getgroupcommand.cpp

   1 /*
   2  *  getgroupcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 2/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getgroupcommand.h"
  11 #include "inputdata.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> GetgroupCommand::setParameters(){
  15         try {
  16                 CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none",false,true); parameters.push_back(pshared);
  17                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  18                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  19
  20                 vector<string> myArray;
  21                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  22                 return myArray;
  23         }
  24         catch(exception& e) {
  25                 m->errorOut(e, "GetgroupCommand", "setParameters");
  26                 exit(1);
  27         }
  28 }
  29 //**********************************************************************************************************************
  30 string GetgroupCommand::getHelpString(){
  31         try {
  32                 string helpString = "";
  33                 helpString += "The get.group command parameter is shared and it's required if you have no valid current file.\n";
  34                 //m->mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the consensus command.\n");
  35                 helpString += "You may not use any parameters with the get.group command.\n";
  36                 helpString += "The get.group command should be in the following format: \n";
  37                 helpString += "get.group()\n";
  38                 helpString += "Example get.group().\n";
  39                 return helpString;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "GetgroupCommand", "getHelpString");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 GetgroupCommand::GetgroupCommand(){
  48         try {
  49                 abort = true; calledHelp = true;
  50                 setParameters();
  51                 vector<string> tempOutNames;
  52                 outputTypes["bootgroup"] = tempOutNames;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 GetgroupCommand::GetgroupCommand(string option)  {
  61         try {
  62                 abort = false; calledHelp = false;
  63
  64                 //allow user to run help
  65                 if(option == "help") { help(); abort = true; calledHelp = true; }
  66                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  67
  68                 else {
  69                         vector<string> myArray = setParameters();
  70
  71                         OptionParser parser(option);
  72                         map<string,string> parameters = parser.getParameters();
  73                         map<string,string>::iterator it;
  74
  75                         ValidParameters validParameter;
  76                         //check to make sure all parameters are valid for command
  77                         for (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["bootgroup"] = 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("shared");
  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["shared"] = inputDir + it->second;           }
  96                                 }
  97                         }
  98
  99                         //get shared file
 100                         sharedfile = validParameter.validFile(parameters, "shared", true);
 101                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 102                         else if (sharedfile == "not found") {
 103                                 //if there is a current shared file, use it
 104                                 sharedfile = m->getSharedFile();
 105                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 106                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 107                         }else { m->setSharedFile(sharedfile); }
 108
 109
 110                         //if the user changes the output directory command factory will send this info to us in the output parameter
 111                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 112                 }
 113         }
 114         catch(exception& e) {
 115                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
 116                 exit(1);
 117         }
 118 }
 119 //**********************************************************************************************************************
 120
 121 int GetgroupCommand::execute(){
 122         try {
 123
 124                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 125
 126                 //open output file
 127                 outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
 128                 m->openOutputFile(outputFile, out);
 129
 130                 InputData input(sharedfile, "sharedfile");
 131                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 132
 133                 for (int i = 0; i < lookup.size(); i++) {
 134                         out << lookup[i]->getGroup() << '\t' << lookup[i]->getGroup() << endl;
 135                         m->mothurOut(lookup[i]->getGroup()); m->mothurOutEndLine();
 136                         delete lookup[i];
 137                 }
 138
 139                 out.close();
 140
 141                 if (m->control_pressed) {  m->mothurRemove(outputFile);   return 0; }
 142
 143                 m->mothurOutEndLine();
 144                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 145                 m->mothurOut(outputFile); m->mothurOutEndLine();        outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
 146                 m->mothurOutEndLine();
 147
 148                 return 0;
 149         }
 150
 151         catch(exception& e) {
 152                 m->errorOut(e, "GetgroupCommand", "execute");
 153                 exit(1);
 154         }
 155 }
 156
 157