string temp;
while(!in.eof()){
+ if (m->control_pressed) { break; }
+
Sequence currSeq(in);
name = currSeq.getName();
- if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
- else { sequence = currSeq.getUnaligned(); }
-
- seqmap[name] = sequence;
- map<string,group>::iterator it = data.find(sequence);
- if (it == data.end()) { //it's unique.
- data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
-// data[sequence].groupnumber = 1;
- data[sequence].names = name;
- }else { // its a duplicate.
- data[sequence].names += "," + name;
-// data[sequence].groupnumber++;
- }
-
+ if (name != "") {
+ if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
+ else { sequence = currSeq.getUnaligned(); }
+
+ seqmap[name] = sequence;
+ map<string,group>::iterator it = data.find(sequence);
+ if (it == data.end()) { //it's unique.
+ data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
+ // data[sequence].groupnumber = 1;
+ data[sequence].names = name;
+ }else { // its a duplicate.
+ data[sequence].names += "," + name;
+ // data[sequence].groupnumber++;
+ }
+ }
gobble(in);
}
in.close();
}
catch(exception& e) {
- errorOut(e, "FastaMap", "readFastaFile");
+ m->errorOut(e, "FastaMap", "readFastaFile");
exit(1);
}
}
map<string,string> oldNameMap;
string name, list;
while(!oldNameFile.eof()){
+ if (m->control_pressed) { break; }
+
oldNameFile >> name >> list;
oldNameMap[name] = list;
gobble(oldNameFile);
openInputFile(inFastaFile, inFASTA);
string sequence;
while(!inFASTA.eof()){
+ if (m->control_pressed) { break; }
+
Sequence currSeq(inFASTA);
name = currSeq.getName();
- if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
- else { sequence = currSeq.getUnaligned(); }
-
- seqmap[name] = sequence;
- map<string,group>::iterator it = data.find(sequence);
- if (it == data.end()) { //it's unique.
- data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
-// data[sequence].groupnumber = 1;
- data[sequence].names = oldNameMap[name];
- }else { // its a duplicate.
- data[sequence].names += "," + oldNameMap[name];
-// data[sequence].groupnumber++;
- }
-
+ if (name != "") {
+ if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
+ else { sequence = currSeq.getUnaligned(); }
+
+ seqmap[name] = sequence;
+ map<string,group>::iterator it = data.find(sequence);
+ if (it == data.end()) { //it's unique.
+ data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
+ // data[sequence].groupnumber = 1;
+ data[sequence].names = oldNameMap[name];
+ }else { // its a duplicate.
+ data[sequence].names += "," + oldNameMap[name];
+ // data[sequence].groupnumber++;
+ }
+ }
gobble(inFASTA);
}
// two column file created with groupname and them list of identical sequence names
for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+ if (m->control_pressed) { break; }
outFile << it->second.groupname << '\t' << it->second.names << endl;
}
outFile.close();
}
catch(exception& e) {
- errorOut(e, "FastaMap", "printNamesFile");
+ m->errorOut(e, "FastaMap", "printNamesFile");
exit(1);
}
}
openOutputFile(outFileName, out);
//creates a fasta file
for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
+ if (m->control_pressed) { break; }
out << ">" << it->second.groupname << endl;
out << it->first << endl;
}
out.close();
}
catch(exception& e) {
- errorOut(e, "FastaMap", "printCondensedFasta");
+ m->errorOut(e, "FastaMap", "printCondensedFasta");
exit(1);
}
}