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, 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                 helpString += "You may not use any parameters with the get.group command.\n";
  35                 helpString += "The get.group command should be in the following format: \n";
  36                 helpString += "get.group()\n";
  37                 helpString += "Example get.group().\n";
  38                 return helpString;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "GetgroupCommand", "getHelpString");
  42                 exit(1);
  43         }
  44 }
  45
  46 //**********************************************************************************************************************
  47 GetgroupCommand::GetgroupCommand(){
  48         try {
  49                 abort = true; calledHelp = true;
  50                 setParameters();
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 GetgroupCommand::GetgroupCommand(string option)  {
  59         try {
  60                 abort = false; calledHelp = false;
  61
  62                 //allow user to run help
  63                 if(option == "help") { help(); abort = true; calledHelp = true; }
  64                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  65
  66                 else {
  67                         vector<string> myArray = setParameters();
  68
  69                         OptionParser parser(option);
  70                         map<string,string> parameters = parser.getParameters();
  71                         map<string,string>::iterator it;
  72
  73                         ValidParameters validParameter;
  74                         //check to make sure all parameters are valid for command
  75                         for (it = parameters.begin(); it != parameters.end(); it++) {
  76                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  77                         }
  78
  79                         //if the user changes the input directory command factory will send this info to us in the output parameter
  80                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  81                         if (inputDir == "not found"){   inputDir = "";          }
  82                         else {
  83                                 string path;
  84                                 it = parameters.find("shared");
  85                                 //user has given a template file
  86                                 if(it != parameters.end()){
  87                                         path = m->hasPath(it->second);
  88                                         //if the user has not given a path then, add inputdir. else leave path alone.
  89                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
  90                                 }
  91                         }
  92
  93                         //get shared file
  94                         sharedfile = validParameter.validFile(parameters, "shared", true);
  95                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
  96                         else if (sharedfile == "not found") {
  97                                 //if there is a current shared file, use it
  98                                 sharedfile = m->getSharedFile();
  99                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 100                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 101                         }else { m->setSharedFile(sharedfile); }
 102
 103
 104                         //if the user changes the output directory command factory will send this info to us in the output parameter
 105                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(sharedfile);             }
 106                 }
 107         }
 108         catch(exception& e) {
 109                 m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
 110                 exit(1);
 111         }
 112 }
 113 //**********************************************************************************************************************
 114
 115 int GetgroupCommand::execute(){
 116         try {
 117
 118                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 119
 120                 InputData input(sharedfile, "sharedfile");
 121                 vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
 122
 123                 for (int i = 0; i < lookup.size(); i++) {
 124                         m->mothurOut(lookup[i]->getGroup()); m->mothurOutEndLine();
 125                         delete lookup[i];
 126                 }
 127
 128                 m->mothurOutEndLine();
 129                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 130                 m->mothurOutEndLine();
 131
 132                 return 0;
 133         }
 134
 135         catch(exception& e) {
 136                 m->errorOut(e, "GetgroupCommand", "execute");
 137                 exit(1);
 138         }
 139 }
 140 //**********************************************************************************************************************
 141
 142