groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true; }
- else {
+ else if (groupfile == "not found") {
+ groupfile = "";
+
+ m->mothurOut("You have not provided a group file. I am assumming all sequence are from the same group."); m->mothurOutEndLine();
+
+ if (treefile != "") { Tree* tree = new Tree(treefile); delete tree; } //extracts names from tree to make faked out groupmap
+
+ globaldata->setGroupFile(groupfile);
+ //read in group map info.
+ treeMap = new TreeMap();
+ for (int i = 0; i < globaldata->Treenames.size(); i++) { treeMap->addSeq(globaldata->Treenames[i], "Group1"); }
+ globaldata->gTreemap = treeMap;
+
+ }else {
globaldata->setGroupFile(groupfile);
//read in group map info.
treeMap = new TreeMap(groupfile);
T[i]->assembleTree();
}
+
+ //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
+ int numNamesInTree;
+ if (namefile != "") {
+ if (numUniquesInName == globaldata->Treenames.size()) { numNamesInTree = nameMap.size(); }
+ else { numNamesInTree = globaldata->Treenames.size(); }
+ }else { numNamesInTree = globaldata->Treenames.size(); }
+
+
//output any names that are in group file but not in tree
- if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
+ if (numNamesInTree < treeMap->getNumSeqs()) {
for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
//is that name in the tree?
int count = 0;
globaldata->gTreemap = treeMap;
}
-
+
return 0;
}
catch(exception& e) {
int ReadTreeCommand::readNamesFile() {
try {
globaldata->names.clear();
+ numUniquesInName = 0;
ifstream in;
m->openInputFile(namefile, in);
while(!in.eof()) {
in >> first >> second; m->gobble(in);
+ numUniquesInName++;
+
itNames = globaldata->names.find(first);
if (itNames == globaldata->names.end()) {
globaldata->names[first] = second;
vector<string> dupNames;
m->splitAtComma(second, dupNames);
- for (int i = 0; i < dupNames.size(); i++) { nameMap[dupNames[i]] = dupNames[i]; }
- }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }
+ for (int i = 0; i < dupNames.size(); i++) { nameMap[dupNames[i]] = dupNames[i]; if ((groupfile == "") && (i != 0)) { globaldata->gTreemap->addSeq(dupNames[i], "Group1"); } }
+ }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); namefile = ""; return 1; }
}
in.close();