Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 19 Oct 2017 16:27:56 +0200
Description: Use Debian packaged jsoncpp as well as get completely rid
 of blatSrc in automake configuration

--- a/gbtools/Makefile.am
+++ b/gbtools/Makefile.am
@@ -10,11 +10,7 @@
 
 libgbtools_la_LIBADD = src/gbtoolsGUI/libgbtoolsGUI.la src/gbtoolsUtils/libgbtoolsUtils.la
 
-if USE_BLATSRC
-libgbtools_la_LIBADD += src/blatSrc/libblatSrc.la
-endif
-
-libgbtools_la_LIBADD += src/jsoncpp/libjsoncpp.la
+libgbtools_la_LIBADD += -ljsoncpp
 
 if USE_LIBCURL
 libgbtools_la_LIBADD += src/gbtoolsCurl/libgbtoolsCurl.la src/gbtoolsPfetch/libgbtoolsPfetch.la
--- a/gbtools/configure.ac
+++ b/gbtools/configure.ac
@@ -19,8 +19,6 @@
 src/gbtoolsCurl/Makefile
 src/gbtoolsTrackhub/Makefile
 src/gbtoolsPfetch/Makefile
-src/jsoncpp/Makefile
-src/blatSrc/Makefile
 ])
 
 
--- a/gbtools/src/Makefile.am
+++ b/gbtools/src/Makefile.am
@@ -1,12 +1,6 @@
 
 SUBDIRS = include gbtoolsUtils gbtoolsGUI
 
-SUBDIRS += jsoncpp
-
-if USE_BLATSRC
-SUBDIRS += blatSrc
-endif
-
 if USE_LIBCURL
 SUBDIRS += gbtoolsCurl gbtoolsPfetch
 SUBDIRS += gbtoolsTrackhub
--- a/gbtools/src/include/Makefile.am
+++ b/gbtools/src/include/Makefile.am
@@ -6,210 +6,6 @@
 gbtools/gbtoolsGUI.hpp \
 gbtools/gbtoolsPfetch.hpp \
 gbtools/gbtoolsUtils.hpp \
-json/json.h \
-json/json-forwards.h \
-blatSrc/ace.h \
-blatSrc/aliType.h \
-blatSrc/annoAssembly.h \
-blatSrc/annoFilter.h \
-blatSrc/annoFormatTab.h \
-blatSrc/annoFormatter.h \
-blatSrc/annoGrateWig.h \
-blatSrc/annoGrator.h \
-blatSrc/annoGratorQuery.h \
-blatSrc/annoOption.h \
-blatSrc/annoRow.h \
-blatSrc/annoStreamBigBed.h \
-blatSrc/annoStreamBigWig.h \
-blatSrc/annoStreamTab.h \
-blatSrc/annoStreamVcf.h \
-blatSrc/annoStreamer.h \
-blatSrc/apacheLog.h \
-blatSrc/asParse.h \
-blatSrc/axt.h \
-blatSrc/bPlusTree.h \
-blatSrc/bamFile.h \
-blatSrc/bandExt.h \
-blatSrc/base64.h \
-blatSrc/basicBed.h \
-blatSrc/bbiFile.h \
-blatSrc/bigBed.h \
-blatSrc/bigWig.h \
-blatSrc/binRange.h \
-blatSrc/bits.h \
-blatSrc/blastParse.h \
-blatSrc/boxClump.h \
-blatSrc/boxLump.h \
-blatSrc/bwgInternal.h \
-blatSrc/cda.h \
-blatSrc/cgi_build_rules.mk \
-blatSrc/chain.h \
-blatSrc/chainBlock.h \
-blatSrc/chainConnect.h \
-blatSrc/chainToAxt.h \
-blatSrc/chainToPsl.h \
-blatSrc/cheapcgi.h \
-blatSrc/cirTree.h \
-blatSrc/codebias.h \
-blatSrc/common.h \
-blatSrc/common.mk \
-blatSrc/correlate.h \
-blatSrc/crTree.h \
-blatSrc/crudeali.h \
-blatSrc/diGraph.h \
-blatSrc/diGraph.h.97 \
-blatSrc/dlist.h \
-blatSrc/dnaLoad.h \
-blatSrc/dnaMarkov.h \
-blatSrc/dnaMotif.h \
-blatSrc/dnaseq.h \
-blatSrc/dnautil.h \
-blatSrc/dtdParse.h \
-blatSrc/dyOut.h \
-blatSrc/dystring.h \
-blatSrc/elmTree.h \
-blatSrc/emblParse.h \
-blatSrc/ens.h \
-blatSrc/errAbort.h \
-blatSrc/errCatch.h \
-blatSrc/fa.h \
-blatSrc/fieldedTable.h \
-blatSrc/filePath.h \
-blatSrc/flydna.h \
-blatSrc/fof.h \
-blatSrc/fq.h \
-blatSrc/fuzzyFind.h \
-blatSrc/gapCalc.h \
-blatSrc/gdf.h \
-blatSrc/genoFind.h \
-blatSrc/genomeRangeTree.h \
-blatSrc/gfClientLib.h \
-blatSrc/gfPcrLib.h \
-blatSrc/gfWebLib.h \
-blatSrc/gff.h \
-blatSrc/gff3.h \
-blatSrc/gfxPoly.h \
-blatSrc/gifLabel.h \
-blatSrc/hacTree.h \
-blatSrc/hash.h \
-blatSrc/hex.h \
-blatSrc/hgGene.h \
-blatSrc/hgap.h \
-blatSrc/hgdb.h \
-blatSrc/histogram.h \
-blatSrc/hmac.h \
-blatSrc/hmmPfamParse.h \
-blatSrc/hmmstats.h \
-blatSrc/htmlPage.h \
-blatSrc/htmshell.h \
-blatSrc/https.h \
-blatSrc/intValTree.h \
-blatSrc/internet.h \
-blatSrc/itsa.h \
-blatSrc/iupac.h \
-blatSrc/jointalign.h \
-blatSrc/jpegSize.h \
-blatSrc/jsonParse.h \
-blatSrc/jsonWrite.h \
-blatSrc/keys.h \
-blatSrc/knetUdc.h \
-blatSrc/kxTok.h \
-blatSrc/linefile.h \
-blatSrc/localEnvironment.mk \
-blatSrc/localmem.h \
-blatSrc/log.h \
-blatSrc/longToList.h \
-blatSrc/maDbRep.h \
-blatSrc/maToFf.h \
-blatSrc/maf.h \
-blatSrc/mailViaPipe.h \
-blatSrc/md5.h \
-blatSrc/memalloc.h \
-blatSrc/memgfx.h \
-blatSrc/meta.h \
-blatSrc/metaWig.h \
-blatSrc/mime.h \
-blatSrc/net.h \
-blatSrc/nib.h \
-blatSrc/nibTwo.h \
-blatSrc/nt4.h \
-blatSrc/obscure.h \
-blatSrc/oldGff.h \
-blatSrc/oligoTm.h \
-blatSrc/ooc.h \
-blatSrc/options.h \
-blatSrc/pairDistance.h \
-blatSrc/pairHmm.h \
-blatSrc/paraFetch.h \
-blatSrc/patSpace.h \
-blatSrc/peakCluster.h \
-blatSrc/phyloTree.h \
-blatSrc/pipeline.h \
-blatSrc/portable.h \
-blatSrc/psGfx.h \
-blatSrc/psPoly.h \
-blatSrc/pscmGfx.h \
-blatSrc/psl.h \
-blatSrc/pslTbl.h \
-blatSrc/pslTransMap.h \
-blatSrc/pthreadDoList.h \
-blatSrc/pthreadWrap.h \
-blatSrc/qa.h \
-blatSrc/quickHeap.h \
-blatSrc/quotedP.h \
-blatSrc/ra.h \
-blatSrc/raToStruct.h \
-blatSrc/rainbow.h \
-blatSrc/rangeTree.h \
-blatSrc/rbTree.h \
-blatSrc/regexHelper.h \
-blatSrc/repMask.h \
-blatSrc/rle.h \
-blatSrc/rnautil.h \
-blatSrc/rql.h \
-blatSrc/rudp.h \
-blatSrc/scoreWindow.h \
-blatSrc/seg.h \
-blatSrc/seqOut.h \
-blatSrc/seqStats.h \
-blatSrc/shaRes.h \
-blatSrc/sig.h \
-blatSrc/slog.h \
-blatSrc/snof.h \
-blatSrc/snofmake.h \
-blatSrc/spaceSaver.h \
-blatSrc/spacedColumn.h \
-blatSrc/spacedSeed.h \
-blatSrc/splatAli.h \
-blatSrc/splix.h \
-blatSrc/sqlList.h \
-blatSrc/sqlNum.h \
-blatSrc/subText.h \
-blatSrc/sufa.h \
-blatSrc/sufx.h \
-blatSrc/supStitch.h \
-blatSrc/synQueue.h \
-blatSrc/tabRow.h \
-blatSrc/textOut.h \
-blatSrc/tokenizer.h \
-blatSrc/trans3.h \
-blatSrc/trix.h \
-blatSrc/twoBit.h \
-blatSrc/udc.h \
-blatSrc/unfin.h \
-blatSrc/userApp.mk \
-blatSrc/vGfx.h \
-blatSrc/vcf.h \
-blatSrc/vcfBits.h \
-blatSrc/verbose.h \
-blatSrc/wormdna.h \
-blatSrc/xAli.h \
-blatSrc/xa.h \
-blatSrc/xap.h \
-blatSrc/xenalign.h \
-blatSrc/xmlEscape.h \
-blatSrc/xp.h \
-blatSrc/zlibFace.h \
 $(NULL)
 
 # Extra files to remove for the maintainer-clean target.
--- a/gbtools/src/Makefile.am.common
+++ b/gbtools/src/Makefile.am.common
@@ -4,7 +4,7 @@
 AM_CPPFLAGS = \
 $(DEPS_CFLAGS) \
 -I$(top_srcdir)/src/include \
--I$(top_srcdir)/src/include/blatSrc
+-I/usr/include/jsoncpp
 
 AM_CXXFLAGS = -std=c++11 -g -Wall
 
--- a/doc/Design_notes/Makefile
+++ b/doc/Design_notes/Makefile
@@ -185,7 +185,7 @@
 CYGPATH_W = echo
 DEFS = -DHAVE_CONFIG_H
 DEPDIR = .deps
-DEPS_CFLAGS = -pthread -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/harfbuzz  
+DEPS_CFLAGS = -pthread -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/harfbuzz
 DEPS_LIBS = -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfontconfig -lgobject-2.0 -lglib-2.0 -lfreetype  
 DEPS_SQLITE3_CFLAGS =  
 DEPS_SQLITE3_LIBS = -lsqlite3  
--- a/doc/Design_notes/modules/Makefile
+++ b/doc/Design_notes/modules/Makefile
@@ -185,7 +185,7 @@
 CYGPATH_W = echo
 DEFS = -DHAVE_CONFIG_H
 DEPDIR = .deps
-DEPS_CFLAGS = -pthread -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/harfbuzz  
+DEPS_CFLAGS = -pthread -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/gtk-2.0 -I/usr/lib/x86_64-linux-gnu/gtk-2.0/include -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/freetype2 -I/usr/include/pixman-1 -I/usr/include/libpng12 -I/usr/include/harfbuzz
 DEPS_LIBS = -lgtk-x11-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lpangocairo-1.0 -lgdk_pixbuf-2.0 -lcairo -lpango-1.0 -lfontconfig -lgobject-2.0 -lglib-2.0 -lfreetype  
 DEPS_SQLITE3_CFLAGS =  
 DEPS_SQLITE3_LIBS = -lsqlite3  
--- a/configure.ac
+++ b/configure.ac
@@ -70,7 +70,7 @@
 AC_CHECK_FUNCS([dup2 floor gethostbyname memset socket sqrt strcasecmp strchr strcspn strerror strncasecmp strrchr strstr strtol uname])
 
 # Check for dependencies required by all executables
-PKG_CHECK_MODULES([DEPS], [glib-2.0 gtk+-2.0 >= 2.10])
+PKG_CHECK_MODULES([DEPS], [glib-2.0 gtk+-2.0 >= 2.10 jsoncpp])
 
 # Check for dependencies required by sqlite code
 PKG_CHECK_MODULES([DEPS_SQLITE3], [sqlite3], [HAVE_SQLITE3=1], [HAVE_SQLITE3=0])