static void splitter_AddSubSeqFeat(AjPFeattable ftable, ajuint start,
ajuint end, const AjPSeq oldseq)
{
AjPFeattable old_feattable = NULL;
AjIList iter = NULL;
old_feattable = ajSeqGetFeatCopy(oldseq);
if(!old_feattable)
return;
iter = ajListIterNewread(old_feattable->Features);
while(!ajListIterDone(iter))
{
AjPFeature gf = ajListIterGet(iter);
AjPFeature copy = NULL;
if (((ajFeatGetEnd(gf) < start + 1) &&
(gf->End2 == 0 || gf->End2 < start + 1)) ||
((ajFeatGetStart(gf) > end + 1) &&
(gf->Start2 == 0 || gf->Start2 > end + 1)))
{
continue;
}
copy = ajFeatNewFeat(gf);
copy->Start = copy->Start - start;
copy->End = copy->End - start;
if (copy->Start2 > 0)
copy->Start2 = copy->Start2 - start;
if (copy->End2 > 0)
copy->End2 = copy->End2 - start;
ajFeatTrimOffRange (copy, 0, 1, end - start + 1, AJTRUE, AJTRUE);
ajFeattableAdd(ftable, copy);
}
ajFeattableDel(&old_feattable);
ajListIterDel(&iter);
return;
}
static void extractfeat_FeatSeqExtract(const AjPSeq seq, AjPSeqout seqout,
AjPFeattable featab, ajint before,
ajint after, AjBool join,
AjBool featinname,
const AjPStr describe)
{
AjIList iter = NULL;
AjPFeature gf = NULL;
AjBool single; /* ajtrue = is not a multiple */
AjBool parent; /* ajtrue = is a parent of a multiple */
AjBool child; /* ajTrue = is a child of a multiple */
AjBool compall; /* ajTrue = reverse comp all of join */
AjBool sense; /* ajTrue = forward sense */
AjBool remote; /* ajTrue = remote ID */
AjPStr type = NULL; /* name of feature */
AjPStr featseq = NULL; /* feature sequence string */
AjPStr tmpseq = NULL; /* temporary sequence string */
ajint firstpos;
ajint lastpos; /* bounds of feature in sequence */
AjPStr describeout = NULL; /* tag names/values to add to descriptions */
ajuint count = 0;
/* For all features... */
if(featab && ajFeattableGetSize(featab))
{
/* initialise details of a feature */
featseq = ajStrNew();
tmpseq = ajStrNew();
type = ajStrNew();
remote = ajFalse;
compall = ajFalse;
sense = ajTrue;
firstpos = 0;
lastpos = 0;
describeout = ajStrNew();
iter = ajListIterNewread(featab->Features);
while(!ajListIterDone(iter))
{
gf = ajListIterGet(iter) ;
/*
** Determine what sort of thing this feature is. Only one of
** these will be true.
** True if this is part of a multiple join and it is not
** the parent
*/
child = ajFalse;
/* True if this is part of a multiple join and it is the parent */
parent = ajFalse;
/* True if this is not part of a multiple join */
single = ajFalse;
if(ajFeatIsMultiple(gf))
{
if(ajFeatIsChild(gf))
child = ajTrue;
else
parent = ajTrue;
}
else
single = ajTrue;
/*
** If not wish to assembling joins(), then force all features
** to be treated as single
*/
if(!join)
{
child = ajFalse;
parent = ajFalse;
single = ajTrue;
}
ajDebug("feature %S %d-%d is parent %B, child %B, single %B\n",
ajFeatGetType(gf), ajFeatGetStart(gf), ajFeatGetEnd(gf),
parent, child, single);
/*
ajUser("feature %S %d-%d is parent %B, child %B, single %B",
ajFeatGetType(gf), ajFeatGetStart(gf), ajFeatGetEnd(gf),
parent, child, single);
*/
/*
** If single or parent, write out any stored previous feature
** sequence
*/
if(count++ && !child)
{
extractfeat_WriteOut(seqout, &featseq, compall, sense,
firstpos, lastpos, before, after, seq,
remote, type,
featinname, describeout);
/* reset joined feature information */
ajStrSetClear(&featseq);
ajStrSetClear(&tmpseq);
ajStrSetClear(&type);
ajStrSetClear(&describeout);
remote = ajFalse;
compall = ajFalse;
sense = ajTrue;
firstpos = 0;
lastpos = 0;
}
/* if parent, note if have Complemented Join */
if(parent)
compall = ajFeatIsCompMult(gf);
/*
** Get the sense of the feature
** NB. if complementing several joined features, then pretend they
** are forward sense until its possible to reverse-complement
** them all together.
*/
if(!compall && ajFeatGetStrand(gf) == '-')
sense = ajFalse;
/* get 'type' name of feature */
if(single || parent)
ajStrAssignS(&type, ajFeatGetType(gf));
/*
** if single or parent, get 'before' + 'after' sequence
** positions
*/
if(single || parent)
{
firstpos = ajFeatGetStart(gf)-1;
lastpos = ajFeatGetEnd(gf)-1;
}
/* if child, update the boundary positions */
if(child)
{
if(sense)
lastpos = ajFeatGetEnd(gf)-1;
else
firstpos = ajFeatGetStart(gf)-1;
}
extractfeat_MatchPatternDescribe(gf, describe, &describeout);
/* get feature sequence(complement if required) */
if(!child)
{
if(join)
ajFeatGetSeqJoin(gf, featab, seq, &tmpseq);
else
ajFeatGetSeq(gf, seq, &tmpseq);
ajDebug("extracted feature = %d bases\n", ajStrGetLen(tmpseq));
/*ajUser("extracted feature = %d bases", ajStrGetLen(tmpseq));*/
ajStrAssignS(&featseq, tmpseq);
}
}
ajListIterDel(&iter) ;
/*
** write out any previous sequence(s)
** - add before + after, complement all
*/
extractfeat_WriteOut(seqout, &featseq, compall, sense,
firstpos, lastpos, before, after,
seq, remote, type,
featinname, describeout);
ajStrDel(&featseq);
ajStrDel(&tmpseq);
ajStrDel(&type);
ajStrDel(&describeout);
}
return;
}
