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/* @source enssequenceedit ****************************************************
**
** Ensembl Sequence Edit functions
**
** @author Copyright (C) 1999 Ensembl Developers
** @author Copyright (C) 2006 Michael K. Schuster
** @version $Revision: 1.35 $
** @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 "enssequenceedit.h"
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== global variables ============================ */
/* ========================================================================= */
/* ========================================================================= */
/* ============================= private data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private constants =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private variables =========================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== private functions =========================== */
/* ========================================================================= */
static int listSequenceeditCompareStartAscending(
const void *item1,
const void *item2);
static int listSequenceeditCompareStartDescending(
const void *item1,
const void *item2);
/* ========================================================================= */
/* ======================= All functions by section ======================== */
/* ========================================================================= */
/* @filesection enssequenceedit ***********************************************
**
** @nam1rule ens Function belongs to the Ensembl library
**
******************************************************************************/
/* @datasection [EnsPSequenceedit] Ensembl Sequence Edit **********************
**
** @nam2rule Sequenceedit Functions for manipulating
** Ensembl Sequence Edit objects
**
** @cc Bio::EnsEMBL::SeqEdit
** @cc CVS Revision: 1.8
** @cc CVS Tag: branch-ensembl-68
**
******************************************************************************/
/* @section constructors ******************************************************
**
** All constructors return a new Ensembl Sequence Edit by pointer.
** It is the responsibility of the user to first destroy any previous
** Sequence Edit. The target pointer does not need to be initialised to
** NULL, but it is good programming practice to do so anyway.
**
** @fdata [EnsPSequenceedit]
**
** @nam3rule New Constructor
** @nam4rule Attribute Constructor with an Ensembl Attribute object
** @nam4rule Cpy Constructor with existing object
** @nam4rule Ini Constructor with initial values
** @nam4rule Ref Constructor by incrementing the reference counter
**
** @argrule Attribute attribute [EnsPAttribute] Ensembl Attribute
** @argrule Cpy se [const EnsPSequenceedit] Ensembl Sequence Edit
** @argrule Ini at [EnsPAttributetype] Ensembl Attribute Type
** @argrule Ini sequence [AjPStr] Alternative sequence
** @argrule Ini start [ajuint] Start coordinate
** @argrule Ini end [ajuint] End coordinate
** @argrule Ref se [EnsPSequenceedit] Ensembl Sequence Edit
**
** @valrule * [EnsPSequenceedit] Ensembl Sequence Edit or NULL
**
** @fcategory new
******************************************************************************/
/* @func ensSequenceeditNewAttribute ******************************************
**
** Constructor for an Ensembl Sequence Edit with an Ensembl Attribute.
**
** @cc Bio::EnsEMBL:SeqEdit::new
** @param [u] attribute [EnsPAttribute] Ensembl Attribute
**
** @return [EnsPSequenceedit] Ensembl Sequence Edit or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPSequenceedit ensSequenceeditNewAttribute(EnsPAttribute attribute)
{
ajint start = 0;
ajint end = 0;
AjPStr altseq = NULL;
EnsPSequenceedit se = NULL;
if (!attribute)
return NULL;
altseq = ajStrNew();
ajFmtScanS(attribute->Value, "%d %d %S", &start, &end, &altseq);
if (start > (end + 1))
{
ajDebug("ensSequenceeditNewAttribute start %d must be less than or "
"equal to end %d + 1 in Ensembl Attribute value '%S'.\n",
start, end, attribute->Value);
return NULL;
}
if (start < 1)
{
ajDebug("ensSequenceeditNewAttribute start %d must be greater than or "
"equal to 1 in Ensembl Attribute value '%S'.\n",
start, attribute->Value);
return NULL;
}
if (end < 0)
{
ajDebug("ensSequenceeditNewAttribute end %d must be greater than or "
"equal to 0 in Ensembl Attribute value '%S' .\n",
end, attribute->Value);
return NULL;
}
AJNEW0(se);
se->Attribute = ensAttributeNewRef(attribute);
if (altseq)
se->Sequence = ajStrNewRef(altseq);
else
se->Sequence = ajStrNew();
se->Start = start;
se->End = end;
se->Use = 1U;
ajStrDel(&altseq);
return se;
}
/* @func ensSequenceeditNewCpy ************************************************
**
** Object-based constructor function, which returns an independent object.
**
** @param [r] se [const EnsPSequenceedit] Ensembl Sequence Edit
**
** @return [EnsPSequenceedit] Ensembl Sequence Edit or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPSequenceedit ensSequenceeditNewCpy(const EnsPSequenceedit se)
{
EnsPSequenceedit pthis = NULL;
AJNEW0(pthis);
pthis->Attribute = ensAttributeNewRef(se->Attribute);
if (se->Sequence)
pthis->Sequence = ajStrNewRef(se->Sequence);
pthis->Start = se->Start;
pthis->End = se->End;
pthis->Use = 1U;
return pthis;
}
/* @func ensSequenceeditNewIni ************************************************
**
** Ensembl Sequence Edit constructor with initial values.
**
** @cc Bio::EnsEMBL:SeqEdit::new
** @param [u] at [EnsPAttributetype] Ensembl Attribute Type
** @param [u] sequence [AjPStr] Alternative sequence
** @param [r] start [ajuint] Start coordinate
** @param [r] end [ajuint] End coordinate
**
** @return [EnsPSequenceedit] Ensembl Sequence Edit or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPSequenceedit ensSequenceeditNewIni(EnsPAttributetype at,
AjPStr sequence,
ajuint start,
ajuint end)
{
AjPStr value = NULL;
EnsPSequenceedit se = NULL;
if (!sequence)
{
ajDebug("ensSequenceeditNewIni requires an alternate sequence.\n");
return NULL;
}
if (start > (end + 1))
{
ajDebug("ensSequenceeditNewIni start %d must be less than or "
"equal to end %d + 1.\n", start, end);
return NULL;
}
if (start < 1)
{
ajDebug("ensSequenceeditNewIni start %d must be greater than or "
"equal to 1.\n", start);
return NULL;
}
value = ajFmtStr("%u %u %S", start, end, sequence);
AJNEW0(se);
se->Attribute = ensAttributeNewIni(at, value);
if (sequence)
se->Sequence = ajStrNewRef(sequence);
else
se->Sequence = ajStrNew();
se->Start = start;
se->End = end;
se->Use = 1U;
ajStrDel(&value);
return se;
}
/* @func ensSequenceeditNewRef ************************************************
**
** Ensembl Object referencing function, which returns a pointer to the
** Ensembl Object passed in and increases its reference count.
**
** @param [u] se [EnsPSequenceedit] Ensembl Sequence Edit
**
** @return [EnsPSequenceedit] Ensembl Sequence Edit or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPSequenceedit ensSequenceeditNewRef(EnsPSequenceedit se)
{
if (!se)
return NULL;
se->Use++;
return se;
}
/* @section destructors *******************************************************
**
** Destruction destroys all internal data structures and frees the memory
** allocated for an Ensembl Sequence Edit object.
**
** @fdata [EnsPSequenceedit]
**
** @nam3rule Del Destroy (free) an Ensembl Sequence Edit
**
** @argrule * Pse [EnsPSequenceedit*] Ensembl Sequence Edit address
**
** @valrule * [void]
**
** @fcategory delete
******************************************************************************/
/* @func ensSequenceeditDel ***************************************************
**
** Default destructor for an Ensembl Sequence Edit.
**
** @param [d] Pse [EnsPSequenceedit*] Ensembl Sequence Edit address
**
** @return [void]
**
** @release 6.4.0
** @@
******************************************************************************/
void ensSequenceeditDel(EnsPSequenceedit *Pse)
{
EnsPSequenceedit pthis = NULL;
if (!Pse)
return;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 1
if (ajDebugTest("ensSequenceeditDel"))
{
ajDebug("ensSequenceeditDel\n"
" *Pse %p\n",
*Pse);
ensSequenceeditTrace(*Pse, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 1 */
if (!(pthis = *Pse) || --pthis->Use)
{
*Pse = NULL;
return;
}
ensAttributeDel(&pthis->Attribute);
ajStrDel(&pthis->Sequence);
ajMemFree((void **) Pse);
return;
}
/* @section member retrieval **************************************************
**
** Functions for returning members of an Ensembl Sequence Edit object.
**
** @fdata [EnsPSequenceedit]
**
** @nam3rule Get Return Sequence Edit attribute(s)
** @nam4rule Attribute Return the Ensembl Attribute
** @nam4rule Sequence Return the alternate sequence
** @nam4rule Start Return the description
** @nam4rule End Return the value
**
** @argrule * se [const EnsPSequenceedit] Sequence Edit
**
** @valrule Attribute [EnsPAttribute] Ensembl Attribute or NULL
** @valrule Sequence [AjPStr] Alternate sequence or NULL
** @valrule Start [ajuint] Start coordinate or 0U
** @valrule End [ajuint] End coordinate or 0U
**
** @fcategory use
******************************************************************************/
/* @func ensSequenceeditGetAttribute ******************************************
**
** Get the Ensembl Attribute member of an Ensembl Sequence Edit.
**
** @cc Bio::EnsEMBL:SeqEdit::get_Attribute
** @param [r] se [const EnsPSequenceedit] Ensembl Sequence Edit
**
** @return [EnsPAttribute] Ensembl Attribute or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
EnsPAttribute ensSequenceeditGetAttribute(const EnsPSequenceedit se)
{
return (se) ? se->Attribute : NULL;
}
/* @func ensSequenceeditGetEnd ************************************************
**
** Get the end coordinate member of an Ensembl Sequence Edit.
**
** Coordinates are inclusive and one-based, which means that inserts are
** unusually represented by a start one base pair higher than the end. Hence,
** start = 1, end = 1 is a replacement of the first base, but
** start = 1, end = 0 is an insert BEFORE the first base.
**
** @cc Bio::EnsEMBL:SeqEdit::end
** @param [r] se [const EnsPSequenceedit] Ensembl Sequence Edit
**
** @return [ajuint] End coordinate or 0U
**
** @release 6.4.0
** @@
******************************************************************************/
ajuint ensSequenceeditGetEnd(const EnsPSequenceedit se)
{
return (se) ? se->End : 0U;
}
/* @func ensSequenceeditGetSequence *******************************************
**
** Get the (alternative) sequence member of an Ensembl Sequence Edit.
**
** The sequence may either be a string of amino acids or nucleotides depending
** on the context in which this Sequence Edit is used.
** In the case of a deletion the replacement sequence is an empty string.
**
** @cc Bio::EnsEMBL:SeqEdit::alt_seq
** @param [r] se [const EnsPSequenceedit] Ensembl Sequence Edit
**
** @return [AjPStr] Alternative sequence or NULL
**
** @release 6.4.0
** @@
******************************************************************************/
AjPStr ensSequenceeditGetSequence(const EnsPSequenceedit se)
{
return (se) ? se->Sequence : NULL;
}
/* @func ensSequenceeditGetStart **********************************************
**
** Get the start coordinate member of an Ensembl Sequence Edit.
**
** Coordinates are inclusive and one-based, which means that inserts are
** unusually represented by a start one base pair higher than the end. Hence,
** start = 1, end = 1 is a replacement of the first base, but
** start = 1, end = 0 is an insert BEFORE the first base.
**
** @cc Bio::EnsEMBL:SeqEdit::start
** @param [r] se [const EnsPSequenceedit] Ensembl Sequence Edit
**
** @return [ajuint] Start coordinate or 0U
**
** @release 6.4.0
** @@
******************************************************************************/
ajuint ensSequenceeditGetStart(const EnsPSequenceedit se)
{
return (se) ? se->Start : 0U;
}
/* @section debugging *********************************************************
**
** Functions for reporting of an Ensembl Sequence Edit object.
**
** @fdata [EnsPSequenceedit]
**
** @nam3rule Trace Report Ensembl Sequence Edit members to debug file
**
** @argrule Trace se [const EnsPSequenceedit] Ensembl Sequence Edit
** @argrule Trace level [ajuint] Indentation level
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensSequenceeditTrace *************************************************
**
** Trace an Ensembl Sequence Edit.
**
** @param [r] se [const EnsPSequenceedit] Ensembl Sequence Edit
** @param [r] level [ajuint] Indentation level
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSequenceeditTrace(const EnsPSequenceedit se, ajuint level)
{
AjPStr indent = NULL;
if (!se)
return ajFalse;
indent = ajStrNew();
ajStrAppendCountK(&indent, ' ', level * 2);
ajDebug("%SensSequenceeditTrace %p\n"
"%S Attribute %p\n"
"%S Sequence '%S'\n"
"%S Start %u\n"
"%S End %u\n"
"%S Use %u\n",
indent, se,
indent, se->Attribute,
indent, se->Sequence,
indent, se->Start,
indent, se->End,
indent, se->Use);
ensAttributeTrace(se->Attribute, level + 1);
ajStrDel(&indent);
return ajTrue;
}
/* @section calculate *********************************************************
**
** Functions for calculating information from an Ensembl Sequence Edit object.
**
** @fdata [EnsPSequenceedit]
**
** @nam3rule Calculate Calculate Ensembl Sequence Edit information
** @nam4rule Difference Calculate the length difference
** @nam4rule Memsize Calculate the memory size in bytes
**
** @argrule * se [const EnsPSequenceedit] Ensembl Sequence Edit
**
** @valrule Difference [ajint] Length difference or 0
** @valrule Memsize [size_t] Memory size in bytes or 0
**
** @fcategory misc
******************************************************************************/
/* @func ensSequenceeditCalculateDifference ***********************************
**
** Calculate the length difference an Ensembl Sequence Edit would cause.
**
** @cc Bio::EnsEMBL:SeqEdit::length_diff
** @param [r] se [const EnsPSequenceedit] Ensembl Sequence Edit
**
** @return [ajint] Length difference or 0
**
** @release 6.4.0
** @@
******************************************************************************/
ajint ensSequenceeditCalculateDifference(const EnsPSequenceedit se)
{
const char *Ptr = NULL;
register ajuint i = 0U;
if (!se)
return 0;
/*
** NOTE: Since ajStrGetLen returns size_t, which exceeds ajint,
** the length of the alternative sequence needs to be determined here.
**
** return ajStrGetLen(se->Sequence) - (se->End - se->Start + 1);
*/
for (i = 0U, Ptr = ajStrGetPtr(se->Sequence); (Ptr && *Ptr); i++, Ptr++)
if (i == UINT_MAX)
ajFatal("ensSequenceeditCalculateDifference exeeded UINT_MAX.");
return i - (se->End - se->Start + 1);
}
/* @func ensSequenceeditCalculateMemsize **************************************
**
** Calculate the memory size in bytes of an Ensembl Sequence Edit.
**
** @param [r] se [const EnsPSequenceedit] Ensembl Sequence Edit
**
** @return [size_t] Memory size in bytes or 0
**
** @release 6.4.0
** @@
******************************************************************************/
size_t ensSequenceeditCalculateMemsize(const EnsPSequenceedit se)
{
size_t size = 0;
if (!se)
return 0;
size += sizeof (EnsOSequenceedit);
size += ensAttributeCalculateMemsize(se->Attribute);
if (se->Sequence)
{
size += sizeof (AjOStr);
size += ajStrGetRes(se->Sequence);
}
return size;
}
/* @section apply *************************************************************
**
** Functions for applying Ensembl Sequence Edit objects.
**
** @fdata [EnsPSequenceedit]
**
** @nam3rule Apply Apply Ensembl Sequence Edit objects
** @nam4rule String Apply an Ensembl Sequence Edit to an AJAX String
**
** @argrule String se [const EnsPSequenceedit] Ensembl Sequence Edit
** @argrule String offset [ajint] Offset into sequence
** @argrule String Psequence [AjPStr*] Sequence address
**
** @valrule String [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensSequenceeditApplyString *******************************************
**
** Apply an Ensembl Sequence Edit to an AJAX String.
**
** @cc Bio::EnsEMBL:SeqEdit::apply_edit
** @cc Bio::EnsEMBL::DBSQL::SequenceAdaptor::_rna_edit
** @param [r] se [const EnsPSequenceedit] Ensembl Sequence Edit
** @param [rE] offset [ajint] Offset into sequence
** @param [u] Psequence [AjPStr*] Sequence address
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensSequenceeditApplyString(const EnsPSequenceedit se,
ajint offset,
AjPStr *Psequence)
{
ajlong pos1 = 0;
ajlong pos2 = 0;
if (!se)
return ajFalse;
if (!Psequence)
return ajFalse;
if (!*Psequence)
return ajFalse;
pos1 = se->Start - offset;
pos2 = se->End - offset;
if (pos2 < 1)
{
ajDebug("ensSequenceeditApplyString got an Ensembl Sequence Edit, "
"which end position (%d) corrected for the offset (%d) lies "
"beyond the sequence start (1).",
se->End, offset);
return ajFalse;
}
if (pos1 > (ajlong) ajStrGetLen(*Psequence))
{
ajDebug("ensSequenceeditApplyString got an Ensembl Sequence Edit, "
"which start position (%d) corrected for the offset (%d) lies "
"beyond the sequence end (%lu).",
se->Start, offset, ajStrGetLen(*Psequence));
/* FIXME: size_t can be shorter than ajulong */
return ajFalse;
}
/* Adjust to zero-based coordinates. */
ajStrCutRange(Psequence, pos1 - 1, pos2 - 1);
ajStrInsertS(Psequence, pos1 - 1, se->Sequence);
return ajTrue;
}
/* @datasection [AjPList] AJAX List *******************************************
**
** @nam2rule List Functions for manipulating AJAX List objects
**
******************************************************************************/
/* @funcstatic listSequenceeditCompareStartAscending **************************
**
** AJAX List of Ensembl Sequence Edit objects comparison function to sort by
** start member in ascending order.
**
** @param [r] item1 [const void*] Ensembl Sequence Edit address 1
** @param [r] item2 [const void*] Ensembl Sequence Edit 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 listSequenceeditCompareStartAscending(
const void *item1,
const void *item2)
{
int result = 0;
EnsPSequenceedit se1 = *(EnsOSequenceedit *const *) item1;
EnsPSequenceedit se2 = *(EnsOSequenceedit *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listSequenceeditCompareStartAscending"))
{
ajDebug("listSequenceeditCompareStartAscending\n"
" se1 %p\n"
" se2 %p\n",
se1,
se2);
ensSequenceeditTrace(se1, 1);
ensSequenceeditTrace(se2, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX list. */
if (se1 && (!se2))
return -1;
if ((!se1) && (!se2))
return 0;
if ((!se1) && se2)
return +1;
if (se1->Start < se2->Start)
result = -1;
if (se1->Start > se2->Start)
result = +1;
return result;
}
/* @funcstatic listSequenceeditCompareStartDescending *************************
**
** AJAX List of Ensembl Sequence Edit objects comparison function to sort by
** start member in descending order.
**
** @param [r] item1 [const void*] Ensembl Sequence Edit address 1
** @param [r] item2 [const void*] Ensembl Sequence Edit 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 listSequenceeditCompareStartDescending(
const void *item1,
const void *item2)
{
int result = 0;
EnsPSequenceedit se1 = *(EnsOSequenceedit *const *) item1;
EnsPSequenceedit se2 = *(EnsOSequenceedit *const *) item2;
#if defined(AJ_DEBUG) && AJ_DEBUG >= 2
if (ajDebugTest("listSequenceeditCompareStartDescending"))
{
ajDebug("listSequenceeditCompareStartDescending\n"
" se1 %p\n"
" se2 %p\n",
se1,
se2);
ensSequenceeditTrace(se1, 1);
ensSequenceeditTrace(se2, 1);
}
#endif /* defined(AJ_DEBUG) && AJ_DEBUG >= 2 */
/* Sort empty values towards the end of the AJAX list. */
if (se1 && (!se2))
return -1;
if ((!se1) && (!se2))
return 0;
if ((!se1) && se2)
return +1;
if (se1->Start < se2->Start)
result = +1;
if (se1->Start > se2->Start)
result = -1;
return result;
}
/* @section list **************************************************************
**
** Functions for manipulating AJAX List objects.
**
** @fdata [AjPList]
**
** @nam3rule Sequenceedit Functions for manipulating AJAX List objects of
** Ensembl Sequence Edit objects
** @nam4rule Sort Sort functions
** @nam5rule Start Sort by start member
** @nam6rule Ascending Sort in ascending order
** @nam6rule Descending Sort in descending order
**
** @argrule Ascending ses [AjPList] AJAX List of Ensembl Sequence Edit objects
** @argrule Descending ses [AjPList] AJAX List of Ensembl Sequence Edit objects
**
** @valrule * [AjBool] ajTrue upon success, ajFalse otherwise
**
** @fcategory misc
******************************************************************************/
/* @func ensListSequenceeditSortStartAscending ********************************
**
** Sort an AJAX List of Ensembl Sequence Edit objects by start member in
** ascending order.
**
** @param [u] ses [AjPList] AJAX List of Ensembl Sequence Edit objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListSequenceeditSortStartAscending(AjPList ses)
{
if (!ses)
return ajFalse;
ajListSort(ses, &listSequenceeditCompareStartAscending);
return ajTrue;
}
/* @func ensListSequenceeditSortStartDescending *******************************
**
** Sort an AJAX List of Ensembl Sequence Edit objects by start member in
** descending order.
**
** @param [u] ses [AjPList] AJAX List of Ensembl Sequence Edit objects
**
** @return [AjBool] ajTrue upon success, ajFalse otherwise
**
** @release 6.4.0
** @@
******************************************************************************/
AjBool ensListSequenceeditSortStartDescending(AjPList ses)
{
if (!ses)
return ajFalse;
ajListSort(ses, &listSequenceeditCompareStartDescending);
return ajTrue;
}
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