//**********************************************************************************************************************
vector<string> DeuniqueTreeCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","tree",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
}
}
//**********************************************************************************************************************
+string DeuniqueTreeCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "tree") { pattern = "[filename],deunique.tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
DeuniqueTreeCommand::DeuniqueTreeCommand(){
try {
abort = true; calledHelp = true;
TreeReader* reader = new TreeReader(treefile, "", namefile);
vector<Tree*> T = reader->getTrees();
- map<string, string> nameMap = reader->getNameMap();
+ map<string, string> nameMap;
+ m->readNames(namefile, nameMap);
delete reader;
//print new Tree
- string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + "deunique.tre";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ string outputFile = getOutputFileName("tree", variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
ofstream out;
m->openOutputFile(outputFile, out);
T[0]->print(out, nameMap);
out.close();
- delete (T[0]->getTreeMap());
+ delete (T[0]->getCountTable());
for (int i = 0; i < T.size(); i++) { delete T[i]; }
//set phylip file as new current phylipfile