+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);
+ it = groupmap.find(seqName);
+
+ if (it != groupmap.end()) { error = 1; m->mothurOut("Your group file contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
+ pairDone = false;
+ }
+ }
+ }
+
+ m->setAllGroups(namesOfGroups);
+ return error;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "readMap");
+ exit(1);
+ }
+}
+/************************************************************/
+int GroupMap::readDesignMap(string filename) {
+ try {
+ groupFileName = filename;
+ m->openInputFile(filename, fileHandle);
+ index = 0;
+ string seqName, seqGroup;
+ int error = 0;
+ string rest = "";
+ char buffer[4096];
+ bool pairDone = false;
+ bool columnOne = true;
+
+ while (!fileHandle.eof()) {
+ if (m->control_pressed) { fileHandle.close(); return 1; }
+
+ fileHandle.read(buffer, 4096);
+ vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
+
+ 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);
+
+ if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
+ m->checkName(seqName);