+++ /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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