TreeMap::TreeMap(string filename) {
m = MothurOut::getInstance();
+ ofstream out2;
+ m->openOutputFileAppend(filename, out2);
+ out2 << endl; out2.close();
groupFileName = filename;
m->openInputFile(filename, fileHandle);
}
/************************************************************/
int TreeMap::readMap(string gf) {
try {
+ ofstream out2;
+ m->openOutputFileAppend(gf, out2);
+ out2 << endl; out2.close();
+
groupFileName = gf;
m->openInputFile(gf, fileHandle);
}
fileHandle.close();
+ if (rest != "") {
+ vector<string> pieces = m->splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { seqName = pieces[i]; columnOne=false; }
+ else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ setNamesOfGroups(seqGroup);
+
+ map<string, GroupIndex>::iterator itCheck = treemap.find(seqName);
+ if (itCheck != treemap.end()) { error = 1; m->mothurOut("[WARNING]: Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ namesOfSeqs.push_back(seqName);
+ treemap[seqName].groupname = seqGroup; //store data in map
+
+ it2 = seqsPerGroup.find(seqGroup);
+ if (it2 == seqsPerGroup.end()) { //if it's a new group
+ seqsPerGroup[seqGroup] = 1;
+ }else {//it's a group we already have
+ seqsPerGroup[seqGroup]++;
+ }
+ }
+ pairDone = false;
+ }
+ }
+ }
+
return error;
}
catch(exception& e) {
}
fileHandle.close();
+ if (rest != "") {
+ vector<string> pieces = m->splitWhiteSpace(rest);
+
+ for (int i = 0; i < pieces.size(); i++) {
+ if (columnOne) { seqName = pieces[i]; columnOne=false; }
+ else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
+
+ if (pairDone) {
+ setNamesOfGroups(seqGroup);
+
+ map<string, GroupIndex>::iterator itCheck = treemap.find(seqName);
+ if (itCheck != treemap.end()) { error = 1; m->mothurOut("[WARNING]: Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ namesOfSeqs.push_back(seqName);
+ treemap[seqName].groupname = seqGroup; //store data in map
+
+ it2 = seqsPerGroup.find(seqGroup);
+ if (it2 == seqsPerGroup.end()) { //if it's a new group
+ seqsPerGroup[seqGroup] = 1;
+ }else {//it's a group we already have
+ seqsPerGroup[seqGroup]++;
+ }
+ }
+ pairDone = false;
+ }
+ }
+ }
+
return error;
}
catch(exception& e) {