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 string DeuniqueTreeCommand::getOutputFileNameTag(string type, string inputName=""){
  47         try {
  48         string outputFileName = "";
  49                 map<string, vector<string> >::iterator it;
  50
  51         //is this a type this command creates
  52         it = outputTypes.find(type);
  53         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  54         else {
  55             if (type == "tree") {  outputFileName =  "deunique.tre"; }
  56             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  57         }
  58         return outputFileName;
  59         }
  60         catch(exception& e) {
  61                 m->errorOut(e, "DeuniqueTreeCommand", "getOutputFileNameTag");
  62                 exit(1);
  63         }
  64 }
  65 //**********************************************************************************************************************
  66 DeuniqueTreeCommand::DeuniqueTreeCommand(){
  67         try {
  68                 abort = true; calledHelp = true;
  69                 setParameters();
  70                 vector<string> tempOutNames;
  71                 outputTypes["tree"] = tempOutNames;
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
  75                 exit(1);
  76         }
  77 }
  78 /***********************************************************/
  79 DeuniqueTreeCommand::DeuniqueTreeCommand(string option)  {
  80         try {
  81                 abort = false; calledHelp = false;
  82
  83                 //allow user to run help
  84                 if(option == "help") { help(); abort = true; calledHelp = true; }
  85                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  86
  87                 else {
  88                         vector<string> myArray = setParameters();
  89
  90                         OptionParser parser(option);
  91                         map<string,string> parameters = parser.getParameters();
  92                         map<string,string>::iterator it;
  93
  94                         ValidParameters validParameter;
  95
  96                         //check to make sure all parameters are valid for command
  97                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  98                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  99                         }
 100
 101                         //initialize outputTypes
 102                         vector<string> tempOutNames;
 103                         outputTypes["tree"] = tempOutNames;
 104
 105                         //if the user changes the input directory command factory will send this info to us in the output parameter
 106                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 107                         if (inputDir == "not found"){   inputDir = "";          }
 108                         else {
 109                                 string path;
 110                                 it = parameters.find("tree");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 116                                 }
 117
 118                                 it = parameters.find("name");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 124                                 }
 125                         }
 126
 127             //check for required parameters
 128                         treefile = validParameter.validFile(parameters, "tree", true);
 129                         if (treefile == "not open") { abort = true; }
 130                         else if (treefile == "not found") {                             //if there is a current design file, use it
 131                                 treefile = m->getTreeFile();
 132                                 if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 133                                 else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
 134                         }else { m->setTreeFile(treefile); }
 135
 136                         namefile = validParameter.validFile(parameters, "name", true);
 137                         if (namefile == "not open") { abort = true; }
 138                         else if (namefile == "not found") {                             //if there is a current design file, use it
 139                                 namefile = m->getNameFile();
 140                                 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 141                                 else {  m->mothurOut("You have no current name file and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
 142                         }else { m->setNameFile(namefile); }
 143
 144                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(treefile);       }
 145                 }
 146
 147         }
 148         catch(exception& e) {
 149                 m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
 150                 exit(1);
 151         }
 152 }
 153
 154 /***********************************************************/
 155 int DeuniqueTreeCommand::execute() {
 156         try {
 157
 158                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 159
 160                 m->setTreeFile(treefile);
 161
 162                 TreeReader* reader = new TreeReader(treefile, "", namefile);
 163         vector<Tree*> T = reader->getTrees();
 164         map<string, string> nameMap;
 165         m->readNames(namefile, nameMap);
 166         delete reader;
 167
 168                 //print new Tree
 169                 string outputFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
 170                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 171                 ofstream out;
 172                 m->openOutputFile(outputFile, out);
 173                 T[0]->print(out, nameMap);
 174                 out.close();
 175
 176         delete (T[0]->getCountTable());
 177                 for (int i = 0; i < T.size(); i++) { delete T[i]; }
 178
 179                 //set phylip file as new current phylipfile
 180                 string current = "";
 181                 itTypes = outputTypes.find("tree");
 182                 if (itTypes != outputTypes.end()) {
 183                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
 184                 }
 185
 186                 m->mothurOutEndLine();
 187                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 188                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 189                 m->mothurOutEndLine();
 190
 191                 return 0;
 192
 193         }
 194         catch(exception& e) {
 195                 m->errorOut(e, "DeuniqueTreeCommand", "execute");
 196                 exit(1);
 197         }
 198 }
 199 /***********************************************************/
 200
 201
 202
 203