Animator::Animator(Object* obj, int frames)
{
addObjs(obj);
_anims.resize(_objs.size());
addSeq(frames);
reset();
}
int GTree::addSequence(int *bid, int n, int L, int seqID) //adds all the L-subseqs
{
n = n-L+1;
if (n<0) n=0;
for(int i=0;i<n;i++)
{
addSeq(bid,L,bid, seqID, gMAXMM, 0);
bid++;
}
return n;
}
bool AceParser::loadContig(int ctgidx, fnLytSeq* seqfn, bool re_pos) {
bool forgetCtg = false;
if (ctgidx>=contigs.Count())
GError("LayoutParser: invalid contig index '%d'\n", ctgidx);
LytCtgData* ctgdata=contigs[ctgidx];
if (re_pos && currentContig!=NULL) { //free previously loaded contig data
currentContig->seqs.Clear(); // unless it was a parse() call
seqinfo.Clear();
}
currentContig=ctgdata;
int ctg_numSeqs=ctgdata->numseqs;
if (re_pos) {
seek(ctgdata->fpos); //position right where the contig definition starts
char *r = linebuf->getLine(f,f_pos);
if (r==NULL) return false;
}
if (seqfn!=NULL) { //process the contig sequence!
char* ctgseq=readSeq();
forgetCtg=(*seqfn)(numContigs, ctgdata, NULL, ctgseq);
GFREE(ctgseq); //obviously the caller should have made a copy
}
//now look for all the component sequences
if (fskipTo("AF ")<0) {
GMessage("AceParser: error finding sequence offsets (AF)"
" for contig '%s' (%d)\n", ctgdata->name, ctgdata->len);
return false;
}
int numseqs=0;
while (startsWith(linebuf->chars(), "AF ",3)) {
if (addSeq(linebuf->chars(), ctgdata)==NULL) {
GMessage("AceParser: error parsing AF entry:\n%s\n",linebuf->chars());
return false;
}
numseqs++;
//read next line:
linebuf->getLine(f,f_pos);
}
if (numseqs!=ctg_numSeqs) {
GMessage("Invalid number of AF entries found (%d) for contig '%s' "
"(length %d, numseqs %d)\n", numseqs,
ctgdata->name, ctgdata->len, ctg_numSeqs);
return false;
}
//now read each sequence entry
off_t seqpos=fskipTo("RD ");
numseqs=0; //count again, now the RD entries
if (seqpos<0) {
GMessage("AceParser: error locating first RD entry for contig '%s'\n",
ctgdata->name);
return false;
}
//int numseqs=0;
//reading the actual component sequence details
while (startsWith(linebuf->chars(), "RD ",3)) {
char* s=linebuf->chars()+3;
char* p=strchrs(s, " \t");
LytSeqInfo* seq;
if (p==NULL) {
GMessage("AceParser: Error parsing RD header line:\n%s\n", linebuf->chars());
return false;
}
*p='\0';
if ((seq=seqinfo.Find(s))==NULL) {
GMessage("AceParser: unknown RD encountered: '%s'\n", s);
return false;
}
p++; //now p is in linebuf after the RD name
seq->fpos=seqpos;
int len;
if (sscanf(p, "%d", &len)!=1) {
GMessage("AceParser: cannot parse RD length for '%s'\n", s);
return false;
}
seq->setLength(len);
//read the sequence data here if a callback fn was given:
char* sseq=NULL;
if (seqfn!=NULL)
sseq=readSeq(seq); //read full sequence here
if (fskipTo("QA ")<0) {
GMessage("AceParser: Error finding QA entry for read %s! (fpos=%llu)\n", seq->name, (unsigned long long)f_pos);
return false;
}
//parse QA entry:
int tmpa, tmpb;
if (sscanf(linebuf->chars()+3, "%d %d %d %d", &tmpa, &tmpb, &seq->left,&seq->right)!=4 ||
seq->left<=0 || seq->right<=0) {
GMessage("AceParser: Error parsing QA entry.\n");
return false;
}
/*
if (fskipTo("DS")<0) {
GMessage("AceParser: Error closing RD entry ('DS' not found).\n");
return false;
}
*/
seqpos=getFilePos()+1;
bool forgetSeq=false;
if (seqfn!=NULL) {
forgetSeq=(*seqfn)(numContigs, ctgdata, seq, sseq);
GFREE(sseq);
}
if (forgetSeq) { //parsing the whole stream -- aceconv)
ctg_numSeqs--;
seqinfo.Remove(seq->name);
ctgdata->seqs.RemovePtr(seq);
}
numseqs++;
if (numseqs<ctgdata->numseqs)
seqpos=fskipTo("RD ", "CO "); //more sequences left to read
}
if (numseqs!=ctgdata->numseqs) {
GMessage("Error: Invalid number of RD entries found (%d) for contig '%s' "
"(length %d, numseqs %d)\n", numseqs,
ctgdata->name, ctgdata->len, ctg_numSeqs);
return false;
}
if (forgetCtg) {
ctgIDs.Remove(ctgdata->name);
ctgdata->seqs.Clear();
seqinfo.Clear();
contigs.RemovePtr(ctgdata);
}
return true;
}
/*
Load contig data; can be called by parse - and then no fseek is needed and
the file position if right after parsing the contig summary data
*/
bool LayoutParser::loadContig(int ctgidx, fnLytSeq* seqfn, bool re_pos) {
bool forgetCtg=false;
char* r=NULL;
if (ctgidx>=contigs.Count())
GError("LayoutParser: invalid contig index '%d'\n", ctgidx);
LytCtgData* ctgdata=contigs[ctgidx];
if (re_pos && currentContig!=NULL) { //free previous contig data
//unless it was a parse() call
currentContig->seqs.Clear();
seqinfo.Clear();
}
currentContig=ctgdata;
if (re_pos) {
seek(ctgdata->fpos); //position right where the contig definition starts
r=linebuf->getLine(f,f_pos);//skip the first line
if (r==NULL) return false;
}
if (seqfn!=NULL)
forgetCtg=(*seqfn)(numContigs, ctgdata, NULL, NULL);
int ctg_numSeqs=ctgdata->numseqs;
int numseqs=0;
while ((r=linebuf->getLine(f,f_pos))!=NULL) {
if (linebuf->length()<4) continue;
if (linebuf->chars()[0]=='>') {
linebuf->pushBack();
break; //reached next contig
}
//sequence data parsing
bool forgetSeq=false;
LytSeqInfo* seq=NULL;
if ((seq=addSeq(linebuf->chars(), ctgdata))==NULL) {
GMessage("LayoutParser: error parsing sequence entry:\n%s\n",linebuf->chars());
return false;
}
/*
// Weird -- why would I MODIFY the given clipping of a sequence?
//--
bool ctg_clipping = (ctgdata->rpos>ctgdata->lpos);
if (ctg_clipping) {
if (ctgdata->lpos > seq->offs && ctgdata->lpos < seq->offs+seq->length())
seq->left = ctgdata->lpos - seq->offs+1;
if (ctgdata->rpos < seq->offs+seq->length() && ctgdata->rpos>seq->offs )
seq->right = ctgdata->rpos-seq->offs+1;
} */
if (seqfn!=NULL)
forgetSeq=(*seqfn)(numContigs, ctgdata, seq, NULL);
if (forgetSeq) {
ctg_numSeqs--;
seqinfo.Remove(seq->name);
ctgdata->seqs.RemovePtr(seq);
}
else {
numseqs++;
}
} //while sequences
if (forgetCtg) {
ctgIDs.Remove(ctgdata->name);
contigs.RemovePtr(ctgdata);
}
if (numseqs!=ctg_numSeqs) {
GMessage("Mismatching number of sequences found (%d) for contig '%s' "
"(length %d, numseqs %d)\n", numseqs,
ctgdata->name, ctgdata->len, ctg_numSeqs);
return false;
}
return true;
}
Animator::Animator(const std::vector<Object*>& objs, int frames) : _objs(objs)
{
_anims.resize(_objs.size());
addSeq(frames);
reset();
}
