deuniquetreecommand.cpp

   1 /*
   2  *  deuniquetreecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/27/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "deuniquetreecommand.h"
  11 #include "treereader.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> DeuniqueTreeCommand::setParameters(){
  15         try {
  16                 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  19                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  20
  21                 vector<string> myArray;
  22                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  23                 return myArray;
  24         }
  25         catch(exception& e) {
  26                 m->errorOut(e, "DeuniqueTreeCommand", "setParameters");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 string DeuniqueTreeCommand::getHelpString(){
  32         try {
  33                 string helpString = "";
  34                 helpString += "The deunique.tree command parameters are tree and name.  Both parameters are required unless you have valid current files.\n";
  35                 helpString += "The deunique.tree command should be in the following format: deunique.tree(tree=yourTreeFile, name=yourNameFile).\n";
  36                 helpString += "Example deunique.tree(tree=abrecovery.tree, name=abrecovery.names).\n";
  37                 helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreeFile).\n";
  38                 return helpString;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "DeuniqueTreeCommand", "getHelpString");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 DeuniqueTreeCommand::DeuniqueTreeCommand(){
  47         try {
  48                 abort = true; calledHelp = true;
  49                 setParameters();
  50                 vector<string> tempOutNames;
  51                 outputTypes["tree"] = tempOutNames;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
  55                 exit(1);
  56         }
  57 }
  58 /***********************************************************/
  59 DeuniqueTreeCommand::DeuniqueTreeCommand(string option)  {
  60         try {
  61                 abort = false; calledHelp = false;
  62
  63                 //allow user to run help
  64                 if(option == "help") { help(); abort = true; calledHelp = true; }
  65                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  66
  67                 else {
  68                         vector<string> myArray = setParameters();
  69
  70                         OptionParser parser(option);
  71                         map<string,string> parameters = parser.getParameters();
  72                         map<string,string>::iterator it;
  73
  74                         ValidParameters validParameter;
  75
  76                         //check to make sure all parameters are valid for command
  77                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  78                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  79                         }
  80
  81                         //initialize outputTypes
  82                         vector<string> tempOutNames;
  83                         outputTypes["tree"] = tempOutNames;
  84
  85                         //if the user changes the input directory command factory will send this info to us in the output parameter
  86                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  87                         if (inputDir == "not found"){   inputDir = "";          }
  88                         else {
  89                                 string path;
  90                                 it = parameters.find("tree");
  91                                 //user has given a template file
  92                                 if(it != parameters.end()){
  93                                         path = m->hasPath(it->second);
  94                                         //if the user has not given a path then, add inputdir. else leave path alone.
  95                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
  96                                 }
  97
  98                                 it = parameters.find("name");
  99                                 //user has given a template file
 100                                 if(it != parameters.end()){
 101                                         path = m->hasPath(it->second);
 102                                         //if the user has not given a path then, add inputdir. else leave path alone.
 103                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 104                                 }
 105                         }
 106
 107             //check for required parameters
 108                         treefile = validParameter.validFile(parameters, "tree", true);
 109                         if (treefile == "not open") { abort = true; }
 110                         else if (treefile == "not found") {                             //if there is a current design file, use it
 111                                 treefile = m->getTreeFile();
 112                                 if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 113                                 else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
 114                         }else { m->setTreeFile(treefile); }
 115
 116                         namefile = validParameter.validFile(parameters, "name", true);
 117                         if (namefile == "not open") { abort = true; }
 118                         else if (namefile == "not found") {                             //if there is a current design file, use it
 119                                 namefile = m->getNameFile();
 120                                 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 121                                 else {  m->mothurOut("You have no current name file and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
 122                         }else { m->setNameFile(namefile); }
 123
 124                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(treefile);       }
 125                 }
 126
 127         }
 128         catch(exception& e) {
 129                 m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
 130                 exit(1);
 131         }
 132 }
 133
 134 /***********************************************************/
 135 int DeuniqueTreeCommand::execute() {
 136         try {
 137
 138                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 139
 140                 m->setTreeFile(treefile);
 141
 142                 TreeReader* reader = new TreeReader(treefile, "", namefile);
 143         vector<Tree*> T = reader->getTrees();
 144         map<string, string> nameMap = reader->getNameMap();
 145         delete reader;
 146
 147                 //print new Tree
 148                 string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + "deunique.tre";
 149                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 150                 ofstream out;
 151                 m->openOutputFile(outputFile, out);
 152                 T[0]->print(out, nameMap);
 153                 out.close();
 154
 155         delete (T[0]->getTreeMap());
 156                 for (int i = 0; i < T.size(); i++) { delete T[i]; }
 157
 158                 //set phylip file as new current phylipfile
 159                 string current = "";
 160                 itTypes = outputTypes.find("tree");
 161                 if (itTypes != outputTypes.end()) {
 162                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
 163                 }
 164
 165                 m->mothurOutEndLine();
 166                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 167                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 168                 m->mothurOutEndLine();
 169
 170                 return 0;
 171
 172         }
 173         catch(exception& e) {
 174                 m->errorOut(e, "DeuniqueTreeCommand", "execute");
 175                 exit(1);
 176         }
 177 }
 178 /***********************************************************/
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