getlabelcommand.cpp

   1 /*
   2  *  GetlabelCommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 1/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getlabelcommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14 vector<string> GetlabelCommand::setParameters(){
  15         try {
  16                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(plist);
  17                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(prabund);
  18                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(psabund);
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "GetlabelCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 GetlabelCommand::GetlabelCommand(){
  33         try {
  34                 abort = true; calledHelp = true;
  35                 setParameters();
  36         }
  37         catch(exception& e) {
  38                 m->errorOut(e, "GetlabelCommand", "CollectCommand");
  39                 exit(1);
  40         }
  41 }
  42 //**********************************************************************************************************************
  43 string GetlabelCommand::getHelpString(){
  44         try {
  45                 string helpString = "";
  46                 helpString += "The get.label command parameters are list, sabund and rabund file. \n";
  47                 helpString += "The get.label command should be in the following format: \n";
  48                 helpString += "get.label()\n";
  49                 helpString += "Example get.label().\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "GetlabelCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58
  59 GetlabelCommand::GetlabelCommand(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 (it = parameters.begin(); it != parameters.end(); it++) {
  78                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  79                         }
  80
  81                         //if the user changes the input directory command factory will send this info to us in the output parameter
  82                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  83                         if (inputDir == "not found"){   inputDir = "";          }
  84                         else {
  85                                 string path;
  86
  87                                 it = parameters.find("rabund");
  88                                 //user has given a template file
  89                                 if(it != parameters.end()){
  90                                         path = m->hasPath(it->second);
  91                                         //if the user has not given a path then, add inputdir. else leave path alone.
  92                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
  93                                 }
  94
  95                                 it = parameters.find("sabund");
  96                                 //user has given a template file
  97                                 if(it != parameters.end()){
  98                                         path = m->hasPath(it->second);
  99                                         //if the user has not given a path then, add inputdir. else leave path alone.
 100                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 101                                 }
 102
 103                                 it = parameters.find("list");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 109                                 }
 110                         }
 111
 112                         //check for required parameters
 113                         listfile = validParameter.validFile(parameters, "list", true);
 114                         if (listfile == "not open") { listfile = ""; abort = true; }
 115                         else if (listfile == "not found") { listfile = ""; }
 116                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 117
 118                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 119                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 120                         else if (sabundfile == "not found") { sabundfile = ""; }
 121                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 122
 123                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 124                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 125                         else if (rabundfile == "not found") { rabundfile = ""; }
 126                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 127
 128                         if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 129                                 //is there are current file available for any of these?
 130                                 //give priority to list, then rabund, then sabund
 131                                 //if there is a current shared file, use it
 132
 133                                 listfile = m->getListFile();
 134                                 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 135                                 else {
 136                                         rabundfile = m->getRabundFile();
 137                                         if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 138                                         else {
 139                                                 sabundfile = m->getSabundFile();
 140                                                 if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 141                                                 else {
 142                                                         m->mothurOut("No valid current files. You must provide a list, sabund or rabund file."); m->mothurOutEndLine();
 143                                                         abort = true;
 144                                                 }
 145                                         }
 146                                 }
 147                         }
 148                 }
 149
 150         }
 151         catch(exception& e) {
 152                 m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
 153                 exit(1);
 154         }
 155 }
 156 //**********************************************************************************************************************
 157
 158 int GetlabelCommand::execute(){
 159         try {
 160
 161                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 162
 163                 InputData* input = new InputData(inputfile, format);
 164                 OrderVector* order = input->getOrderVector();
 165                 string label = order->getLabel();
 166
 167                 while (order != NULL) {
 168
 169                         if (m->control_pressed) { delete input;  delete order; return 0; }
 170
 171                         label = order->getLabel();
 172
 173                         m->mothurOut(label); m->mothurOutEndLine();
 174
 175                         delete order;
 176                         order = input->getOrderVector();
 177                 }
 178
 179                 delete input;
 180
 181                 return 0;
 182         }
 183
 184         catch(exception& e) {
 185                 m->errorOut(e, "GetlabelCommand", "execute");
 186                 exit(1);
 187         }
 188 }
 189 //**********************************************************************************************************************
 190
 191