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/* @source ensslice ***********************************************************
**
** Ensembl Slice functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.68 $
** @modified 2009 by Alan Bleasby for incorporation into EMBOSS core
** @modified $Date: 2013/02/17 13:02:40 $ by $Author: mks $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA 02110-1301, USA.
**
******************************************************************************/
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "enscache.h"
#include "ensassemblyexception.h"
#include "ensassemblymapper.h"
#include "ensattribute.h"
#include "ensmapper.h"
#include "ensprojectionsegment.h"
#include "enssequence.h"
#include "enssequenceedit.h"
#include "ensslice.h"
#include "ensrepeat.h"
#include "enstable.h"
#include "enstranslation.h"
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== global variables ============================ */
/* ========================================================================= */
/* ========================================================================= */
/* ============================= private data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private constants =========================== */
/* ========================================================================= */
/* @conststatic sliceKSequenceeditCode ****************************************
**
** Ensembl Sequence Edit objects for Ensembl Slice objects are a sub-set of
** Ensembl Attribute objects that provide information about modifications of
** the Slice sequence. Ensembl Attribute objects with the following codes are
** Sequence Edit objects on the Slice-level.
**
** _rna_edit: General sequence edit
**
******************************************************************************/
static const char *sliceKSequenceeditCode[] =
{
"_rna_edit",
(const char *) NULL
};
/* @conststatic sliceKType ****************************************************
**
** The Ensembl Slice Type member is enumerated in both, the SQL table
** definition and the data structure. The following strings are used for
** conversion in database operations and correspond to EnsESliceType.
**
******************************************************************************/
static const char *const sliceKType[] =
{
"",
"Linear",
"Circular",
"LocusReferenceGenome",
(const char *) NULL
};
/* @conststatic sliceadaptorKCacheMaxBytes ************************************
**
** Maximum memory size in bytes the Ensembl Slice Adaptor-internal
** Ensembl Cache can use.
**
** 1 << 26 = 64 MiB
**
******************************************************************************/
static const size_t sliceadaptorKCacheMaxBytes = 1U << 26U;
/* @conststatic sliceadaptorKCacheMaxCount ************************************
**
** Maximum number of Ensembl Slice objects the Ensembl Slice Adaptor-internal
** Ensembl Cache can hold.
**
** 1 << 16 = 64 Ki
**
******************************************************************************/
static const ajuint sliceadaptorKCacheMaxCount = 1U << 16U;
/* @conststatic sliceadaptorKCacheMaxSize *************************************
**
** Maximum memory size in bytes of an Ensembl Slice to be allowed into the
** Ensembl Slice Adaptor-internal Ensembl Cache.
**
******************************************************************************/
static const size_t sliceadaptorKCacheMaxSize = 0U;
/* ========================================================================= */
/* =========================== private variables =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private functions =========================== */
/* ========================================================================= */
static EnsPProjectionsegment sliceConstrain(EnsPSlice slice);
static AjBool sliceProject(EnsPSlice slice,
EnsPCoordsystem trgcs,
AjPList pss);
static int listSliceCompareIdentifierAscending(
const void *item1,
const void *item2);
static int listSliceCompareIdentifierDescending(
const void *item1,
const void *item2);
static int listSliceCompareNameAscending(
const void *item1,
const void *item2);
static int listSliceCompareNameDescending(
const void *item1,
const void *item2);
static void sliceadaptorCacheDelete(void **Pvalue);
/* ========================================================================= */
/* ======================= All functions by section ======================== */
/* ========================================================================= */
/* @filesection ensslice ******************************************************
**
** @nam1rule ens Function belongs to the Ensembl library
**
******************************************************************************/
/* @datasection [EnsPSlice] Ensembl Slice *************************************
**
** @nam2rule Slice Functions for manipulating Ensembl Slice objects
**
** @cc Bio::EnsEMBL::Slice
** @cc CVS Revision: 1.301
** @cc CVS Tag: branch-ensembl-68
**
** @cc Bio::EnsEMBL::CircularSlice
** @cc CVS Revision: 1.12
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Slice by pointer.
** It is the responsibility of the user to first destroy any previous
** Slice. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPSlice]
**
** @nam3rule New Constructor
** @nam4rule Cpy Constructor with existing object
** @nam4rule Ini Constructor with initial values
** @nam4rule Ref Constructor by incrementing the reference counter
** @nam4rule Seq Constructor with a sequence
**
** @argrule Cpy slice [const EnsPSlice] Ensembl Slice
** @argrule Ini sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @argrule Ini sr [EnsPSeqregion] Ensembl Sequence Region
** @argrule Ini start [ajint] Ensembl Sequence Region start
** @argrule Ini end [ajint] Ensembl Sequence Region end
** @argrule Ini strand [ajint] Ensembl Sequence Region strand
** @argrule Ref slice [EnsPSlice] Ensembl Slice
** @argrule Seq sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @argrule Seq sr [EnsPSeqregion] Ensembl Sequence Region
** @argrule Seq start [ajint] Ensembl Sequence Region start
** @argrule Seq end [ajint] Ensembl Sequence Region end
** @argrule Seq strand [ajint] Ensembl Sequence Region strand
** @argrule Seq sequence [AjPStr] Sequence (optional)
**
** @valrule * [EnsPSlice] Ensembl Slice or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensSliceNewCpy *******************************************************
**
** Object-based constructor function, which returns an independent object.
**
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [EnsPSlice] Ensembl Slice or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPSlice ensSliceNewCpy(const EnsPSlice slice)
{
EnsPSlice pthis = NULL;
if (!slice)
return NULL;
AJNEW0(pthis);
pthis->Adaptor = slice->Adaptor;
pthis->Seqregion = ensSeqregionNewRef(slice->Seqregion);
if (slice->Sequence)
pthis->Sequence = ajStrNewRef(slice->Sequence);
pthis->Topology = slice->Topology;
pthis->Type = slice->Type;
pthis->Start = slice->Start;
pthis->End = slice->End;
pthis->Strand = slice->Strand;
pthis->Use = 1U;
return pthis;
}
/* @func ensSliceNewIni *******************************************************
**
** Constructor for an Ensembl Slice with initial values.
**
** @cc Bio::EnsEMBL::Slice::new
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [u] sr [EnsPSeqregion] Ensembl Sequence Region
** @param [r] start [ajint] Ensembl Sequence Region start
** @param [r] end [ajint] Ensembl Sequence Region end
** @param [r] strand [ajint] Ensembl Sequence Region strand
**
** @return [EnsPSlice] Ensembl Slice or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPSlice ensSliceNewIni(EnsPSliceadaptor sla,
EnsPSeqregion sr,
ajint start,
ajint end,
ajint strand)
{
EnsPSlice slice = NULL;
if (!sr)
{
ajDebug("ensSliceNewIni requires an Ensembl Sequence Region.\n");
return NULL;
}
if (ensCoordsystemGetToplevel(ensSeqregionGetCoordsystem(sr)))
{
ajDebug("ensSliceNewIni cannot create a Slice on a Sequence Region "
"with a top-level Coordinate System.\n");
return NULL;
}
if ((strand != 1) && (strand != -1))
{
ajDebug("ensSliceNewIni requires a strand of either 1 or -1 "
"not %d.\n", strand);
return NULL;
}
AJNEW0(slice);
slice->Adaptor = sla;
slice->Seqregion = ensSeqregionNewRef(sr);
slice->Sequence = NULL;
slice->Topology = ensESliceTopologyNULL;
slice->Type = ensSliceTypeFromSeqregion(sr);
slice->Start = start;
slice->End = end;
slice->Strand = strand;
slice->Use = 1U;
return slice;
}
/* @func ensSliceNewRef *******************************************************
**
** Ensembl Object referencing function, which returns a pointer to the
** Ensembl Object passed in and increases its reference count.
**
** @param [u] slice [EnsPSlice] Ensembl Slice
**
** @return [EnsPSlice] Ensembl Slice or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPSlice ensSliceNewRef(EnsPSlice slice)
{
if (!slice)
return NULL;
slice->Use++;
return slice;
}
/* @func ensSliceNewSeq *******************************************************
**
** Construct a new Ensembl Slice with sequence information.
**
** @cc Bio::EnsEMBL::Slice::new
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [u] sr [EnsPSeqregion] Ensembl Sequence Region
** @param [r] start [ajint] Ensembl Sequence Region start
** @param [r] end [ajint] Ensembl Sequence Region end
** @param [r] strand [ajint] Ensembl Sequence Region strand
** @param [u] sequence [AjPStr] Sequence (optional)
**
** @return [EnsPSlice] Ensembl Slice or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPSlice ensSliceNewSeq(EnsPSliceadaptor sla,
EnsPSeqregion sr,
ajint start,
ajint end,
ajint strand,
AjPStr sequence)
{
EnsPSlice slice = NULL;
if (!sr)
{
ajDebug("ensSliceNewSeq requires an Ensembl Sequence Region.\n");
return NULL;
}
if (ensCoordsystemGetToplevel(ensSeqregionGetCoordsystem(sr)))
{
ajDebug("ensSliceNewSeq cannot create a Slice on a Sequence Region "
"with a top-level Coordinate System.\n");
return NULL;
}
if (!start)
start = 1;
if (!end)
end = ensSeqregionGetLength(sr);
if (start > (end + 1))
{
ajDebug("ensSliceNewSeq requires that the start coordinate %d is "
"less than or equal to the end coordinate %d + 1.\n",
start, end);
return NULL;
}
if (!strand)
strand = 1;
if ((strand != 1) && (strand != -1))
{
ajDebug("ensSliceNewSeq requires a strand of either 1 or -1 "
"not %d.\n", strand);
return NULL;
}
if (sequence &&
(ajStrGetLen(sequence) != (ajuint) ensSeqregionGetLength(sr)))
{
ajDebug("ensSliceNewSeq requires that the Sequence Region length %d "
"matches the length of the Sequence string %u.\n",
ensSeqregionGetLength(sr), ajStrGetLen(sequence));
return NULL;
}
AJNEW0(slice);
slice->Adaptor = sla;
slice->Seqregion = ensSeqregionNewRef(sr);
if (sequence)
slice->Sequence = ajStrNewRef(sequence);
slice->Topology = ensESliceTopologyNULL;
slice->Type = ensSliceTypeFromSeqregion(sr);
slice->Start = start;
slice->End = end;
slice->Strand = strand;
slice->Use = 1U;
return slice;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Slice object.
**
** @fdata [EnsPSlice]
**
** @nam3rule Del Destroy (free) an Ensembl Slice
**
** @argrule * Pslice [EnsPSlice*] Ensembl Slice address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensSliceDel **********************************************************
**
** Default destructor for an Ensembl Slice.
**
** @param [d] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensSliceDel(EnsPSlice *Pslice)
{
EnsPSlice pthis = NULL;
if (!Pslice)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensSliceDel"))
{
ajDebug("ensSliceDel\n"
" *Pslice %p\n",
*Pslice);
ensSliceTrace(*Pslice, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Pslice) || --pthis->Use)
{
*Pslice = NULL;
return;
}
ensSeqregionDel(&pthis->Seqregion);
ajStrDel(&pthis->Sequence);
ajMemFree((void **) Pslice);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Slice object.
**
** @fdata [EnsPSlice]
**
** @nam3rule Get Return Slice attribute(s)
** @nam4rule Adaptor Return the Ensembl Slice Adaptor
** @nam4rule End Return the end
** @nam4rule Seqregion Return the Ensembl Sequence Region
** @nam4rule Sequence Return the sequence
** @nam4rule Start Return the start
** @nam4rule Strand Return the strand
**
** @argrule * slice [const EnsPSlice] Slice
**
** @valrule Adaptor [EnsPSliceadaptor] Ensembl Slice Adaptor or NULL
** @valrule End [ajint] End or 0
** @valrule Seqregion [EnsPSeqregion] Ensembl Sequence Region or NULL
** @valrule Sequence [const AjPStr] Sequence or NULL
** @valrule Start [ajint] Start or 0
** @valrule Strand [ajint] Strand or 0
**
** @fcategory use
******************************************************************************/
/* @func ensSliceGetAdaptor ***************************************************
**
** Get the Ensembl Slice Adaptor member an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::adaptor
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [EnsPSliceadaptor] Ensembl Slice Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPSliceadaptor ensSliceGetAdaptor(const EnsPSlice slice)
{
return (slice) ? slice->Adaptor : NULL;
}
/* @func ensSliceGetEnd *******************************************************
**
** Get the end coordinate member of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::end
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [ajint] End coordinate or 0
**
** @release 6.2.0
** @@
******************************************************************************/
ajint ensSliceGetEnd(const EnsPSlice slice)
{
return (slice) ? slice->End : 0;
}
/* @func ensSliceGetSeqregion *************************************************
**
** Get the Ensembl Sequence Region member of an Ensembl Slice.
**
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [EnsPSeqregion] Ensembl Sequence Region or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPSeqregion ensSliceGetSeqregion(const EnsPSlice slice)
{
return (slice) ? slice->Seqregion : NULL;
}
/* @func ensSliceGetSequence **************************************************
**
** Get the sequence member of an Ensembl Slice.
**
** NOTE: This function returns only the sequence member that has been set for
** an Ensembl Slice object that is not based on an Ensembl Sequence Region.
** For Ensembl Slice objects based on Ensembl Sequence Region objects the
** sequence is fetched dynamically via ensSliceFetchSequence functions.
**
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [const AjPStr] Sequence or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
const AjPStr ensSliceGetSequence(const EnsPSlice slice)
{
return (slice) ? slice->Sequence : NULL;
}
/* @func ensSliceGetStart *****************************************************
**
** Get the start coordinate member of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::start
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [ajint] Start coordinate or 0
**
** @release 6.2.0
** @@
******************************************************************************/
ajint ensSliceGetStart(const EnsPSlice slice)
{
return (slice) ? slice->Start : 0;
}
/* @func ensSliceGetStrand ****************************************************
**
** Get the strand member of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::strand
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [ajint] Strand information or 0
**
** @release 6.2.0
** @@
******************************************************************************/
ajint ensSliceGetStrand(const EnsPSlice slice)
{
return (slice) ? slice->Strand : 0;
}
/* @section load on demand ****************************************************
**
** Functions for returning members of an Ensembl Slice object,
** which may need loading from an Ensembl SQL database on demand.
**
** @fdata [EnsPSlice]
**
** @nam3rule Load Return Ensembl Slice attribute(s) loaded on demand
** @nam4rule Topology Return the topology
**
** @argrule * slice [EnsPSlice] Ensembl Slice
**
** @valrule Topology [EnsESliceTopology] Topology or ensESliceTopologyNULL
**
** @fcategory use
******************************************************************************/
/* @func ensSliceLoadTopology *************************************************
**
** Load the topology member of an Ensembl Slice.
**
** This is not a simple accessor function, since it will attempt fetching
** Ensembl Attribute objects from the Ensembl database associated with the
** Ensembl Sequence Region.
**
** @cc Bio::EnsEMBL::Slice::is_circular
** @param [u] slice [EnsPSlice] Ensembl Slice
**
** @return [EnsESliceTopology] Topology or ensESliceTopologyNULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsESliceTopology ensSliceLoadTopology(EnsPSlice slice)
{
AjPList attributes = NULL;
AjPStr code = NULL;
EnsPAttribute attribute = NULL;
if (!slice)
return ensESliceTopologyNULL;
if (slice->Topology == ensESliceTopologyNULL)
{
if (slice->Seqregion == NULL)
return ensESliceTopologyNULL;
code = ajStrNewC("circular_seq");
attributes = ajListNew();
ensSliceFetchAllAttributes(slice, code, attributes);
if (ajListGetLength(attributes) > 0)
slice->Topology = ensESliceTopologyCircular;
else
slice->Topology = ensESliceTopologyLinear;
while (ajListPop(attributes, (void **) &attribute))
ensAttributeDel(&attribute);
ajListFree(&attributes);
ajStrDel(&code);
}
return slice->Topology;
}
/* @section member assignment *************************************************
**
** Functions for assigning members of an Ensembl Slice object.
**
** @fdata [EnsPSlice]
**
** @nam3rule Set Set one member of a Slice
** @nam4rule Adaptor Set the Ensembl Slice Adaptor
** @nam4rule Sequence Set the sequence
** @nam4rule Topology Set the topology
**
** @argrule * slice [EnsPSlice] Ensembl Slice object
** @argrule Adaptor sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @argrule Sequence sequence [AjPStr] Sequence
** @argrule Topology sltp [EnsESliceTopology] Ensembl Slice Topology
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory modify
******************************************************************************/
/* @func ensSliceSetAdaptor ***************************************************
**
** Set the Ensembl Slice Adaptor member of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::adaptor
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceSetAdaptor(EnsPSlice slice, EnsPSliceadaptor sla)
{
if (!slice)
return ajFalse;
slice->Adaptor = sla;
return ajTrue;
}
/* @func ensSliceSetSequence **************************************************
**
** Set the sequence member of an Ensembl Slice.
**
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] sequence [AjPStr] Sequence
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceSetSequence(EnsPSlice slice, AjPStr sequence)
{
if (!slice)
return ajFalse;
ajStrDel(&slice->Sequence);
if (sequence)
{
if (ajStrGetLen(sequence) == ensSliceCalculateLength(slice))
slice->Sequence = ajStrNewRef(sequence);
else
ajFatal("ensSliceSetSequence got sequence of length %u, "
"which does not match the length of the Slice %u.\n",
ajStrGetLen(sequence),
ensSliceCalculateLength(slice));
}
return ajTrue;
}
/* @func ensSliceSetTopology **************************************************
**
** Set the Ensembl Slice Topology member of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::is_circular
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] sltp [EnsESliceTopology] Ensembl Slice Topology
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceSetTopology(EnsPSlice slice, EnsESliceTopology sltp)
{
if (!slice)
return ajFalse;
slice->Topology = sltp;
return ajTrue;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Slice object.
**
** @fdata [EnsPSlice]
**
** @nam3rule Trace Report Ensembl Slice members to debug file
**
** @argrule Trace slice [const EnsPSlice] Ensembl Slice
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensSliceTrace ********************************************************
**
** Trace an Ensembl Slice.
**
** @param [r] slice [const EnsPSlice] Ensembl Slice
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceTrace(const EnsPSlice slice, ajuint level)
{
AjPStr indent = NULL;
if (!slice)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensSliceTrace %p\n"
"%S Adaptor %p\n"
"%S Seqregion %p\n"
"%S Sequence %p\n"
"%S Topology %d\n"
"%S Start %d\n"
"%S End %d\n"
"%S Strand %d\n"
"%S Use %u\n",
indent, slice,
indent, slice->Adaptor,
indent, slice->Seqregion,
indent, slice->Sequence,
indent, slice->Topology,
indent, slice->Start,
indent, slice->End,
indent, slice->Strand,
indent, slice->Use);
ensSeqregionTrace(slice->Seqregion, level + 1);
ajStrDel(&indent);
return ajTrue;
}
/* @section convenience functions *********************************************
**
** Ensembl Slice convenience functions
**
** @fdata [EnsPSlice]
**
** @nam3rule Get Get member(s) of associated objects
** @nam4rule Coordsystem Get Ensembl Coordinate System member(s)
** @nam5rule Name Get the name
** @nam5rule Object Get the Ensembl Coordinate System object
** @nam5rule Version Get the version
** @nam4rule Seqregion Get Ensembl Sequence Region member(s)
** @nam5rule Identifier Get the SQL database-internal identifier
** @nam5rule Length Get the length
** @nam5rule Name Get the name
** @nam4rule Translation Get an AJAX Translation
**
** @argrule Coordsystem slice [const EnsPSlice] Ensembl Slice
** @argrule Seqregion slice [const EnsPSlice] Ensembl Slice
** @argrule Translation slice [EnsPSlice] Ensembl Slice
**
** @valrule CoordsystemObject [EnsPCoordsystem] Ensembl Coordinate System or
** NULL
** @valrule Identifier [ajuint] SQL database-internal identifier or 0U
** @valrule Name [const AjPStr] Name or NULL
** @valrule Length [ajint] Length or 0
** @valrule Version [const AjPStr] Version or NULL
** @valrule Translation [const AjPTrn] AJAX Translation or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensSliceGetCoordsystemName *******************************************
**
** Get the name member of the Ensembl Coordinate System member of the
** Ensembl Sequence Region member of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::coord_system_name
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [const AjPStr] Ensembl Coordinate System name
**
** @release 6.2.0
** @@
******************************************************************************/
const AjPStr ensSliceGetCoordsystemName(const EnsPSlice slice)
{
return (slice) ?
ensCoordsystemGetName(
ensSeqregionGetCoordsystem(slice->Seqregion)) : NULL;
}
/* @func ensSliceGetCoordsystemObject *****************************************
**
** Get the Ensembl Coordinate System member of the
** Ensembl Sequence Region member of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::coord_system
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [EnsPCoordsystem] Ensembl Coordinate System
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPCoordsystem ensSliceGetCoordsystemObject(const EnsPSlice slice)
{
return (slice) ? ensSeqregionGetCoordsystem(slice->Seqregion) : NULL;
}
/* @func ensSliceGetCoordsystemVersion ****************************************
**
** Get the version member of the Ensembl Coordinate System member of the
** Ensembl Sequence Region member of an Ensembl Slice.
**
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [const AjPStr] Ensembl Coordinate System version or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
const AjPStr ensSliceGetCoordsystemVersion(const EnsPSlice slice)
{
return (slice) ?
ensCoordsystemGetVersion(
ensSeqregionGetCoordsystem(slice->Seqregion)) : NULL;
}
/* @func ensSliceGetSeqregionIdentifier ***************************************
**
** Get the identifier member of the Ensembl Sequence Region member of an
** Ensembl Slice.
**
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [ajuint] Ensembl Sequence Region identifier or 0U
**
** @release 6.2.0
** @@
******************************************************************************/
ajuint ensSliceGetSeqregionIdentifier(const EnsPSlice slice)
{
return (slice) ? ensSeqregionGetIdentifier(slice->Seqregion) : 0U;
}
/* @func ensSliceGetSeqregionLength *******************************************
**
** Calculate the length of the Ensembl Sequence Region member of an
** Ensembl Slice.
**
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [ajint] Ensembl Sequence Region length or 0
**
** @release 6.2.0
** @@
******************************************************************************/
ajint ensSliceGetSeqregionLength(const EnsPSlice slice)
{
return (slice) ? ensSeqregionGetLength(slice->Seqregion) : 0;
}
/* @func ensSliceGetSeqregionName *********************************************
**
** Get the name member of the Ensembl Sequence Region member of an
** Ensembl Slice.
**
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [const AjPStr] Ensembl Sequence Region name or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
const AjPStr ensSliceGetSeqregionName(const EnsPSlice slice)
{
return (slice) ? ensSeqregionGetName(slice->Seqregion) : NULL;
}
/* @func ensSliceGetTranslation ***********************************************
**
** Get an AJAX Translation for an Ensembl Slice.
**
** The AJAX Translation will match the codon table defined as an
** Ensembl Attribute of code "codon_table" associated with an Ensembl Slice.
** If no Attribute is associated with this Slice, an AJAX Translation based on
** codon table 0, the standard code with translation start at AUG only,
** will be returned.
**
** @param [u] slice [EnsPSlice] Ensembl Slice
**
** @return [const AjPTrn] AJAX Translation or NULL
**
** @release 6.3.0
** @@
******************************************************************************/
const AjPTrn ensSliceGetTranslation(EnsPSlice slice)
{
ajuint codontable = 0U;
AjPList attributes = NULL;
AjPStr code = NULL;
AjPStr value = NULL;
EnsPAttribute attribute = NULL;
if (!slice)
return NULL;
code = ajStrNewC("codon_table");
attributes = ajListNew();
ensSliceFetchAllAttributes(slice, code, attributes);
ajStrDel(&code);
while (ajListPop(attributes, (void **) &attribute))
{
value = ensAttributeGetValue(attribute);
if (value && ajStrGetLen(value))
{
if (!ajStrToUint(value, &codontable))
ajWarn("ensSliceGetTranslation Could not parse "
"Ensembl Attribute value '%S' into an "
"unsigned integer value.",
value);
}
else
{
ajDebug("ensSliceGetTranslation got Ensembl Attribute %p with an "
"empty value.",
attribute);
ensAttributeTrace(attribute, 1);
}
ensAttributeDel(&attribute);
}
ajListFree(&attributes);
return ensTranslationCacheGet(codontable);
}
/* @section calculate *********************************************************
**
** Functions for calculating information from an Ensembl Slice object.
**
** @fdata [EnsPSlice]
**
** @nam3rule Calculate Calculate Ensembl Slice information
** @nam4rule Centrepoint Calculate the centre point
** @nam4rule Length Calculate the length
** @nam4rule Memsize Calculate the memory size in bytes
** @nam4rule Region Calculate the length of a region
**
** @argrule Centrepoint slice [EnsPSlice] Ensembl Slice
** @argrule Length slice [EnsPSlice] Ensembl Slice
** @argrule Memsize slice [const EnsPSlice] Ensembl Slice
** @argrule Region slice [EnsPSlice] Ensembl Slice
** @argrule Region start [ajint] Start
** @argrule Region end [ajint] End
**
** @valrule Centrepoint [ajint] Centre point or 0
** @valrule Length [ajuint] Length or 0U
** @valrule Memsize [size_t] Memory size in bytes or 0
** @valrule Region [ajuint] Length or 0U
**
** @fcategory misc
******************************************************************************/
/* @func ensSliceCalculateCentrepoint *****************************************
**
** Calculate the centre point coordinate of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::centrepoint
** @cc Bio::EnsEMBL::CircularSlice::centrepoint
** @param [u] slice [EnsPSlice] Ensembl Slice
**
** @return [ajint] Centre point coordinate or 0
**
** @release 6.4.0
** @@
******************************************************************************/
ajint ensSliceCalculateCentrepoint(EnsPSlice slice)
{
ajint mpoint = 0;
if (!slice)
return 0;
mpoint = slice->Start + ensSliceCalculateLength(slice) / 2;
if (mpoint > ensSeqregionGetLength(slice->Seqregion))
mpoint -= ensSeqregionGetLength(slice->Seqregion);
return mpoint;
}
/* @func ensSliceCalculateLength **********************************************
**
** Calculate the length of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::length
** @cc Bio::EnsEMBL::CircularSlice::length
** @param [u] slice [EnsPSlice] Ensembl Slice
**
** @return [ajuint] Ensembl Slice length or 0U
**
** @release 6.4.0
** @@
******************************************************************************/
ajuint ensSliceCalculateLength(EnsPSlice slice)
{
return (slice) ?
ensSliceCalculateRegion(slice, slice->Start, slice->End) : 0U;
}
/* @func ensSliceCalculateMemsize *********************************************
**
** Calculate the memory size in bytes of an Ensembl Slice.
**
** @param [r] slice [const EnsPSlice] Ensembl Slice
**
** @return [size_t] Memory size in bytes or 0
**
** @release 6.4.0
** @@
******************************************************************************/
size_t ensSliceCalculateMemsize(const EnsPSlice slice)
{
size_t size = 0;
if (!slice)
return 0;
size += sizeof (EnsOSlice);
size += ensSeqregionCalculateMemsize(slice->Seqregion);
if (slice->Sequence)
{
size += sizeof (AjOStr);
size += ajStrGetRes(slice->Sequence);
}
return size;
}
/* @func ensSliceCalculateRegion **********************************************
**
** Calculate the length of a region spanning a (circular) Ensembl Slice.
**
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] start [ajint] Start
** @param [r] end [ajint] End
**
** @return [ajuint] Length or 0U
**
** @release 6.4.0
** @@
** Linear Slice:
** length = start - end + 1
** Circular Slice (start > end): in two sections
** length = (Sequence Region Length - start + 1) + (end - 1 + 1)
** length = Sequence Region Length - start + 1 + end
******************************************************************************/
ajuint ensSliceCalculateRegion(EnsPSlice slice, ajint start, ajint end)
{
ajuint length = 0U;
AjBool circular = AJFALSE;
if (!slice)
return 0U;
if (start > end)
{
if (ensSliceIsCircular(slice, &circular))
{
if (circular == ajTrue)
length = ensSliceGetSeqregionLength(slice) - start + 1U + end;
else
ajFatal("ensSliceCalculateRegion cannot calculate the length "
"of a region on a linear Ensembl Slice, where the "
"start coordinate (%d) is greater than the "
"end coordinate (%d).", start, end);
}
else
ajFatal("ensSliceCalculateSpan cannot determine the "
"Ensembl Slice topology.");
}
else
length = end - start + 1U;
/*
** NOTE: This could be rewritten to:
**
** length = end - start + 1U;
**
** if ((start > end) && (circular == ajTrue))
** length += ensSliceGetSeqregionLength(slice);
*/
return length;
}
/* @section fetch *************************************************************
**
** Functions for fetching objects of an Ensembl Slice object.
**
** @fdata [EnsPSlice]
**
** @nam3rule Fetch Fetch Ensembl Slice objects
** @nam4rule All Fetch all objects
** @nam5rule Attributes Fetch all Ensembl Attribute objects
** @nam5rule Repeatfeatures Fetch all Repeat Feature objects
** @nam5rule Sequenceedits Fetch all Sequence Edit objects
** @nam4rule Name Fetch the name
** @nam4rule Sequence Fetch the sequence
** @nam5rule All Fetch the complete sequence
** @nam5rule Sub Fetch a sub-sequence
** @nam6rule Seq Fetch as AJAX Sequence object
** @nam6rule Str Fetch as AJAX String object
** @nam4rule Sliceexpanded Fetch an expanded Ensembl Slice
** @nam4rule Sliceinverted Fetch an inverted Ensembl Slice
** @nam4rule Slicesub Fetch a sub-Slice
**
** @argrule AllAttributes slice [EnsPSlice] Ensembl Slice
** @argrule AllAttributes code [const AjPStr] Ensembl Attribute code
** @argrule AllAttributes attributes [AjPList]
** AJAX List of Ensembl Attribute objects
** @argrule AllRepeatfeatures slice [EnsPSlice] Ensembl Slice
** @argrule AllRepeatfeatures anname [const AjPStr] Ensembl Analysis name
** @argrule AllRepeatfeatures rctype [const AjPStr]
** Ensembl Repeat Consensus type
** @argrule AllRepeatfeatures rcclass [const AjPStr]
** Ensembl Repeat Consensus class
** @argrule AllRepeatfeatures rcname [const AjPStr]
** Ensembl Repeat Consensus name
** @argrule AllRepeatfeatures rfs [AjPList]
** AJAX List of Ensembl Repeat Feature objects
** @argrule AllSequenceedits slice [EnsPSlice] Ensembl Slice
** @argrule AllSequenceedits ses [AjPList]
** AJAX List of Ensembl Sequence Edit objects
** @argrule Name slice [const EnsPSlice] Ensembl Slice
** @argrule Name Pname [AjPStr*] Name
** @argrule Sequence slice [EnsPSlice] Ensembl Slice
** @argrule Sub start [ajint] Start coordinate
** @argrule Sub end [ajint] End coordinate
** @argrule Sub strand [ajint] Strand information
** @argrule Seq Psequence [AjPSeq*] AJAX Sequence address
** @argrule Str Psequence [AjPStr*] AJAX String address
** @argrule Sliceinverted slice [EnsPSlice] Ensembl Slice
** @argrule Sliceinverted Pslice [EnsPSlice*] Sliceinverted Ensembl Slice
** @argrule Sliceexpanded slice [EnsPSlice] Ensembl Slice
** @argrule Sliceexpanded five [ajint]
** Number of bases to expand the 5' region
** @argrule Sliceexpanded three [ajint]
** Number of bases to expand the 3' region
** @argrule Sliceexpanded force [AjBool] Force Slice contraction
** @argrule Sliceexpanded Pfshift [ajint*]
** Maximum possible 5' shift when "force" is set
** @argrule Sliceexpanded Ptshift [ajint*]
** Maximum possible 3' shift when "force" is set
** @argrule Sliceexpanded Pslice [EnsPSlice*] Ensembl Slice address
** @argrule Slicesub slice [EnsPSlice] Ensembl Slice
** @argrule Slicesub start [ajint] Start coordinate
** @argrule Slicesub end [ajint] End coordinate
** @argrule Slicesub strand [ajint] Strand information
** @argrule Slicesub Pslice [EnsPSlice*] Ensembl Slice address
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensSliceFetchAllAttributes *******************************************
**
** Fetch all Ensembl Attribute objects for an Ensembl Slice.
** The caller is responsible for deleting the Ensembl Attribute objects before
** deleting the AJAX List.
**
** @cc Bio::EnsEMBL::Slice::get_all_Attributes
** @cc Bio::EnsEMBL::CircularSlice::get_all_Attributes
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [rN] code [const AjPStr] Ensembl Attribute code
** @param [u] attributes [AjPList] AJAX List of Ensembl Attribute objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceFetchAllAttributes(EnsPSlice slice,
const AjPStr code,
AjPList attributes)
{
if (!slice)
return ajFalse;
if (!attributes)
return ajFalse;
if (!slice->Seqregion)
{
ajDebug("ensSliceFetchAllAttributes cannot fetch "
"Ensembl Attribute objects for an "
"Ensembl Slice without an "
"Ensembl Sequence Region.\n");
return ajFalse;
}
ensSeqregionFetchAllAttributes(slice->Seqregion, code, attributes);
return ajTrue;
}
/* @func ensSliceFetchAllRepeatfeatures ***************************************
**
** Fetch all Ensembl Repeat Feature objects on an Ensembl Slice.
**
** The caller is responsible for deleting the Ensembl Repeat Feture objects
** before deleting the AJAX List.
**
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] anname [const AjPStr] Ensembl Analysis name
** @param [r] rctype [const AjPStr] Ensembl Repeat Consensus type
** @param [r] rcclass [const AjPStr] Ensembl Repeat Consensus class
** @param [r] rcname [const AjPStr] Ensembl Repeat Consensus name
** @param [u] rfs [AjPList] AJAX List of Ensembl Repeat Feature objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceFetchAllRepeatfeatures(EnsPSlice slice,
const AjPStr anname,
const AjPStr rctype,
const AjPStr rcclass,
const AjPStr rcname,
AjPList rfs)
{
if (ajDebugTest("ensSliceFetchAllRepeatfeatures"))
ajDebug("ensSliceFetchAllRepeatfeatures\n"
" slice %p\n"
" anname '%S'\n"
" rctype '%S'\n"
" rcclass '%S'\n"
" rcname '%S'\n"
" rfs %p\n",
slice,
anname,
rctype,
rcclass,
rcname,
rfs);
if (!slice)
return ajFalse;
if (!slice->Adaptor)
{
ajDebug("ensSliceFetchAllRepeatfeatures cannot get Repeat Feature "
"objects without a Slice Adaptor attached to the Slice.\n");
return ajFalse;
}
return ensRepeatfeatureadaptorFetchAllbySlice(
ensRegistryGetRepeatfeatureadaptor(
ensSliceadaptorGetDatabaseadaptor(slice->Adaptor)),
slice,
anname,
rctype,
rcclass,
rcname,
rfs);
}
/* @func ensSliceFetchAllSequenceedits ****************************************
**
** Fetch all Ensembl Sequence Edit objects of an Ensembl Slice.
**
** The caller is responsible for deleting the Ensembl Sequence Edit objects
** before deleting the AJAX List.
**
** @cc Bio::EnsEMBL::DBSQL::SequenceAdaptor::_rna_edit
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] ses [AjPList] AJAX List of Ensembl Sequence Edit objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** Ensembl Sequence Edit objects are Ensembl Attribute objects, which codes
** have to be defined in the static const char *sliceKSequenceeditCode array.
******************************************************************************/
AjBool ensSliceFetchAllSequenceedits(EnsPSlice slice,
AjPList ses)
{
register ajuint i = 0U;
AjPList attributes = NULL;
AjPStr code = NULL;
EnsPAttribute at = NULL;
EnsPSequenceedit se = NULL;
if (!slice)
return ajFalse;
if (!ses)
return ajFalse;
code = ajStrNew();
attributes = ajListNew();
for (i = 0U; sliceKSequenceeditCode[i]; i++)
{
ajStrAssignC(&code, sliceKSequenceeditCode[i]);
ensSliceFetchAllAttributes(slice, code, attributes);
}
while (ajListPop(attributes, (void **) &at))
{
se = ensSequenceeditNewAttribute(at);
ajListPushAppend(ses, (void *) se);
ensAttributeDel(&at);
}
ajListFree(&attributes);
ajStrDel(&code);
return ajTrue;
}
/* @func ensSliceFetchName ****************************************************
**
** Fetch the name of an Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::name
** @param [r] slice [const EnsPSlice] Ensembl Slice
** @param [wP] Pname [AjPStr*] Name String address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceFetchName(const EnsPSlice slice, AjPStr *Pname)
{
EnsPCoordsystem cs = NULL;
if (!slice)
return ajFalse;
if (!Pname)
return ajFalse;
cs = ensSeqregionGetCoordsystem(slice->Seqregion);
if (*Pname)
*Pname = ajFmtPrintS(
Pname,
"%S:%S:%S:%d:%d:%d",
ensCoordsystemGetName(cs),
ensCoordsystemGetVersion(cs),
ensSeqregionGetName(slice->Seqregion),
slice->Start,
slice->End,
slice->Strand);
else
*Pname = ajFmtStr(
"%S:%S:%S:%d:%d:%d",
ensCoordsystemGetName(cs),
ensCoordsystemGetVersion(cs),
ensSeqregionGetName(slice->Seqregion),
slice->Start,
slice->End,
slice->Strand);
return ajTrue;
}
/* @func ensSliceFetchSequenceAllSeq ******************************************
**
** Fetch the sequence of an Ensembl Slice as AJAX Sequence.
**
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [wP] Psequence [AjPSeq*] AJAX Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceFetchSequenceAllSeq(EnsPSlice slice, AjPSeq *Psequence)
{
AjPStr name = NULL;
AjPStr sequence = NULL;
if (!slice)
return ajFalse;
if (!Psequence)
return ajFalse;
/*
** It is sligtly more efficient, if undefined AJAX String objects are
** directly allocated by the following functions to their final size.
*/
ensSliceFetchName(slice, &name);
ensSliceFetchSequenceAllStr(slice, &sequence);
if (*Psequence)
{
ajSeqClear(*Psequence);
ajSeqAssignNameS(*Psequence, name);
ajSeqAssignSeqS(*Psequence, sequence);
}
else
*Psequence = ajSeqNewNameS(sequence, name);
ajSeqSetNuc(*Psequence);
ajStrDel(&sequence);
ajStrDel(&name);
return ajTrue;
}
/* @func ensSliceFetchSequenceAllStr ******************************************
**
** Fetch the sequence of an Ensembl Slice as AJAX String.
**
** @cc Bio::EnsEMBL::Slice::seq
** @cc Bio::EnsEMBL::CircularSlice::seq
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [wP] Psequence [AjPStr*] Sequence String address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceFetchSequenceAllStr(EnsPSlice slice, AjPStr *Psequence)
{
AjBool circular = AJFALSE;
AjPStr sequence1 = NULL;
AjPStr sequence2 = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPSequenceadaptor sqa = NULL;
EnsPSlice slice1 = NULL;
EnsPSlice slice2 = NULL;
if (!slice)
return ajFalse;
if (!Psequence)
return ajFalse;
if (*Psequence)
ajStrAssignClear(Psequence);
else
*Psequence = ajStrNewRes(ensSliceCalculateLength(slice) + 1);
/* Special case for "in-between" (insertion) coordinates. */
if (slice->Start == (slice->End + 1))
return ajTrue;
if (slice->Sequence)
{
/*
** Since the Slice has sequence attached, check whether its
** Slice length matches its sequence length.
*/
if (ajStrGetLen(slice->Sequence) != ensSliceCalculateLength(slice))
ajFatal("ensSliceFetchSequenceAllStr got a Slice, "
"which sequence length %u does not match its length %u.\n",
ajStrGetLen(slice->Sequence),
ensSliceCalculateLength(slice));
ajStrAssignS(Psequence, slice->Sequence);
}
else if (slice->Adaptor)
{
/*
** Since the Slice has a Slice Adaptor attached, it is possible to
** retrieve the sequence from the database.
*/
dba = ensSliceadaptorGetDatabaseadaptor(slice->Adaptor);
sqa = ensRegistryGetSequenceadaptor(dba);
ensSliceIsCircular(slice, &circular);
if ((circular == ajTrue) && (slice->Start > slice->End))
{
slice1 = ensSliceNewCpy(slice);
slice2 = ensSliceNewCpy(slice);
slice1->End = ensSeqregionGetLength(slice1->Seqregion);
slice2->Start = 1;
/*
** FIXME: The Perl API uses two linear Slice objects here
** and passes in undef for the end. The above copies may
** therefore not work.
*/
/*
** It is sligtly more efficient, if undefined AJAX String objects
** are directly allocated by the following functions to their
** final size.
*/
ensSequenceadaptorFetchSliceAllStr(sqa, slice1, &sequence1);
ensSequenceadaptorFetchSliceAllStr(sqa, slice2, &sequence2);
ajStrAssignS(Psequence, sequence1);
ajStrAppendS(Psequence, sequence2);
ajStrDel(&sequence1);
ajStrDel(&sequence2);
ensSliceDel(&slice1);
ensSliceDel(&slice2);
}
else
ensSequenceadaptorFetchSliceAllStr(sqa, slice, Psequence);
}
else
{
/*
** The Slice has no sequence and no Slice Adaptor attached,
** so just return Ns.
*/
ajStrAppendCountK(Psequence, 'N', ensSliceCalculateLength(slice));
}
if (ajStrGetLen(*Psequence) != ensSliceCalculateLength(slice))
ajWarn("ensSliceFetchSequenceAllStr got sequence of length %u "
"for Ensembl Slice of length %u.\n",
ajStrGetLen(*Psequence),
ensSliceCalculateLength(slice));
return ajTrue;
}
/* @func ensSliceFetchSequenceSubSeq ******************************************
**
** Fetch a sub-sequence of an Ensembl Slice as AJAX Sequence.
**
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] start [ajint] Start coordinate
** @param [r] end [ajint] End coordinate
** @param [r] strand [ajint] Strand information
** @param [wP] Psequence [AjPSeq*] Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceFetchSequenceSubSeq(EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPSeq *Psequence)
{
ajint srstart = 0;
ajint srend = 0;
ajint srstrand = 0;
AjPStr name = NULL;
AjPStr sequence = NULL;
if (!slice)
return ajFalse;
if (!strand)
strand = 1;
if (!Psequence)
return ajFalse;
/*
** Construct the Slice name, but convert relative Slice coordinates into
** absolute Sequence Region coordinates.
*/
if (slice->Strand >= 0)
{
srstart = slice->Start + start - 1;
srend = slice->Start + end - 1;
}
else
{
srstart = slice->End - end + 1;
srend = slice->End - start + 1;
}
srstrand = slice->Strand * strand;
name = ajFmtStr("%S:%S:%S:%d:%d:%d",
ensSliceGetCoordsystemName(slice),
ensSliceGetCoordsystemVersion(slice),
ensSliceGetSeqregionName(slice),
srstart,
srend,
srstrand);
/*
** Fetch the Slice sequence.
**
** It is sligtly more efficient, if undefined AJAX String objects are
** directly allocated by the following functions to their final size.
*/
ensSliceFetchSequenceSubStr(slice, start, end, strand, &sequence);
if (*Psequence)
{
ajSeqClear(*Psequence);
ajSeqAssignNameS(*Psequence, name);
ajSeqAssignSeqS(*Psequence, sequence);
}
else
*Psequence = ajSeqNewNameS(sequence, name);
ajSeqSetNuc(*Psequence);
ajStrDel(&sequence);
ajStrDel(&name);
return ajTrue;
}
/* @func ensSliceFetchSequenceSubStr ******************************************
**
** Fetch a sub-sequence of an Ensembl Slice as AJAX String
** in releative coordinates.
**
** @cc Bio::EnsEMBL::Slice::subseq
** @cc Bio::EnsEMBL::CircularSlice::subseq
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] start [ajint] Start coordinate
** @param [r] end [ajint] End coordinate
** @param [r] strand [ajint] Strand information
** @param [wP] Psequence [AjPStr*] Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceFetchSequenceSubStr(EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPStr *Psequence)
{
ajint region1 = 0;
ajint region2 = 0;
ajint slength = 0;
ajuint rlength = 0U;
AjBool circular = AJFALSE;
AjPStr sequence1 = NULL;
AjPStr sequence2 = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPSequenceadaptor sqa = NULL;
if (ajDebugTest("ensSliceFetchSequenceSubStr"))
ajDebug("ensSliceFetchSequenceSubStr\n"
" slice %p\n"
" start %d\n"
" end %d\n"
" strand %d\n"
" Psequence %p\n",
slice,
start,
end,
strand,
Psequence);
if (!slice)
return ajFalse;
if (!Psequence)
return ajFalse;
/* For "in-between" (insertion) coordinates return an empty string. */
if (start == (end + 1))
return ajTrue;
ensSliceIsCircular(slice, &circular);
if ((circular == ajFalse) && (start > (end + 1)))
{
ajDebug("ensSliceFetchSequenceSubStr requires for linear Slices that "
"the start coordinate %d is less than the "
"end coordinate %d + 1.\n",
start, end);
return ajFalse;
}
if (!strand)
strand = 1;
if ((circular == ajTrue) && (start > end))
{
region1 = ensSeqregionGetLength(slice->Seqregion) - start;
region2 = end;
rlength = region1 + region2 + 1;
}
else
rlength = end - start + 1;
if (*Psequence)
ajStrAssignClear(Psequence);
else
*Psequence = ajStrNewRes(rlength + 1);
if (slice->Sequence)
{
/*
** Since the Slice has sequence attached, check whether
** Slice length and sequence length match.
*/
if (ajStrGetLen(slice->Sequence) != ensSliceCalculateLength(slice))
ajFatal("ensSliceFetchSequenceSubStr got a Slice, "
"which sequence length (%Lu) does not match its "
"length (%u).\n",
ajStrGetLen(slice->Sequence),
ensSliceCalculateLength(slice));
/* FIXME: size_t can be shorter than ajulong */
/* Relative Slice coordinates range from 1 to length. */
/* Check for a gap at the beginning and pad it with Ns. */
if (start < 1)
{
ajStrAppendCountK(Psequence, 'N', 1 - start);
start = 1;
}
ajStrAppendSubS(Psequence,
slice->Sequence,
start - 1,
end - start + 1);
/* Check that the Slice is within signed integer range. */
if (ensSliceCalculateLength(slice) <= INT_MAX)
slength = (ajint) ensSliceCalculateLength(slice);
else
ajFatal("ensSliceFetchSequenceSubStr got an "
"Ensembl Slice, which length (%u) exceeds the "
"maximum integer limit (%d).\n",
ensSliceCalculateLength(slice), INT_MAX);
/* Check for a gap at the end and pad it again with Ns. */
if (end > slength)
ajStrAppendCountK(Psequence, 'N', (ajuint) (end - slength));
if (strand < 0)
ajSeqstrReverse(Psequence);
}
else if (slice->Adaptor)
{
/*
** Since the Slice has a Slice Adaptor attached, it is possible to
** retrieve the sequence from the database.
*/
dba = ensSliceadaptorGetDatabaseadaptor(slice->Adaptor);
sqa = ensRegistryGetSequenceadaptor(dba);
if ((circular == ajTrue) && (start > end))
{
sequence1 = ajStrNewRes(rlength);
sequence2 = ajStrNewRes(rlength);
ensSequenceadaptorFetchSliceSubStr(
sqa,
slice,
start,
ensSeqregionGetLength(slice->Seqregion),
strand,
&sequence1);
ensSequenceadaptorFetchSliceSubStr(
sqa,
slice,
1,
end,
strand,
&sequence2);
ajStrAppendS(Psequence, sequence1);
ajStrAppendS(Psequence, sequence2);
ajStrDel(&sequence1);
ajStrDel(&sequence2);
}
else
ensSequenceadaptorFetchSliceSubStr(sqa,
slice,
start,
end,
strand,
Psequence);
}
else
{
/*
** The Slice has no sequence and no Slice Adaptor attached,
** so just return Ns.
*/
ajStrAppendCountK(Psequence, 'N', rlength);
}
if (ajStrGetLen(*Psequence) != rlength)
ajWarn("ensSliceFetchSequenceSubStr got sequence of length %Lu "
"for region of length %u.\n",
ajStrGetLen(*Psequence),
rlength);
/* FIXME: size_t can be shorter than ajulong */
return ajTrue;
}
/* @func ensSliceFetchSliceexpanded *******************************************
**
** Fetch an expanded copy of an Ensembl Slice, which remains unchanged.
** The start and end are moved outwards from the centre of the Slice if
** positive values are provided and moved inwards if negative values are
** provided. A Slice may not be contracted below 1 base pair but may grow
** to be arbitrarily large.
**
** The caller is responsible for deleting the Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::expand
** @cc Bio::EnsEMBL::CircularSlice::expand
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] five [ajint] Number of bases to expand the 5' region
** Positive values expand the Slice, negative values contract it
** @param [r] three [ajint] Number of bases to expand the 3' region
** Positive values expand the Slice, negative values contract it
** @param [r] force [AjBool] Force Slice contraction, even when shifts for
** "five" and "three" overlap. In that case "five" and
** "three" will be set to a maximum possible number
** resulting in a Slice, which would have only 2 base
** pairs.
** @param [w] Pfshift [ajint*] Maximum possible 5' shift when "force" is set
** @param [w] Ptshift [ajint*] Maximum possible 3' shift when "force" is set
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** NOTE: Currently, this function fetches the expanded Slice via a
** Slice Adaptor, if one is set for this Slice. The Slice Adaptor registers
** Slice objects in the internal cache, which minimises memory requirements.
** However, registering many Slice objects, the LRU cache may drop important
** Slice objects.
******************************************************************************/
AjBool ensSliceFetchSliceexpanded(EnsPSlice slice,
ajint five,
ajint three,
AjBool force,
ajint *Pfshift,
ajint *Ptshift,
EnsPSlice *Pslice)
{
ajint sshift = 0;
ajint eshift = 0;
ajint srstart = 0;
ajint srend = 0;
AjBool circular = AJFALSE;
if (ajDebugTest("ensSliceFetchSliceexpanded"))
ajDebug("ensSliceFetchSliceexpanded\n"
" slice %p\n"
" five %d\n"
" three %d\n"
" force '%B'\n"
" Pfshift %p\n"
" Ptshift %p\n"
" Pslice %p\n",
slice,
five,
three,
force,
Pfshift,
Ptshift,
Pslice);
if (!slice)
return ajFalse;
if (!Pfshift)
return ajFalse;
if (!Ptshift)
return ajFalse;
if (!Pslice)
return ajFalse;
*Pslice = NULL;
if (slice->Sequence)
{
ajDebug("ensSliceFetchSliceexpanded cannot expand an Ensembl Slice "
"with an attached sequence.\n");
return ajFalse;
}
if (slice->Strand > 0)
{
sshift = five;
eshift = three;
}
else
{
sshift = three;
eshift = five;
}
srstart = slice->Start - sshift;
srend = slice->End + eshift;
ensSliceIsCircular(slice, &circular);
if (
(
(srstart <= 0)
||
(srstart > ensSliceGetSeqregionLength(slice))
||
(srend <= 0)
||
(srend > ensSliceGetSeqregionLength(slice))
)
&&
(circular == ajTrue)
)
{
if (srstart <= 0)
srstart += ensSliceGetSeqregionLength(slice);
if (srstart > ensSliceGetSeqregionLength(slice))
srstart -= ensSliceGetSeqregionLength(slice);
if (srend <= 0)
srend += ensSliceGetSeqregionLength(slice);
if (srend > ensSliceGetSeqregionLength(slice))
srend -= ensSliceGetSeqregionLength(slice);
}
if ((srstart > srend) && (circular == ajFalse))
{
if (force)
{
/* Apply the maximal possible shift, if force is set. */
if (sshift < 0)
{
/*
** If we are contracting the Slice from the start,
** move the start just before the end.
*/
srstart = srend - 1;
sshift = slice->Start - srstart;
}
else
{
/*
** If the Slice still has a negative length,
** try to move the end.
*/
if (eshift < 0)
{
srend = srstart + 1;
eshift = srend - slice->End;
}
*Pfshift = (slice->Strand >= 0) ? eshift : sshift;
*Ptshift = (slice->Strand >= 0) ? sshift : eshift;
}
}
if (srstart > srend)
{
/* If the Slice still has a negative length, return NULL. */
ajDebug("ensSliceFetchSliceexpanded requires the Slice "
"start %d to be less than the Slice end %d "
"coordinate.\n",
srstart, srend);
return ajFalse;
}
}
if (slice->Adaptor)
ensSliceadaptorFetchBySeqregionIdentifier(
slice->Adaptor,
ensSeqregionGetIdentifier(slice->Seqregion),
srstart,
srend,
slice->Strand,
Pslice);
else
*Pslice = ensSliceNewIni(slice->Adaptor,
slice->Seqregion,
srstart,
srend,
slice->Strand);
return ajTrue;
}
/* @func ensSliceFetchSliceinverted *******************************************
**
** Fetch an inverted Slice from an Ensembl Slice.
**
** The caller is responsible for deleting the Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::invert
** @cc Bio::EnsEMBL::CircularSlice::invert
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
** @see ensSliceadaptorFetchBySlice
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** NOTE: Currently, this function fetches the expanded Slice via a
** Slice Adaptor, if one is set for this Slice. The Slice Adaptor registers
** Slice objects in the internal cache, which minimises memory requirements.
** However, registering many Slice objects, the LRU cache may drop important
** Slice objects.
******************************************************************************/
AjBool ensSliceFetchSliceinverted(EnsPSlice slice, EnsPSlice *Pslice)
{
AjPStr sequence = NULL;
if (!slice)
return ajFalse;
if (!Pslice)
return ajFalse;
*Pslice = NULL;
/*
** Retrieve the inverted Slice via the Slice Adaptor if one is attached.
** This will automatically register the new Slice in the
** Slice Adaptor-internal cache and will also take care of
** an eventual Slice-internal sequence.
** Use relative Slice coordinates, which range from 1 to length.
*/
if (slice->Adaptor)
{
ensSliceadaptorFetchBySlice(slice->Adaptor,
slice,
1,
(ajint) ensSliceCalculateLength(slice),
-1,
Pslice);
return ajTrue;
}
if (slice->Sequence)
{
/* Reverse (and complement) the sequence if one has been defined. */
sequence = ajStrNewS(slice->Sequence);
ajSeqstrReverse(&sequence);
*Pslice = ensSliceNewSeq(slice->Adaptor,
slice->Seqregion,
slice->Start,
slice->End,
slice->Strand * -1,
sequence);
ajStrDel(&sequence);
}
else
*Pslice = ensSliceNewIni(slice->Adaptor,
slice->Seqregion,
slice->Start,
slice->End,
slice->Strand * -1);
return ajTrue;
}
/* @func ensSliceFetchSlicesub ************************************************
**
** Fetch a Sub-Slice from an Ensembl Slice.
**
** If a Slice is requested, which lies outside the boundaries of this Slice,
** this function will return NULL. This means that the behaviour will be
** consistent whether or not the Slice is attached to the database
** (i.e. if there is attached sequence to the Slice).
** Alternatively, the ensSliceFetchSliceexpanded or
** ensSliceAdaptorFetchByRegion functions could be used instead.
**
** The caller is responsible for deleting the Ensembl Slice.
**
** @cc Bio::EnsEMBL::Slice::sub_Slice
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] start [ajint] Start coordinate
** @param [r] end [ajint] End coordinate
** @param [r] strand [ajint] Strand information
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
** @see ensSliceadaptorFetchBySlice
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** NOTE: Currently, this function fetches the expanded Slice via a
** Slice Adaptor, if one is set for this Slice. The Slice Adaptor registers
** Slice objects in the internal cache, which minimises memory requirements.
** However, registering many Slice objects, the LRU cache may drop important
** Slice objects.
******************************************************************************/
AjBool ensSliceFetchSlicesub(EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
EnsPSlice *Pslice)
{
ajint srstart = 0;
ajint srend = 0;
ajint srstrand = 0;
AjPStr sequence = NULL;
if (!slice)
{
ajDebug("ensSliceGetSubSlice requires an Ensembl Slice.\n");
return ajFalse;
}
if (!Pslice)
return ajFalse;
*Pslice = NULL;
if ((start < 1) || (start > slice->End))
{
ajDebug("ensSliceGetSubSlice requires the start coordinate %d "
"to be greater than or equal to 1 and less than or equal to "
"the end coordinate %d of the Ensembl Slice.\n",
start, slice->End);
return ajFalse;
}
if ((end < start) || (end > slice->End))
{
ajDebug("ensSliceGetSubSlice requires the end coordinate %d "
"to be greater than or equal to the start coordinate %d "
"and to be less than or equal to the "
"end coordinate %d of the Ensembl Slice.\n",
end, start, slice->End);
return ajFalse;
}
if (!strand)
strand = 1;
/*
** Retrieve the Sub-Slice via the Slice Adaptor if one is attached.
** This will automatically register the new Slice in the
** Slice Adaptor-internal cache and will also take care of
** an eventual Slice-internal sequence.
*/
if (slice->Adaptor)
{
ensSliceadaptorFetchBySlice(slice->Adaptor,
slice,
start,
end,
strand,
Pslice);
return ajTrue;
}
/* Transform relative into absolute Slice coordinates. */
if (slice->Strand >= 0)
{
srstart = slice->Start + start - 1;
srend = slice->Start + end - 1;
}
else
{
srstart = slice->End - end + 1;
srend = slice->End - start + 1;
}
srstrand = slice->Strand * strand;
if (slice->Sequence)
{
sequence = ajStrNewRes(end - start + 1);
ensSliceFetchSequenceSubStr(slice,
start,
end,
strand,
&sequence);
*Pslice = ensSliceNewSeq(slice->Adaptor,
slice->Seqregion,
srstart,
srend,
srstrand,
sequence);
ajStrDel(&sequence);
}
else
*Pslice = ensSliceNewIni(slice->Adaptor,
slice->Seqregion,
srstart,
srend,
srstrand);
return ajTrue;
}
/* @section comparison ********************************************************
**
** Functions for comparing Ensembl Slice objects.
**
** @fdata [EnsPSlice]
**
** @nam3rule Compare Functions for comparing Ensembl Slice objects
** @nam4rule Identifier Compare the SQL database-internal identifier
** @nam5rule Ascending Sort in ascending order
** @nam5rule Descending Sort in descending order
**
** @argrule * slice1 [const EnsPSlice] Ensembl Slice
** @argrule * slice2 [const EnsPSlice] Ensembl Slice
**
** @valrule * [int] Integer less than, equal or greater than 0
**
** @fcategory misc
******************************************************************************/
/* @func ensSliceCompareIdentifierAscending ***********************************
**
** Comparison function to sort Ensembl Slice objects by their
** Ensembl Sequence Region identifier in ascending order.
**
** Ensembl Slice objects without Ensembl Sequence Region objects sort towards
** the end of the AJAX List.
**
** @param [r] slice1 [const EnsPSlice] Ensembl Slice 1
** @param [r] slice2 [const EnsPSlice] Ensembl Slice 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.3.0
** @@
******************************************************************************/
int ensSliceCompareIdentifierAscending(const EnsPSlice slice1,
const EnsPSlice slice2)
{
int result = 0;
ajuint srid1 = 0U;
ajuint srid2 = 0U;
/* Sort empty values towards the end of the AJAX List. */
if (slice1 && (!slice2))
return -1;
if ((!slice1) && (!slice2))
return 0;
if ((!slice1) && slice2)
return +1;
srid1 = ensSliceGetSeqregionIdentifier(slice1);
srid2 = ensSliceGetSeqregionIdentifier(slice2);
if (srid1 < srid2)
result = -1;
if (srid1 > srid2)
result = +1;
return result;
}
/* @section comparison ********************************************************
**
** Functions for matching Ensembl Slice objects.
**
** @fdata [EnsPSlice]
**
** @nam3rule Match Functions for matching Ensembl Slice objects
** @nam3rule Similarity Functions for matching Ensembl Slice objects
**
** @argrule * slice1 [const EnsPSlice] Ensembl Slice
** @argrule * slice2 [const EnsPSlice] Ensembl Slice
**
** @valrule * [AjBool] ajTrue if the Slice objects match
**
** @fcategory misc
******************************************************************************/
/* @func ensSliceMatch ********************************************************
**
** Test for matching two Ensembl Slice objects.
**
** @param [r] slice1 [const EnsPSlice] First Ensembl Slice
** @param [r] slice2 [const EnsPSlice] Second Ensembl Slice
**
** @return [AjBool] ajTrue if the Slice objects are equal
**
** @release 6.2.0
** @@
** The comparison is based on an initial pointer equality test and if that
** fails, the Coordinate System, the Sequence Region, as well as the Slice
** start, end and strand members are compared. In case the Slice has a
** sequence String attached, it is compared as well.
******************************************************************************/
AjBool ensSliceMatch(const EnsPSlice slice1, const EnsPSlice slice2)
{
if (ajDebugTest("ensSliceMatch"))
{
ajDebug("ensSliceMatch\n"
" slice1 %p\n"
" slice2 %p\n",
slice1,
slice2);
ensSliceTrace(slice1, 1);
ensSliceTrace(slice2, 1);
}
if (!slice1)
return ajFalse;
if (!slice2)
return ajFalse;
/* Try a direct pointer comparison first. */
if (slice1 == slice2)
return ajTrue;
if (!ensSeqregionMatch(slice1->Seqregion, slice2->Seqregion))
return ajFalse;
if (slice1->Start != slice2->Start)
return ajFalse;
if (slice1->End != slice2->End)
return ajFalse;
if (slice1->Strand != slice2->Strand)
return ajFalse;
if ((slice1->Sequence || slice2->Sequence) &&
(!ajStrMatchS(slice1->Sequence, slice2->Sequence)))
return ajFalse;
return ajTrue;
}
/* @func ensSliceSimilarity ***************************************************
**
** Test two Ensembl Slice objects for similarity.
**
** For similarity Ensembl Slice objects have to be defined on the same
** Ensembl Sequence Region, but can have different start end and strand
** coordinates. If a sequence has been set, it has to match perfectly.
**
** @param [r] slice1 [const EnsPSlice] First Ensembl Slice
** @param [r] slice2 [const EnsPSlice] Second Ensembl Slice
**
** @return [AjBool] ajTrue if the Slice objects are equal
**
** @release 6.4.0
** @@
** The comparison is based on an initial pointer equality test and if that
** fails, the Ensembl Sequence Region objects are compared. In case one of the
** Ensembl Slice objects has a sequence attached, it is compared as well.
******************************************************************************/
AjBool ensSliceSimilarity(const EnsPSlice slice1, const EnsPSlice slice2)
{
if (ajDebugTest("ensSliceSimilarity"))
{
ajDebug("ensSliceSimilarity\n"
" slice1 %p\n"
" slice2 %p\n",
slice1,
slice2);
ensSliceTrace(slice1, 1);
ensSliceTrace(slice2, 1);
}
if (!slice1)
return ajFalse;
if (!slice2)
return ajFalse;
/* Try a direct pointer comparison first. */
if (slice1 == slice2)
return ajTrue;
if (!ensSeqregionMatch(slice1->Seqregion, slice2->Seqregion))
return ajFalse;
/* Sequence members are optional. */
if (((slice1->Sequence != NULL) || (slice2->Sequence != NULL)) &&
(ajStrMatchS(slice1->Sequence, slice2->Sequence) == ajFalse))
return ajFalse;
return ajTrue;
}
/* @section query *************************************************************
**
** Functions for querying the properties of an Ensembl Slice.
**
** @fdata [EnsPSlice]
**
** @nam3rule Is Check whether an Ensembl Slice represents a certain property
** @nam4rule Circular Check for a circular Ensembl Slice
** @nam4rule Nonreference Check for a non-reference Ensembl Slice
** @nam4rule Toplevel Check for a top-level Ensembl Slice
**
** @argrule * slice [EnsPSlice] Ensembl Slice
** @argrule * Presult [AjBool*] Boolean result
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensSliceIsCircular ***************************************************
**
** Check whether an Ensembl Slice is circular based on an Ensembl Sequence
** Region, which has an Ensembl Attribute of code "circular_seq" set.
**
** @cc Bio::EnsEMBL::Slice::is_circular
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] Presult [AjBool*] ajTrue if the Ensembl Sequence Region has an
** Ensembl Attribute of code "circular_seq" set
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** NOTE: In this implementation, the "circular" property relies on
** Ensembl Attribute objects are linked to Ensembl Sequence Region objects
** that are at the base of Ensembl Slice objects. Although Ensembl Sequence
** Region objects cache all Ensembl Attribute objects, one SQL query is still
** needed for each new Ensembl Sequence Region object.
** The Perl API caches the information for all Ensembl Sequence Region objects
** at once, but does not formalise the information within
** Ensembl Attribute objects.
******************************************************************************/
AjBool ensSliceIsCircular(EnsPSlice slice, AjBool *Presult)
{
EnsESliceTopology sltp = ensESliceTopologyNULL;
if (!slice)
return ajFalse;
if (!Presult)
return ajFalse;
sltp = ensSliceLoadTopology(slice);
if (sltp == ensESliceTopologyCircular)
*Presult = ajTrue;
else
*Presult = ajFalse;
return ajTrue;
}
/* @func ensSliceIsNonreference ***********************************************
**
** Check whether an Ensembl Slice is based on an Ensembl Sequence Region, which
** has an Ensembl Attribute of code "non_ref" set.
**
** @cc Bio::EnsEMBL::Slice::is_reference
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] Presult [AjBool*] ajTrue if the Ensembl Sequence Region has an
** Ensembl Attribute of code "non_ref" set
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceIsNonreference(EnsPSlice slice, AjBool *Presult)
{
if (!slice)
return ajFalse;
if (!Presult)
return ajFalse;
if (!slice->Seqregion)
{
ajDebug("ensSliceIsNonreference requires the Ensembl Slice to have an "
"Ensembl Sequence region attached.\n");
return ajFalse;
}
return ensSeqregionIsNonreference(slice->Seqregion, Presult);
}
/* @func ensSliceIsToplevel ***************************************************
**
** Check whether an Ensembl Slice is based on an Ensembl Sequence Region, which
** has an Ensembl Attribute of code "toplevel" set.
**
** @cc Bio::EnsEMBL::Slice::is_toplevel
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] Presult [AjBool*] ajTrue if the Ensembl Sequence Region has an
** Ensembl Attribute of code "toplevel" set
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceIsToplevel(EnsPSlice slice, AjBool *Presult)
{
if (!slice)
return ajFalse;
if (!Presult)
return ajFalse;
if (!slice->Seqregion)
{
ajDebug("ensSliceIsToplevel requires the Ensembl Slice to have an "
"Ensembl Sequence region attached.\n");
return ajFalse;
}
return ensSeqregionIsToplevel(slice->Seqregion, Presult);
}
/* @section map ***************************************************************
**
** Functions for mapping Ensembl Slice objects.
**
** @fdata [EnsPSlice]
**
** @nam3rule Project Project an Ensembl Slice onto another
** Ensembl Coordinate System
** @nam3rule Projectslice Project an Ensembl Slice onto another
** Ensembl Slice
**
** @argrule Project slice [EnsPSlice] Ensembl Slice
** @argrule Project csname [const AjPStr] Ensembl Coordinate System name
** @argrule Project csversion [const AjPStr] Ensembl Coordinate System version
** @argrule Project pss [AjPList] AJAX List of
** Ensembl Projection Segment objects
** @argrule Projectslice srcslice [EnsPSlice] Source Ensembl Slice
** @argrule Projectslice trgslice [EnsPSlice] Target Ensembl Slice
** @argrule Projectslice pss [AjPList] AJAX List of
** Ensembl Projection Segment objects
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @funcstatic sliceConstrain *************************************************
**
** Constrain an Ensembl Slice to its Ensembl Sequence Region member.
**
** The caller is responsible for deleting the Ensembl Projection Segment.
**
** @cc Bio::EnsEMBL::Slice::_constrain_to_region
** @cc Bio::EnsEMBL::CircularSlice::_constrain_to_region
** @param [u] slice [EnsPSlice] Ensembl Slice
**
** @return [EnsPProjectionsegment] Ensembl Projection Segment or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
static EnsPProjectionsegment sliceConstrain(EnsPSlice slice)
{
ajint five = 0;
ajint three = 0;
ajint fshift = 0;
ajint tshift = 0;
EnsPProjectionsegment ps = NULL;
EnsPSlice nslice = NULL;
if (!slice)
{
ajDebug("sliceConstrain requires an Ensembl Slice.\n");
return NULL;
}
/* Return NULL, if this Slice does not overlap with its Sequence Region. */
if ((slice->Start > ensSeqregionGetLength(slice->Seqregion)) ||
(slice->End < 1))
return NULL;
/*
** If the Slice has negative coordinates or coordinates exceeding the
** length of the Sequence Region the Slice needs shrinking to the
** defined Sequence Region.
*/
if (slice->Start < 1)
five = slice->Start - 1;
if (slice->End > ensSeqregionGetLength(slice->Seqregion))
three = ensSeqregionGetLength(slice->Seqregion) - slice->End;
if (five || three)
{
if (slice->Strand >= 0)
ensSliceFetchSliceexpanded(slice,
five,
three,
ajFalse,
&fshift,
&tshift,
&nslice);
else
ensSliceFetchSliceexpanded(slice,
three,
five,
ajFalse,
&fshift,
&tshift,
&nslice);
}
else
nslice = ensSliceNewRef(slice);
ps = ensProjectionsegmentNewIni(1 - five,
ensSliceCalculateLength(slice) + three,
nslice);
ensSliceDel(&nslice);
return ps;
}
/* @funcstatic sliceProject ***************************************************
**
** Ensembl Slice project helper function.
**
** The caller is responsible for deleting the Ensembl Projection Segment
** objects before deleting the AJAX List.
**
** @cc Bio::EnsEMBL::Slice::project
** @cc Bio::EnsEMBL::CircularSlice::project
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] trgcs [EnsPCoordsystem] Ensembl Coordinate System
** @param [u] pss [AjPList] AJAX List of Ensembl Projection Segment objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
static AjBool sliceProject(EnsPSlice slice,
EnsPCoordsystem trgcs,
AjPList pss)
{
ajint end = 0;
ajint start = 1;
ajint length = 0;
AjBool debug = AJFALSE;
AjBool circular = AJFALSE;
AjPList nrmpss = NULL;
AjPList mrs = NULL;
EnsPAssemblymapper am = NULL;
EnsPAssemblymapperadaptor ama = NULL;
EnsPCoordsystem srccs = NULL;
EnsPCoordsystem nrmcs = NULL;
EnsPCoordsystem mrcs = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPProjectionsegment nrmps = NULL;
EnsPProjectionsegment ps = NULL;
EnsPMapperresult mr = NULL;
const EnsPSlice nrmslice = NULL;
EnsPSlice newslice = NULL;
/* Deliberately connect debug requests to ensSliceProject. */
debug = ajDebugTest("ensSliceProject");
if (debug)
{
ajDebug("sliceProject\n"
" slice %p\n"
" trgcs %p\n"
" pss %p\n",
slice,
trgcs,
pss);
ensSliceTrace(slice, 1);
ensCoordsystemTrace(trgcs, 1);
}
if (!slice)
return ajFalse;
if (!trgcs)
return ajFalse;
if (!pss)
return ajFalse;
if (!slice->Adaptor)
{
ajDebug("sliceProject requires that an Ensembl Slice Adaptor has "
"been set in the Ensembl Slice.\n");
return ajFalse;
}
dba = ensSliceadaptorGetDatabaseadaptor(slice->Adaptor);
/*
** Get the source Coordinate System, which is the
** Ensembl Coordinate System member of the
** Ensembl Sequence Region member of this Ensembl Slice.
*/
if (!slice->Seqregion)
{
ajDebug("sliceProject requires that an Ensembl Sequence Region "
"has been set in the Ensembl Slice.\n");
return ajFalse;
}
srccs = ensSeqregionGetCoordsystem(slice->Seqregion);
if (!srccs)
{
ajDebug("sliceProject requires that an Ensembl Coordinate System "
"member has been set in the Ensembl Sequence Region member "
"of the Ensembl Slice.\n");
return ajFalse;
}
/*
** No mapping is needed if the requested Ensembl Coordinate System is the
** one this Ensembl Slice is based upon, but we do need to check if some
** of the Slice is outside of defined regions.
*/
if (ensCoordsystemMatch(srccs, trgcs))
{
ajListPushAppend(pss, (void *) sliceConstrain(slice));
return ajTrue;
}
/*
** Decompose this Slice into its symlinked components, which allows
** handling of haplotypes (HAPs) and pseudo-autosomal region (PARs).
*/
ama = ensRegistryGetAssemblymapperadaptor(dba);
nrmpss = ajListNew();
ensSliceadaptorRetrieveNormalisedprojection(slice->Adaptor,
slice,
nrmpss);
while (ajListPop(nrmpss, (void **) &nrmps))
{
nrmslice = ensProjectionsegmentGetTargetSlice(nrmps);
nrmcs = ensSeqregionGetCoordsystem(nrmslice->Seqregion);
ensAssemblymapperadaptorFetchByCoordsystems(ama, nrmcs, trgcs, &am);
mrs = ajListNew();
if (am)
ensAssemblymapperMapSlice(am, nrmslice, ajFalse, mrs);
else
{
if (debug)
ajDebug("sliceProject could not fetch an "
"Ensembl Assembly Mapper between "
"Ensembl Coordinate System objects "
"'%S:%S' and '%S:%S', which implies an "
"Ensembl Mapper Result of type "
"ensEMapperresultTypeGap.\n",
ensCoordsystemGetName(nrmcs),
ensCoordsystemGetVersion(nrmcs),
ensCoordsystemGetName(trgcs),
ensCoordsystemGetVersion(trgcs));
mr = ensMapperresultNewGap(nrmslice->Start, nrmslice->End, 0);
ajListPushAppend(mrs, (void *) mr);
}
ensAssemblymapperDel(&am);
/* Construct a projection from the mapping results and return it. */
while (ajListPop(mrs, (void **) &mr))
{
switch (ensMapperresultGetType(mr))
{
case ensEMapperresultTypeCoordinate:
/*
** Calculate the Ensembl Mapper Result length for circular
** or linear Ensembl Slice objects.
*/
if (ensMapperresultGetCoordinateStart(mr) >
ensMapperresultGetCoordinateEnd(mr))
length
= ensSliceGetSeqregionLength(nrmslice)
+ ensMapperresultGetCoordinateStart(mr)
+ ensMapperresultGetCoordinateEnd(mr)
+ 1;
else
length
= ensMapperresultGetCoordinateEnd(mr)
- ensMapperresultGetCoordinateStart(mr)
+ 1;
mrcs = ensMapperresultGetCoordsystem(mr);
/*
** If the normalised projection just ended up mapping to
** the same Coordinate System we were already in then we
** should just return the original region. This can happen
** for example, if we were on a PAR region on Y, which
** referred to X and a projection to "toplevel" was
** requested.
*/
if (ensCoordsystemMatch(mrcs, nrmcs))
{
/* Trim off regions, which are not defined. */
ajListPushAppend(pss, (void *) sliceConstrain(slice));
/*
** Delete this Ensembl Mapper Result and the rest of
** the Ensembl Mapper Results including the AJAX List.
*/
ensMapperresultDel(&mr);
while (ajListPop(mrs, (void **) &mr))
ensMapperresultDel(&mr);
ajListFree(&mrs);
/*
** Delete this normalised Projection Segment and the
** rest of the normalised Projection Segment objects
** including the AJAX List.
*/
ensProjectionsegmentDel(&nrmps);
while (ajListPop(nrmpss, (void **) &nrmps))
ensProjectionsegmentDel(&nrmps);
ajListFree(&nrmpss);
return ajTrue;
}
else
{
/* Create a Slice in the target Coordinate System. */
ensSliceadaptorFetchByMapperresult(slice->Adaptor,
mr,
&newslice);
end = start + length - 1;
ensSliceIsCircular(newslice, &circular);
if ((circular == ajTrue) &&
(end > ensSliceGetSeqregionLength(newslice)))
end -= ensSliceGetSeqregionLength(newslice);
ps = ensProjectionsegmentNewIni(start, end, newslice);
ajListPushAppend(pss, (void *) ps);
ensSliceDel(&newslice);
}
break;
case ensEMapperresultTypeGap:
/*
** Skip gaps, but calculate the Ensembl Mapper Result
** length for circular or linear Ensembl Slice objects.
*/
if (ensMapperresultGetGapStart(mr) >
ensMapperresultGetGapEnd(mr))
length
= ensSliceGetSeqregionLength(nrmslice)
+ ensMapperresultGetGapStart(mr)
+ ensMapperresultGetGapEnd(mr)
+ 1;
else
length
= ensMapperresultGetGapEnd(mr)
- ensMapperresultGetGapStart(mr)
+1;
break;
case ensEMapperresultTypeInDel:
/*
** Calculate the Ensembl Mapper Result length for circular
** or linear Ensembl Slice objects.
** NOTE: The Ensembl Mapper Result Coordinate member is
** most likely the one to be used here. The Perl API just
** specifies code for Bio::EnsEMBL::Mapper::Coordinate
** objects.
*/
if (ensMapperresultGetCoordinateStart(mr) >
ensMapperresultGetCoordinateEnd(mr))
length
= ensSliceGetSeqregionLength(nrmslice)
+ ensMapperresultGetCoordinateStart(mr)
+ ensMapperresultGetCoordinateEnd(mr)
+ 1;
else
length
= ensMapperresultGetCoordinateEnd(mr)
- ensMapperresultGetCoordinateStart(mr)
+ 1;
ajWarn("sliceProject got an unexpected "
"Ensembl Mapper Result of type "
"ensEMapperresultTypeInDel.");
break;
default:
ajWarn("sliceProject got an unexpected "
"Ensembl Mapper Result of type %d.",
ensMapperresultGetType(mr));
}
start += length;
ensMapperresultDel(&mr);
}
ajListFree(&mrs);
ensProjectionsegmentDel(&nrmps);
}
ajListFree(&nrmpss);
return ajTrue;
}
/* @func ensSliceProject ******************************************************
**
** Project an Ensembl Slice onto another Ensembl Coordinate System.
**
** Projecting an Ensembl Slice onto an Ensembl Coordinate System that the
** Slice is assembled from is analogous to retrieving a tiling path.
** This method may also be used to project up-wards to a higher-level
** Ensembl Coordinate System.
**
** The caller is responsible for deleting the Ensembl Projection Segment
** objects before deleting the AJAX List.
**
** @cc Bio::EnsEMBL::Slice::project
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] csname [const AjPStr] Ensembl Coordinate System name
** @param [rN] csversion [const AjPStr] Ensembl Coordinate System version
** @param [u] pss [AjPList] AJAX List of Ensembl Projection Segment objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceProject(EnsPSlice slice,
const AjPStr csname,
const AjPStr csversion,
AjPList pss)
{
AjBool circular = AJFALSE;
AjBool result = AJFALSE;
EnsPCoordsystem cs = NULL;
EnsPCoordsystemadaptor csa = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPSlice slice1 = NULL;
EnsPSlice slice2 = NULL;
if (ajDebugTest("ensSliceProject"))
{
ajDebug("ensSliceProject\n"
" slice %p\n"
" csname '%S'\n"
" cvsversion '%S'\n"
" pss %p\n",
slice,
csname,
csversion,
pss);
ensSliceTrace(slice, 1);
}
if (!slice)
{
ajDebug("ensSliceProject requires an Ensembl Slice.\n");
return ajFalse;
}
if (!csname)
{
ajDebug("ensSliceProject requires an "
"Ensembl Coordinate System name.\n");
return ajFalse;
}
/*
** A Coordinate System version is not strictly required,
** since ensCoordsystemadaptorFetchByName does not require one.
*/
if (!pss)
{
ajDebug("ensSliceProject requires an AJAX List of "
"Ensembl Projection Segment objects.\n");
return ajFalse;
}
if (!slice->Adaptor)
{
ajDebug("ensSliceProject requires that an Ensembl Slice Adaptor has "
"been set in the Ensembl Slice.\n");
return ajFalse;
}
if (!slice->Seqregion)
{
ajDebug("ensSliceProject requires that an Ensembl Sequence Region "
"has been set in the Ensembl Slice.\n");
return ajFalse;
}
if (!ensSliceIsCircular(slice, &circular))
return ajFalse;
/* Fetch the target Coordinate System. */
dba = ensSliceadaptorGetDatabaseadaptor(slice->Adaptor);
csa = ensRegistryGetCoordsystemadaptor(dba);
ensCoordsystemadaptorFetchByName(csa, csname, csversion, &cs);
if (!cs)
{
ajDebug("ensSliceProject cannot project to an unknown "
"Ensembl Coordinate System '%S:%S'.\n", csname, csversion);
return ajFalse;
}
if ((circular == ajTrue) && (slice->Start > slice->End))
{
slice1 = ensSliceNewCpy(slice);
slice2 = ensSliceNewCpy(slice);
slice1->End = ensSeqregionGetLength(slice1->Seqregion);
slice2->Start = 1;
if (!sliceProject(slice1, cs, pss))
result = ajFalse;
if (!sliceProject(slice2, cs, pss))
result = ajFalse;
ensSliceDel(&slice1);
ensSliceDel(&slice2);
}
else
{
if (!sliceProject(slice, cs, pss))
result = ajFalse;
}
ensCoordsystemDel(&cs);
return result;
}
/* @func ensSliceProjectslice *************************************************
**
** Project an Ensembl Slice onto another Ensembl Slice.
**
** Needed for cases where multiple assembly mappings exist and a specific
** mapping is specified.
**
** The caller is responsible for deleting the Ensembl Projection Segment
** objects before deleting the AJAX List.
**
** @cc Bio::EnsEMBL::Slice::project_to_slice
** @param [u] srcslice [EnsPSlice] Ensembl Slice
** @param [u] trgslice [EnsPSlice] Target Ensembl Slice
** @param [u] pss [AjPList] AJAX List of Ensembl Projection Segment objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceProjectslice(EnsPSlice srcslice,
EnsPSlice trgslice,
AjPList pss)
{
ajint start = 0;
ajint length = 0;
ajuint last = 0U;
AjPList nrmpss = NULL;
AjPList mrs = NULL;
EnsPAssemblymapper am = NULL;
EnsPAssemblymapperadaptor ama = NULL;
EnsPCoordsystem srccs = NULL;
EnsPCoordsystem trgcs = NULL;
EnsPCoordsystem nrmcs = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPProjectionsegment nrmps = NULL;
EnsPProjectionsegment ps = NULL;
EnsPMapperresult mr = NULL;
const EnsPSlice nrmslice = NULL;
EnsPSlice newslice = NULL;
if (!srcslice)
return ajFalse;
if (!trgslice)
return ajFalse;
dba = ensSliceadaptorGetDatabaseadaptor(srcslice->Adaptor);
ama = ensRegistryGetAssemblymapperadaptor(dba);
/*
** Get the source Ensembl Coordinate System, which is the
** Ensembl Coordinate System member of the
** Ensembl Sequence Region member of this Ensembl Slice.
*/
srccs = ensSeqregionGetCoordsystem(srcslice->Seqregion);
if (!srccs)
{
ajDebug("ensSliceProjectslice requires that an "
"Ensembl Coordinate System member has been set in the "
"Ensembl Sequence Region member of the source "
"Ensembl Slice.\n");
return ajFalse;
}
/*
** Get the target Coordinate System, which is the
** Ensembl Coordinate System member of the
** Ensembl Sequence Region member of this Ensembl Slice.
*/
trgcs = ensSeqregionGetCoordsystem(trgslice->Seqregion);
if (!trgcs)
{
ajDebug("ensSliceProjectslice requires that an "
"Ensembl Coordinate System member has been set in the "
"Ensembl Sequence Region member of the target "
"Ensembl Slice.\n");
return ajFalse;
}
/*
** Decompose this Slice into its symlinked components, which allows
** handling of haplotypes (HAPs) and pseudo-autosomal region (PARs).
*/
nrmpss = ajListNew();
ensSliceadaptorRetrieveNormalisedprojection(srcslice->Adaptor,
srcslice,
nrmpss);
while (ajListPop(nrmpss, (void **) &nrmps))
{
nrmslice = ensProjectionsegmentGetTargetSlice(nrmps);
nrmcs = ensSeqregionGetCoordsystem(nrmslice->Seqregion);
ensAssemblymapperadaptorFetchByCoordsystems(ama, nrmcs, trgcs, &am);
mrs = ajListNew();
if (am)
ensAssemblymapperMapToSlice(am, nrmslice, trgslice, ajFalse, mrs);
else
{
ajDebug("ensSliceProjectslice got no Ensembl Assemblymapper -> "
"Ensembl Mapper Result of type gap\n");
mr = ensMapperresultNewGap(nrmslice->Start, nrmslice->End, 0);
ajListPushAppend(mrs, (void *) mr);
}
ensAssemblymapperDel(&am);
/* Construct a projection from the mapping results and return it. */
while (ajListPop(mrs, (void **) &mr))
{
length = ensMapperresultCalculateLengthResult(mr);
/*
** Reset the start coordinate, if a new target Sequence Region
** was encountered.
*/
if (last != ensMapperresultGetRank(mr))
start = 1;
last = ensMapperresultGetRank(mr);
/* Skip gaps. */
if (ensMapperresultGetType(mr) == ensEMapperresultTypeCoordinate)
{
/* For multiple mappings only get the correct one. */
if (ensMapperresultGetObjectidentifier(mr) ==
ensSliceGetSeqregionIdentifier(trgslice))
{
/* Create a Slice in the target Coordinate System. */
ensSliceadaptorFetchByMapperresult(srcslice->Adaptor,
mr,
&newslice);
ps = ensProjectionsegmentNewIni(start,
start + length - 1,
newslice);
ajListPushAppend(pss, (void *) ps);
ensSliceDel(&newslice);
}
}
start += length;
ensMapperresultDel(&mr);
}
ajListFree(&mrs);
ensProjectionsegmentDel(&nrmps);
}
ajListFree(&nrmpss);
ensCoordsystemDel(&trgcs);
/*
** Delete the Ensembl Assembly Mapper Adaptor cache,
** as the next mapping may include a different set.
*/
ensAssemblymapperadaptorClear(ama);
return ajTrue;
}
/* @datasection [EnsESliceType] Ensembl Slice Type ****************************
**
** @nam2rule Slice Functions for manipulating
** Ensembl Slice objects
** @nam3rule SliceType Functions for manipulating
** Ensembl Slice Type enumerations
**
******************************************************************************/
/* @section Misc **************************************************************
**
** Functions for returning an Ensembl Slice Type enumeration.
**
** @fdata [EnsESliceType]
**
** @nam4rule From Ensembl Slice Type query
** @nam5rule Seqregion Ensembl Sequence Region
** @nam5rule Str AJAX String object query
**
** @argrule Seqregion sr [EnsPSeqregion] Ensembl Sequence Region
** @argrule Str type [const AjPStr] Type string
**
** @valrule * [EnsESliceType] Ensembl Slice Type enumeration or
** ensESliceTypeNULL
**
** @fcategory misc
******************************************************************************/
/* @func ensSliceTypeFromSeqregion ********************************************
**
** Convert an Ensembl Sequence Region into an Ensembl Slice Type enumeration.
**
** @param [u] sr [EnsPSeqregion] Ensembl Sequence Region
**
** @return [EnsESliceType] Ensembl Slice Type enumeration or
** ensESliceTypeNULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsESliceType ensSliceTypeFromSeqregion(EnsPSeqregion sr)
{
AjBool result = AJFALSE;
if (!sr)
return ensESliceTypeNULL;
ensSeqregionIsLocusreferencegenomic(sr, &result);
if (result == ajTrue)
return ensESliceTypeLrg;
else
return ensESliceTypeLinear;
}
/* @func ensSliceTypeFromStr **************************************************
**
** Convert an AJAX String into an Ensembl Slice Type enumeration.
**
** @param [r] type [const AjPStr] Type string
**
** @return [EnsESliceType] Ensembl Slice Type enumeration or
** ensESliceTypeNULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsESliceType ensSliceTypeFromStr(const AjPStr type)
{
register EnsESliceType i = ensESliceTypeNULL;
EnsESliceType ste = ensESliceTypeNULL;
for (i = ensESliceTypeNULL;
sliceKType[i];
i++)
if (ajStrMatchC(type, sliceKType[i]))
ste = i;
if (!ste)
ajDebug("ensSliceTypeFromStr encountered "
"unexpected string '%S'.\n", type);
return ste;
}
/* @section Cast **************************************************************
**
** Functions for returning attributes of an
** Ensembl Slice Type enumeration.
**
** @fdata [EnsESliceType]
**
** @nam4rule To Return Ensembl Slice Type enumeration
** @nam5rule Char Return C character string value
**
** @argrule To ste [EnsESliceType] Ensembl Slice Type enumeration
**
** @valrule Char [const char*] Ensembl Slice Type C-type (char *) string
**
** @fcategory cast
******************************************************************************/
/* @func ensSliceTypeToChar ***************************************************
**
** Convert an Ensembl Slice Type enumeration into a C-type (char *) string.
**
** @param [u] ste [EnsESliceType] Ensembl Slice Type enumeration
**
** @return [const char*] Ensembl Slice Type C-type (char *) string
**
** @release 6.4.0
** @@
******************************************************************************/
const char* ensSliceTypeToChar(EnsESliceType ste)
{
register EnsESliceType i = ensESliceTypeNULL;
for (i = ensESliceTypeNULL;
sliceKType[i] && (i < ste);
i++);
if (!sliceKType[i])
ajDebug("ensSliceTypeToChar "
"encountered an out of boundary error on "
"Ensembl Slice Type "
"enumeration %d.\n",
ste);
return sliceKType[i];
}
/* @datasection [AjPList] AJAX List *******************************************
**
** @nam2rule List Functions for manipulating AJAX List objects
**
******************************************************************************/
/* @section list **************************************************************
**
** Functions for manipulating AJAX List objects.
**
** @fdata [AjPList]
**
** @nam3rule Slice Functions for manipulating AJAX List objects of
** Ensembl Slice objects
** @nam4rule Remove Remove functions
** @nam5rule Duplications Remove duplications
** @nam4rule Sort Sort functions
** @nam5rule Identifier Sort by Ensembl Sequence Region identifier member
** @nam5rule Name Sort by Ensembl Sequence Region name member
** @nam6rule Ascending Sort in ascending order
** @nam6rule Descending Sort in descending order
**
** @argrule * slices [AjPList] AJAX List of Ensembl Slice objects
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensListSliceRemoveDuplications ***************************************
**
** Process an AJAX List of Ensembl Slice objects and remove duplicate regions.
**
** This function checks each Ensembl Slice object on the AJAX List for
** duplicate regions and if positive, replaces the Ensembl Slice object by one
** or more Ensembl Slice objects representing the unique sequence.
**
** Ensembl Slice objects of complete mammalian Y chromosomes contain duplictaed
** regions where the pseudo autosomal regions (PARs) on both chromosome ends
** represent unique sequence, while the bulk of the chromosome is copied
** (duplicated) from the X chromosome. Therefore, this function would remove an
** Ensembl Slice spanning the Y chromosome and replace it with two Ensembl
** Slice objects representing just the PAR regions.
**
** The caller is responsible for deleting the Ensembl Slice objects before
** deleting the AJAX List.
**
** @param [u] slices [AjPList] AJAX List of Ensembl Slice objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListSliceRemoveDuplications(AjPList slices)
{
AjIList iter = NULL;
AjPList aes = NULL;
AjPList pss = NULL;
EnsPAssemblyexception ae = NULL;
EnsPAssemblyexceptionadaptor aea = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPProjectionsegment ps = NULL;
EnsPSlice psslice = NULL;
EnsPSlice srslice = NULL;
if (!slices)
return ajFalse;
aes = ajListNew();
pss = ajListNew();
iter = ajListIterNew(slices);
while (!ajListIterDone(iter))
{
srslice = (EnsPSlice) ajListIterGet(iter);
dba = ensSliceadaptorGetDatabaseadaptor(srslice->Adaptor);
aea = ensRegistryGetAssemblyexceptionadaptor(dba);
ensAssemblyexceptionadaptorFetchAllbyReferenceSeqregion(
aea,
ensSliceGetSeqregionIdentifier(srslice),
aes);
if (ajListGetLength(aes))
{
/*
** This Ensembl Slice may have duplicate regions, so de-reference
** symlinked assembly regions and remove any Ensembl Slice objects,
** which have a symlink, because these are duplicates.
** Replace them with any symlinked Ensembl Slice objects based on
** the same Ensembl Sequence Region and Ensembl Coordinate System
** as the original Ensembl Slice.
*/
ajListIterRemove(iter);
ensSliceadaptorRetrieveNormalisedprojection(srslice->Adaptor,
srslice,
pss);
while (ajListPop(pss, (void **) &ps))
{
psslice = ensProjectionsegmentGetTargetSlice(ps);
if (ensSeqregionMatch(psslice->Seqregion,
srslice->Seqregion))
{
ajListIterInsert(iter, (void *) ensSliceNewRef(psslice));
/* Advance the AJAX List Iterator after the insert. */
(void) ajListIterGet(iter);
}
ensProjectionsegmentDel(&ps);
}
ensSliceDel(&srslice);
}
while (ajListPop(aes, (void **) &ae))
ensAssemblyexceptionDel(&ae);
}
ajListIterDel(&iter);
ajListFree(&aes);
ajListFree(&pss);
return ajTrue;
}
/* @funcstatic listSliceCompareIdentifierAscending ****************************
**
** AJAX List of Ensembl Slice objects comparison function to sort by
** Ensembl Sequence Region identifier in ascending order.
**
** @param [r] item1 [const void*] Ensembl Slice address 1
** @param [r] item2 [const void*] Ensembl Slice address 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.4.0
** @@
******************************************************************************/
static int listSliceCompareIdentifierAscending(
const void *item1,
const void *item2)
{
ajuint srid1 = 0U;
ajuint srid2 = 0U;
EnsPSlice slice1 = *(EnsOSlice *const *) item1;
EnsPSlice slice2 = *(EnsOSlice *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listSliceCompareIdentifierAscending"))
ajDebug("listSliceCompareIdentifierAscending\n"
" slice1 %p\n"
" slice2 %p\n",
slice1,
slice2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (slice1 && (!slice2))
return -1;
if ((!slice1) && (!slice2))
return 0;
if ((!slice1) && slice2)
return +1;
srid1 = ensSliceGetSeqregionIdentifier(slice1);
srid2 = ensSliceGetSeqregionIdentifier(slice2);
if (srid1 && (!srid2))
return -1;
if ((!srid1) && (!srid2))
return 0;
if ((!srid1) && srid2)
return +1;
if (srid1 < srid2)
return -1;
if (srid1 > srid2)
return +1;
return 0;
}
/* @func ensListSliceSortIdentifierAscending **********************************
**
** Sort an AJAX List of Ensembl Slice objects by their
** Ensembl Sequence Region identifier in ascending order.
**
** @param [u] slices [AjPList] AJAX List of Ensembl Slice objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListSliceSortIdentifierAscending(AjPList slices)
{
if (!slices)
return ajFalse;
ajListSort(slices, &listSliceCompareIdentifierAscending);
return ajTrue;
}
/* @funcstatic listSliceCompareIdentifierDescending ***************************
**
** AJAX List of Ensembl Slice objects comparison function to sort by
** Ensembl Sequence Region identifier in descending order.
**
** @param [r] item1 [const void*] Ensembl Slice address 1
** @param [r] item2 [const void*] Ensembl Slice address 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.4.0
** @@
******************************************************************************/
static int listSliceCompareIdentifierDescending(
const void *item1,
const void *item2)
{
ajuint srid1 = 0U;
ajuint srid2 = 0U;
EnsPSlice slice1 = *(EnsOSlice *const *) item1;
EnsPSlice slice2 = *(EnsOSlice *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listSliceCompareIdentifierDescending"))
ajDebug("listSliceCompareIdentifierDescending\n"
" slice1 %p\n"
" slice2 %p\n",
slice1,
slice2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (slice1 && (!slice2))
return -1;
if ((!slice1) && (!slice2))
return 0;
if ((!slice1) && slice2)
return +1;
srid1 = ensSliceGetSeqregionIdentifier(slice1);
srid2 = ensSliceGetSeqregionIdentifier(slice2);
if (srid1 && (!srid2))
return -1;
if ((!srid1) && (!srid2))
return 0;
if ((!srid1) && srid2)
return +1;
if (srid1 > srid2)
return -1;
if (srid1 < srid2)
return +1;
return 0;
}
/* @func ensListSliceSortIdentifierDescending *********************************
**
** Sort an AJAX List of Ensembl Slice objects by their
** Ensembl Sequence Region identifier in descending order.
**
** @param [u] slices [AjPList] AJAX List of Ensembl Slice objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListSliceSortIdentifierDescending(AjPList slices)
{
if (!slices)
return ajFalse;
ajListSort(slices, &listSliceCompareIdentifierDescending);
return ajTrue;
}
/* @funcstatic listSliceCompareNameAscending **********************************
**
** AJAX List of Ensembl Slice objects comparison function to sort by
** Ensembl Sequence Region name in ascending order.
**
** @param [r] item1 [const void*] Ensembl Slice address 1
** @param [r] item2 [const void*] Ensembl Slice address 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.4.0
** @@
******************************************************************************/
static int listSliceCompareNameAscending(
const void *item1,
const void *item2)
{
const AjPStr srname1 = NULL;
const AjPStr srname2 = NULL;
EnsPSlice slice1 = *(EnsOSlice *const *) item1;
EnsPSlice slice2 = *(EnsOSlice *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listSliceCompareNameAscending"))
ajDebug("listSliceCompareNameAscending\n"
" slice1 %p\n"
" slice2 %p\n",
slice1,
slice2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (slice1 && (!slice2))
return -1;
if ((!slice1) && (!slice2))
return 0;
if ((!slice1) && slice2)
return +1;
srname1 = ensSliceGetSeqregionName(slice1);
srname2 = ensSliceGetSeqregionName(slice2);
if (srname1 && (!srname2))
return -1;
if ((!srname1) && (!srname2))
return 0;
if ((!srname1) && srname2)
return +1;
return ajStrCmpS(srname1, srname2);
}
/* @func ensListSliceSortNameAscending ****************************************
**
** Sort an AJAX List of Ensembl Slice objects by their
** Ensembl Sequence Region name in ascending order.
**
** @param [u] slices [AjPList] AJAX List of Ensembl Slice objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListSliceSortNameAscending(AjPList slices)
{
if (!slices)
return ajFalse;
ajListSort(slices, &listSliceCompareNameAscending);
return ajTrue;
}
/* @funcstatic listSliceCompareNameDescending *********************************
**
** AJAX List of Ensembl Slice objects comparison function to sort by
** Ensembl Sequence Region name in descending order.
**
** @param [r] item1 [const void*] Ensembl Slice address 1
** @param [r] item2 [const void*] Ensembl Slice address 2
** @see ajListSort
**
** @return [int] The comparison function returns an integer less than,
** equal to, or greater than zero if the first argument is
** considered to be respectively less than, equal to, or
** greater than the second.
**
** @release 6.4.0
** @@
******************************************************************************/
static int listSliceCompareNameDescending(
const void *item1,
const void *item2)
{
const AjPStr srname1 = NULL;
const AjPStr srname2 = NULL;
EnsPSlice slice1 = *(EnsOSlice *const *) item1;
EnsPSlice slice2 = *(EnsOSlice *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listSliceCompareNameDescending"))
ajDebug("listSliceCompareNameDescending\n"
" slice1 %p\n"
" slice2 %p\n",
slice1,
slice2);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX List. */
if (slice1 && (!slice2))
return -1;
if ((!slice1) && (!slice2))
return 0;
if ((!slice1) && slice2)
return +1;
srname1 = ensSliceGetSeqregionName(slice1);
srname2 = ensSliceGetSeqregionName(slice2);
if (srname1 && (!srname2))
return -1;
if ((!srname1) && (!srname2))
return 0;
if ((!srname1) && srname2)
return +1;
return -1 * ajStrCmpS(srname1, srname2);
}
/* @func ensListSliceSortNameDescending ***************************************
**
** Sort an AJAX List of Ensembl Slice objects by their
** Ensembl Sequence Region name in descending order.
**
** @param [u] slices [AjPList] AJAX List of Ensembl Slice objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListSliceSortNameDescending(AjPList slices)
{
if (!slices)
return ajFalse;
ajListSort(slices, &listSliceCompareNameDescending);
return ajTrue;
}
/* @datasection [EnsPSliceadaptor] Ensembl Slice Adaptor **********************
**
** @nam2rule Sliceadaptor Functions for manipulating
** Ensembl Slice Adaptor objects
**
** @cc Bio::EnsEMBL::DBSQL::SliceAdaptor
** @cc CVS Revision: 1.134
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @funcstatic sliceadaptorCacheDelete ****************************************
**
** Wrapper function to delete an Ensembl Slice from an Ensembl Cache.
**
** @param [d] Pvalue [void**] Ensembl Slice address
** @see ensCacheNew
**
** @return [void]
**
** @release 6.3.0
** @@
** When deleting from the Cache, this function also removes and deletes the
** Ensembl Slice from the name cache, which is based on a
** conventional AJAX Table.
******************************************************************************/
static void sliceadaptorCacheDelete(void **Pvalue)
{
ajint start = 0;
ajint end = 0;
ajint strand = 0;
AjPStr key = NULL;
EnsPCoordsystem cs = NULL;
EnsPSlice oldslice = NULL;
EnsPSlice newslice = NULL;
if (!Pvalue)
return;
if (!*Pvalue)
return;
/*
** Synchronise the deletion of this Sequence Region from the
** identifier cache, which is based on an Ensembl (LRU) Cache,
** with the name cache, based on a conventional AJAX Table,
** both in the Sequence Adaptor.
*/
newslice = *((EnsPSlice *) Pvalue);
if (newslice->Adaptor && newslice->Adaptor->CacheByName)
{
cs = ensSeqregionGetCoordsystem(newslice->Seqregion);
start = newslice->Start;
end = newslice->End;
strand = newslice->Strand;
if ((start == 1) &&
(end == ensSeqregionGetLength(newslice->Seqregion)) &&
(strand == 1))
{
start = 0;
end = 0;
strand = 0;
}
/* Remove from the name cache. */
key = ajFmtStr("%S:%S:%S:%d:%d:%d",
ensCoordsystemGetName(cs),
ensCoordsystemGetVersion(cs),
ensSeqregionGetName(newslice->Seqregion),
start, end, strand);
oldslice = (EnsPSlice) ajTableRemove(
newslice->Adaptor->CacheByName,
(const void *) key);
ensSliceDel(&oldslice);
ajStrDel(&key);
}
ensSliceDel((EnsPSlice *) Pvalue);
return;
}
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Slice Adaptor by pointer.
** It is the responsibility of the user to first destroy any previous
** Slice Adaptor. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPSliceadaptor]
**
** @nam3rule New Constructor
**
** @argrule New dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @valrule * [EnsPSliceadaptor] Ensembl Slice Adaptor or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensSliceadaptorNew ***************************************************
**
** Default constructor for an Ensembl Slice Adaptor.
**
** Ensembl Object Adaptors are singleton objects in the sense that a single
** instance of an Ensembl Object Adaptor connected to a particular database is
** sufficient to instantiate any number of Ensembl Objects from the database.
** Each Ensembl Object will have a weak reference to the Object Adaptor that
** instantiated it. Therefore, Ensembl Object Adaptors should not be
** instantiated directly, but rather obtained from the Ensembl Registry,
** which will in turn call this function if neccessary.
**
** @see ensRegistryGetDatabaseadaptor
** @see ensRegistryGetSliceadaptor
**
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [EnsPSliceadaptor] Ensembl Slice Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPSliceadaptor ensSliceadaptorNew(
EnsPDatabaseadaptor dba)
{
EnsPSliceadaptor sla = NULL;
if (!dba)
return NULL;
AJNEW0(sla);
sla->Adaptor = dba;
sla->CacheByIdentifier = ensCacheNew(
ensECacheTypeAlphaNumeric,
sliceadaptorKCacheMaxBytes,
sliceadaptorKCacheMaxCount,
sliceadaptorKCacheMaxSize,
(void *(*)(void *)) &ensSliceNewRef,
&sliceadaptorCacheDelete,
(size_t (*)(const void *)) &ensSliceCalculateMemsize,
(void *(*)(const void *key)) NULL,
(AjBool (*)(const void *value)) NULL,
ajFalse,
"Slice");
sla->CacheByName = ajTablestrNew(0U);
ajTableSetDestroyvalue(sla->CacheByName, (void (*)(void **)) &ensSliceDel);
return sla;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Slice Adaptor object.
**
** @fdata [EnsPSliceadaptor]
**
** @nam3rule Del Destroy (free) an Ensembl Slice Adaptor
**
** @argrule * Psla [EnsPSliceadaptor*] Ensembl Slice Adaptor address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensSliceadaptorDel ***************************************************
**
** Default destructor for an Ensembl Slice Adaptor.
**
** This function also clears the internal Sequence Region caches.
**
** Ensembl Object Adaptors are singleton objects that are registered in the
** Ensembl Registry and weakly referenced by Ensembl Objects that have been
** instantiated by it. Therefore, Ensembl Object Adaptors should never be
** destroyed directly. Upon exit, the Ensembl Registry will call this function
** if required.
**
** @param [d] Psla [EnsPSliceadaptor*] Ensembl Slice Adaptor address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensSliceadaptorDel(EnsPSliceadaptor *Psla)
{
EnsPSliceadaptor pthis = NULL;
if (!Psla)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensSliceadaptorDel"))
ajDebug("ensSliceadaptorDel\n"
" *Psla %p\n",
*Psla);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Psla))
return;
/*
** Clear the identifier cache, which is based on an Ensembl LRU Cache.
** Clearing the Ensembl LRU Cache automatically clears the name cache
** via sliceadaptorCacheDelete.
*/
ensCacheDel(&pthis->CacheByIdentifier);
ajTableDel(&pthis->CacheByName);
ajMemFree((void **) Psla);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Slice Adaptor object.
**
** @fdata [EnsPSliceadaptor]
**
** @nam3rule Get Return Ensembl Slice Adaptor attribute(s)
** @nam4rule Databaseadaptor Return the Ensembl Database Adaptor
**
** @argrule * sla [EnsPSliceadaptor] Ensembl Slice Adaptor
**
** @valrule Databaseadaptor [EnsPDatabaseadaptor] Ensembl Database Adaptor
** or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensSliceadaptorGetDatabaseadaptor ************************************
**
** Get the Ensembl Database Adaptor member of an Ensembl Slice Adaptor.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPDatabaseadaptor ensSliceadaptorGetDatabaseadaptor(
EnsPSliceadaptor sla)
{
return (sla) ? sla->Adaptor : NULL;
}
/* @section member retrieval **************************************************
**
** Functions for manipulating an Ensembl Slice Adaptor cache.
**
** @fdata [EnsPSliceadaptor]
**
** @nam3rule Cache Manupulate an Ensembl Slice Adaptor cache
** @nam4rule Insert Insert an Ensembl Slice
**
** @argrule * sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @argrule Insert Pslice [EnsPSlice*] Ensembl Slice
** address
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensSliceadaptorCacheInsert *******************************************
**
** Insert an Ensembl Slice into the Slice Adaptor-internal cache.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceadaptorCacheInsert(EnsPSliceadaptor sla, EnsPSlice *Pslice)
{
ajint start = 0;
ajint end = 0;
ajint strand = 0;
AjPStr ikey = NULL;
AjPStr nkey = NULL;
EnsPCoordsystem cs = NULL;
EnsPSlice slice1 = NULL;
EnsPSlice slice2 = NULL;
if (!sla)
return ajFalse;
if (!Pslice)
return ajFalse;
if (ajDebugTest("ensSliceadaptorCacheInsert"))
{
ajDebug("ensSliceadaptorCacheInsert\n"
" sla %p\n"
" *Pslice %p\n",
sla,
*Pslice);
ensSliceTrace(*Pslice, 1);
}
if (!*Pslice)
return ajFalse;
cs = ensSeqregionGetCoordsystem((*Pslice)->Seqregion);
start = (*Pslice)->Start;
end = (*Pslice)->End;
strand = (*Pslice)->Strand;
/*
** For Ensembl Slice objects that cover an entire Ensembl Sequence Region,
** zero all coordinates.
*/
if ((start == 1) &&
(end == ensSeqregionGetLength((*Pslice)->Seqregion)) &&
(strand == 1))
{
start = 0;
end = 0;
strand = 0;
}
/* Search the identifier cache. */
ikey = ajFmtStr("%u:%d:%d:%d",
ensSeqregionGetIdentifier((*Pslice)->Seqregion),
start, end, strand);
ensCacheFetch(sla->CacheByIdentifier,
(void *) ikey,
(void **) &slice1);
/* Search the name cache. */
nkey = ajFmtStr("%S:%S:%S:%d:%d:%d",
ensCoordsystemGetName(cs),
ensCoordsystemGetVersion(cs),
ensSeqregionGetName((*Pslice)->Seqregion),
start, end, strand);
slice2 = (EnsPSlice) ajTableFetchmodS(sla->CacheByName, nkey);
if ((!slice1) && (!slice2))
{
/*
** None of the caches returned an identical Ensembl Slice so add this
** one to both caches. The Ensembl LRU Cache automatically references
** the Ensembl Slice via the sliceadaptorCacheReference function,
** while the AJAX Table-based cache needs manual referencing.
*/
ensCacheStore(sla->CacheByIdentifier,
(void *) ikey,
(void **) Pslice);
ajTablePut(sla->CacheByName,
(void *) ajStrNewS(nkey),
(void *) ensSliceNewRef(*Pslice));
}
if (slice1 && slice2 && (slice1 == slice2))
{
/*
** Both caches returned the same Ensembl Slice so delete it and
** return a pointer to the one already in the cache.
*/
ensSliceDel(Pslice);
*Pslice = ensSliceNewRef(slice2);
}
if (slice1 && slice2 && (slice1 != slice2))
ajDebug("ensSliceadaptorCacheInsert detected Slice objects in the "
"identifier '%S' and name '%S' cache with "
"different addresses (%p and %p).\n",
ikey, nkey, slice1, slice2);
if (slice1 && (!slice2))
ajDebug("ensSliceadaptorCacheInsert detected a Slice in "
"the identifier, but not in the name cache.\n");
if ((!slice1) && slice2)
ajDebug("ensSliceadaptorCacheInsert detected a Slice in "
"the name, but not in the identifier cache.\n");
ensSliceDel(&slice1);
ajStrDel(&ikey);
ajStrDel(&nkey);
return ajTrue;
}
/* @section canonical object retrieval ****************************************
**
** Functions for fetching Ensembl Slice objects from an
** Ensembl SQL database.
**
** @fdata [EnsPSliceadaptor]
**
** @nam3rule Fetch Fetch Ensembl Slice object(s)
** @nam4rule All Fetch all Ensembl Slice objects
** @nam4rule Allby Fetch all Ensembl Slice objects matching a criterion
** @nam5rule Regionunique Fetch all Ensembl Slice objects representing the
** unique parts of an Ensembl Sequence Region
** @nam4rule By Fetch one Ensembl Slice object matching a criterion
** @nam5rule Feature Fetch by an Ensembl Feature
** @nam5rule Location Fetch by a top-level location
** @nam5rule Mapperresult Fetch by an Ensembl Mapper Result
** @nam5rule Name Fetch by a name
** @nam5rule Region Fetch by a region
** @nam5rule Seqregion Fetch by an Ensembl Sequence Region member
** @nam6rule Identifier Fetch by an SQL database-internal identifier
** @nam6rule Name Fetch by a name
** @nam5rule Slice Fetch by an Ensembl Slice
**
** @argrule * sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @argrule All csname [const AjPStr] Ensembl Coordinate System name
** @argrule All csversion [const AjPStr] Ensembl Coordinate System version
** @argrule All nonreference [AjBool]
** Include non-reference Ensembl Sequence Region objects
** @argrule All duplicates [AjBool]
** Include duplicate Ensembl Sequence Region objects
** @argrule All lrg [AjBool] Include Locus Reference Genomic
** @argrule All slices [AjPList] AJAX List of Ensembl Slice objects
** @argrule AllbyRegionunique csname [const AjPStr]
** Ensembl Coordinate System name
** @argrule AllbyRegionunique csversion [const AjPStr]
** Ensembl Coordinate System version
** @argrule AllbyRegionunique srname [const AjPStr]
** Ensembl Sequence Region name
** @argrule AllbyRegionunique srstart [ajint] Start coordinate
** @argrule AllbyRegionunique srend [ajint] End coordinate
** @argrule AllbyRegionunique srstrand [ajint] Strand information
** @argrule Allby slices [AjPList] AJAX List of Ensembl Slice objects
** @argrule ByLocation location [const AjPStr] Top-level location
** @argrule ByMapperresult mr [const EnsPMapperresult] Ensembl Mapper Result
** @argrule ByName name [const AjPStr] Ensembl Slice name
** @argrule ByRegion csname [const AjPStr] Ensembl Coordinate System name
** @argrule ByRegion csversion [const AjPStr] Ensembl Coordinate System version
** @argrule ByRegion srname [const AjPStr] Ensembl Sequence Region name
** @argrule ByRegion srstart [ajint] Start coordinate
** @argrule ByRegion srend [ajint] End coordinate
** @argrule ByRegion srstrand [ajint] Strand information
** @argrule BySeqregionIdentifier srid [ajuint]
** Ensembl Sequence Region identifier
** @argrule BySeqregionIdentifier srstart [ajint] Start coordinate
** @argrule BySeqregionIdentifier srend [ajint] End coordinate
** @argrule BySeqregionIdentifier srstrand [ajint] Strand information
** @argrule BySeqregionName csname [const AjPStr]
** Ensembl Coordinate System name
** @argrule BySeqregionName csversion [const AjPStr]
** Ensembl Coordinate System version
** @argrule BySeqregionName srname [const AjPStr] Ensembl Sequence Region name
** @argrule BySlice slice [EnsPSlice] Ensembl Slice
** @argrule BySlice start [ajint] Start coordinate
** @argrule BySlice end [ajint] End coordinate
** @argrule BySlice strand [ajint] Strand information
** @argrule ByFeature feature [const EnsPFeature] Ensembl Feature
** @argrule ByFeature flank [ajint] Flanking region in base pair coordinates
** @argrule By Pslice [EnsPSlice*] Ensembl Slice address
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensSliceadaptorFetchAll **********************************************
**
** Fetch all Ensembl Slice objects representing Ensembl Sequence Region objects
** of a given Ensembl Coordinate System.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [r] csname [const AjPStr] Ensembl Coordinate System name
** @param [rN] csversion [const AjPStr] Ensembl Coordinate System version
** @param [r] nonreference [AjBool]
** Include non-reference Ensembl Sequence Region objects
** @param [r] duplicates [AjBool]
** Include duplicate Ensembl Sequence Region objects
** @param [r] lrg [AjBool] Include Locus Reference Genomic
** @param [u] slices [AjPList] An AJAX List of Ensembl Slice objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
** The Coordinate System name may be the name of an actual Coordinate System
** or an alias like "seqlevel" or "toplevel".
** If the Coordinate System name provided is "toplevel", all non-redundant,
** top-level Slice objects are returned. The Coordinate System version will be
** ignored in that case.
** Non-reference Slice objects reflect alternative haplotype assemblies.
** Examples for human NCBI36 would be c5_H2, c6_COX, c6_QBL and c22_H2.
** If the duplicate option is not set and a pseudo-autosomal region (PAR) is
** at the beginning of the Sequence Region, then the resulting Slice will not
** start at position 1, so that coordinates retrieved from this Slice might
** not be what was expected.
******************************************************************************/
AjBool ensSliceadaptorFetchAll(EnsPSliceadaptor sla,
const AjPStr csname,
const AjPStr csversion,
AjBool nonreference,
AjBool duplicates,
AjBool lrg,
AjPList slices)
{
AjBool debug = AJFALSE;
AjBool result = AJFALSE;
AjPList srs = NULL;
EnsPCoordsystem cs = NULL;
EnsPCoordsystemadaptor csa = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPSeqregion sr = NULL;
EnsPSeqregionadaptor sra = NULL;
EnsPSlice slice = NULL;
debug = ajDebugTest("ensSliceadaptorFetchAll");
if (debug)
ajDebug("ensSliceadaptorFetchAll\n"
" sla %p\n"
" csname '%S'\n"
" csversion '%S'\n"
" nonreference '%B'\n"
" duplicates '%B'\n"
" lrg '%B'\n"
" slices %p\n",
sla,
csname,
csversion,
nonreference,
duplicates,
lrg,
slices);
if (!sla)
return ajFalse;
if (!csname)
return ajFalse;
if (!slices)
return ajFalse;
dba = ensSliceadaptorGetDatabaseadaptor(sla);
csa = ensRegistryGetCoordsystemadaptor(dba);
sra = ensRegistryGetSeqregionadaptor(dba);
ensCoordsystemadaptorFetchByName(csa, csname, csversion, &cs);
if (!cs)
{
ajWarn("ensSliceadaptorFetchAll could not retrieve Coordinate System "
"for name '%S' and version '%S'.\n", csname, csversion);
return ajTrue;
}
/* Fetch the Ensembl Sequence Region objects from the database. */
srs = ajListNew();
ensSeqregionadaptorFetchAllbyCoordsystem(sra, cs, srs);
while (ajListPop(srs, (void **) &sr))
{
/* Check for non-reference Ensembl Sequence Region objects. */
if (nonreference == ajFalse)
{
if (!ensSeqregionIsNonreference(sr, &result))
{
ajDebug("ensSliceadaptorFetchAll could not call "
"ensSeqregionIsNonreference successfully.\n");
ensSeqregionTrace(sr, 1);
ensSeqregionDel(&sr);
continue;
}
if (result == ajTrue)
{
if (debug)
{
ajDebug("ensSliceadaptorFetchAll removed non-reference "
"Ensembl Sequence Region %p.\n", sr);
ensSeqregionTrace(sr, 1);
}
ensSeqregionDel(&sr);
continue;
}
}
/*
** Check for Locus Reference Genomic (LRG)
** Ensembl Sequence Region objects.
*/
if (lrg == ajFalse)
{
if (!ensSeqregionIsLocusreferencegenomic(sr, &result))
{
ajDebug("ensSliceadaptorFetchAll could not call "
"ensSeqregionIsLocusreferencegenomic successfully.\n");
ensSeqregionTrace(sr, 1);
ensSeqregionDel(&sr);
continue;
}
if (result == ajTrue)
{
if (debug)
{
ajDebug("ensSliceadaptorFetchAll removed LRG "
"Ensembl Sequence Region %p.\n", sr);
ensSeqregionTrace(sr, 1);
}
ensSeqregionDel(&sr);
continue;
}
}
/* Create a new Slice spanning the entire Sequence Region. */
slice = ensSliceNewIni(sla, sr, 1, ensSeqregionGetLength(sr), 1);
ajListPushAppend(slices, (void *) slice);
ensSeqregionDel(&sr);
}
if (duplicates == ajFalse)
ensListSliceRemoveDuplications(slices);
ajListFree(&srs);
ensCoordsystemDel(&cs);
return ajTrue;
}
/* @func ensSliceadaptorFetchAllbyRegionunique ********************************
**
** Fetch Ensembl Slice objects representing the unique parts of an
** Ensembl Sequence Region. At a minimum the name of an
** Ensembl Sequence Region must be provided. If no Coordinate System name is
** provided then a Slice of the highest ranked Coordinate System with a
** matching Sequence Region name will be returned.
**
** The caller is responsible for deleting the Ensembl Slice objects before
** deleting the AJAX List.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [rN] csname [const AjPStr] Ensembl Coordinate System name
** @param [rN] csversion [const AjPStr] Ensembl Coordinate System version
** @param [r] srname [const AjPStr] Ensembl Sequence Region name
** @param [r] srstart [ajint] Start coordinate
** @param [r] srend [ajint] End coordinate
** @param [r] srstrand [ajint] Strand information
** @param [u] slices [AjPList] AJAX List of Ensembl Slice objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
**
** NOTE: The Ensembl Core Perl API performs some fuzzy matching, if no exact
** match for the provided Sequence Region name can be found. This allows clones
** to be fetched even when their sequence version is not known.
** For example ensSliceadaptorFetchByRegion(..., "clone", "AC008066", ...)
** will retrieve the Sequence Region with name "AC008066.4".
**
** The fuzzy matching can be turned off by setting the $no_fuzz argument to a
** true value.
**
** This has not been implemented here.
******************************************************************************/
AjBool ensSliceadaptorFetchAllbyRegionunique(EnsPSliceadaptor sla,
const AjPStr csname,
const AjPStr csversion,
const AjPStr srname,
ajint srstart,
ajint srend,
ajint srstrand,
AjPList slices)
{
AjBool result = AJFALSE;
EnsPSlice slice = NULL;
if (!sla)
return ajFalse;
if (!(srname && ajStrGetLen(srname)))
return ajFalse;
if (!slices)
return ajFalse;
result = ensSliceadaptorFetchByRegion(
sla,
csname,
csversion,
srname,
srstart,
srend,
srstrand,
&slice);
ajListPushAppend(slices, (void *) slice);
ensListSliceRemoveDuplications(slices);
return result;
}
/* @func ensSliceadaptorFetchByFeature ****************************************
**
** Fetch an Ensembl Slice around an Ensembl Feature.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [r] feature [const EnsPFeature] Ensembl Feature
** @param [r] flank [ajint] Flanking region in base pair coordinates
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
** All this really does is return a resized version of the Slice that the
** Feature is already on. Note that Slice objects returned from this function
** are always on the forward strand of the Sequence Region regardless of the
** strandedness of the Feature passed in.
******************************************************************************/
AjBool ensSliceadaptorFetchByFeature(EnsPSliceadaptor sla,
const EnsPFeature feature,
ajint flank,
EnsPSlice *Pslice)
{
ajuint srid = 0U;
ajint srstart = 0;
ajint srend = 0;
AjBool result = AJFALSE;
EnsPSlice slice = NULL;
if (ajDebugTest("ensSliceadaptorFetchByFeature"))
{
ajDebug("ensSliceadaptorFetchByFeature\n"
" sla %p\n"
" feature %p\n"
" flank %d\n"
" Pslice %p\n",
sla,
feature,
flank,
Pslice);
ensFeatureTrace(feature, 1);
}
if (!sla)
{
ajDebug("ensSliceadaptorFetchByFeature requires an "
"Ensembl Slice Adaptor.\n");
return ajFalse;
}
if (!feature)
{
ajDebug("ensSliceadaptorFetchByFeature requires an "
"Ensembl Feature.\n");
return ajFalse;
}
if (!Pslice)
return ajFalse;
*Pslice = NULL;
slice = ensFeatureGetSlice(feature);
if (!slice)
{
ajDebug("ensSliceadaptorFetchByFeature requires an "
"Ensembl Slice attached to the Ensembl Feature.\n");
return ajFalse;
}
srid = ensSliceGetSeqregionIdentifier(slice);
/* Convert the Feature Slice coordinates to Sequence Region coordinates. */
if (slice->Strand >= 0)
{
srstart = slice->Start + ensFeatureGetStart(feature) - 1;
srend = slice->Start + ensFeatureGetEnd(feature) - 1;
}
else
{
srstart = slice->End - ensFeatureGetEnd(feature) + 1;
srend = slice->End - ensFeatureGetStart(feature) + 1;
}
result = ensSliceadaptorFetchBySeqregionIdentifier(
sla,
srid,
srstart - flank,
srend + flank,
1,
Pslice);
return result;
}
/* @func ensSliceadaptorFetchByLocation ***************************************
**
** Fetch an Ensembl Slice based on a top-level location.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [r] location [const AjPStr] Top-leve location
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.5.0
** @@
******************************************************************************/
AjBool ensSliceadaptorFetchByLocation(EnsPSliceadaptor sla,
const AjPStr location,
EnsPSlice *Pslice)
{
ajint srstart = 0;
ajint srend = 0;
AjBool result = AJFALSE;
AjPRegexp re = NULL;
AjPStr csname = NULL;
AjPStr csversion = NULL;
AjPStr localstr = NULL;
AjPStr srname = NULL;
AjPStr number = NULL;
if (!sla)
return ajFalse;
if ((!location) && (!ajStrGetLen(location)))
return ajFalse;
if (!Pslice)
return ajFalse;
localstr = ajStrNewS(location);
/* Cleanup any nomenclature like 1_000 or 1 000 or 1,000 */
ajStrRemoveSetC(&localstr, " _,");
/* NOTE: This needs adjusting to more complex patterns. */
re = ajRegCompC("^(\\w+):?(\\d+)?(?:-|[.]{2})?(\\d+)?$");
if (ajRegExec(re, localstr))
{
srname = ajStrNew();
ajRegSubI(re, 1, &srname);
if (ajRegLenI(re, 2))
{
number = ajStrNew();
ajRegSubI(re, 2, &number);
ajStrToInt(number, &srstart);
ajStrDel(&number);
}
if (ajRegLenI(re, 3))
{
number = ajStrNew();
ajRegSubI(re, 3, &number);
ajStrToInt(number, &srend);
ajStrDel(&number);
}
csname = ajStrNewC("toplevel");
csversion = ajStrNew();
result = ensSliceadaptorFetchByRegion(
sla,
csname,
csversion,
srname,
srstart,
srend,
1,
Pslice);
ajStrDel(&csname);
ajStrDel(&csversion);
ajStrDel(&srname);
}
ajRegFree(&re);
ajStrDel(&localstr);
return result;
}
/* @func ensSliceadaptorFetchByMapperresult ***********************************
**
** Fetch an Ensembl Slice based on an Ensembl Mapper Result.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [r] mr [const EnsPMapperresult] Ensembl Mapper Result
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceadaptorFetchByMapperresult(EnsPSliceadaptor sla,
const EnsPMapperresult mr,
EnsPSlice *Pslice)
{
if (!sla)
return ajFalse;
if (!mr)
return ajFalse;
if (!Pslice)
return ajFalse;
return ensSliceadaptorFetchBySeqregionIdentifier(
sla,
ensMapperresultGetObjectidentifier(mr),
ensMapperresultGetCoordinateStart(mr),
ensMapperresultGetCoordinateEnd(mr),
ensMapperresultGetCoordinateStrand(mr),
Pslice);
}
/* @func ensSliceadaptorFetchByName *******************************************
**
** Fetch an Ensembl Slice by name, which consists of the following
** colon-separated fields:
** Coordinate System name,
** Coordinate System version,
** Sequence Region start,
** Sequence Region end and
** Sequence Region strand
**
** csname:csversion:srname:srstart:srend:srstrand
**
** The caller is responsible for deleting the Ensembl Slice.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [r] name [const AjPStr] Ensembl Slice name
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceadaptorFetchByName(EnsPSliceadaptor sla,
const AjPStr name,
EnsPSlice *Pslice)
{
ajint start = 0;
ajint end = 0;
ajint strand = 0;
AjBool debug = AJFALSE;
AjBool error = AJFALSE;
AjBool result = AJFALSE;
AjPStr csname = NULL;
AjPStr csversion = NULL;
AjPStr srname = NULL;
AjPStr srstart = NULL;
AjPStr srend = NULL;
AjPStr srstrand = NULL;
AjPStrTok token = NULL;
debug = ajDebugTest("ensSliceadaptorFetchByName");
if (debug)
ajDebug("ensSliceadaptorFetchByName\n"
" sla %p\n"
" name '%S'\n"
" Pslice %p\n",
sla,
name,
Pslice);
if (!sla)
return ajFalse;
if (!(name && ajStrGetLen(name)))
return ajFalse;
if (!Pslice)
return ajFalse;
/* Check the Slice Adaptor-internal cache for the name, first. */
*Pslice = (EnsPSlice) ajTableFetchmodS(sla->CacheByName, name);
if (*Pslice)
{
/*
** For any object returned by the AJAX Table the reference counter
** needs to be incremented manually.
*/
ensSliceNewRef(*Pslice);
return ajTrue;
}
token = ajStrTokenNewC(name, ":");
csname = ajStrNew();
csversion = ajStrNew();
srname = ajStrNew();
srstart = ajStrNew();
srend = ajStrNew();
srstrand = ajStrNew();
if (ajStrTokenNextParseNoskip(token, &csname) &&
ajStrTokenNextParseNoskip(token, &csversion) &&
ajStrTokenNextParseNoskip(token, &srname) &&
ajStrTokenNextParseNoskip(token, &srstart) &&
ajStrTokenNextParseNoskip(token, &srend) &&
ajStrTokenNextParseNoskip(token, &srstrand))
{
/*
** Convert AJAX String objects into AJAX integers.
** Empty AJAX String objects are not converted and default to 0, to
** discriminate them from out of range and other errors reported by
** ajStrToInt.
*/
if (ajStrGetLen(srstart))
if (!ajStrToInt(srstart, &start))
{
ajWarn("ensSliceadaptorFetchByName could not convert '%S' "
"into an integer.",
srstart);
error = ajTrue;
}
if (ajStrGetLen(srend))
if (!ajStrToInt(srend, &end))
{
ajWarn("ensSliceadaptorFetchByName could not convert '%S' "
"into an integer.",
srend);
error = ajTrue;
}
if (ajStrGetLen(srstrand))
if (!ajStrToInt(srstrand, &strand))
{
ajWarn("ensSliceadaptorFetchByName could not convert '%S' "
"into an integer.",
srstrand);
error = ajTrue;
}
if (debug)
ajDebug("ensSliceadaptorFetchByName parsed name '%S' into:\n"
" csname '%S'\n"
" csversion '%S'\n"
" srname '%S'\n"
" srstart '%S' %d\n"
" srend '%S' %d\n"
" srstrand '%S' %d\n",
name,
csname,
csversion,
srname,
srstart, start,
srend, end,
srstrand, strand);
if (error == ajFalse)
{
if (start == 0 && end == 0)
result = ensSliceadaptorFetchBySeqregionName(
sla,
csname,
csversion,
srname,
Pslice);
else
result = ensSliceadaptorFetchByRegion(
sla,
csname,
csversion,
srname,
start,
end,
strand,
Pslice);
}
}
else
ajDebug("ensSliceadaptorFetchByName got a malformed Ensembl Slice "
"name '%S', should be something like "
"chromosome:NCBI36:X:1000000:2000000:1\n"
" csname '%S'\n"
" csversion '%S'\n"
" srname '%S'\n"
" srstart '%S'\n"
" srend '%S'\n"
" srstrand '%S'\n",
name,
csname,
csversion,
srname,
srstart,
srend,
srstrand);
ajStrDel(&csname);
ajStrDel(&csversion);
ajStrDel(&srname);
ajStrDel(&srstart);
ajStrDel(&srend);
ajStrDel(&srstrand);
ajStrTokenDel(&token);
return result;
}
/* @func ensSliceadaptorFetchByRegion *****************************************
**
** Fetch an Ensembl Slice by region information. At a minimum the name of an
** Ensembl Sequence Region must be provided. If no Coordinate System name is
** provided then a Slice of the highest ranked Coordinate System with a
** matching Sequence Region name will be returned.
**
** The caller is responsible for deleting the Ensembl Slice.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [rN] csname [const AjPStr] Ensembl Coordinate System name
** @param [rN] csversion [const AjPStr] Ensembl Coordinate System version
** @param [r] srname [const AjPStr] Ensembl Sequence Region name
** @param [r] srstart [ajint] Start coordinate
** @param [r] srend [ajint] End coordinate
** @param [r] srstrand [ajint] Strand information
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
**
** NOTE: The Ensembl Core Perl API performs some fuzzy matching, if no exact
** match for the provided Sequence Region name can be found. This allows clones
** to be fetched even when their sequence version is not known.
** For example ensSliceadaptorFetchByRegion(..., "clone", "AC008066", ...)
** will retrieve the Sequence Region with name "AC008066.4".
**
** The fuzzy matching can be turned off by setting the $no_fuzz argument to a
** true value.
**
** This has not been implemented here.
******************************************************************************/
AjBool ensSliceadaptorFetchByRegion(EnsPSliceadaptor sla,
const AjPStr csname,
const AjPStr csversion,
const AjPStr srname,
ajint srstart,
ajint srend,
ajint srstrand,
EnsPSlice *Pslice)
{
AjPStr key = NULL;
EnsPCoordsystem cs = NULL;
EnsPCoordsystemadaptor csa = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPSeqregion sr = NULL;
EnsPSeqregionadaptor sra = NULL;
if (ajDebugTest("ensSliceadaptorFetchByRegion"))
ajDebug("ensSliceadaptorFetchByRegion\n"
" sla %p\n"
" csname '%S'\n"
" csversion '%S'\n"
" srname '%S'\n"
" srstart %d\n"
" srend %d\n"
" srstrand %d\n"
" Pslice %p\n",
sla,
csname,
csversion,
srname,
srstart,
srend,
srstrand,
Pslice);
if (!sla)
{
ajDebug("ensSliceadaptorFetchByRegion requires an "
"Ensembl Slice Adaptor.\n");
return ajFalse;
}
if ((srname == NULL) || (ajStrGetLen(srname) == 0))
{
ajDebug("ensSliceadaptorFetchByRegion requires an "
"Ensembl Sequence Region name.\n");
return ajFalse;
}
if (!Pslice)
return ajFalse;
*Pslice = NULL;
/*
** Initially, search the cache, which can only return an Ensembl Slice,
** which is associated with a name and version of a regular Ensembl
** Coordinate System. For requests specifying the top-level Coordinate
** System or no Coordinate System at all the database needs to be queried
** for the Sequence Region associated with the Coordinate System of the
** highest rank. However, all Slice objects will be inserted into the cache
** with their true Coordinate System, keeping at least the memory
** requirements minimal.
*/
key = ajFmtStr("%S:%S:%S:%d:%d:%d",
csname,
csversion,
srname,
srstart,
srend,
srstrand);
*Pslice = (EnsPSlice) ajTableFetchmodS(sla->CacheByName, key);
ajStrDel(&key);
if (*Pslice)
{
/*
** For any object returned by the AJAX Table the reference counter
** needs to be incremented manually.
*/
ensSliceNewRef(*Pslice);
return ajTrue;
}
dba = ensSliceadaptorGetDatabaseadaptor(sla);
/* Load the Ensembl Coordinate System if a name has been provided. */
if (csname && ajStrGetLen(csname))
{
csa = ensRegistryGetCoordsystemadaptor(dba);
ensCoordsystemadaptorFetchByName(csa, csname, csversion, &cs);
if (!cs)
{
ajDebug("ensSliceadaptorFetchByRegion could not load an Ensembl "
"Coordinate System for name '%S' and version '%S'.\n",
csname, csversion);
return ajTrue;
}
}
/* Load the Ensembl Sequence Region by name. */
sra = ensRegistryGetSeqregionadaptor(dba);
ensSeqregionadaptorFetchByName(sra, cs, srname, &sr);
if (!sr)
{
ajDebug("ensSliceadaptorFetchByRegion could not load an Ensembl "
"Sequence Region for name '%S' and Coordinate System "
"identifier %d.\n", srname, ensCoordsystemGetIdentifier(cs));
ensCoordsystemTrace(cs, 1);
/* NOTE: The Perl implementation also performs a fuzzy search. */
ensSeqregionadaptorFetchBySynonym(sra, srname, &sr);
}
if (!sr)
{
ajDebug("ensSliceadaptorFetchByRegion could not load an Ensembl "
"Sequence Region for synonym '%S'.\n",
srname);
}
if (srstrand == 0)
srstrand = 1;
/*
** NOTE: The Perl API tests the Coordinate System name whether it matches
** a meta table entry with meta_key = 'LRG' to create a Bio::EnsEMBL::Slice
** or Bio::EnsEMBL::LRGSlice object. This implementation leaves this to the
** ensSliceNewIni function.
*/
if (sr)
{
*Pslice = ensSliceNewIni(sla, sr, srstart, srend, srstrand);
/*
** This implentation does not have a
** Bio::EnsEMBL::CircularSlice object.
*/
if (srstart > (srend + 1))
ensSliceSetTopology(*Pslice, ensESliceTopologyCircular);
ensSliceadaptorCacheInsert(sla, Pslice);
}
ensCoordsystemDel(&cs);
ensSeqregionDel(&sr);
return ajTrue;
}
/* @func ensSliceadaptorFetchBySeqregionIdentifier ****************************
**
** Fetch an Ensembl Slice by an Ensembl Sequence Region identifier.
** The caller is responsible for deleting the Ensembl Slice.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [r] srid [ajuint] Ensembl Sequence Region identifier
** @param [r] srstart [ajint] Start coordinate
** @param [r] srend [ajint] End coordinate
** @param [r] srstrand [ajint] Strand information
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceadaptorFetchBySeqregionIdentifier(EnsPSliceadaptor sla,
ajuint srid,
ajint srstart,
ajint srend,
ajint srstrand,
EnsPSlice *Pslice)
{
AjPStr key = NULL;
EnsPSeqregion sr = NULL;
if (ajDebugTest("ensSliceadaptorFetchBySeqregionIdentifier"))
ajDebug("ensSliceadaptorFetchBySeqregionIdentifier\n"
" sla %p\n"
" srid %u\n"
" srstart %d\n"
" srend %d\n"
" srstrand %d\n"
" Pslice %p\n",
sla,
srid,
srstart,
srend,
srstrand,
Pslice);
if (!sla)
{
ajDebug("ensSliceadaptorFetchBySeqregionIdentifier requires an "
"Ensembl Slice Adaptor.\n");
return ajFalse;
}
if (!srid)
{
ajDebug("ensSliceadaptorFetchBySeqregionIdentifier requires an "
"Ensembl Sequence Region identifier.\n");
return ajFalse;
}
if (!Pslice)
return ajFalse;
*Pslice = NULL;
/* Check the cache first. */
key = ajFmtStr("%u:%d:%d:%d", srid, srstart, srend, srstrand);
ensCacheFetch(sla->CacheByIdentifier, (void *) key, (void **) Pslice);
ajStrDel(&key);
if (*Pslice)
return ajTrue;
ensSeqregionadaptorFetchByIdentifier(
ensRegistryGetSeqregionadaptor(
ensSliceadaptorGetDatabaseadaptor(sla)),
srid,
&sr);
if (!sr)
{
ajDebug("ensSliceadaptorFetchBySeqregionIdentifier could not load an "
"Ensembl Sequence Region for identifier %d.\n", srid);
return ajTrue;
}
if (!srstart)
srstart = 1;
if (!srend)
srend = ensSeqregionGetLength(sr);
if (srstart > (srend + 1))
ajFatal("ensSliceadaptorFetchBySeqregionIdentifier requires the Slice "
"start %d to be less than or equal to the end %d + 1 for "
"Ensembl Sequence Region identifier %d.",
srstart, srend, srid);
if (!srstrand)
srstrand = 1;
*Pslice = ensSliceNewIni(sla, sr, srstart, srend, srstrand);
ensSliceadaptorCacheInsert(sla, Pslice);
ensSeqregionDel(&sr);
return ajTrue;
}
/* @func ensSliceadaptorFetchBySeqregionName **********************************
**
** Fetch an Ensembl Slice by an Ensembl Sequence Region name, which must be
** provided at a minimum. If no Coordinate System name has been specified,
** an Ensembl Slice of the highest ranked Ensembl Coordinate System with a
** matching Sequence Region name will be returned.
**
** The caller is responsible for deleting the Ensembl Slice.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [rN] csname [const AjPStr] Ensembl Coordinate System name
** @param [rN] csversion [const AjPStr] Ensembl Coordinate System version
** @param [r] srname [const AjPStr] Ensembl Sequence Region name
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
**
** NOTE: The Ensembl Core Perl API performs some fuzzy matching, if no exact
** match for the provided Sequence Region name can be found. This allows clones
** to be fetched even when their sequence version is not known.
** For example ensSliceadaptorFetchByRegion(..., "clone", "AC008066", ...)
** will retrieve the Sequence Region with name "AC008066.4".
**
** The fuzzy matching can be turned off by setting the $no_fuzz argument to a
** true value.
**
** This has not been implemented here.
******************************************************************************/
AjBool ensSliceadaptorFetchBySeqregionName(EnsPSliceadaptor sla,
const AjPStr csname,
const AjPStr csversion,
const AjPStr srname,
EnsPSlice *Pslice)
{
AjPStr key = NULL;
EnsPCoordsystem cs = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPSeqregion sr = NULL;
if (ajDebugTest("ensSliceadaptorFetchBySeqregionName"))
ajDebug("ensSliceadaptorFetchBySeqregionName\n"
" sla %p\n"
" csname '%S'\n"
" csversion '%S'\n"
" srname '%S'\n"
" Pslice %p\n",
sla,
csname,
csversion,
srname,
Pslice);
if (!sla)
return ajFalse;
if (!(srname && ajStrGetLen(srname)))
return ajFalse;
if (!Pslice)
return ajFalse;
*Pslice = NULL;
/*
** Initially, search the cache, which can only return an Ensembl Slice,
** which is associated with a name and version of a regular Ensembl
** Coordinate System. For requests specifying the top-level Coordinate
** System or no Coordinate System at all the database needs to be queried
** for the Sequence Region associated with the Coordinate System of the
** highest rank. However, all Slice objects will be inserted into the cache
** with their true Coordinate System, keeping at least the memory
** requirements minimal.
*/
key = ajFmtStr("%S:%S:%S:0:0:0",
csname,
csversion,
srname);
*Pslice = (EnsPSlice) ajTableFetchmodS(sla->CacheByName, key);
ajStrDel(&key);
if (*Pslice)
{
/*
** For any object returned by the AJAX Table the reference counter
** needs to be incremented manually.
*/
ensSliceNewRef(*Pslice);
return ajTrue;
}
dba = ensSliceadaptorGetDatabaseadaptor(sla);
/* Load the Ensembl Coordinate System if a name has been provided. */
if (csname && ajStrGetLen(csname))
{
ensCoordsystemadaptorFetchByName(
ensRegistryGetCoordsystemadaptor(dba),
csname,
csversion,
&cs);
if (!cs)
{
ajDebug("ensSliceadaptorFetchBySeqregionName could not load an "
"Ensembl Coordinate System for name '%S' and "
"version '%S'.\n",
csname, csversion);
return ajTrue;
}
}
/* Load the Ensembl Sequence Region. */
ensSeqregionadaptorFetchByName(
ensRegistryGetSeqregionadaptor(dba),
cs,
srname,
&sr);
if (!sr)
{
ajDebug("ensSliceadaptorFetchBySeqregionName could not load an "
"Ensembl Sequence Region for name '%S' and Coordinate System "
"identifier %d.\n", srname, ensCoordsystemGetIdentifier(cs));
ensCoordsystemTrace(cs, 1);
ensCoordsystemDel(&cs);
return ajTrue;
}
/*
** NOTE: The Perl API tests the Coordinate System name whether it matches
** a meta table entry with meta_key = 'LRG' to create a Bio::EnsEMBL::Slice
** or Bio::EnsEMBL::LRGSlice object. This implementation leaves this to the
** ensSliceNewIni function.
*/
*Pslice = ensSliceNewIni(sla, sr, 1, ensSeqregionGetLength(sr), 1);
ensSliceadaptorCacheInsert(sla, Pslice);
ensCoordsystemDel(&cs);
ensSeqregionDel(&sr);
return ajTrue;
}
/* @func ensSliceadaptorFetchBySlice ******************************************
**
** Fetch an Ensembl Slice by an Ensembl Slice in relative coordinates.
**
** This function is experimental, but the advantage of going through the
** Slice Adaptor would be that a (Sub-)Slice would be registered in the
** Slice Adaptor-internal cache, which in turn reduces memory consumption.
** The caller is responsible for deleting the Ensembl Slice.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [r] start [ajint] Start coordinate
** @param [r] end [ajint] End coordinate
** @param [r] strand [ajint] Strand information
** @param [wP] Pslice [EnsPSlice*] Ensembl Slice address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensSliceadaptorFetchBySlice(EnsPSliceadaptor sla,
EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
EnsPSlice *Pslice)
{
ajuint srid = 0U;
ajint srstart = 0;
ajint srend = 0;
ajint srstrand = 0;
if (!sla)
return ajFalse;
if (!slice)
return ajFalse;
if (start > (end + 1))
{
ajDebug("ensSliceadaptorFetchBySlice requires the start coordinate %d "
"to be less than the end coordinate %d + 1.\n",
start, end);
return ajFalse;
}
if (!strand)
strand = 1;
if (!Pslice)
return ajFalse;
*Pslice = NULL;
/* Transform relative into absolute Sequence Region coordinates. */
/*
**
** s e
** SS \ +1 / SE
** 1 \ |-------| / length
** \ |------Slice------| /
** |--------Seqregion--------|
** |------Slice------|
** / |-------| \
** SS / -1 \ SE
** e s
**
*/
srid = ensSeqregionGetIdentifier(slice->Seqregion);
if (slice->Strand >= 0)
{
srstart = slice->Start + start - 1;
srend = slice->Start + end - 1;
}
else
{
srstart = slice->End - end + 1;
srend = slice->End - start + 1;
}
srstrand = slice->Strand * strand;
ensSliceadaptorFetchBySeqregionIdentifier(sla,
srid,
srstart,
srend,
srstrand,
Pslice);
if (!*Pslice)
return ajFalse;
/* Adjust the sequence in case the Slice has one associated. */
if (slice->Sequence)
ensSliceFetchSequenceSubStr(slice,
start,
end,
strand,
&((*Pslice)->Sequence));
return ajTrue;
}
/* @section accessory object retrieval ****************************************
**
** Functions for retrieving objects releated to Ensembl Slice objects
** from an Ensembl SQL database.
**
** @fdata [EnsPSliceadaptor]
**
** @nam3rule Retrieve Retrieve Ensembl Slice-releated object(s)
** @nam4rule Normalisedprojection Retrieve all Ensembl Projection Segment
** objects for a normalised projection
**
** @argrule * sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @argrule Normalisedprojection slice [EnsPSlice] Ensembl Slice
** @argrule Normalisedprojection pss [AjPList] AJAX List of
** Ensembl Projection Segment objects
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensSliceadaptorRetrieveNormalisedprojection **************************
**
** Retrieve all Ensembl Projection Segment objects required for a normalised
** projection of an Ensembl Slice.
**
** This function returns an AJAX List of Ensembl Projection Segment objects
** where symbolic links exist for the given Ensembl Slice.
**
** The caller is resposible for deleting the Ensembl Projection Segment objects
** before deleting the AJAX List.
**
** @param [u] sla [EnsPSliceadaptor] Ensembl Slice Adaptor
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] pss [AjPList] AJAX List of Ensembl Projection Segment objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSliceadaptorRetrieveNormalisedprojection(EnsPSliceadaptor sla,
EnsPSlice slice,
AjPList pss)
{
ajint difference = 0;
ajuint excsrid = 0U;
ajuint excstart = 1U;
ajuint excend = 0U;
ajuint exclength = 0U;
ajuint refsrid = 0U;
ajuint refstart = 1U;
ajuint refend = 0U;
ajuint reflength = 0U;
ajuint start = 1U;
/* ajuint srid = 0U; */
AjBool debug = AJFALSE;
AjPList aes = NULL;
AjPList haps = NULL;
AjPList pars = NULL;
AjPList syms = NULL;
AjPList mrs = NULL;
AjPStr source = NULL;
AjPStr target = NULL;
EnsPAssemblyexception ae = NULL;
EnsPAssemblyexceptionadaptor aea = NULL;
EnsPMapper mapper = NULL;
EnsPMapperresult mr = NULL;
EnsPSlice excslice = NULL;
EnsPSlice prjslice = NULL;
EnsPSlice refslice = NULL;
debug = ajDebugTest("ensSliceadaptorRetrieveNormalisedprojection");
if (debug)
{
ajDebug("ensSliceadaptorRetrieveNormalisedprojection\n"
" sla %p\n"
" slice %p\n"
" pss %p\n",
sla,
slice,
pss);
ensSliceTrace(slice, 1);
}
if (!sla)
{
ajDebug("ensSliceadaptorRetrieveNormalisedprojection requires an "
"Ensembl Slice Adaptor.\n");
return ajFalse;
}
if (!slice)
{
ajDebug("ensSliceadaptorRetrieveNormalisedprojection requires an "
"Ensembl Slice.\n");
return ajFalse;
}
if (!pss)
{
ajDebug("ensSliceadaptorRetrieveNormalisedprojection requires an "
"AJAX List of Ensembl Projection Segment objects.\n");
return ajFalse;
}
aea = ensRegistryGetAssemblyexceptionadaptor(
ensSliceadaptorGetDatabaseadaptor(sla));
refsrid = ensSliceGetSeqregionIdentifier(slice);
haps = ajListNew();
pars = ajListNew();
aes = ajListNew();
ensAssemblyexceptionadaptorFetchAllbyReferenceSeqregion(aea, refsrid, aes);
while (ajListPop(aes, (void **) &ae))
{
/*
** Select all overlapping pseudo-autosomal regions (PARs) and all
** haplotype regions (HAPs) if any.
*/
switch (ensAssemblyexceptionGetType(ae))
{
case ensEAssemblyexceptionTypePAR:
if (((ajint) ensAssemblyexceptionGetReferenceStart(ae)
<= slice->End) &&
((ajint) ensAssemblyexceptionGetReferenceEnd(ae)
>= slice->Start))
ajListPushAppend(pars, (void *) ae);
else
ensAssemblyexceptionDel(&ae);
break;
default:
ajListPushAppend(haps, (void *) ae);
}
}
ajListFree(&aes);
if ((!ajListGetLength(haps)) && (!ajListGetLength(pars)))
{
/*
** There are no haplotypes and no pseudo-autosomal regions,
** so return just a Projection Segment for this Slice.
*/
if (debug)
ajDebug("ensSliceadaptorRetrieveNormalisedprojection "
"found no Ensembl Assembly Exception objects overlapping "
"this Ensembl Slice.\n");
ajListFree(&haps);
ajListFree(&pars);
ajListPushAppend(
pss,
(void *) ensProjectionsegmentNewIni(
1,
ensSliceCalculateLength(slice),
slice));
return ajTrue;
}
syms = ajListNew();
if (ajListGetLength(haps) > 0)
{
/*
** We want the region of the haplotype inverted, which means that we
** want the two regions of the Slice that are not covered by the
** haplotype as Projection Segment objects.
**
** Haplotype: *******
** Reference: -------------------
** Projection Segment objects: ++++++ ++++++
*/
ensListAssemblyexceptionSortReferenceEndAscending(haps);
ajListPeekFirst(haps, (void **) &ae);
ensSliceadaptorFetchBySeqregionIdentifier(
sla,
ensAssemblyexceptionGetReferenceSeqregion(ae),
0,
0,
0,
&refslice);
ensSliceadaptorFetchBySeqregionIdentifier(
sla,
ensAssemblyexceptionGetExceptionSeqregion(ae),
0,
0,
0,
&excslice);
excsrid = ensAssemblyexceptionGetExceptionSeqregion(ae);
excstart = 1;
excend = 0;
exclength = ensSliceCalculateLength(excslice);
refstart = 1;
refend = 0;
reflength = ensSliceCalculateLength(refslice);
ensSliceDel(&refslice);
ensSliceDel(&excslice);
while (ajListPop(haps, (void **) &ae))
{
excend = ensAssemblyexceptionGetReferenceStart(ae) - 1;
refend = ensAssemblyexceptionGetExceptionStart(ae) - 1;
/*
** Add an Ensembl Assembly Exception for a haplotype (HAP) at
** the start or the end of the reference Slice.
*/
if ((excend > 0) && (excstart < reflength))
ajListPushAppend(
syms,
(void *) ensAssemblyexceptionNewIni(
(EnsPAssemblyexceptionadaptor) NULL,
0,
ensAssemblyexceptionGetReferenceSeqregion(ae),
excstart,
excend,
ensAssemblyexceptionGetExceptionSeqregion(ae),
refstart,
refend,
1,
ensEAssemblyexceptionTypeNULL));
refstart
= refend
+ ensAssemblyexceptionCalculateExceptionLength(ae)
+ 1;
excstart
= excend
+ ensAssemblyexceptionCalculateReferenceLength(ae)
+ 1;
ensAssemblyexceptionDel(&ae);
}
/*
** For the last segment from the end of the
** Ensembl Assembly Exception to the end of the Ensembl Slice objects.
*/
excend = reflength;
refend = exclength;
difference = (excend - excstart) - (refend - refstart);
if (difference > 0)
ajListPushAppend(
syms,
ensAssemblyexceptionNewIni(
(EnsPAssemblyexceptionadaptor) NULL,
0,
refsrid,
excstart,
excend,
excsrid,
refstart,
refend + difference,
1,
ensEAssemblyexceptionTypeNULL));
else if (difference < 0)
ajListPushAppend(
syms,
ensAssemblyexceptionNewIni(
(EnsPAssemblyexceptionadaptor) NULL,
0,
refsrid,
excstart,
excend - difference,
excsrid,
refstart,
refend,
1,
ensEAssemblyexceptionTypeNULL));
else
ajListPushAppend(
syms,
ensAssemblyexceptionNewIni(
(EnsPAssemblyexceptionadaptor) NULL,
0,
refsrid,
excstart,
excend,
excsrid,
refstart,
refend,
1,
ensEAssemblyexceptionTypeNULL));
}
ajListFree(&haps);
/*
** The ajListPushlist function adds all nodes from the second AJAX List to
** the first and deletes the second.
*/
ajListPushlist(syms, &pars);
source = ajStrNewC("sym");
target = ajStrNewC("org");
mapper = ensMapperNewIni(source,
target,
ensSliceGetCoordsystemObject(slice),
ensSliceGetCoordsystemObject(slice));
while (ajListPop(syms, (void **) &ae))
{
ensMapperAddCoordinates(mapper,
ensAssemblyexceptionGetReferenceSeqregion(ae),
ensAssemblyexceptionGetReferenceStart(ae),
ensAssemblyexceptionGetReferenceEnd(ae),
1,
ensAssemblyexceptionGetExceptionSeqregion(ae),
ensAssemblyexceptionGetExceptionStart(ae),
ensAssemblyexceptionGetExceptionEnd(ae));
ensAssemblyexceptionDel(&ae);
}
ajListFree(&syms);
mrs = ajListNew();
ensMapperMap(mapper,
refsrid,
slice->Start,
slice->End,
slice->Strand,
source,
mrs);
ajStrDel(&source);
ajStrDel(&target);
while (ajListPop(mrs, (void **) &mr))
{
switch (ensMapperresultGetType(mr))
{
case ensEMapperresultTypeCoordinate:
if (debug)
{
ajDebug("ensSliceadaptorRetrieveNormalisedprojection "
" got Ensembl Mapper Result %p.\n", mr);
ensMapperresultTrace(mr, 1);
}
ensSliceadaptorFetchByMapperresult(sla, mr, &prjslice);
ajListPushAppend(
pss,
(void *) ensProjectionsegmentNewIni(
start,
start + ensMapperresultCalculateLengthResult(mr) - 1,
prjslice));
ensSliceDel(&prjslice);
break;
case ensEMapperresultTypeGap:
if (debug)
ajDebug("ensSliceadaptorRetrieveNormalisedprojection\n"
" Ensembl Mapper Result gap %d:%d\n",
ensMapperresultGetGapStart(mr),
ensMapperresultGetGapEnd(mr));
prjslice = ensSliceNewIni(sla,
slice->Seqregion,
ensMapperresultGetGapStart(mr),
ensMapperresultGetGapEnd(mr),
slice->Strand);
ajListPushAppend(
pss,
(void *) ensProjectionsegmentNewIni(
start,
start + ensMapperresultCalculateLengthGap(mr) - 1,
prjslice));
ensSliceDel(&prjslice);
break;
default:
ajWarn("ensSliceadaptorRetrieveNormalisedprojection got "
"an unexpected Ensembl Mapper Result type %d.\n",
ensMapperresultGetType(mr));
}
start += ensMapperresultCalculateLengthResult(mr);
ensMapperresultDel(&mr);
}
ajListFree(&mrs);
ensMapperDel(&mapper);
return ajTrue;
}
/* @datasection [EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice ***********
**
** @nam2rule Repeatmaskedslice Functions for manipulating
** Ensembl Repeat-Masked Slice objects
**
** @cc Bio::EnsEMBL::RepeatMaskedSlice
** @cc CVS Revision: 1.21
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Repeat-Masked Slice by pointer.
** It is the responsibility of the user to first destroy any previous
** Repeat-Masked Slice. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPRepeatmaskedslice]
**
** @nam3rule New Constructor
** @nam4rule Cpy Constructor with existing object
** @nam4rule Ini Constructor with initial values
** @nam4rule Ref Constructor by incrementing the reference counter
**
** @argrule Cpy rmslice [const EnsPRepeatmaskedslice] Ensembl Repeat-Masked
** Slice
** @argrule Ini slice [EnsPSlice] Ensembl Slice
** @argrule Ini annames [AjPList]
** AJAX List of AJAX String (Ensembl Analysis name) objects
** @argrule Ini masking [AjPTable]
** AJAX Table of AJAX String key data and
** Ensembl Repeat Mask Type enumeration value data
** to override masking types
** @argrule Ref rmslice [EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice
**
** @valrule * [EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensRepeatmaskedsliceNewCpy *******************************************
**
** Object-based constructor function, which returns an independent object.
**
** @param [r] rmslice [const EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice
**
** @return [EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPRepeatmaskedslice ensRepeatmaskedsliceNewCpy(
const EnsPRepeatmaskedslice rmslice)
{
void **keyarray = NULL;
void **valarray = NULL;
register ajuint i = 0U;
EnsERepeatMaskType *Pmsktyp = NULL;
AjIList iter = NULL;
AjPStr key = NULL;
EnsPRepeatmaskedslice pthis = NULL;
if (!rmslice)
return NULL;
AJNEW0(pthis);
pthis->Slice = ensSliceNewRef(rmslice->Slice);
/* Copy the AJAX List of (Ensembl Analysis name) AJAX String objects. */
if (rmslice->Analysisnames)
{
pthis->Analysisnames = ajListstrNew();
iter = ajListIterNew(rmslice->Analysisnames);
while (!ajListIterDone(iter))
{
key = (AjPStr) ajListIterGet(iter);
if (key && ajStrGetLen(key))
ajListPushAppend(pthis->Analysisnames,
(void *) ajStrNewS(key));
}
ajListIterDel(&iter);
}
/* Copy the AJAX Table of AJAX String key and AJAX Enum masking types. */
if (rmslice->Masking)
{
pthis->Masking = ajTablestrNew(0U);
ajTableSetDestroyvalue(pthis->Masking, &ajMemFree);
ajTableToarrayKeysValues(rmslice->Masking, &keyarray, &valarray);
for (i = 0U; keyarray[i]; i++)
{
key = ajStrNewS((AjPStr) keyarray[i]);
AJNEW0(Pmsktyp);
*Pmsktyp = *((EnsERepeatMaskType *) valarray[i]);
ajTablePut(pthis->Masking, (void *) key, (void *) Pmsktyp);
}
AJFREE(keyarray);
AJFREE(valarray);
}
pthis->Use = 1U;
return pthis;
}
/* @func ensRepeatmaskedsliceNewIni *******************************************
**
** Constructor for an Ensembl Repeat-Masked Slice with initial values.
**
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [uN] annames [AjPList]
** AJAX List of AJAX String (Ensembl Analysis name) objects
** @param [uN] masking [AjPTable]
** AJAX Table of AJAX String key data and
** Ensembl Repeat Mask Type enumeration value data
** to override masking types
**
** @return [EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPRepeatmaskedslice ensRepeatmaskedsliceNewIni(EnsPSlice slice,
AjPList annames,
AjPTable masking)
{
void **keyarray = NULL;
void **valarray = NULL;
register ajuint i = 0U;
EnsERepeatMaskType *Pmsktyp = NULL;
AjIList iter = NULL;
AjPStr key = NULL;
EnsPRepeatmaskedslice rmslice = NULL;
if (ajDebugTest("ensRepeatmaskedsliceNewIni"))
{
ajDebug("ensRepeatmaskedsliceNewIni\n"
" slice %p\n"
" annames %p\n"
" masking %p\n",
slice,
annames,
masking);
ensSliceTrace(slice, 1);
}
if (!slice)
return NULL;
AJNEW0(rmslice);
rmslice->Slice = ensSliceNewRef(slice);
/* Copy the AJAX List of (Ensembl Analysis name) AJAX String objects. */
if (annames)
{
rmslice->Analysisnames = ajListstrNew();
iter = ajListIterNew(annames);
while (!ajListIterDone(iter))
{
key = (AjPStr) ajListIterGet(iter);
if (key && ajStrGetLen(key))
ajListPushAppend(rmslice->Analysisnames,
(void *) ajStrNewS(key));
}
ajListIterDel(&iter);
}
/* Copy the AJAX Table of AJAX String key and AJAX Enum masking types. */
if (masking)
{
rmslice->Masking = ajTablestrNew(0U);
ajTableSetDestroyvalue(rmslice->Masking, &ajMemFree);
ajTableToarrayKeysValues(masking, &keyarray, &valarray);
for (i = 0U; keyarray[i]; i++)
{
key = ajStrNewS((AjPStr) keyarray[i]);
AJNEW0(Pmsktyp);
*Pmsktyp = *((EnsERepeatMaskType *) valarray[i]);
ajTablePut(rmslice->Masking, (void *) key, (void *) Pmsktyp);
}
AJFREE(keyarray);
AJFREE(valarray);
}
rmslice->Use = 1U;
return rmslice;
}
/* @func ensRepeatmaskedsliceNewRef *******************************************
**
** Ensembl Object referencing function, which returns a pointer to the
** Ensembl Object passed in and increases its reference count.
**
** @param [u] rmslice [EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice
**
** @return [EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPRepeatmaskedslice ensRepeatmaskedsliceNewRef(
EnsPRepeatmaskedslice rmslice)
{
if (!rmslice)
return NULL;
rmslice->Use++;
return rmslice;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Repeat-Masked Slice object.
**
** @fdata [EnsPRepeatmaskedslice]
**
** @nam3rule Del Destroy (free) an Ensembl Repeat-Masked Slice
**
** @argrule * Prmslice [EnsPRepeatmaskedslice*]
** Ensembl Repeat-Masked Slice address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensRepeatmaskedsliceDel **********************************************
**
** Default destructor for an Ensembl Repeat-Masked Slice.
**
** @param [d] Prmslice [EnsPRepeatmaskedslice*]
** Ensembl Repeat-Masked Slice address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensRepeatmaskedsliceDel(EnsPRepeatmaskedslice *Prmslice)
{
EnsPRepeatmaskedslice pthis = NULL;
if (!Prmslice)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("ensRepeatmaskedsliceDel"))
{
ajDebug("ensRepeatmaskedsliceDel\n"
" *Prmslice %p\n",
*Prmslice);
ensRepeatmaskedsliceTrace(*Prmslice, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Prmslice) || --pthis->Use)
{
*Prmslice = NULL;
return;
}
ensSliceDel(&pthis->Slice);
/*
** Clear and delete the AJAX List of
** (Ensembl Analysis name) AJAX String objects.
*/
ajListstrFreeData(&pthis->Analysisnames);
ajTableDel(&pthis->Masking);
ajMemFree((void **) Prmslice);
return;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Repeat-Masked Slice object.
**
** @fdata [EnsPRepeatmaskedslice]
**
** @nam3rule Trace Report Ensembl Repeat-Masked Slice members to debug file
**
** @argrule Trace rmslice [const EnsPRepeatmaskedslice]
** Ensembl Repeat-Masked Slice
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensRepeatmaskedsliceTrace ********************************************
**
** Trace an Ensembl Repeat-Masked Slice.
**
** @param [r] rmslice [const EnsPRepeatmaskedslice]
** Ensembl Repeat-Masked Slice
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensRepeatmaskedsliceTrace(const EnsPRepeatmaskedslice rmslice,
ajuint level)
{
AjPStr indent = NULL;
if (!rmslice)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensRepeatmaskedsliceTrace %p\n"
"%S Slice %p\n"
"%S Analysisnames %p\n"
"%S Masking %p\n"
"%S Use %u\n",
indent, rmslice,
indent, rmslice->Slice,
indent, rmslice->Analysisnames,
indent, rmslice->Masking,
indent, rmslice->Use);
ensSliceTrace(rmslice->Slice, level + 1);
ajStrDel(&indent);
return ajTrue;
}
/* @section fetch *************************************************************
**
** Functions for fetching objects of an Ensembl Repeat-Masked Slice object.
**
** @fdata [EnsPRepeatmaskedslice]
**
** @nam3rule Fetch Fetch Ensembl Repeat-Masked Slice objects
** @nam4rule All Fetch all objects
** @nam4rule Sequence Fetch the sequence
** @nam5rule Seq Fetch as AJAX Sequence object
** @nam5rule Str Fetch as AJAX String object
**
** @argrule Sequence rmslice [EnsPRepeatmaskedslice] Ensembl Repeat-Masked
** Slice
** @argrule Sequence mtype [EnsERepeatMaskType] Repeat masking type
** @argrule Seq Psequence [AjPSeq*] AJAX Sequence address
** @argrule Str Psequence [AjPStr*] AJAX String address
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensRepeatmaskedsliceFetchSequenceSeq *********************************
**
** Fetch the (masked) sequence of an Ensembl Repeat-Masked Slice as
** AJAX Sequence.
**
** @param [u] rmslice [EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice
** @param [u] mtype [EnsERepeatMaskType] Repeat masking type
** @param [wP] Psequence [AjPSeq*] Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
******************************************************************************/
AjBool ensRepeatmaskedsliceFetchSequenceSeq(EnsPRepeatmaskedslice rmslice,
EnsERepeatMaskType mtype,
AjPSeq *Psequence)
{
AjPStr name = NULL;
AjPStr sequence = NULL;
if (!rmslice)
return ajFalse;
if (!Psequence)
return ajFalse;
name = ajStrNew();
ensSliceFetchName(rmslice->Slice, &name);
sequence = ajStrNew();
ensRepeatmaskedsliceFetchSequenceStr(rmslice, mtype, &sequence);
if (*Psequence)
{
ajSeqClear(*Psequence);
ajSeqAssignSeqS(*Psequence, sequence);
ajSeqAssignNameS(*Psequence, name);
}
else
*Psequence = ajSeqNewNameS(sequence, name);
ajSeqSetNuc(*Psequence);
ajStrDel(&sequence);
ajStrDel(&name);
return ajTrue;
}
/* @func ensRepeatmaskedsliceFetchSequenceStr *********************************
**
** Fetch the (masked) sequence for an Ensembl Repeat-Masked Slice as
** AJAX String.
**
** @cc Bio::EnsEMBL::RepeatMaskedSlice::seq
** @cc Bio::EnsEMBL::Slice::_mask_features
** @param [u] rmslice [EnsPRepeatmaskedslice] Ensembl Repeat-Masked Slice
** @param [u] mtype [EnsERepeatMaskType] Repeat masking type
** @param [wP] Psequence [AjPStr*] Sequence String address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.2.0
** @@
** NOTE: The Bio::EnsEMBL::RepeatMaskedSlice::subseq method has not been
** implemented, because the Ensembl Base Adaptor has no global Ensembl Feature
** cache. Handling of polymorphic Bio::EnsEMBL::Feature subclasses is simple in
** object-oriented Perl, but quite complex in ANSI C. The Perl method
** retrieves Bio::EnsEMBL::RepeatFeature objects for larger blocks
** (2^18 or 256 Ki base pairs) for more efficient caching of subsequent
** requests.
** However, the performance hit should be minimal, as the relational database
** management system (RDBMS) caches the underlying queries. It is also possible
** to fetch the (masked) sequence for the whole Repeat-Masked Slice and
** subsequently extract the sub sequence with correspoinding AJAX functions.
** Therefore, the Bio::EnsEMBL::RepeatMaskedSlice::subseq method offers
** only small benefits over Bio::EnsEMBL::RepeatMaskedSlice::seq.
** As a consequence, the private Bio::EnsEMBL::Slice::_mask_features method
** has been merged into this function to simplify parameter checking if both,
** sequence and Repeat Feature objects are fetched from the same Slice.
******************************************************************************/
AjBool ensRepeatmaskedsliceFetchSequenceStr(EnsPRepeatmaskedslice rmslice,
EnsERepeatMaskType mtype,
AjPStr *Psequence)
{
ajint start = 0;
ajint end = 0;
EnsERepeatMaskType msktyp = ensERepeatMaskTypeNULL;
EnsERepeatMaskType *Pmsktyp = NULL;
AjIList iter = NULL;
AjPList rfs = NULL;
AjPStr key = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPFeature feature = NULL;
EnsPRepeatconsensus rc = NULL;
EnsPRepeatfeature rf = NULL;
EnsPRepeatfeatureadaptor rfa = NULL;
EnsPSliceadaptor sla = NULL;
if (ajDebugTest("ensRepeatmaskedsliceFetchSequenceStr"))
ajDebug("ensRepeatmaskedsliceFetchSequenceStr\n"
" rmslice %p\n"
" mtype %d\n"
" *Psequence %p\n",
rmslice,
mtype,
*Psequence);
if (!rmslice)
return ajFalse;
if (!Psequence)
return ajFalse;
if (*Psequence)
ajStrAssignClear(Psequence);
else
*Psequence = ajStrNew();
if ((mtype <= ensERepeatMaskTypeNULL) || (mtype > ensERepeatMaskTypeHard))
{
ajDebug("ensRepeatmaskedsliceFetchSequenceStr got unsupported "
"masking type %d\n", mtype);
return ajFalse;
}
if (!rmslice->Slice)
{
ajDebug("ensRepeatmaskedsliceFetchSequenceStr got an "
"Ensembl Repeat-Masked Slice without an "
"Ensembl Slice.\n");
return ajFalse;
}
ensSliceFetchSequenceAllStr(rmslice->Slice, Psequence);
/* Sanity check */
if (ensSliceCalculateLength(rmslice->Slice) != ajStrGetLen(*Psequence))
ajWarn("ensRepeatmaskedsliceFetchSequenceStr got Slice of length %u, "
"but DNA sequence of length %u.\n",
ensSliceCalculateLength(rmslice->Slice),
ajStrGetLen(*Psequence));
sla = ensSliceGetAdaptor(rmslice->Slice);
dba = ensSliceadaptorGetDatabaseadaptor(sla);
rfa = ensRegistryGetRepeatfeatureadaptor(dba);
rfs = ajListNew();
if (rmslice->Analysisnames)
{
iter = ajListIterNew(rmslice->Analysisnames);
while (!ajListIterDone(iter))
{
key = (AjPStr) ajListIterGet(iter);
ensRepeatfeatureadaptorFetchAllbySlice(rfa,
rmslice->Slice,
key,
(AjPStr) NULL,
(AjPStr) NULL,
(AjPStr) NULL,
rfs);
}
ajListIterDel(&iter);
}
else
ensRepeatfeatureadaptorFetchAllbySlice(rfa,
rmslice->Slice,
(AjPStr) NULL,
(AjPStr) NULL,
(AjPStr) NULL,
(AjPStr) NULL,
rfs);
while (ajListPop(rfs, (void **) &rf))
{
/*
** NOTE: Since this function merges methods from the RepeatMaskedSlice
** and Slice classes the Repeat Feature objects are automatically
** fetched from the same Slice and do not need transforming back onto
** the Slice that has been passed into the second method. It is also
** not necessary to check whether the Feature objects overlap with the
** Slice.
**
** For the AJAX String masking functions, the start and end coordinates
** of Repeat Feature objects partly outside the Slice need to be
** trimmed.
*/
feature = ensRepeatfeatureGetFeature(rf);
start = (ensFeatureGetStart(feature) >= 1) ?
ensFeatureGetStart(feature) :
1;
end = (ensFeatureGetEnd(feature) <=
(ajint) ensSliceCalculateLength(rmslice->Slice)) ?
ensFeatureGetEnd(feature) :
(ajint) ensSliceCalculateLength(rmslice->Slice);
if (rmslice->Masking)
{
rc = ensRepeatfeatureGetRepeatconsensus(rf);
/* Get the masking type for the Repeat Consensus type. */
key = ajFmtStr("repeat_type_%S", ensRepeatconsensusGetType(rc));
Pmsktyp = (EnsERepeatMaskType *) ajTableFetchmodV(
rmslice->Masking,
(const void *) key);
if (Pmsktyp)
msktyp = *Pmsktyp;
ajStrDel(&key);
/* Get the masking type for the Repeat Consensus class. */
key = ajFmtStr("repeat_class_%S", ensRepeatconsensusGetClass(rc));
Pmsktyp = (EnsERepeatMaskType *) ajTableFetchmodV(
rmslice->Masking,
(const void *) key);
if (Pmsktyp)
msktyp = *Pmsktyp;
ajStrDel(&key);
/* Get the masking type for the Repeat Consensus name. */
key = ajFmtStr("repeat_name_%S", ensRepeatconsensusGetName(rc));
Pmsktyp = (EnsERepeatMaskType *) ajTableFetchmodV(
rmslice->Masking,
(const void *) key);
if (Pmsktyp)
msktyp = *Pmsktyp;
ajStrDel(&key);
}
/* Set the default masking type, if no other type has been defined. */
if (!msktyp)
msktyp = mtype;
/* Mask the DNA sequence. */
switch (msktyp)
{
case ensERepeatMaskTypeNULL:
break;
case ensERepeatMaskTypeSoft:
ajStrFmtLowerSub(Psequence, start - 1, end - 1);
break;
case ensERepeatMaskTypeHard:
ajStrMaskRange(Psequence, start - 1, end - 1, 'N');
break;
default:
ajDebug("ensRepeatmaskedsliceFetchSequenceStr got unsupported "
"Ensembl Repeat Mask Type enumeration %d\n", msktyp);
}
ensRepeatfeatureDel(&rf);
}
ajListFree(&rfs);
return ajTrue;
}
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