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/*
* 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","tree",false,true,true); parameters.push_back(ptree);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
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";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "DeuniqueTreeCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
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->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "DeuniqueTreeCommand", "getOutputPattern");
exit(1);
}
}
/***********************************************************/
DeuniqueTreeCommand::DeuniqueTreeCommand(string option) : Command() {
try {
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
treefile = validParameter.validFile(parameters, "tree");
if (treefile == "not open") { abort = true; }
else if (treefile == "not found") { //if there is a current design file, use it
treefile = current->getTreeFile();
if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter.\n"); }
else { m->mothurOut("You have no current tree file and the tree parameter is required.\n"); abort = true; }
}else { current->setTreeFile(treefile); }
namefile = validParameter.validFile(parameters, "name");
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { //if there is a current design file, use it
namefile = current->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter.\n"); }
else { m->mothurOut("You have no current name file and the name parameter is required.\n"); abort = true; }
}else { current->setNameFile(namefile); }
if (outputdir == ""){ outputdir = util.hasPath(treefile); }
}
}
catch(exception& e) {
m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
exit(1);
}
}
/***********************************************************/
int DeuniqueTreeCommand::execute() {
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
current->setTreeFile(treefile);
TreeReader* reader = new TreeReader(treefile, "", namefile);
vector<Tree*> T = reader->getTrees();
map<string, string> nameMap;
util.readNames(namefile, nameMap);
delete reader;
//print new Tree
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(treefile));
string outputFile = getOutputFileName("tree", variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
ofstream out;
util.openOutputFile(outputFile, out);
T[0]->print(out, nameMap);
out.close();
delete (T[0]->getCountTable());
for (int i = 0; i < T.size(); i++) { delete T[i]; }
//set phylip file as new current phylipfile
string currentName = "";
itTypes = outputTypes.find("tree");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setTreeFile(currentName); }
}
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "DeuniqueTreeCommand", "execute");
exit(1);
}
}
/***********************************************************/
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