numNodes = T->getNumNodes();
numLeaves = T->getNumLeaves();
- readTreeString();
+ readTreeString();
+
//save trees for later commands
globaldata->gTree.push_back(T);
gobble(filehandle);
numLeaves = T->getNumLeaves();
//read tree info
- readTreeString();
+ readTreeString();
+
//save trees for later commands
globaldata->gTree.push_back(T);
}
}
-
}
catch(exception& e) {
cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
//adds sequence names that are not in group file to the "xxx" group
if(n1 == -1) {
- cerr << "Name: " << name << " not found in your groupfile and it will be ignored. \n";
- globaldata->gTreemap->namesOfSeqs.push_back(name);
- globaldata->gTreemap->treemap[name].groupname = "xxx";
- globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
+ cerr << "Name: " << name << " not found in your groupfile.. \n"; exit(1);
- map<string, int>::iterator it;
- it = globaldata->gTreemap->seqsPerGroup.find("xxx");
- if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
- globaldata->gTreemap->namesOfGroups.push_back("xxx");
- globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
- }else {
- globaldata->gTreemap->seqsPerGroup["xxx"]++;
- }
+ //globaldata->gTreemap->namesOfSeqs.push_back(name);
+ //globaldata->gTreemap->treemap[name].groupname = "xxx";
+ //globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
+
+ //map<string, int>::iterator it;
+ //it = globaldata->gTreemap->seqsPerGroup.find("xxx");
+ //if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
+ // globaldata->gTreemap->namesOfGroups.push_back("xxx");
+ // globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
+ //}else {
+ // globaldata->gTreemap->seqsPerGroup["xxx"]++;
+ //}
//find index in tree of name
- n1 = T->getIndex(name);
- group = "xxx";
+ //n1 = T->getIndex(name);
+ //group = "xxx";
+ //numLeaves++;
+ //numNodes = 2*numLeaves - 1;
}
T->tree[n1].setGroup(group);
-
T->tree[n1].setChildren(-1,-1);
if(blen == 1){