示例#1
0
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;
}
示例#2
0
文件: trimest.c 项目: WenchaoLin/JAMg
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;
}
示例#3
0
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;
}