--- /dev/null
+/*
+ * deuniquetreecommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 5/27/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "deuniquetreecommand.h"
+#include "treereader.h"
+
+//**********************************************************************************************************************
+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);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string DeuniqueTreeCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The deunique.tree command parameters are tree and name. Both parameters are required unless you have valid current files.\n";
+ helpString += "The deunique.tree command should be in the following format: deunique.tree(tree=yourTreeFile, name=yourNameFile).\n";
+ helpString += "Example deunique.tree(tree=abrecovery.tree, name=abrecovery.names).\n";
+ helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreeFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DeuniqueTreeCommand::DeuniqueTreeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
+ exit(1);
+ }
+}
+/***********************************************************/
+DeuniqueTreeCommand::DeuniqueTreeCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("tree");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["tree"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+ }
+
+ //check for required parameters
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { abort = true; }
+ else if (treefile == "not found") { //if there is a current design file, use it
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setTreeFile(treefile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { abort = true; }
+ else if (namefile == "not found") { //if there is a current design file, use it
+ namefile = m->getNameFile();
+ if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current name file and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setNameFile(namefile); }
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(treefile); }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
+ exit(1);
+ }
+}
+
+/***********************************************************/
+int DeuniqueTreeCommand::execute() {
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ m->setTreeFile(treefile);
+
+ TreeReader* reader = new TreeReader(treefile, "", namefile);
+ vector<Tree*> T = reader->getTrees();
+ map<string, string> nameMap = reader->getNameMap();
+ delete reader;
+
+ //print new Tree
+ string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + "deunique.tre";
+ 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());
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }
+
+ //set phylip file as new current phylipfile
+ string current = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeuniqueTreeCommand", "execute");
+ exit(1);
+ }
+}
+/***********************************************************/
+
+
+
+
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