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/* @source enssequence ********************************************************
**
** Ensembl Sequence functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.46 $
** @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 "ensprojectionsegment.h"
#include "enssequence.h"
#include "enssequenceedit.h"
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== global variables ============================ */
/* ========================================================================= */
/* ========================================================================= */
/* ============================= private data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private constants =========================== */
/* ========================================================================= */
/* @conststatic sequenceKChunkPower *******************************************
**
** The Ensembl Sequence Adaptor handles sequences in larger chunks internally.
** Both, memory allocation and SQL database operations become more efficient,
** since requests for neighbouring regions are likely to be returned from the
** same block.
**
** 1 << 18 = 256 KiB, about the size of a BAC clone
**
******************************************************************************/
static const ajuint sequenceKChunkPower = 18U;
/* @conststatic sequenceadaptorKCacheMaxBytes *********************************
**
** The maximum memory size in bytes the Ensembl Sequence Adaptor-internal
** Ensembl Cache can use.
**
** 1 << 26 = 64 MiB
**
******************************************************************************/
static const size_t sequenceadaptorKCacheMaxBytes = 1U << 26U;
/* @conststatic sequenceadaptorKCacheMaxCount *********************************
**
** The mamximum number of sequence chunks the Ensembl Sequence Adaptor-internal
** Ensembl Cache can hold.
**
** 1 << 16 = 64 Ki
**
******************************************************************************/
static const ajuint sequenceadaptorKCacheMaxCount = 1U << 16U;
/* @conststatic sequenceadaptorKCacheMaxSize **********************************
**
** Maximum size of a sequence chunk to be allowed into the
** Ensembl Sequence Adaptor-internal Ensembl Cache.
**
******************************************************************************/
static const size_t sequenceadaptorKCacheMaxSize = 0U;
/* @conststatic sequenceadaptorKCacheMaxLength ********************************
**
** Maximum length of a sequence request up to which it gets chunked and cached.
** Larger request are returned directly.
**
** 1 << 21 = 2 Mi, or about 8 BAC clones
**
******************************************************************************/
static const ajuint sequenceadaptorKCacheMaxLength = 1U << 21U;
/* ========================================================================= */
/* =========================== private variables =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private functions =========================== */
/* ========================================================================= */
static size_t sequenceadaptorCacheSize(const void *value);
static AjBool sequenceadaptorFetchCircularsliceSubStr(
EnsPSequenceadaptor sqa,
EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPStr *Psequence);
/* ========================================================================= */
/* ======================= All functions by section ======================== */
/* ========================================================================= */
/* @filesection enssequence ***************************************************
**
** @nam1rule ens Function belongs to the Ensembl library
**
******************************************************************************/
/* @datasection [EnsPSequenceadaptor] Ensembl Sequence Adaptor ****************
**
** @nam2rule Sequenceadaptor Functions for manipulating
** Ensembl Sequence Adaptor objects
**
** @cc Bio::EnsEMBL::DBSQL::Sequenceadaptor
** @cc CVS Revision: 1.54
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @funcstatic sequenceadaptorCacheSize ***************************************
**
** Wrapper function to calculate the memory size of an Ensembl Sequence
** (i.e. an AJAX String) from an Ensembl Cache.
**
** @param [r] value [const void*] AJAX String
**
** @return [size_t] Memory size in bytes or 0
**
** @release 6.3.0
** @@
******************************************************************************/
static size_t sequenceadaptorCacheSize(const void *value)
{
size_t size = 0;
if (!value)
return 0;
size += sizeof (AjOStr);
size += ajStrGetRes((const AjPStr) value);
return size;
}
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Sequence Adaptor by pointer.
** It is the responsibility of the user to first destroy any previous
** Sequence Adaptor. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPSequenceadaptor]
**
** @nam3rule New Constructor
**
** @argrule New dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
** @argrule Obj object [EnsPSequenceadaptor] Ensembl Sequence Adaptor
** @argrule Ref object [EnsPSequenceadaptor] Ensembl Sequence Adaptor
**
** @valrule * [EnsPSequenceadaptor] Ensembl Sequence Adaptor or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensSequenceadaptorNew ************************************************
**
** Default constructor for an Ensembl Sequence 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 ensRegistryGetSequenceadaptor
**
** @cc Bio::EnsEMBL::DBSQL::Sequenceadaptor::new
** @param [u] dba [EnsPDatabaseadaptor] Ensembl Database Adaptor
**
** @return [EnsPSequenceadaptor] Ensembl Sequence Adaptor or NULL
**
** @release 6.2.0
** @@
******************************************************************************/
EnsPSequenceadaptor ensSequenceadaptorNew(
EnsPDatabaseadaptor dba)
{
EnsPSequenceadaptor sqa = NULL;
if (!dba)
return NULL;
if (ajDebugTest("ensSequenceadaptorNew"))
ajDebug("ensSequenceadaptorNew\n"
" dba %p\n",
dba);
AJNEW0(sqa);
sqa->Adaptor = dba;
sqa->Cache = ensCacheNew(
ensECacheTypeAlphaNumeric,
sequenceadaptorKCacheMaxBytes,
sequenceadaptorKCacheMaxCount,
sequenceadaptorKCacheMaxSize,
(void *(*)(void *)) &ajStrNewRef,
(void (*)(void **)) &ajStrDel,
&sequenceadaptorCacheSize,
(void *(*)(const void *)) NULL,
(AjBool (*)(const void *)) NULL,
ajFalse,
"Sequence");
return sqa;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Sequence Adaptor object.
**
** @fdata [EnsPSequenceadaptor]
**
** @nam3rule Del Destroy (free) an Ensembl Sequence Adaptor
**
** @argrule * Psqa [EnsPSequenceadaptor*] Ensembl Sequence Adaptor address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensSequenceadaptorDel ************************************************
**
** Default destructor for an Ensembl Sequence Adaptor.
**
** 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] Psqa [EnsPSequenceadaptor*] Ensembl Sequence Adaptor address
**
** @return [void]
**
** @release 6.2.0
** @@
******************************************************************************/
void ensSequenceadaptorDel(EnsPSequenceadaptor *Psqa)
{
EnsPSequenceadaptor pthis = NULL;
if (!Psqa)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensSequenceadaptorDel"))
ajDebug("ensSequenceadaptorDel\n"
" *Psqa %p\n",
*Psqa);
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Psqa))
return;
ensCacheDel(&pthis->Cache);
ajMemFree((void **) Psqa);
return;
}
/* @section cache *************************************************************
**
** Functions for maintaining the Ensembl Sequence Adaptor-internal cache.
**
** @fdata [EnsPSequenceadaptor]
**
** @nam3rule Cache
** @nam4rule Clear Clear the Ensembl Sequence Adaptor-internal cache
**
** @argrule * sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensSequenceadaptorCacheClear *****************************************
**
** Clear the internal cache of an Ensembl Sequence Adaptor.
**
** @cc Bio::EnsEMBL::DBSQL::SequenceAdaptor::clear_cache
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.5.0
** @@
******************************************************************************/
AjBool ensSequenceadaptorCacheClear(EnsPSequenceadaptor sqa)
{
if (!sqa)
return ajFalse;
return ensCacheClear(sqa->Cache);
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an
** Ensembl Sequence Adaptor object.
**
** @fdata [EnsPSequenceadaptor]
**
** @nam3rule Get Return Ensembl Sequence Adaptor attribute(s)
** @nam4rule Databaseadaptor Return the Ensembl Database Adaptor
**
** @argrule * sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
**
** @valrule Databaseadaptor [EnsPDatabaseadaptor]
** Ensembl Database Adaptor or NULL
**
** @fcategory use
******************************************************************************/
/* @func ensSequenceadaptorGetDatabaseadaptor ***************************
**
** Get the Ensembl Database Adaptor of an Ensembl Sequence Adaptor.
**
** @param [u] sqa [EnsPSequenceadaptor]
** Ensembl Sequence Adaptor
**
** @return [EnsPDatabaseadaptor] Ensembl Database Adaptor or NULL
**
** @release 6.5.0
** @@
******************************************************************************/
EnsPDatabaseadaptor ensSequenceadaptorGetDatabaseadaptor(
EnsPSequenceadaptor sqa)
{
return (sqa) ? sqa->Adaptor : NULL;
}
/* @section object fetching ***************************************************
**
** Functions for retrieving Sequence objects from an Ensembl Core database.
**
** @fdata [EnsPSequenceadaptor]
**
** @nam3rule Fetch Fetch Ensembl Sequence object(s)
** @nam4rule Seqregion Fetch by an Ensembl Sequence Region
** @nam4rule Slice Fetch by an Ensembl Slice
** @nam5rule All Fetch the complete sequence
** @nam5rule Sub Fetch a sub-sequence
** @nam6rule Str Fetch as an AJAX String
** @nam6rule Seq Fetch as an AJAX Sequence
**
** @argrule * sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
** @argrule Seqregion sr [const EnsPSeqregion] Ensembl Sequence Region
** @argrule SeqregionSub start [ajuint] Start coordinate
** @argrule SeqregionSub length [ajuint] Sequence length
** @argrule Slice slice [EnsPSlice] Ensembl Slice
** @argrule SliceSub start [ajint] Start
** @argrule SliceSub end [ajint] End
** @argrule SliceSub strand [ajint] Strand
** @argrule Str Psequence [AjPStr*] AJAX String address
** @argrule Seq Psequence [AjPSeq*] AJAX Sequence address
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory use
******************************************************************************/
/* @func ensSequenceadaptorFetchSeqregionAllSeq *******************************
**
** Fetch the sequence of an Ensembl Sequence Region as an AJAX Sequence.
**
** The caller is responsible for deleting the AJAX String.
**
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
** @param [r] sr [const EnsPSeqregion] Ensembl Sequence Region
** @param [wP] Psequence [AjPSeq*] AJAX Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** This function will only return biological sequence information for
** Ensembl Sequence Region objects, which are in the sequence-level
** Ensembl Coordinate System. All other Ensembl Sequence Region objects do not
** have sequence attached so that their sequence can only be fetched in the
** context of an Ensembl Slice, which is subsequently mapped to the
** sequence-level Ensembl Coordinate System. See the description of the
** ensSequenceadaptorFetchSliceAllSeq function for further details.
******************************************************************************/
AjBool ensSequenceadaptorFetchSeqregionAllSeq(EnsPSequenceadaptor sqa,
const EnsPSeqregion sr,
AjPSeq *Psequence)
{
return ensSequenceadaptorFetchSeqregionSubSeq(
sqa,
sr,
1,
(ajuint) ensSeqregionGetLength(sr),
Psequence);
}
/* @func ensSequenceadaptorFetchSeqregionAllStr *******************************
**
** Fetch the sequence of an Ensembl Sequence Region as an AJAX String.
**
** The caller is responsible for deleting the AJAX String.
**
** @cc Bio::EnsEMBL::DBSQL::Sequenceadaptor::_fetch_seq
** @see ensSequenceadaptorFetchSliceAllStr
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
** @param [r] sr [const EnsPSeqregion] Ensembl Sequence Region
** @param [u] Psequence [AjPStr*] Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** This function will only return biological sequence information for
** Ensembl Sequence Region objects, which are in the sequence-level
** Ensembl Coordinate System. All other Ensembl Sequence Region objects do not
** have sequence attached so that their sequence can only be fetched in the
** context of an Ensembl Slice, which is subsequently mapped to the
** sequence-level Ensembl Coordinate System. See the description of the
** ensSequenceadaptorFetchSliceAllStr function for further details.
******************************************************************************/
AjBool ensSequenceadaptorFetchSeqregionAllStr(EnsPSequenceadaptor sqa,
const EnsPSeqregion sr,
AjPStr *Psequence)
{
return ensSequenceadaptorFetchSeqregionSubStr(
sqa,
sr,
1,
(ajuint) ensSeqregionGetLength(sr),
Psequence);
}
/* @func ensSequenceadaptorFetchSeqregionSubSeq *******************************
**
** Fetch a sub-sequence of an Ensembl Sequence Region as an AJAX Sequence.
** The start coordinate is one-based, as in the SQL SUBSTRING function.
** A start of 1 and a length equal the Sequence Region length covers the whole
** Sequence Region.
**
** The caller is responsible for deleting the AJAX Sequence.
**
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
** @param [r] sr [const EnsPSeqregion] Ensembl Sequence Region
** @param [r] start [ajuint] Start coordinate
** @param [r] length [ajuint] Sequence length
** @param [wP] Psequence [AjPSeq*] AJAX Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** This function will only return biological sequence information for
** Ensembl Sequence Region objects, which are in the sequence-level
** Ensembl Coordinate System. All other Ensembl Sequence Region objects do not
** have sequence attached so that their sequence can only be fetched in the
** context of an Ensembl Slice, which is subsequently mapped to the
** sequence-level Ensembl Coordinate System. See the description of the
** ensSequenceadaptorFetchSliceAllSeq function for further details.
******************************************************************************/
AjBool ensSequenceadaptorFetchSeqregionSubSeq(EnsPSequenceadaptor sqa,
const EnsPSeqregion sr,
ajuint start,
ajuint length,
AjPSeq *Psequence)
{
AjBool result = AJFALSE;
AjPStr name = NULL;
AjPStr sequence = NULL;
if (ajDebugTest("ensSequenceadaptorFetchSeqregionSubSeq"))
{
ajDebug("ensSequenceadaptorFetchSeqregionSubSeq\n"
" sqa %p\n"
" sr %p\n"
" start %u\n"
" length %u\n"
" Psequence %p\n",
sqa,
sr,
start,
length,
Psequence);
ensSeqregionTrace(sr, 1);
}
if (!sqa)
return ajFalse;
if (!sr)
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.
*/
name = ajFmtStr(
"%S:%S:%S:%u:%u:1",
ensCoordsystemGetName(ensSeqregionGetCoordsystem(sr)),
ensCoordsystemGetVersion(ensSeqregionGetCoordsystem(sr)),
ensSeqregionGetName(sr),
start,
start + length - 1);
result = ensSequenceadaptorFetchSeqregionSubStr(
sqa,
sr,
start,
length,
&sequence);
if (*Psequence)
{
ajSeqClear(*Psequence);
ajSeqAssignNameS(*Psequence, name);
ajSeqAssignSeqS(*Psequence, sequence);
}
else
*Psequence = ajSeqNewNameS(sequence, name);
ajSeqSetNuc(*Psequence);
ajStrDel(&name);
ajStrDel(&sequence);
return result;
}
/* @func ensSequenceadaptorFetchSeqregionSubStr *******************************
**
** Fetch a sub-sequence of an Ensembl Sequence Region as an AJAX String.
** The start coordinate is one-based, as in the SQL SUBSTRING function.
** A start of 1 and a length equal the Sequence Region length covers the whole
** Sequence Region.
**
** The caller is responsible for deleting the AJAX String.
**
** @cc Bio::EnsEMBL::DBSQL::Sequenceadaptor::_fetch_seq
** @see ensSequenceadaptorFetchSliceSubStr
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
** @param [r] sr [const EnsPSeqregion] Ensembl Sequence Region
** @param [r] start [ajuint] Start coordinate
** @param [r] length [ajuint] Sequence length
** @param [u] Psequence [AjPStr*] Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
** This function will only return biological sequence information for
** Ensembl Sequence Region objects, which are in the sequence-level
** Ensembl Coordinate System. All other Ensembl Sequence Region objects do not
** have sequence attached so that their sequence can only be fetched in the
** context of an Ensembl Slice, which is subsequently mapped to the
** sequence-level Ensembl Coordinate System. See the description of the
** ensSequenceadaptorFetchSliceSubStr function for further details.
******************************************************************************/
AjBool ensSequenceadaptorFetchSeqregionSubStr(EnsPSequenceadaptor sqa,
const EnsPSeqregion sr,
ajuint start,
ajuint length,
AjPStr *Psequence)
{
register ajuint i = 0U;
ajuint chkmin = 0U;
ajuint chkmax = 0U;
ajuint posmin = 0U;
AjPSqlstatement sqls = NULL;
AjISqlrow sqli = NULL;
AjPSqlrow sqlr = NULL;
AjPStr chkstr = NULL;
AjPStr tmpstr = NULL;
AjPStr key = NULL;
AjPStr statement = NULL;
EnsPDatabaseadaptor dba = NULL;
if (ajDebugTest("ensSequenceadaptorFetchSeqregionSubStr"))
{
ajDebug("ensSequenceadaptorFetchSeqregionSubStr\n"
" sqa %p\n"
" sr %p\n"
" start %d\n"
" length %d\n",
sqa,
sr,
start,
length);
ensSeqregionTrace(sr, 1);
}
if (!sqa)
return ajFalse;
if (!sr)
return ajFalse;
if (!Psequence)
return ajFalse;
/*
** Reserve sequence space in larger blocks based on the requested length
** plus one position for the 'nul' string terminator.
*/
if (*Psequence)
ajStrAssignClear(Psequence);
else
*Psequence = ajStrNewRes((((length + 1) >> sequenceKChunkPower) + 1)
<< sequenceKChunkPower);
dba = ensSequenceadaptorGetDatabaseadaptor(sqa);
if (length < sequenceadaptorKCacheMaxLength)
{
chkmin = (start - 1) >> sequenceKChunkPower;
chkmax = (start + length - 1) >> sequenceKChunkPower;
/*
** Allocate an AJAX String and reserve space for the number of
** sequence chunks plus one for the 'nul' string terminator.
*/
tmpstr = ajStrNewRes(((1 << sequenceKChunkPower) + 1) *
(chkmax - chkmin + 1));
/* Piece together sequence from cached sequence chunks. */
for (i = chkmin; i <= chkmax; i++)
{
key = ajFmtStr("%u:%u", ensSeqregionGetIdentifier(sr), i);
chkstr = NULL;
ensCacheFetch(sqa->Cache, (void *) key, (void **) &chkstr);
if (chkstr)
{
ajStrAppendS(&tmpstr, chkstr);
ajStrDel(&chkstr);
}
else
{
/* Fetch uncached sequence chunks. */
posmin = (i << sequenceKChunkPower) + 1;
statement = ajFmtStr(
"SELECT "
"SUBSTRING(dna.sequence FROM %u FOR %u) "
"FROM "
"dna "
"WHERE "
"dna.seq_region_id = %u",
posmin,
1 << sequenceKChunkPower,
ensSeqregionGetIdentifier(sr));
sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
sqli = ajSqlrowiterNew(sqls);
while (!ajSqlrowiterDone(sqli))
{
sqlr = ajSqlrowiterGet(sqli);
/*
** Allocate an AJAX String and reserve space for the
** maximum sequence chunk length plus the 'nul' string
** terminator.
*/
chkstr = ajStrNewRes((1 << sequenceKChunkPower) + 1);
ajSqlcolumnToStr(sqlr, &chkstr);
/*
** Always store upper case sequence
** so that it can be properly soft-masked.
*/
ajStrFmtUpper(&chkstr);
ensCacheStore(sqa->Cache, (void *) key, (void **) &chkstr);
ajStrAppendS(&tmpstr, chkstr);
ajStrDel(&chkstr);
}
ajSqlrowiterDel(&sqli);
ensDatabaseadaptorSqlstatementDel(dba, &sqls);
ajStrDel(&statement);
}
ajStrDel(&key);
}
/* Return only the requested portion of the entire sequence. */
posmin = (chkmin << sequenceKChunkPower) + 1;
ajStrAssignSubS(Psequence,
tmpstr,
start - posmin,
start - posmin + length - 1);
ajStrDel(&tmpstr);
}
else
{
/* Do not attempt any caching for requests of very large sequences. */
statement = ajFmtStr(
"SELECT "
"SUBSTRING(dna.sequence FROM %u FOR %u) "
"FROM dna "
"WHERE "
"dna.seq_region_id = %u",
start,
length,
ensSeqregionGetIdentifier(sr));
sqls = ensDatabaseadaptorSqlstatementNew(dba, statement);
sqli = ajSqlrowiterNew(sqls);
while (!ajSqlrowiterDone(sqli))
{
sqlr = ajSqlrowiterGet(sqli);
/*
** Allocate an AJAX String and reserve space of the length plus
** the 'nul' string terminator.
*/
chkstr = ajStrNewRes((length + 1));
ajSqlcolumnToStr(sqlr, &chkstr);
/*
** Always return upper case sequence
** so that it can be properly soft-masked.
*/
ajStrFmtUpper(&chkstr);
ajStrAssignS(Psequence, chkstr);
ajStrDel(&chkstr);
}
ajSqlrowiterDel(&sqli);
ensDatabaseadaptorSqlstatementDel(dba, &sqls);
ajStrDel(&statement);
}
return ajTrue;
}
/* @func ensSequenceadaptorFetchSliceAllSeq ***********************************
**
** Fetch the sequence of an Ensembl Slice as an AJAX Sequence.
**
** The caller is responsible for deleting the AJAX Sequence.
**
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
** @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 ensSequenceadaptorFetchSliceAllSeq(EnsPSequenceadaptor sqa,
EnsPSlice slice,
AjPSeq *Psequence)
{
return ensSequenceadaptorFetchSliceSubSeq(
sqa,
slice,
1,
ensSliceCalculateLength(slice),
1,
Psequence);
}
/* @func ensSequenceadaptorFetchSliceAllStr ***********************************
**
** Fetch the sequence of an Ensembl Slice as an AJAX String.
**
** The caller is responsible for deleting the AJAX String.
**
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence Adaptor
** @param [u] slice [EnsPSlice] Ensembl Slice
** @param [u] Psequence [AjPStr*] Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSequenceadaptorFetchSliceAllStr(EnsPSequenceadaptor sqa,
EnsPSlice slice,
AjPStr *Psequence)
{
return ensSequenceadaptorFetchSliceSubStr(
sqa,
slice,
1,
ensSliceCalculateLength(slice),
1,
Psequence);
}
/* @func ensSequenceadaptorFetchSliceSubSeq ***********************************
**
** Fetch a sub-sequence of an Ensembl Slice as an AJAX Sequence.
** Coordinates are relative to the Slice and one-based.
** A start of 1 and an end equal the Slice length covers the whole Slice.
**
** The caller is responsible for deleting the AJAX Sequence.
**
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence 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] Psequence [AjPSeq*] AJAX Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSequenceadaptorFetchSliceSubSeq(EnsPSequenceadaptor sqa,
EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPSeq *Psequence)
{
ajint srstart = 0;
ajint srend = 0;
ajint srstrand = 0;
AjBool result = AJFALSE;
AjPStr name = NULL;
AjPStr sequence = NULL;
if (!sqa)
return ajFalse;
if (!slice)
return ajFalse;
if (!strand)
strand = 1;
if (!Psequence)
return ajFalse;
/* Transform relative into absolute coordinates for the Slice name. */
if (ensSliceGetStrand(slice) > 0)
{
srstart = ensSliceGetStart(slice) + start - 1;
srend = ensSliceGetStart(slice) + end - 1;
srstrand = +strand;
}
else
{
srstart = ensSliceGetEnd(slice) - end + 1;
srend = ensSliceGetEnd(slice) - start + 1;
srstrand = -strand;
}
/*
** It is sligtly more efficient, if undefined AJAX String objects are
** directly allocated by the following functions to their final size.
*/
name = ajFmtStr(
"%S:%S:%S:%d:%d:%d",
ensSliceGetCoordsystemName(slice),
ensSliceGetCoordsystemVersion(slice),
ensSliceGetSeqregionName(slice),
srstart,
srend,
srstrand);
result = ensSequenceadaptorFetchSliceSubStr(
sqa,
slice,
start,
end,
strand,
&sequence);
if (*Psequence)
{
ajSeqClear(*Psequence);
ajSeqAssignNameS(*Psequence, name);
ajSeqAssignSeqS(*Psequence, sequence);
}
else
*Psequence = ajSeqNewNameS(sequence, name);
ajSeqSetNuc(*Psequence);
ajStrDel(&name);
ajStrDel(&sequence);
return result;
}
/* @func ensSequenceadaptorFetchSliceSubStr ***********************************
**
** Fetch a sub-sequence of an Ensembl Slice as an AJAX String.
** Coordinates are relative to the Slice and one-based.
** A start of 1 and an end equal the Slice length covers the whole Slice.
**
** The caller is responsible for deleting the AJAX String.
**
** @cc Bio::EnsEMBL::DBSQL::Sequenceadaptor::fetch_by_Slice_start_end_strand
** @see ensSequenceadaptorFetchSliceAllStr
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence 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 [u] Psequence [AjPStr*] Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSequenceadaptorFetchSliceSubStr(EnsPSequenceadaptor sqa,
EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPStr *Psequence)
{
const char *Ptr = NULL;
register ajuint i = 0U;
ajint five = 0;
ajint three = 0;
ajint fshift = 0;
ajint tshift = 0;
ajuint padding = 0U;
ajuint total = 0U;
AjBool circular = AJFALSE;
AjBool debug = AJFALSE;
AjPList pslist = NULL;
AjPList ses = NULL;
AjPStr tmpstr = NULL;
EnsPCoordsystem seqlvlcs = NULL;
EnsPCoordsystemadaptor csa = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPProjectionsegment ps = NULL;
EnsPSequenceedit se = NULL;
EnsPSlice eslice = NULL;
EnsPSlice nslice = NULL;
EnsPSlice sslice = NULL;
EnsPSliceadaptor sla = NULL;
debug = ajDebugTest("ensSequenceadaptorFetchSliceSubStr");
if (debug)
{
ajDebug("ensSequenceadaptorFetchSliceSubStr\n"
" sqa %p\n"
" slice %p\n"
" start %d\n"
" end %d\n"
" strand %d\n"
" Psequence %p\n",
sqa,
slice,
start,
end,
strand,
Psequence);
ensSliceTrace(slice, 1);
}
if (!sqa)
return ajFalse;
if (!slice)
return ajFalse;
if (!Psequence)
return ajFalse;
if (!ensSliceIsCircular(slice, &circular))
return ajFalse;
if (circular == ajTrue)
{
if (start > end)
return sequenceadaptorFetchCircularsliceSubStr(
sqa,
slice,
start,
end,
strand,
Psequence);
if (start < 0)
start += ensSliceGetSeqregionLength(slice);
if (end < 0)
end += ensSliceGetSeqregionLength(slice);
if (ensSliceGetStart(slice) > ensSliceGetEnd(slice))
return sequenceadaptorFetchCircularsliceSubStr(
sqa,
slice,
ensSliceGetStart(slice),
ensSliceGetEnd(slice),
strand,
Psequence);
}
if (start > end)
{
ajDebug("ensSequenceadaptorFetchSliceSubStr requires the start %d "
"to be less than or equal to the end %d coordinate.\n",
start, end);
return ajFalse;
}
if (!strand)
strand = 1;
/*
** Reserve sequence space in larger blocks based on the requested length
** plus one position for the 'nul' string terminator.
*/
if (*Psequence)
ajStrAssignClear(Psequence);
else
*Psequence = ajStrNewRes(
(((ensSliceCalculateRegion(slice, start, end) + 1)
>> sequenceKChunkPower) + 1) << sequenceKChunkPower);
dba = ensSequenceadaptorGetDatabaseadaptor(sqa);
csa = ensRegistryGetCoordsystemadaptor(dba);
sla = ensRegistryGetSliceadaptor(dba);
/*
** Get a new Slice that spans the exact region to retrieve DNA from.
** Only this short region of the Slice needs mapping into the
** sequence-level coordinate system.
*/
/* Relative Slice coordinates range from 1 to length. */
five = 1 - start;
three = end - ensSliceCalculateLength(slice);
if (five || three)
ensSliceFetchSliceexpanded(slice,
five,
three,
ajFalse,
&fshift,
&tshift,
&eslice);
else
eslice = ensSliceNewRef(slice);
/*
** Retrieve normalised, non-symlinked Slice objects, which allows fetching
** of haplotypes (HAPs) and pseudo-autosomal regions (PARs).
*/
pslist = ajListNew();
ensSliceadaptorRetrieveNormalisedprojection(sla, eslice, pslist);
if (!ajListGetLength(pslist))
ajFatal("ensSequenceadaptorFetchSliceSubStr could not "
"retrieve normalised Slices. Database contains incorrect "
"information in the 'assembly_exception' table.\n");
/*
** Call this method again with any Slice that was sym-linked to by this
** Slice.
*/
ajListPeekFirst(pslist, (void **) &ps);
if ((ajListGetLength(pslist) != 1) ||
(!ensSliceMatch(ensProjectionsegmentGetTargetSlice(ps), slice)))
{
tmpstr = ajStrNew();
while (ajListPop(pslist, (void **) &ps))
{
nslice = ensProjectionsegmentGetTargetSlice(ps);
ensSequenceadaptorFetchSliceAllStr(sqa, nslice, &tmpstr);
ajStrAppendS(Psequence, tmpstr);
ensProjectionsegmentDel(&ps);
}
ajStrDel(&tmpstr);
ajListFree(&pslist);
if (strand < 0)
ajSeqstrReverse(Psequence);
ensSliceDel(&eslice);
return ajTrue;
}
/*
** Clear the AJAX List of Ensembl Projection Segment objects resulting
** from the projection of the expanded Slice object to normalised
** Slice objects.
*/
while (ajListPop(pslist, (void **) &ps))
ensProjectionsegmentDel(&ps);
/*
** Now, this Slice needs projecting onto the sequence-level Coordinate
** System even if it is already in this Coordinate System, because
** flanking gaps need trimming out the Slice is past the edges of
** the Sequence Region.
*/
ensCoordsystemadaptorFetchSeqlevel(csa, &seqlvlcs);
ensSliceProject(slice,
ensCoordsystemGetName(seqlvlcs),
ensCoordsystemGetVersion(seqlvlcs),
pslist);
ensCoordsystemDel(&seqlvlcs);
/*
** Fetch the sequence for each of the Ensembl Sequence Region objects
** projected onto. Allocate space for 512 KiB (1 << 19) that should fit
** one BAC clone.
*/
tmpstr = ajStrNewRes((1 << 19) + 1);
while (ajListPop(pslist, (void **) &ps))
{
/*
** Check for gaps between Ensembl Projection Segment objects and
** pad them with Ns.
*/
padding = ensProjectionsegmentGetSourceStart(ps) - total - 1;
if (padding)
{
ajStrAppendCountK(Psequence, 'N', padding);
if (debug)
ajDebug("ensSequenceadaptorFetchSliceSubStr got total %u "
"and Projection Segment source start %u, "
"therefore added %u N padding between.\n",
total,
ensProjectionsegmentGetSourceStart(ps),
padding);
}
sslice = ensProjectionsegmentGetTargetSlice(ps);
ensSequenceadaptorFetchSeqregionSubStr(
sqa,
ensSliceGetSeqregion(sslice),
ensSliceGetStart(sslice),
ensSliceCalculateLength(sslice),
&tmpstr);
if (ensSliceGetStrand(sslice) < 0)
ajSeqstrReverse(&tmpstr);
ajStrAppendS(Psequence, tmpstr);
total = ensProjectionsegmentGetSourceEnd(ps);
ensProjectionsegmentDel(&ps);
}
ajStrDel(&tmpstr);
ajListFree(&pslist);
/* Check for any remaining gaps at the end. */
padding = ensSliceCalculateLength(slice) - total;
if (padding)
{
ajStrAppendCountK(Psequence, 'N', padding);
if (debug)
ajDebug("ensSequenceadaptorFetchSliceSubStr got total %u "
"and Ensembl Slice length %u, "
"therefore added %u N padding.\n",
total,
ensSliceCalculateLength(slice),
padding);
}
/*
** If the sequence is too short, because we came in with a sequence-level
** Slice that was partially off the Sequence Region, pad the end with Ns
** to make it long enough.
** NOTE: Since ajStrGetLen returns size_t, which exceeds ajint,
** the sequence length needs to be determined here.
** padding = ensSliceCalculateLength(slice) - ajStrGetLen(*Psequence);
*/
for (i = 0U, Ptr = ajStrGetPtr(*Psequence); (Ptr && *Ptr); i++, Ptr++)
if (i == UINT_MAX)
ajFatal("ensSequenceadaptorFetchSliceSubStr exeeded UINT_MAX.");
padding = ensSliceCalculateLength(slice) - i;
if (padding)
{
ajStrAppendCountK(Psequence, 'N', padding);
if (debug)
ajDebug("ensSequenceadaptorFetchSliceSubStr got "
"sequence length %u, but Slice length %u, "
"therefore added %u N final padding.\n",
ajStrGetLen(*Psequence),
ensSliceCalculateLength(slice),
padding);
}
/* Apply Sequence Edits. */
ses = ajListNew();
ensSliceFetchAllSequenceedits(slice, ses);
/*
** Sort Sequence Edits in reverse order to avoid the complication of
** adjusting down-stream Sequence Edit coordinates.
*/
ensListSequenceeditSortStartDescending(ses);
while (ajListPop(ses, (void **) &se))
{
/* Adjust Sequence Edit coordinates to the Sub-Slice. */
ensSequenceeditApplyString(se,
ensSliceGetStart(eslice) - 1,
Psequence);
ensSequenceeditDel(&se);
}
ajListFree(&ses);
/* Reverse sequence if requested. */
if (strand < 0)
ajSeqstrReverse(Psequence);
ensSliceDel(&eslice);
return ajTrue;
}
/* @funcstatic sequenceadaptorFetchCircularsliceSubStr ************************
**
** Fetch a sub-sequence of a (circular) Ensembl Slice as an AJAX String.
** Coordinates are relative to the Slice and one-based.
** A start of 1 and an end equal the Slice length covers the whole Slice.
**
** The caller is responsible for deleting the AJAX String.
**
** @cc Bio::EnsEMBL::DBSQL::Sequenceadaptor::
** _fetch_by_Slice_start_end_strand_circular
** @param [u] sqa [EnsPSequenceadaptor] Ensembl Sequence 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 [u] Psequence [AjPStr*] Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
static AjBool sequenceadaptorFetchCircularsliceSubStr(EnsPSequenceadaptor sqa,
EnsPSlice slice,
ajint start,
ajint end,
ajint strand,
AjPStr *Psequence)
{
const char *Ptr = NULL;
register ajuint i = 0U;
ajint mpoint = 0;
ajint five = 0;
ajint three = 0;
ajint fshift = 0;
ajint tshift = 0;
ajuint padding = 0U;
ajuint total = 0U;
AjBool circular = AJFALSE;
AjBool debug = AJFALSE;
AjPList pslist = NULL;
AjPList ses = NULL;
AjPStr sequence1 = NULL;
AjPStr sequence2 = NULL;
AjPStr tmpstr = NULL;
EnsPCoordsystem seqlvlcs = NULL;
EnsPCoordsystemadaptor csa = NULL;
EnsPDatabaseadaptor dba = NULL;
EnsPProjectionsegment ps = NULL;
EnsPSequenceedit se = NULL;
EnsPSlice eslice = NULL;
EnsPSlice nslice = NULL;
EnsPSlice sslice = NULL;
EnsPSliceadaptor sla = NULL;
debug = ajDebugTest("sequenceadaptorFetchCircularsliceSubStr");
if (debug)
{
ajDebug("sequenceadaptorFetchCircularsliceSubStr\n"
" sqa %p\n"
" slice %p\n"
" start %d\n"
" end %d\n"
" strand %d\n"
" Psequence %p\n",
sqa,
slice,
start,
end,
strand,
Psequence);
ensSliceTrace(slice, 1);
}
if (!sqa)
return ajFalse;
if (!slice)
return ajFalse;
if (!Psequence)
return ajFalse;
if (*Psequence)
ajStrAssignClear(Psequence);
else
*Psequence = ajStrNewRes(
(((ensSliceCalculateRegion(slice, start, end) + 1)
>> sequenceKChunkPower) + 1) << sequenceKChunkPower);
if (!ensSliceIsCircular(slice, &circular))
return ajFalse;
dba = ensSequenceadaptorGetDatabaseadaptor(sqa);
csa = ensRegistryGetCoordsystemadaptor(dba);
sla = ensRegistryGetSliceadaptor(dba);
if ((start > end) && (circular == ajTrue))
{
mpoint
= ensSliceGetSeqregionLength(slice)
- ensSliceGetStart(slice)
+ 1;
sequence1 = ajStrNew();
sequence2 = ajStrNew();
sequenceadaptorFetchCircularsliceSubStr(
sqa,
slice,
1,
mpoint,
1,
&sequence1);
sequenceadaptorFetchCircularsliceSubStr(
sqa,
slice,
mpoint + 1,
ensSliceCalculateLength(slice),
1,
&sequence1);
if (ensSliceGetStrand(slice) >= 0)
{
ajStrAppendS(Psequence, sequence1);
ajStrAppendS(Psequence, sequence2);
}
else
{
ajStrAppendS(Psequence, sequence2);
ajStrAppendS(Psequence, sequence1);
ajSeqstrReverse(Psequence);
}
ajStrDel(&sequence1);
ajStrDel(&sequence2);
return ajTrue;
}
/* Get a new Slice that spans the exact region to retrieve DNA from. */
/* Relative Slice coordinates range from 1 to length. */
five = 1 - start;
three = end - ensSliceCalculateLength(slice);
if (five || three)
{
if (ensSliceGetStrand(slice) >= 0)
ensSliceFetchSliceexpanded(slice,
five,
three,
ajFalse,
&fshift,
&tshift,
&eslice);
else
ensSliceFetchSliceexpanded(slice,
three,
five,
ajFalse,
&tshift,
&fshift,
&eslice);
}
/*
** Retrieve normalized non-symlinked Slice objects, which allows fetching
** of haplotypes (HAPs) and pseudo-autosomal regions (PARs).
*/
pslist = ajListNew();
ensSliceadaptorRetrieveNormalisedprojection(sla, eslice, pslist);
if (!ajListGetLength(pslist))
ajFatal("sequenceadaptorFetchCircularsliceSubStr could not "
"retrieve normalised Slices. Database contains incorrect "
"information in the 'assembly_exception' table.\n");
/*
** Call this method again with any Slice that was sym-linked to by this
** Slice.
*/
ajListPeekFirst(pslist, (void **) &ps);
if ((ajListGetLength(pslist) != 1) ||
(!ensSliceMatch(ensProjectionsegmentGetTargetSlice(ps), slice)))
{
tmpstr = ajStrNew();
while (ajListPop(pslist, (void **) &ps))
{
nslice = ensProjectionsegmentGetTargetSlice(ps);
ensSequenceadaptorFetchSliceAllStr(sqa, nslice, &tmpstr);
ajStrAppendS(Psequence, tmpstr);
ensProjectionsegmentDel(&ps);
}
ajStrDel(&tmpstr);
ajListFree(&pslist);
if (strand < 0)
ajSeqstrReverse(Psequence);
ensSliceDel(&eslice);
return ajTrue;
}
/*
** Clear the AJAX List of Ensembl Projection Segment objects resulting
** from the projection of the expanded Slice object to normalised
** Slice objects.
*/
while (ajListPop(pslist, (void **) &ps))
ensProjectionsegmentDel(&ps);
/*
** Now, this Slice needs projecting onto the sequence-level Coordinate
** System even if it is already in this Coordinate System, because
** flanking gaps need trimming out the Slice is past the edges of
** the Sequence Region.
*/
ensCoordsystemadaptorFetchSeqlevel(csa, &seqlvlcs);
ensSliceProject(slice,
ensCoordsystemGetName(seqlvlcs),
ensCoordsystemGetVersion(seqlvlcs),
pslist);
ensCoordsystemDel(&seqlvlcs);
/*
** Fetch the sequence for each of the Ensembl Sequence Region objects
** projected onto. Allocate space for 512 KiB (1 << 19) that should fit
** one BAC clone.
*/
tmpstr = ajStrNewRes((1 << 19) + 1);
while (ajListPop(pslist, (void **) &ps))
{
/*
** Check for gaps between Ensembl Projection Segment objects and
** pad them with Ns.
*/
padding = ensProjectionsegmentGetSourceStart(ps) - total - 1;
if (padding)
{
ajStrAppendCountK(Psequence, 'N', padding);
if (debug)
ajDebug("sequenceadaptorFetchCircularsliceSubStr got total %u "
"and Projection Segment source start %u, "
"therefore added %u N padding between.\n",
total,
ensProjectionsegmentGetSourceStart(ps),
padding);
}
sslice = ensProjectionsegmentGetTargetSlice(ps);
ensSequenceadaptorFetchSeqregionSubStr(
sqa,
ensSliceGetSeqregion(sslice),
ensSliceGetStart(sslice),
ensSliceCalculateLength(sslice),
&tmpstr);
if (ensSliceGetStrand(sslice) < 0)
ajSeqstrReverse(&tmpstr);
ajStrAppendS(Psequence, tmpstr);
total = ensProjectionsegmentGetSourceEnd(ps);
ensProjectionsegmentDel(&ps);
}
/* Check for any remaining gaps at the end. */
padding = ensSliceCalculateLength(slice) - total;
if (padding)
{
ajStrAppendCountK(Psequence, 'N', padding);
if (debug)
ajDebug("sequenceadaptorFetchCircularsliceSubStr got total %u "
"and Ensembl Slice length %u, "
"therefore added %u N padding.\n",
total,
ensSliceCalculateLength(slice),
padding);
}
/*
** If the sequence is too short, because we came in with a sequence-level
** Slice that was partially off the Sequence Region, pad the end with Ns
** to make it long enough.
** NOTE: Since ajStrGetLen returns size_t, which exceeds ajint,
** the sequence length needs to be determined here.
** padding = ensSliceCalculateLength(slice) - ajStrGetLen(*Psequence);
*/
for (i = 0U, Ptr = ajStrGetPtr(*Psequence); (Ptr && *Ptr); i++, Ptr++)
if (i == UINT_MAX)
ajFatal("sequenceadaptorFetchCircularsliceSubStr exeeded "
"UINT_MAX.");
padding = ensSliceCalculateLength(slice) - i;
if (padding)
{
ajStrAppendCountK(Psequence, 'N', padding);
if (debug)
ajDebug("sequenceadaptorFetchCircularsliceSubStr got "
"sequence length %u, but Slice length %u, "
"therefore added %u N final padding.\n",
ajStrGetLen(*Psequence),
ensSliceCalculateLength(slice),
padding);
}
/* Apply Sequence Edits. */
ses = ajListNew();
ensSliceFetchAllSequenceedits(slice, ses);
/*
** Sort Sequence Edits in reverse order to avoid the complication of
** adjusting down-stream Sequence Edit coordinates.
*/
ensListSequenceeditSortStartDescending(ses);
while (ajListPop(ses, (void **) &se))
{
/* Adjust Sequence Edit coordinates to the Sub-Slice. */
ensSequenceeditApplyString(se,
ensSliceGetStart(eslice) - 1,
Psequence);
ensSequenceeditDel(&se);
}
ajListFree(&ses);
/* Reverse sequence if requested. */
if (strand < 0)
ajSeqstrReverse(Psequence);
ensSliceDel(&eslice);
return ajTrue;
}
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