Subject: castor.util was renamed castor.core.util Author: Vincent Fourmond Description: 1.3.1 castor packages use castor.core.util in stead of castor.util. The patch was generated using find src | perl -pi -e 's/castor\.util/castor.core.util/g' Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentAnnotation.java 2011-10-17 23:43:32.628672117 +0200 @@ -143,27 +143,27 @@ if (temp._seqrefs == null) return false; if (this._seqrefs != temp._seqrefs) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._seqrefs); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._seqrefs); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._seqrefs); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._seqrefs); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqrefs); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); } ; return false; } if (!thcycle) { if (!this._seqrefs.equals(temp._seqrefs)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqrefs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._seqrefs); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqrefs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqrefs); } } } else if (temp._seqrefs != null) @@ -172,29 +172,29 @@ if (temp._provenance == null) return false; if (this._provenance != temp._provenance) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._provenance); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._provenance); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } ; return false; } if (!thcycle) { if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } } } else if (temp._provenance != null) @@ -299,14 +299,14 @@ long tmp; result = 37 * result + (_graph ? 0 : 1); if (_seqrefs != null - && !org.castor.util.CycleBreaker.startingToCycle(_seqrefs)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_seqrefs)) { result = 37 * result + _seqrefs.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_seqrefs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_seqrefs); } if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentSequenceAnnotation.java 2011-10-17 23:43:32.624672117 +0200 @@ -101,29 +101,29 @@ if (temp._provenance == null) return false; if (this._provenance != temp._provenance) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._provenance); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._provenance); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } ; return false; } if (!thcycle) { if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } } } else if (temp._provenance != null) @@ -177,9 +177,9 @@ long tmp; result = 37 * result + (_graph ? 0 : 1); if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AppData.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AppData.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AppData.java 2011-10-17 23:43:32.644672117 +0200 @@ -89,18 +89,18 @@ if (temp._choiceValue == null) return false; if (this._choiceValue != temp._choiceValue) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._choiceValue); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._choiceValue); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._choiceValue); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._choiceValue); } ; @@ -108,14 +108,14 @@ } if (!thcycle) { if (!this._choiceValue.equals(temp._choiceValue)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._choiceValue); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._choiceValue); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._choiceValue); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._choiceValue); } } } else if (temp._choiceValue != null) @@ -124,27 +124,27 @@ if (temp._data == null) return false; if (this._data != temp._data) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._data); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._data); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._data); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._data); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._data); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._data); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._data); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._data); } ; return false; } if (!thcycle) { if (!java.util.Arrays.equals(this._data, temp._data)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._data); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._data); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._data); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._data); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._data); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._data); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._data); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._data); } } } else if (temp._data != null) @@ -153,18 +153,18 @@ if (temp._dataReference == null) return false; if (this._dataReference != temp._dataReference) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._dataReference); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._dataReference); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._dataReference); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._dataReference); } ; @@ -172,15 +172,15 @@ } if (!thcycle) { if (!this._dataReference.equals(temp._dataReference)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._dataReference); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._dataReference); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._dataReference); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._dataReference); } } @@ -232,18 +232,18 @@ long tmp; if (_choiceValue != null - && !org.castor.util.CycleBreaker.startingToCycle(_choiceValue)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_choiceValue)) { result = 37 * result + _choiceValue.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_choiceValue); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_choiceValue); } - if (_data != null && !org.castor.util.CycleBreaker.startingToCycle(_data)) { + if (_data != null && !org.castor.core.util.CycleBreaker.startingToCycle(_data)) { result = 37 * result + _data.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_data); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_data); } if (_dataReference != null - && !org.castor.util.CycleBreaker.startingToCycle(_dataReference)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_dataReference)) { result = 37 * result + _dataReference.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_dataReference); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_dataReference); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Attachment.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Attachment.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Attachment.java 2011-10-17 23:43:32.624672117 +0200 @@ -112,27 +112,27 @@ if (temp._type == null) return false; if (this._type != temp._type) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._type); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._type); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._type); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._type); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); } ; return false; } if (!thcycle) { if (!this._type.equals(temp._type)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); } } } else if (temp._type != null) @@ -141,29 +141,29 @@ if (temp._objectref == null) return false; if (this._objectref != temp._objectref) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._objectref); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._objectref); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._objectref); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._objectref); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._objectref); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._objectref); } ; return false; } if (!thcycle) { if (!this._objectref.equals(temp._objectref)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._objectref); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._objectref); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._objectref); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._objectref); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._objectref); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._objectref); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._objectref); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._objectref); } } } else if (temp._objectref != null) @@ -172,27 +172,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -268,18 +268,18 @@ long tmp; result = 37 * result + (_compressed ? 0 : 1); - if (_type != null && !org.castor.util.CycleBreaker.startingToCycle(_type)) { + if (_type != null && !org.castor.core.util.CycleBreaker.startingToCycle(_type)) { result = 37 * result + _type.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_type); } if (_objectref != null - && !org.castor.util.CycleBreaker.startingToCycle(_objectref)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_objectref)) { result = 37 * result + _objectref.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_objectref); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_objectref); } - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Glyph.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Glyph.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Glyph.java 2011-10-17 23:43:32.628672117 +0200 @@ -89,27 +89,27 @@ if (temp._content == null) return false; if (this._content != temp._content) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } ; return false; } if (!thcycle) { if (!this._content.equals(temp._content)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } } } else if (temp._content != null) @@ -118,27 +118,27 @@ if (temp._dict == null) return false; if (this._dict != temp._dict) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._dict); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._dict); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._dict); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._dict); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._dict); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dict); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dict); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dict); } ; return false; } if (!thcycle) { if (!this._dict.equals(temp._dict)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._dict); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dict); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dict); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dict); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._dict); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dict); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dict); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dict); } } } else if (temp._dict != null) @@ -183,13 +183,13 @@ long tmp; if (_content != null - && !org.castor.util.CycleBreaker.startingToCycle(_content)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) { result = 37 * result + _content.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_content); } - if (_dict != null && !org.castor.util.CycleBreaker.startingToCycle(_dict)) { + if (_dict != null && !org.castor.core.util.CycleBreaker.startingToCycle(_dict)) { result = 37 * result + _dict.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_dict); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_dict); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Input.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Input.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Input.java 2011-10-17 23:43:32.640672117 +0200 @@ -120,27 +120,27 @@ if (temp._name == null) return false; if (this._name != temp._name) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } ; return false; } if (!thcycle) { if (!this._name.equals(temp._name)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } } } else if (temp._name != null) @@ -149,27 +149,27 @@ if (temp._objRef == null) return false; if (this._objRef != temp._objRef) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._objRef); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._objRef); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._objRef); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._objRef); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._objRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._objRef); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._objRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._objRef); } ; return false; } if (!thcycle) { if (!this._objRef.equals(temp._objRef)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._objRef); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._objRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._objRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._objRef); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._objRef); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._objRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._objRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._objRef); } } } else if (temp._objRef != null) @@ -252,14 +252,14 @@ int result = super.hashCode(); long tmp; - if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) { + if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) { result = 37 * result + _name.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_name); } if (_objRef != null - && !org.castor.util.CycleBreaker.startingToCycle(_objRef)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_objRef)) { result = 37 * result + _objRef.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_objRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_objRef); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Instance.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Instance.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Instance.java 2011-10-17 23:43:32.640672117 +0200 @@ -79,27 +79,27 @@ if (temp._urn == null) return false; if (this._urn != temp._urn) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._urn); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._urn); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._urn); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._urn); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._urn); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._urn); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._urn); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._urn); } ; return false; } if (!thcycle) { if (!this._urn.equals(temp._urn)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._urn); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._urn); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._urn); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._urn); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._urn); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._urn); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._urn); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._urn); } } } else if (temp._urn != null) @@ -130,9 +130,9 @@ int result = super.hashCode(); long tmp; - if (_urn != null && !org.castor.util.CycleBreaker.startingToCycle(_urn)) { + if (_urn != null && !org.castor.core.util.CycleBreaker.startingToCycle(_urn)) { result = 37 * result + _urn.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_urn); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_urn); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Link.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Link.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Link.java 2011-10-17 23:43:32.640672117 +0200 @@ -85,27 +85,27 @@ if (temp._content == null) return false; if (this._content != temp._content) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } ; return false; } if (!thcycle) { if (!this._content.equals(temp._content)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } } } else if (temp._content != null) @@ -114,27 +114,27 @@ if (temp._href == null) return false; if (this._href != temp._href) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._href); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._href); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._href); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._href); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._href); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._href); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._href); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._href); } ; return false; } if (!thcycle) { if (!this._href.equals(temp._href)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._href); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._href); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._href); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._href); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._href); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._href); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._href); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._href); } } } else if (temp._href != null) @@ -177,13 +177,13 @@ long tmp; if (_content != null - && !org.castor.util.CycleBreaker.startingToCycle(_content)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) { result = 37 * result + _content.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_content); } - if (_href != null && !org.castor.util.CycleBreaker.startingToCycle(_href)) { + if (_href != null && !org.castor.core.util.CycleBreaker.startingToCycle(_href)) { result = 37 * result + _href.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_href); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_href); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Map.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Map.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Map.java 2011-10-17 23:43:32.628672117 +0200 @@ -85,27 +85,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -136,9 +136,9 @@ int result = super.hashCode(); long tmp; - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/MapType.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/MapType.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/MapType.java 2011-10-17 23:43:32.632672117 +0200 @@ -83,27 +83,27 @@ if (temp._local == null) return false; if (this._local != temp._local) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._local); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._local); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._local); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._local); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._local); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._local); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._local); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._local); } ; return false; } if (!thcycle) { if (!this._local.equals(temp._local)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._local); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._local); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._local); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._local); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._local); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._local); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._local); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._local); } } } else if (temp._local != null) @@ -112,27 +112,27 @@ if (temp._mapped == null) return false; if (this._mapped != temp._mapped) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._mapped); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._mapped); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._mapped); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._mapped); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._mapped); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapped); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapped); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapped); } ; return false; } if (!thcycle) { if (!this._mapped.equals(temp._mapped)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._mapped); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapped); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapped); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapped); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._mapped); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapped); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapped); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapped); } } } else if (temp._mapped != null) @@ -172,14 +172,14 @@ int result = super.hashCode(); long tmp; - if (_local != null && !org.castor.util.CycleBreaker.startingToCycle(_local)) { + if (_local != null && !org.castor.core.util.CycleBreaker.startingToCycle(_local)) { result = 37 * result + _local.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_local); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_local); } if (_mapped != null - && !org.castor.util.CycleBreaker.startingToCycle(_mapped)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_mapped)) { result = 37 * result + _mapped.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_mapped); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_mapped); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/NodeType.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/NodeType.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/NodeType.java 2011-10-17 23:43:32.628672117 +0200 @@ -176,27 +176,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -205,29 +205,29 @@ if (temp._modifiable == null) return false; if (this._modifiable != temp._modifiable) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._modifiable); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._modifiable); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } ; return false; } if (!thcycle) { if (!this._modifiable.equals(temp._modifiable)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } } } else if (temp._modifiable != null) @@ -236,27 +236,27 @@ if (temp._name == null) return false; if (this._name != temp._name) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } ; return false; } if (!thcycle) { if (!this._name.equals(temp._name)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } } } else if (temp._name != null) @@ -265,18 +265,18 @@ if (temp._description == null) return false; if (this._description != temp._description) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._description); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._description); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._description); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._description); } ; @@ -284,14 +284,14 @@ } if (!thcycle) { if (!this._description.equals(temp._description)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._description); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._description); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._description); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._description); } } } else if (temp._description != null) @@ -300,29 +300,29 @@ if (temp._vrefList == null) return false; if (this._vrefList != temp._vrefList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._vrefList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._vrefList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._vrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vrefList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._vrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vrefList); } ; return false; } if (!thcycle) { if (!this._vrefList.equals(temp._vrefList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._vrefList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._vrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vrefList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._vrefList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._vrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vrefList); } } } else if (temp._vrefList != null) @@ -331,18 +331,18 @@ if (temp._propertyList == null) return false; if (this._propertyList != temp._propertyList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._propertyList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._propertyList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); } ; @@ -350,14 +350,14 @@ } if (!thcycle) { if (!this._propertyList.equals(temp._propertyList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList); } } } else if (temp._propertyList != null) @@ -524,33 +524,33 @@ int result = super.hashCode(); long tmp; - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_modifiable != null - && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) { result = 37 * result + _modifiable.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable); } - if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) { + if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) { result = 37 * result + _name.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_name); } if (_description != null - && !org.castor.util.CycleBreaker.startingToCycle(_description)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_description)) { result = 37 * result + _description.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_description); } if (_vrefList != null - && !org.castor.util.CycleBreaker.startingToCycle(_vrefList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_vrefList)) { result = 37 * result + _vrefList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_vrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_vrefList); } if (_propertyList != null - && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Param.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Param.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Param.java 2011-10-17 23:43:32.628672117 +0200 @@ -92,27 +92,27 @@ if (temp._content == null) return false; if (this._content != temp._content) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } ; return false; } if (!thcycle) { if (!this._content.equals(temp._content)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } } } else if (temp._content != null) @@ -121,27 +121,27 @@ if (temp._name == null) return false; if (this._name != temp._name) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } ; return false; } if (!thcycle) { if (!this._name.equals(temp._name)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } } } else if (temp._name != null) @@ -150,27 +150,27 @@ if (temp._type == null) return false; if (this._type != temp._type) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._type); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._type); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._type); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._type); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); } ; return false; } if (!thcycle) { if (!this._type.equals(temp._type)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); } } } else if (temp._type != null) @@ -224,17 +224,17 @@ long tmp; if (_content != null - && !org.castor.util.CycleBreaker.startingToCycle(_content)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) { result = 37 * result + _content.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_content); } - if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) { + if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) { result = 37 * result + _name.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_name); } - if (_type != null && !org.castor.util.CycleBreaker.startingToCycle(_type)) { + if (_type != null && !org.castor.core.util.CycleBreaker.startingToCycle(_type)) { result = 37 * result + _type.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_type); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Property.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Property.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Property.java 2011-10-17 23:43:32.628672117 +0200 @@ -92,27 +92,27 @@ if (temp._content == null) return false; if (this._content != temp._content) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } ; return false; } if (!thcycle) { if (!this._content.equals(temp._content)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } } } else if (temp._content != null) @@ -121,27 +121,27 @@ if (temp._name == null) return false; if (this._name != temp._name) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } ; return false; } if (!thcycle) { if (!this._name.equals(temp._name)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } } } else if (temp._name != null) @@ -150,27 +150,27 @@ if (temp._type == null) return false; if (this._type != temp._type) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._type); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._type); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._type); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._type); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); } ; return false; } if (!thcycle) { if (!this._type.equals(temp._type)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); } } } else if (temp._type != null) @@ -224,17 +224,17 @@ long tmp; if (_content != null - && !org.castor.util.CycleBreaker.startingToCycle(_content)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) { result = 37 * result + _content.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_content); } - if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) { + if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) { result = 37 * result + _name.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_name); } - if (_type != null && !org.castor.util.CycleBreaker.startingToCycle(_type)) { + if (_type != null && !org.castor.core.util.CycleBreaker.startingToCycle(_type)) { result = 37 * result + _type.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_type); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/RangeAnnotation.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/RangeAnnotation.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/RangeAnnotation.java 2011-10-17 23:43:32.644672117 +0200 @@ -288,27 +288,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -317,29 +317,29 @@ if (temp._modifiable == null) return false; if (this._modifiable != temp._modifiable) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._modifiable); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._modifiable); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } ; return false; } if (!thcycle) { if (!this._modifiable.equals(temp._modifiable)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } } } else if (temp._modifiable != null) @@ -348,27 +348,27 @@ if (temp._group == null) return false; if (this._group != temp._group) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._group); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._group); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._group); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._group); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._group); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._group); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._group); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._group); } ; return false; } if (!thcycle) { if (!this._group.equals(temp._group)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._group); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._group); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._group); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._group); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._group); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._group); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._group); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._group); } } } else if (temp._group != null) @@ -377,27 +377,27 @@ if (temp._type == null) return false; if (this._type != temp._type) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._type); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._type); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._type); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._type); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); } ; return false; } if (!thcycle) { if (!this._type.equals(temp._type)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._type); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._type); } } } else if (temp._type != null) @@ -406,27 +406,27 @@ if (temp._label == null) return false; if (this._label != temp._label) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._label); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._label); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._label); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._label); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._label); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._label); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._label); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._label); } ; return false; } if (!thcycle) { if (!this._label.equals(temp._label)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._label); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._label); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._label); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._label); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._label); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._label); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._label); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._label); } } } else if (temp._label != null) @@ -435,18 +435,18 @@ if (temp._description == null) return false; if (this._description != temp._description) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._description); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._description); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._description); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._description); } ; @@ -454,14 +454,14 @@ } if (!thcycle) { if (!this._description.equals(temp._description)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._description); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._description); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._description); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._description); } } } else if (temp._description != null) @@ -470,27 +470,27 @@ if (temp._status == null) return false; if (this._status != temp._status) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._status); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._status); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._status); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._status); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._status); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._status); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._status); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._status); } ; return false; } if (!thcycle) { if (!this._status.equals(temp._status)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._status); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._status); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._status); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._status); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._status); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._status); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._status); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._status); } } } else if (temp._status != null) @@ -499,18 +499,18 @@ if (temp._annotationElementList == null) return false; if (this._annotationElementList != temp._annotationElementList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._annotationElementList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._annotationElementList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._annotationElementList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._annotationElementList); } ; @@ -519,15 +519,15 @@ if (!thcycle) { if (!this._annotationElementList .equals(temp._annotationElementList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._annotationElementList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._annotationElementList); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._annotationElementList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._annotationElementList); } } @@ -537,29 +537,29 @@ if (temp._scoreList == null) return false; if (this._scoreList != temp._scoreList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._scoreList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._scoreList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._scoreList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._scoreList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._scoreList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._scoreList); } ; return false; } if (!thcycle) { if (!this._scoreList.equals(temp._scoreList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._scoreList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._scoreList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._scoreList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._scoreList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._scoreList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._scoreList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._scoreList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._scoreList); } } } else if (temp._scoreList != null) @@ -568,29 +568,29 @@ if (temp._linkList == null) return false; if (this._linkList != temp._linkList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._linkList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._linkList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList); } ; return false; } if (!thcycle) { if (!this._linkList.equals(temp._linkList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList); } } } else if (temp._linkList != null) @@ -599,18 +599,18 @@ if (temp._propertyList == null) return false; if (this._propertyList != temp._propertyList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._propertyList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._propertyList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); } ; @@ -618,14 +618,14 @@ } if (!thcycle) { if (!this._propertyList.equals(temp._propertyList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList); } } } else if (temp._propertyList != null) @@ -942,57 +942,57 @@ int result = super.hashCode(); long tmp; - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_modifiable != null - && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) { result = 37 * result + _modifiable.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable); } - if (_group != null && !org.castor.util.CycleBreaker.startingToCycle(_group)) { + if (_group != null && !org.castor.core.util.CycleBreaker.startingToCycle(_group)) { result = 37 * result + _group.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_group); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_group); } - if (_type != null && !org.castor.util.CycleBreaker.startingToCycle(_type)) { + if (_type != null && !org.castor.core.util.CycleBreaker.startingToCycle(_type)) { result = 37 * result + _type.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_type); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_type); } - if (_label != null && !org.castor.util.CycleBreaker.startingToCycle(_label)) { + if (_label != null && !org.castor.core.util.CycleBreaker.startingToCycle(_label)) { result = 37 * result + _label.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_label); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_label); } if (_description != null - && !org.castor.util.CycleBreaker.startingToCycle(_description)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_description)) { result = 37 * result + _description.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_description); } if (_status != null - && !org.castor.util.CycleBreaker.startingToCycle(_status)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_status)) { result = 37 * result + _status.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_status); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_status); } if (_annotationElementList != null - && !org.castor.util.CycleBreaker + && !org.castor.core.util.CycleBreaker .startingToCycle(_annotationElementList)) { result = 37 * result + _annotationElementList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_annotationElementList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_annotationElementList); } if (_scoreList != null - && !org.castor.util.CycleBreaker.startingToCycle(_scoreList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_scoreList)) { result = 37 * result + _scoreList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_scoreList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_scoreList); } if (_linkList != null - && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_linkList)) { result = 37 * result + _linkList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_linkList); } if (_propertyList != null - && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/RangeType.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/RangeType.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/RangeType.java 2011-10-17 23:43:32.644672117 +0200 @@ -157,18 +157,18 @@ if (temp._choiceValue == null) return false; if (this._choiceValue != temp._choiceValue) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._choiceValue); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._choiceValue); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._choiceValue); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._choiceValue); } ; @@ -176,14 +176,14 @@ } if (!thcycle) { if (!this._choiceValue.equals(temp._choiceValue)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._choiceValue); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._choiceValue); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._choiceValue); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._choiceValue); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._choiceValue); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._choiceValue); } } } else if (temp._choiceValue != null) @@ -192,27 +192,27 @@ if (temp._posList == null) return false; if (this._posList != temp._posList) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._posList); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._posList); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._posList); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._posList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._posList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._posList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._posList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._posList); } ; return false; } if (!thcycle) { if (!this._posList.equals(temp._posList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._posList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._posList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._posList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._posList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._posList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._posList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._posList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._posList); } } } else if (temp._posList != null) @@ -221,27 +221,27 @@ if (temp._segList == null) return false; if (this._segList != temp._segList) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._segList); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._segList); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._segList); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._segList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._segList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._segList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._segList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._segList); } ; return false; } if (!thcycle) { if (!this._segList.equals(temp._segList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._segList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._segList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._segList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._segList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._segList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._segList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._segList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._segList); } } } else if (temp._segList != null) @@ -378,19 +378,19 @@ long tmp; if (_choiceValue != null - && !org.castor.util.CycleBreaker.startingToCycle(_choiceValue)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_choiceValue)) { result = 37 * result + _choiceValue.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_choiceValue); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_choiceValue); } if (_posList != null - && !org.castor.util.CycleBreaker.startingToCycle(_posList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_posList)) { result = 37 * result + _posList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_posList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_posList); } if (_segList != null - && !org.castor.util.CycleBreaker.startingToCycle(_segList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_segList)) { result = 37 * result + _segList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_segList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_segList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/ReferenceType.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/ReferenceType.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/ReferenceType.java 2011-10-17 23:43:32.640672117 +0200 @@ -128,27 +128,27 @@ if (temp._content == null) return false; if (this._content != temp._content) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } ; return false; } if (!thcycle) { if (!this._content.equals(temp._content)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } } } else if (temp._content != null) @@ -157,27 +157,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -186,27 +186,27 @@ if (temp._refs == null) return false; if (this._refs != temp._refs) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._refs); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._refs); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._refs); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._refs); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._refs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refs); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._refs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refs); } ; return false; } if (!thcycle) { if (!this._refs.equals(temp._refs)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._refs); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._refs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refs); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._refs); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._refs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refs); } } } else if (temp._refs != null) @@ -302,17 +302,17 @@ long tmp; if (_content != null - && !org.castor.util.CycleBreaker.startingToCycle(_content)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) { result = 37 * result + _content.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_content); } - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } - if (_refs != null && !org.castor.util.CycleBreaker.startingToCycle(_refs)) { + if (_refs != null && !org.castor.core.util.CycleBreaker.startingToCycle(_refs)) { result = 37 * result + _refs.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_refs); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_refs); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Score.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Score.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Score.java 2011-10-17 23:43:32.628672117 +0200 @@ -100,27 +100,27 @@ if (temp._name == null) return false; if (this._name != temp._name) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } ; return false; } if (!thcycle) { if (!this._name.equals(temp._name)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } } } else if (temp._name != null) @@ -171,9 +171,9 @@ long tmp; result = 37 * result + java.lang.Float.floatToIntBits(_content); - if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) { + if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) { result = 37 * result + _name.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_name); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/SequenceMapping.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/SequenceMapping.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/SequenceMapping.java 2011-10-17 23:43:32.628672117 +0200 @@ -94,27 +94,27 @@ if (temp._loc == null) return false; if (this._loc != temp._loc) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._loc); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._loc); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._loc); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._loc); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._loc); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._loc); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._loc); } ; return false; } if (!thcycle) { if (!this._loc.equals(temp._loc)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._loc); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._loc); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._loc); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._loc); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._loc); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._loc); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._loc); } } } else if (temp._loc != null) @@ -123,27 +123,27 @@ if (temp._map == null) return false; if (this._map != temp._map) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._map); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._map); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._map); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._map); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._map); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._map); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._map); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._map); } ; return false; } if (!thcycle) { if (!this._map.equals(temp._map)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._map); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._map); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._map); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._map); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._map); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._map); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._map); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._map); } } } else if (temp._map != null) @@ -152,27 +152,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -181,29 +181,29 @@ if (temp._provenance == null) return false; if (this._provenance != temp._provenance) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._provenance); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._provenance); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } ; return false; } if (!thcycle) { if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } } } else if (temp._provenance != null) @@ -263,22 +263,22 @@ int result = super.hashCode(); long tmp; - if (_loc != null && !org.castor.util.CycleBreaker.startingToCycle(_loc)) { + if (_loc != null && !org.castor.core.util.CycleBreaker.startingToCycle(_loc)) { result = 37 * result + _loc.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_loc); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_loc); } - if (_map != null && !org.castor.util.CycleBreaker.startingToCycle(_map)) { + if (_map != null && !org.castor.core.util.CycleBreaker.startingToCycle(_map)) { result = 37 * result + _map.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_map); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_map); } - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Treenode.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Treenode.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Treenode.java 2011-10-17 23:43:32.628672117 +0200 @@ -122,27 +122,27 @@ if (temp._treeId == null) return false; if (this._treeId != temp._treeId) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._treeId); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._treeId); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._treeId); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._treeId); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeId); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeId); } ; return false; } if (!thcycle) { if (!this._treeId.equals(temp._treeId)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeId); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeId); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeId); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeId); } } } else if (temp._treeId != null) @@ -151,29 +151,29 @@ if (temp._nodespec == null) return false; if (this._nodespec != temp._nodespec) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._nodespec); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._nodespec); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._nodespec); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._nodespec); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._nodespec); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._nodespec); } ; return false; } if (!thcycle) { if (!this._nodespec.equals(temp._nodespec)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._nodespec); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._nodespec); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._nodespec); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._nodespec); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._nodespec); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._nodespec); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._nodespec); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._nodespec); } } } else if (temp._nodespec != null) @@ -261,14 +261,14 @@ long tmp; if (_treeId != null - && !org.castor.util.CycleBreaker.startingToCycle(_treeId)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_treeId)) { result = 37 * result + _treeId.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_treeId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeId); } if (_nodespec != null - && !org.castor.util.CycleBreaker.startingToCycle(_nodespec)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_nodespec)) { result = 37 * result + _nodespec.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_nodespec); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_nodespec); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/test/simpleclient/simpleapp/VamsasDatastore.java 2011-10-17 23:43:32.608672117 +0200 @@ -40,7 +40,7 @@ /* * * static { - * org.exolab.castor.util.LocalConfiguration.getInstance().getProperties().setProperty( + * org.exolab.castor.core.util.LocalConfiguration.getInstance().getProperties().setProperty( * "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); } * */ Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Alignment.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Alignment.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Alignment.java 2011-10-17 23:43:32.628672117 +0200 @@ -282,27 +282,27 @@ if (temp._gapChar == null) return false; if (this._gapChar != temp._gapChar) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._gapChar); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._gapChar); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._gapChar); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._gapChar); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._gapChar); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._gapChar); } ; return false; } if (!thcycle) { if (!this._gapChar.equals(temp._gapChar)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._gapChar); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._gapChar); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._gapChar); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._gapChar); } } } else if (temp._gapChar != null) @@ -315,27 +315,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -344,29 +344,29 @@ if (temp._modifiable == null) return false; if (this._modifiable != temp._modifiable) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._modifiable); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._modifiable); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } ; return false; } if (!thcycle) { if (!this._modifiable.equals(temp._modifiable)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } } } else if (temp._modifiable != null) @@ -375,18 +375,18 @@ if (temp._alignmentAnnotationList == null) return false; if (this._alignmentAnnotationList != temp._alignmentAnnotationList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._alignmentAnnotationList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._alignmentAnnotationList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentAnnotationList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentAnnotationList); } ; @@ -395,15 +395,15 @@ if (!thcycle) { if (!this._alignmentAnnotationList .equals(temp._alignmentAnnotationList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentAnnotationList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentAnnotationList); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentAnnotationList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentAnnotationList); } } @@ -413,29 +413,29 @@ if (temp._treeList == null) return false; if (this._treeList != temp._treeList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._treeList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._treeList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList); } ; return false; } if (!thcycle) { if (!this._treeList.equals(temp._treeList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList); } } } else if (temp._treeList != null) @@ -444,18 +444,18 @@ if (temp._alignmentSequenceList == null) return false; if (this._alignmentSequenceList != temp._alignmentSequenceList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._alignmentSequenceList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._alignmentSequenceList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentSequenceList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentSequenceList); } ; @@ -464,15 +464,15 @@ if (!thcycle) { if (!this._alignmentSequenceList .equals(temp._alignmentSequenceList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentSequenceList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentSequenceList); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentSequenceList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentSequenceList); } } @@ -482,18 +482,18 @@ if (temp._propertyList == null) return false; if (this._propertyList != temp._propertyList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._propertyList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._propertyList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); } ; @@ -501,14 +501,14 @@ } if (!thcycle) { if (!this._propertyList.equals(temp._propertyList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList); } } } else if (temp._propertyList != null) @@ -517,29 +517,29 @@ if (temp._provenance == null) return false; if (this._provenance != temp._provenance) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._provenance); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._provenance); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } ; return false; } if (!thcycle) { if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } } } else if (temp._provenance != null) @@ -841,46 +841,46 @@ long tmp; if (_gapChar != null - && !org.castor.util.CycleBreaker.startingToCycle(_gapChar)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_gapChar)) { result = 37 * result + _gapChar.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_gapChar); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_gapChar); } result = 37 * result + (_aligned ? 0 : 1); - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_modifiable != null - && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) { result = 37 * result + _modifiable.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable); } if (_alignmentAnnotationList != null - && !org.castor.util.CycleBreaker + && !org.castor.core.util.CycleBreaker .startingToCycle(_alignmentAnnotationList)) { result = 37 * result + _alignmentAnnotationList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentAnnotationList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentAnnotationList); } if (_treeList != null - && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) { result = 37 * result + _treeList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList); } if (_alignmentSequenceList != null - && !org.castor.util.CycleBreaker + && !org.castor.core.util.CycleBreaker .startingToCycle(_alignmentSequenceList)) { result = 37 * result + _alignmentSequenceList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceList); } if (_propertyList != null - && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList); } if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentSequence.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AlignmentSequence.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AlignmentSequence.java 2011-10-17 23:43:32.624672117 +0200 @@ -132,27 +132,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -161,27 +161,27 @@ if (temp._refid == null) return false; if (this._refid != temp._refid) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._refid); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._refid); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._refid); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._refid); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._refid); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid); } ; return false; } if (!thcycle) { if (!this._refid.equals(temp._refid)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._refid); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._refid); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid); } } } else if (temp._refid != null) @@ -190,18 +190,18 @@ if (temp._alignmentSequenceAnnotationList == null) return false; if (this._alignmentSequenceAnnotationList != temp._alignmentSequenceAnnotationList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._alignmentSequenceAnnotationList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._alignmentSequenceAnnotationList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentSequenceAnnotationList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentSequenceAnnotationList); } ; @@ -210,15 +210,15 @@ if (!thcycle) { if (!this._alignmentSequenceAnnotationList .equals(temp._alignmentSequenceAnnotationList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentSequenceAnnotationList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentSequenceAnnotationList); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentSequenceAnnotationList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentSequenceAnnotationList); } } @@ -323,19 +323,19 @@ int result = super.hashCode(); long tmp; - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } - if (_refid != null && !org.castor.util.CycleBreaker.startingToCycle(_refid)) { + if (_refid != null && !org.castor.core.util.CycleBreaker.startingToCycle(_refid)) { result = 37 * result + _refid.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_refid); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_refid); } if (_alignmentSequenceAnnotationList != null - && !org.castor.util.CycleBreaker + && !org.castor.core.util.CycleBreaker .startingToCycle(_alignmentSequenceAnnotationList)) { result = 37 * result + _alignmentSequenceAnnotationList.hashCode(); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(_alignmentSequenceAnnotationList); } Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AnnotationElement.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/AnnotationElement.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/AnnotationElement.java 2011-10-17 23:43:32.632672117 +0200 @@ -213,27 +213,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -242,18 +242,18 @@ if (temp._description == null) return false; if (this._description != temp._description) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._description); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._description); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._description); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._description); } ; @@ -261,14 +261,14 @@ } if (!thcycle) { if (!this._description.equals(temp._description)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._description); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._description); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._description); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._description); } } } else if (temp._description != null) @@ -277,29 +277,29 @@ if (temp._glyphList == null) return false; if (this._glyphList != temp._glyphList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._glyphList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._glyphList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._glyphList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._glyphList); } ; return false; } if (!thcycle) { if (!this._glyphList.equals(temp._glyphList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._glyphList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._glyphList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._glyphList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._glyphList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._glyphList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._glyphList); } } } else if (temp._glyphList != null) @@ -308,29 +308,29 @@ if (temp._valueList == null) return false; if (this._valueList != temp._valueList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._valueList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._valueList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._valueList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._valueList); } ; return false; } if (!thcycle) { if (!this._valueList.equals(temp._valueList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._valueList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._valueList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._valueList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._valueList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._valueList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._valueList); } } } else if (temp._valueList != null) @@ -519,24 +519,24 @@ long tmp; result = 37 * result + (int) (_position ^ (_position >>> 32)); result = 37 * result + (_after ? 0 : 1); - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_description != null - && !org.castor.util.CycleBreaker.startingToCycle(_description)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_description)) { result = 37 * result + _description.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_description); } if (_glyphList != null - && !org.castor.util.CycleBreaker.startingToCycle(_glyphList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_glyphList)) { result = 37 * result + _glyphList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_glyphList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_glyphList); } if (_valueList != null - && !org.castor.util.CycleBreaker.startingToCycle(_valueList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_valueList)) { result = 37 * result + _valueList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_valueList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_valueList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/ApplicationData.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/ApplicationData.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/ApplicationData.java 2011-10-17 23:43:32.624672117 +0200 @@ -173,27 +173,27 @@ if (temp._version == null) return false; if (this._version != temp._version) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._version); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._version); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version); } ; return false; } if (!thcycle) { if (!this._version.equals(temp._version)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._version); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._version); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version); } } } else if (temp._version != null) @@ -202,27 +202,27 @@ if (temp._name == null) return false; if (this._name != temp._name) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } ; return false; } if (!thcycle) { if (!this._name.equals(temp._name)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } } } else if (temp._name != null) @@ -231,29 +231,29 @@ if (temp._userList == null) return false; if (this._userList != temp._userList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._userList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._userList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._userList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._userList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._userList); } ; return false; } if (!thcycle) { if (!this._userList.equals(temp._userList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._userList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._userList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._userList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._userList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._userList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._userList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._userList); } } } else if (temp._userList != null) @@ -262,27 +262,27 @@ if (temp._common == null) return false; if (this._common != temp._common) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._common); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._common); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._common); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._common); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._common); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._common); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._common); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._common); } ; return false; } if (!thcycle) { if (!this._common.equals(temp._common)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._common); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._common); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._common); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._common); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._common); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._common); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._common); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._common); } } } else if (temp._common != null) @@ -291,18 +291,18 @@ if (temp._instanceList == null) return false; if (this._instanceList != temp._instanceList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._instanceList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._instanceList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._instanceList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._instanceList); } ; @@ -310,14 +310,14 @@ } if (!thcycle) { if (!this._instanceList.equals(temp._instanceList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._instanceList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._instanceList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._instanceList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._instanceList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._instanceList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._instanceList); } } } else if (temp._instanceList != null) @@ -476,28 +476,28 @@ long tmp; if (_version != null - && !org.castor.util.CycleBreaker.startingToCycle(_version)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_version)) { result = 37 * result + _version.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_version); } - if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) { + if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) { result = 37 * result + _name.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_name); } if (_userList != null - && !org.castor.util.CycleBreaker.startingToCycle(_userList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_userList)) { result = 37 * result + _userList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_userList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_userList); } if (_common != null - && !org.castor.util.CycleBreaker.startingToCycle(_common)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_common)) { result = 37 * result + _common.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_common); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_common); } if (_instanceList != null - && !org.castor.util.CycleBreaker.startingToCycle(_instanceList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_instanceList)) { result = 37 * result + _instanceList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_instanceList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_instanceList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DataSet.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/DataSet.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DataSet.java 2011-10-17 23:43:32.644672117 +0200 @@ -295,27 +295,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -324,18 +324,18 @@ if (temp._sequenceList == null) return false; if (this._sequenceList != temp._sequenceList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._sequenceList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._sequenceList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._sequenceList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._sequenceList); } ; @@ -343,14 +343,14 @@ } if (!thcycle) { if (!this._sequenceList.equals(temp._sequenceList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._sequenceList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._sequenceList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._sequenceList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequenceList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequenceList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequenceList); } } } else if (temp._sequenceList != null) @@ -359,18 +359,18 @@ if (temp._sequenceMappingList == null) return false; if (this._sequenceMappingList != temp._sequenceMappingList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._sequenceMappingList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._sequenceMappingList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._sequenceMappingList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._sequenceMappingList); } ; @@ -378,15 +378,15 @@ } if (!thcycle) { if (!this._sequenceMappingList.equals(temp._sequenceMappingList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._sequenceMappingList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._sequenceMappingList); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._sequenceMappingList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._sequenceMappingList); } } @@ -396,18 +396,18 @@ if (temp._dataSetAnnotationsList == null) return false; if (this._dataSetAnnotationsList != temp._dataSetAnnotationsList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._dataSetAnnotationsList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._dataSetAnnotationsList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._dataSetAnnotationsList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._dataSetAnnotationsList); } ; @@ -416,15 +416,15 @@ if (!thcycle) { if (!this._dataSetAnnotationsList .equals(temp._dataSetAnnotationsList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._dataSetAnnotationsList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._dataSetAnnotationsList); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._dataSetAnnotationsList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._dataSetAnnotationsList); } } @@ -434,18 +434,18 @@ if (temp._alignmentList == null) return false; if (this._alignmentList != temp._alignmentList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._alignmentList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._alignmentList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentList); } ; @@ -453,15 +453,15 @@ } if (!thcycle) { if (!this._alignmentList.equals(temp._alignmentList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentList); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._alignmentList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._alignmentList); } } @@ -471,29 +471,29 @@ if (temp._treeList == null) return false; if (this._treeList != temp._treeList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._treeList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._treeList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList); } ; return false; } if (!thcycle) { if (!this._treeList.equals(temp._treeList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList); } } } else if (temp._treeList != null) @@ -502,29 +502,29 @@ if (temp._provenance == null) return false; if (this._provenance != temp._provenance) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._provenance); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._provenance); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } ; return false; } if (!thcycle) { if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } } } else if (temp._provenance != null) @@ -842,40 +842,40 @@ int result = super.hashCode(); long tmp; - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_sequenceList != null - && !org.castor.util.CycleBreaker.startingToCycle(_sequenceList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_sequenceList)) { result = 37 * result + _sequenceList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequenceList); } if (_sequenceMappingList != null - && !org.castor.util.CycleBreaker.startingToCycle(_sequenceMappingList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_sequenceMappingList)) { result = 37 * result + _sequenceMappingList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequenceMappingList); } if (_dataSetAnnotationsList != null - && !org.castor.util.CycleBreaker + && !org.castor.core.util.CycleBreaker .startingToCycle(_dataSetAnnotationsList)) { result = 37 * result + _dataSetAnnotationsList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_dataSetAnnotationsList); } if (_alignmentList != null - && !org.castor.util.CycleBreaker.startingToCycle(_alignmentList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_alignmentList)) { result = 37 * result + _alignmentList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_alignmentList); } if (_treeList != null - && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) { result = 37 * result + _treeList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList); } if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DataSetAnnotations.java 2011-10-17 23:43:32.640672117 +0200 @@ -120,27 +120,27 @@ if (temp._seqRef == null) return false; if (this._seqRef != temp._seqRef) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._seqRef); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._seqRef); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._seqRef); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._seqRef); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqRef); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqRef); } ; return false; } if (!thcycle) { if (!this._seqRef.equals(temp._seqRef)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqRef); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._seqRef); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._seqRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._seqRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._seqRef); } } } else if (temp._seqRef != null) @@ -149,29 +149,29 @@ if (temp._provenance == null) return false; if (this._provenance != temp._provenance) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._provenance); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._provenance); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } ; return false; } if (!thcycle) { if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } } } else if (temp._provenance != null) @@ -255,14 +255,14 @@ long tmp; if (_seqRef != null - && !org.castor.util.CycleBreaker.startingToCycle(_seqRef)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_seqRef)) { result = 37 * result + _seqRef.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_seqRef); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_seqRef); } if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DbRef.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/DbRef.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/DbRef.java 2011-10-17 23:43:32.644672117 +0200 @@ -231,27 +231,27 @@ if (temp._source == null) return false; if (this._source != temp._source) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._source); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._source); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._source); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._source); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._source); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._source); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._source); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._source); } ; return false; } if (!thcycle) { if (!this._source.equals(temp._source)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._source); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._source); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._source); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._source); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._source); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._source); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._source); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._source); } } } else if (temp._source != null) @@ -260,27 +260,27 @@ if (temp._version == null) return false; if (this._version != temp._version) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._version); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._version); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version); } ; return false; } if (!thcycle) { if (!this._version.equals(temp._version)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._version); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._version); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version); } } } else if (temp._version != null) @@ -289,18 +289,18 @@ if (temp._accessionId == null) return false; if (this._accessionId != temp._accessionId) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._accessionId); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._accessionId); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._accessionId); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._accessionId); } ; @@ -308,14 +308,14 @@ } if (!thcycle) { if (!this._accessionId.equals(temp._accessionId)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._accessionId); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._accessionId); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._accessionId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._accessionId); } } } else if (temp._accessionId != null) @@ -324,27 +324,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -353,27 +353,27 @@ if (temp._mapList == null) return false; if (this._mapList != temp._mapList) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._mapList); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._mapList); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._mapList); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._mapList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapList); } ; return false; } if (!thcycle) { if (!this._mapList.equals(temp._mapList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._mapList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._mapList); } } } else if (temp._mapList != null) @@ -382,29 +382,29 @@ if (temp._linkList == null) return false; if (this._linkList != temp._linkList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._linkList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._linkList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList); } ; return false; } if (!thcycle) { if (!this._linkList.equals(temp._linkList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._linkList); } } } else if (temp._linkList != null) @@ -413,18 +413,18 @@ if (temp._propertyList == null) return false; if (this._propertyList != temp._propertyList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._propertyList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._propertyList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); } ; @@ -432,14 +432,14 @@ } if (!thcycle) { if (!this._propertyList.equals(temp._propertyList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList); } } } else if (temp._propertyList != null) @@ -666,38 +666,38 @@ long tmp; if (_source != null - && !org.castor.util.CycleBreaker.startingToCycle(_source)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_source)) { result = 37 * result + _source.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_source); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_source); } if (_version != null - && !org.castor.util.CycleBreaker.startingToCycle(_version)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_version)) { result = 37 * result + _version.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_version); } if (_accessionId != null - && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_accessionId)) { result = 37 * result + _accessionId.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_accessionId); } - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_mapList != null - && !org.castor.util.CycleBreaker.startingToCycle(_mapList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_mapList)) { result = 37 * result + _mapList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_mapList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_mapList); } if (_linkList != null - && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_linkList)) { result = 37 * result + _linkList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_linkList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_linkList); } if (_propertyList != null - && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Entry.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Entry.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Entry.java 2011-10-17 23:43:32.640672117 +0200 @@ -225,27 +225,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -254,27 +254,27 @@ if (temp._user == null) return false; if (this._user != temp._user) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._user); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._user); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._user); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._user); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._user); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._user); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._user); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._user); } ; return false; } if (!thcycle) { if (!this._user.equals(temp._user)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._user); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._user); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._user); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._user); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._user); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._user); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._user); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._user); } } } else if (temp._user != null) @@ -283,27 +283,27 @@ if (temp._app == null) return false; if (this._app != temp._app) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._app); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._app); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._app); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._app); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._app); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._app); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._app); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._app); } ; return false; } if (!thcycle) { if (!this._app.equals(temp._app)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._app); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._app); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._app); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._app); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._app); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._app); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._app); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._app); } } } else if (temp._app != null) @@ -312,27 +312,27 @@ if (temp._action == null) return false; if (this._action != temp._action) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._action); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._action); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._action); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._action); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._action); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._action); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._action); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._action); } ; return false; } if (!thcycle) { if (!this._action.equals(temp._action)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._action); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._action); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._action); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._action); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._action); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._action); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._action); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._action); } } } else if (temp._action != null) @@ -341,27 +341,27 @@ if (temp._date == null) return false; if (this._date != temp._date) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._date); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._date); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._date); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._date); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._date); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._date); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._date); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._date); } ; return false; } if (!thcycle) { if (!this._date.equals(temp._date)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._date); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._date); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._date); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._date); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._date); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._date); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._date); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._date); } } } else if (temp._date != null) @@ -370,18 +370,18 @@ if (temp._propertyList == null) return false; if (this._propertyList != temp._propertyList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._propertyList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._propertyList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); } ; @@ -389,14 +389,14 @@ } if (!thcycle) { if (!this._propertyList.equals(temp._propertyList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList); } } } else if (temp._propertyList != null) @@ -405,29 +405,29 @@ if (temp._paramList == null) return false; if (this._paramList != temp._paramList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._paramList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._paramList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._paramList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._paramList); } ; return false; } if (!thcycle) { if (!this._paramList.equals(temp._paramList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._paramList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._paramList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._paramList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._paramList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._paramList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._paramList); } } } else if (temp._paramList != null) @@ -436,29 +436,29 @@ if (temp._inputList == null) return false; if (this._inputList != temp._inputList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._inputList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._inputList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._inputList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._inputList); } ; return false; } if (!thcycle) { if (!this._inputList.equals(temp._inputList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._inputList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._inputList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._inputList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._inputList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._inputList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._inputList); } } } else if (temp._inputList != null) @@ -689,41 +689,41 @@ int result = super.hashCode(); long tmp; - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } - if (_user != null && !org.castor.util.CycleBreaker.startingToCycle(_user)) { + if (_user != null && !org.castor.core.util.CycleBreaker.startingToCycle(_user)) { result = 37 * result + _user.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_user); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_user); } - if (_app != null && !org.castor.util.CycleBreaker.startingToCycle(_app)) { + if (_app != null && !org.castor.core.util.CycleBreaker.startingToCycle(_app)) { result = 37 * result + _app.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_app); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_app); } if (_action != null - && !org.castor.util.CycleBreaker.startingToCycle(_action)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_action)) { result = 37 * result + _action.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_action); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_action); } - if (_date != null && !org.castor.util.CycleBreaker.startingToCycle(_date)) { + if (_date != null && !org.castor.core.util.CycleBreaker.startingToCycle(_date)) { result = 37 * result + _date.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_date); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_date); } if (_propertyList != null - && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList); } if (_paramList != null - && !org.castor.util.CycleBreaker.startingToCycle(_paramList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_paramList)) { result = 37 * result + _paramList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_paramList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_paramList); } if (_inputList != null - && !org.castor.util.CycleBreaker.startingToCycle(_inputList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_inputList)) { result = 37 * result + _inputList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_inputList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_inputList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/LockFile.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/LockFile.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/LockFile.java 2011-10-17 23:43:32.624672117 +0200 @@ -81,27 +81,27 @@ if (temp._content == null) return false; if (this._content != temp._content) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } ; return false; } if (!thcycle) { if (!this._content.equals(temp._content)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } } } else if (temp._content != null) @@ -134,9 +134,9 @@ long tmp; if (_content != null - && !org.castor.util.CycleBreaker.startingToCycle(_content)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) { result = 37 * result + _content.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_content); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Newick.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Newick.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Newick.java 2011-10-17 23:43:32.628672117 +0200 @@ -97,27 +97,27 @@ if (temp._content == null) return false; if (this._content != temp._content) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._content); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._content); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._content); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._content); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } ; return false; } if (!thcycle) { if (!this._content.equals(temp._content)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._content); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._content); } } } else if (temp._content != null) @@ -126,27 +126,27 @@ if (temp._title == null) return false; if (this._title != temp._title) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._title); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._title); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._title); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._title); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title); } ; return false; } if (!thcycle) { if (!this._title.equals(temp._title)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._title); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._title); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title); } } } else if (temp._title != null) @@ -155,27 +155,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -184,29 +184,29 @@ if (temp._modifiable == null) return false; if (this._modifiable != temp._modifiable) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._modifiable); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._modifiable); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } ; return false; } if (!thcycle) { if (!this._modifiable.equals(temp._modifiable)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } } } else if (temp._modifiable != null) @@ -268,22 +268,22 @@ long tmp; if (_content != null - && !org.castor.util.CycleBreaker.startingToCycle(_content)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_content)) { result = 37 * result + _content.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_content); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_content); } - if (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) { + if (_title != null && !org.castor.core.util.CycleBreaker.startingToCycle(_title)) { result = 37 * result + _title.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_title); } - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_modifiable != null - && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) { result = 37 * result + _modifiable.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Provenance.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Provenance.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Provenance.java 2011-10-17 23:43:32.640672117 +0200 @@ -116,29 +116,29 @@ if (temp._entryList == null) return false; if (this._entryList != temp._entryList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._entryList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._entryList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._entryList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._entryList); } ; return false; } if (!thcycle) { if (!this._entryList.equals(temp._entryList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._entryList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._entryList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._entryList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._entryList); } } } else if (temp._entryList != null) @@ -213,9 +213,9 @@ long tmp; if (_entryList != null - && !org.castor.util.CycleBreaker.startingToCycle(_entryList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_entryList)) { result = 37 * result + _entryList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_entryList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_entryList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Sequence.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Sequence.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Sequence.java 2011-10-17 23:43:32.640672117 +0200 @@ -170,27 +170,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -199,29 +199,29 @@ if (temp._dictionary == null) return false; if (this._dictionary != temp._dictionary) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._dictionary); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._dictionary); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dictionary); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dictionary); } ; return false; } if (!thcycle) { if (!this._dictionary.equals(temp._dictionary)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dictionary); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dictionary); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._dictionary); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dictionary); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dictionary); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dictionary); } } } else if (temp._dictionary != null) @@ -230,29 +230,29 @@ if (temp._dbRefList == null) return false; if (this._dbRefList != temp._dbRefList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._dbRefList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._dbRefList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dbRefList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); } ; return false; } if (!thcycle) { if (!this._dbRefList.equals(temp._dbRefList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dbRefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._dbRefList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dbRefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dbRefList); } } } else if (temp._dbRefList != null) @@ -261,29 +261,29 @@ if (temp._vxrefList == null) return false; if (this._vxrefList != temp._vxrefList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._vxrefList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._vxrefList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vxrefList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); } ; return false; } if (!thcycle) { if (!this._vxrefList.equals(temp._vxrefList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vxrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._vxrefList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._vxrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._vxrefList); } } } else if (temp._vxrefList != null) @@ -431,24 +431,24 @@ int result = super.hashCode(); long tmp; - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_dictionary != null - && !org.castor.util.CycleBreaker.startingToCycle(_dictionary)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_dictionary)) { result = 37 * result + _dictionary.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_dictionary); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_dictionary); } if (_dbRefList != null - && !org.castor.util.CycleBreaker.startingToCycle(_dbRefList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_dbRefList)) { result = 37 * result + _dbRefList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_dbRefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_dbRefList); } if (_vxrefList != null - && !org.castor.util.CycleBreaker.startingToCycle(_vxrefList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_vxrefList)) { result = 37 * result + _vxrefList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_vxrefList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_vxrefList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/SequenceType.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/SequenceType.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/SequenceType.java 2011-10-17 23:43:32.624672117 +0200 @@ -171,29 +171,29 @@ if (temp._sequence == null) return false; if (this._sequence != temp._sequence) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._sequence); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._sequence); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequence); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequence); } ; return false; } if (!thcycle) { if (!this._sequence.equals(temp._sequence)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequence); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequence); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._sequence); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._sequence); } } } else if (temp._sequence != null) @@ -202,27 +202,27 @@ if (temp._name == null) return false; if (this._name != temp._name) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._name); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._name); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } ; return false; } if (!thcycle) { if (!this._name.equals(temp._name)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._name); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._name); } } } else if (temp._name != null) @@ -231,18 +231,18 @@ if (temp._description == null) return false; if (this._description != temp._description) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._description); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._description); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._description); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._description); } ; @@ -250,14 +250,14 @@ } if (!thcycle) { if (!this._description.equals(temp._description)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._description); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._description); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._description); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._description); } } } else if (temp._description != null) @@ -266,18 +266,18 @@ if (temp._propertyList == null) return false; if (this._propertyList != temp._propertyList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._propertyList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._propertyList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); } ; @@ -285,14 +285,14 @@ } if (!thcycle) { if (!this._propertyList.equals(temp._propertyList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList); } } } else if (temp._propertyList != null) @@ -434,23 +434,23 @@ result = 37 * result + (int) (_start ^ (_start >>> 32)); result = 37 * result + (int) (_end ^ (_end >>> 32)); if (_sequence != null - && !org.castor.util.CycleBreaker.startingToCycle(_sequence)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_sequence)) { result = 37 * result + _sequence.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_sequence); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_sequence); } - if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) { + if (_name != null && !org.castor.core.util.CycleBreaker.startingToCycle(_name)) { result = 37 * result + _name.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_name); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_name); } if (_description != null - && !org.castor.util.CycleBreaker.startingToCycle(_description)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_description)) { result = 37 * result + _description.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_description); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_description); } if (_propertyList != null - && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Tree.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/Tree.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/Tree.java 2011-10-17 23:43:32.624672117 +0200 @@ -219,27 +219,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -248,29 +248,29 @@ if (temp._modifiable == null) return false; if (this._modifiable != temp._modifiable) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._modifiable); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._modifiable); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } ; return false; } if (!thcycle) { if (!this._modifiable.equals(temp._modifiable)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } } } else if (temp._modifiable != null) @@ -279,27 +279,27 @@ if (temp._title == null) return false; if (this._title != temp._title) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._title); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._title); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._title); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._title); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title); } ; return false; } if (!thcycle) { if (!this._title.equals(temp._title)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._title); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._title); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._title); } } } else if (temp._title != null) @@ -308,29 +308,29 @@ if (temp._newickList == null) return false; if (this._newickList != temp._newickList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._newickList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._newickList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._newickList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._newickList); } ; return false; } if (!thcycle) { if (!this._newickList.equals(temp._newickList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._newickList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._newickList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._newickList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._newickList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._newickList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._newickList); } } } else if (temp._newickList != null) @@ -339,18 +339,18 @@ if (temp._treenodeList == null) return false; if (this._treenodeList != temp._treenodeList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._treenodeList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._treenodeList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._treenodeList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._treenodeList); } ; @@ -358,14 +358,14 @@ } if (!thcycle) { if (!this._treenodeList.equals(temp._treenodeList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._treenodeList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._treenodeList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._treenodeList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treenodeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treenodeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treenodeList); } } } else if (temp._treenodeList != null) @@ -374,18 +374,18 @@ if (temp._propertyList == null) return false; if (this._propertyList != temp._propertyList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._propertyList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._propertyList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); } ; @@ -393,14 +393,14 @@ } if (!thcycle) { if (!this._propertyList.equals(temp._propertyList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._propertyList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._propertyList); } } } else if (temp._propertyList != null) @@ -409,29 +409,29 @@ if (temp._provenance == null) return false; if (this._provenance != temp._provenance) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._provenance); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._provenance); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } ; return false; } if (!thcycle) { if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } } } else if (temp._provenance != null) @@ -651,38 +651,38 @@ int result = super.hashCode(); long tmp; - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_modifiable != null - && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) { result = 37 * result + _modifiable.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable); } - if (_title != null && !org.castor.util.CycleBreaker.startingToCycle(_title)) { + if (_title != null && !org.castor.core.util.CycleBreaker.startingToCycle(_title)) { result = 37 * result + _title.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_title); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_title); } if (_newickList != null - && !org.castor.util.CycleBreaker.startingToCycle(_newickList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_newickList)) { result = 37 * result + _newickList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_newickList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_newickList); } if (_treenodeList != null - && !org.castor.util.CycleBreaker.startingToCycle(_treenodeList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_treenodeList)) { result = 37 * result + _treenodeList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_treenodeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_treenodeList); } if (_propertyList != null - && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_propertyList)) { result = 37 * result + _propertyList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_propertyList); } if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/User.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/User.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/User.java 2011-10-17 23:43:32.640672117 +0200 @@ -85,29 +85,29 @@ if (temp._fullname == null) return false; if (this._fullname != temp._fullname) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._fullname); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._fullname); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._fullname); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._fullname); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._fullname); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._fullname); } ; return false; } if (!thcycle) { if (!this._fullname.equals(temp._fullname)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._fullname); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._fullname); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._fullname); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._fullname); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._fullname); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._fullname); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._fullname); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._fullname); } } } else if (temp._fullname != null) @@ -116,18 +116,18 @@ if (temp._organization == null) return false; if (this._organization != temp._organization) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._organization); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._organization); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._organization); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._organization); } ; @@ -135,14 +135,14 @@ } if (!thcycle) { if (!this._organization.equals(temp._organization)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._organization); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._organization); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._organization); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._organization); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._organization); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._organization); } } } else if (temp._organization != null) @@ -183,14 +183,14 @@ long tmp; if (_fullname != null - && !org.castor.util.CycleBreaker.startingToCycle(_fullname)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_fullname)) { result = 37 * result + _fullname.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_fullname); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_fullname); } if (_organization != null - && !org.castor.util.CycleBreaker.startingToCycle(_organization)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_organization)) { result = 37 * result + _organization.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_organization); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_organization); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/VAMSAS.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/VAMSAS.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/VAMSAS.java 2011-10-17 23:43:32.624672117 +0200 @@ -168,27 +168,27 @@ if (temp._id == null) return false; if (this._id != temp._id) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } ; return false; } if (!thcycle) { if (!this._id.equals(temp._id)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._id); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id); } } } else if (temp._id != null) @@ -197,29 +197,29 @@ if (temp._modifiable == null) return false; if (this._modifiable != temp._modifiable) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._modifiable); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._modifiable); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } ; return false; } if (!thcycle) { if (!this._modifiable.equals(temp._modifiable)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable); } } } else if (temp._modifiable != null) @@ -228,29 +228,29 @@ if (temp._treeList == null) return false; if (this._treeList != temp._treeList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._treeList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._treeList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList); } ; return false; } if (!thcycle) { if (!this._treeList.equals(temp._treeList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList); } } } else if (temp._treeList != null) @@ -259,18 +259,18 @@ if (temp._dataSetList == null) return false; if (this._dataSetList != temp._dataSetList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._dataSetList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._dataSetList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._dataSetList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._dataSetList); } ; @@ -278,14 +278,14 @@ } if (!thcycle) { if (!this._dataSetList.equals(temp._dataSetList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._dataSetList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._dataSetList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._dataSetList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._dataSetList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dataSetList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dataSetList); } } } else if (temp._dataSetList != null) @@ -432,24 +432,24 @@ int result = super.hashCode(); long tmp; - if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) { + if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) { result = 37 * result + _id.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_id); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_id); } if (_modifiable != null - && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) { result = 37 * result + _modifiable.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable); } if (_treeList != null - && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) { result = 37 * result + _treeList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_treeList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList); } if (_dataSetList != null - && !org.castor.util.CycleBreaker.startingToCycle(_dataSetList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_dataSetList)) { result = 37 * result + _dataSetList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_dataSetList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_dataSetList); } return result; Index: libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/VamsasDocument.java =================================================================== --- libvamsas-client-java-0.2+git2011.10.17+1b42648.orig/src/uk/ac/vamsas/objects/core/VamsasDocument.java 2011-10-17 23:31:53.000000000 +0200 +++ libvamsas-client-java-0.2+git2011.10.17+1b42648/src/uk/ac/vamsas/objects/core/VamsasDocument.java 2011-10-17 23:43:32.644672117 +0200 @@ -218,27 +218,27 @@ if (temp._version == null) return false; if (this._version != temp._version) { - thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version); - tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version); + thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._version); + tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._version); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version); } ; return false; } if (!thcycle) { if (!this._version.equals(temp._version)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._version); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._version); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._version); } } } else if (temp._version != null) @@ -247,29 +247,29 @@ if (temp._lockFile == null) return false; if (this._lockFile != temp._lockFile) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._lockFile); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._lockFile); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._lockFile); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._lockFile); } ; return false; } if (!thcycle) { if (!this._lockFile.equals(temp._lockFile)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._lockFile); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._lockFile); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._lockFile); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._lockFile); } } } else if (temp._lockFile != null) @@ -278,29 +278,29 @@ if (temp._provenance == null) return false; if (this._provenance != temp._provenance) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._provenance); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._provenance); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } ; return false; } if (!thcycle) { if (!this._provenance.equals(temp._provenance)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._provenance); } } } else if (temp._provenance != null) @@ -309,29 +309,29 @@ if (temp._VAMSASList == null) return false; if (this._VAMSASList != temp._VAMSASList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._VAMSASList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._VAMSASList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); } ; return false; } if (!thcycle) { if (!this._VAMSASList.equals(temp._VAMSASList)) { - org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); return false; } - org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); - org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(this._VAMSASList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList); } } } else if (temp._VAMSASList != null) @@ -340,18 +340,18 @@ if (temp._applicationDataList == null) return false; if (this._applicationDataList != temp._applicationDataList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._applicationDataList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._applicationDataList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._applicationDataList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._applicationDataList); } ; @@ -359,15 +359,15 @@ } if (!thcycle) { if (!this._applicationDataList.equals(temp._applicationDataList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._applicationDataList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._applicationDataList); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._applicationDataList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._applicationDataList); } } @@ -377,18 +377,18 @@ if (temp._attachmentList == null) return false; if (this._attachmentList != temp._attachmentList) { - thcycle = org.castor.util.CycleBreaker + thcycle = org.castor.core.util.CycleBreaker .startingToCycle(this._attachmentList); - tmcycle = org.castor.util.CycleBreaker + tmcycle = org.castor.core.util.CycleBreaker .startingToCycle(temp._attachmentList); if (thcycle != tmcycle) { if (!thcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._attachmentList); } ; if (!tmcycle) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._attachmentList); } ; @@ -396,15 +396,15 @@ } if (!thcycle) { if (!this._attachmentList.equals(temp._attachmentList)) { - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._attachmentList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._attachmentList); return false; } - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(this._attachmentList); - org.castor.util.CycleBreaker + org.castor.core.util.CycleBreaker .releaseCycleHandle(temp._attachmentList); } } @@ -622,34 +622,34 @@ long tmp; if (_version != null - && !org.castor.util.CycleBreaker.startingToCycle(_version)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_version)) { result = 37 * result + _version.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_version); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_version); } if (_lockFile != null - && !org.castor.util.CycleBreaker.startingToCycle(_lockFile)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_lockFile)) { result = 37 * result + _lockFile.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_lockFile); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_lockFile); } if (_provenance != null - && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_provenance)) { result = 37 * result + _provenance.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_provenance); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_provenance); } if (_VAMSASList != null - && !org.castor.util.CycleBreaker.startingToCycle(_VAMSASList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_VAMSASList)) { result = 37 * result + _VAMSASList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_VAMSASList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_VAMSASList); } if (_applicationDataList != null - && !org.castor.util.CycleBreaker.startingToCycle(_applicationDataList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_applicationDataList)) { result = 37 * result + _applicationDataList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_applicationDataList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_applicationDataList); } if (_attachmentList != null - && !org.castor.util.CycleBreaker.startingToCycle(_attachmentList)) { + && !org.castor.core.util.CycleBreaker.startingToCycle(_attachmentList)) { result = 37 * result + _attachmentList.hashCode(); - org.castor.util.CycleBreaker.releaseCycleHandle(_attachmentList); + org.castor.core.util.CycleBreaker.releaseCycleHandle(_attachmentList); } return result;