static void tranalign_AddGaps(AjPSeq newseq,
const AjPSeq nseq, const AjPSeq pseq,
ajlong npos)
{
AjPStr newstr = NULL;
ajuint ppos = 0;
newstr = ajStrNew();
for(; ppos<ajSeqGetLen(pseq); ppos++)
if(ajSeqGetSeqC(pseq)[ppos] == '-')
ajStrAppendC(&newstr, "---");
else
{
ajStrAppendSubS(&newstr, ajSeqGetSeqS(nseq), npos, npos+2);
npos+=3;
}
ajDebug("aligned seq=%S\n", newstr);
ajSeqAssignSeqS(newseq, newstr);
ajStrDel(&newstr);
return;
}
static void trimest_tolower(AjPStr *strng, ajint start, ajint end)
{
AjPStr substr;
substr = ajStrNew();
/* extract the region and lowercase */
ajStrAppendSubS(&substr, *strng, start, end);
ajStrFmtLower(&substr);
/* remove and replace the lowercased region */
ajStrCutRange(strng, start, end);
ajStrInsertS(strng, start, substr);
ajStrDel(&substr);
return;
}
static void extractfeat_GetRegionPad(const AjPSeq seq, AjPStr *featstr,
ajint start, ajint end, AjBool sense,
AjBool beginning)
{
ajint tmp;
ajint pad;
AjPStr result;
ajDebug("In extractfeat_GetRegionPad start=%d, end=%d\n", start, end);
result = ajStrNew();
if(start > end)
return;
if(start < 0)
{
pad = -start;
if(ajSeqIsNuc(seq))
ajStrAppendCountK(&result, 'N', pad);
else
ajStrAppendCountK(&result, 'X', pad);
start = 0;
}
if(end > (ajint) ajSeqGetLen(seq)-1)
tmp = ajSeqGetLen(seq)-1;
else
tmp = end;
if(start <= (ajint) ajSeqGetLen(seq) && tmp >= 0)
{
ajDebug("Get subsequence %d-%d\n", start, tmp);
ajStrAppendSubS(&result, ajSeqGetSeqS(seq), start, tmp);
ajDebug("result=%S\n", result);
}
if(end > (ajint) ajSeqGetLen(seq)-1)
{
pad = end - ajSeqGetLen(seq)+1;
if(ajSeqIsNuc(seq))
ajStrAppendCountK(&result, 'N', pad);
else
ajStrAppendCountK(&result, 'X', pad);
ajDebug("result=%S\n", result);
}
/* if feature was in reverse sense, then get reverse complement */
if(!sense)
{
ajDebug("get reverse sense of subsequence\n");
ajSeqstrReverse(&result);
ajDebug("result=%S\n", result);
}
if(beginning)
{
ajDebug("Prepend to featstr: %S\n", result);
ajStrInsertS(featstr, 0, result);
}
else
{
ajDebug("Append to featstr: %S\n", result);
ajStrAppendS(featstr, result);
}
ajDebug("featstr=%S\n", *featstr);
ajStrDel(&result);
return;
}