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); parameters.push_back(plist);
  17                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
  18                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
  19                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  20                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  21                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  22
  23                 vector<string> myArray;
  24                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  25                 return myArray;
  26         }
  27         catch(exception& e) {
  28                 m->errorOut(e, "GetlabelCommand", "setParameters");
  29                 exit(1);
  30         }
  31 }
  32 //**********************************************************************************************************************
  33 GetlabelCommand::GetlabelCommand(){
  34         try {
  35                 abort = true; calledHelp = true;
  36                 setParameters();
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "GetlabelCommand", "CollectCommand");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 string GetlabelCommand::getHelpString(){
  45         try {
  46                 string helpString = "";
  47                 helpString += "The get.label command parameters are list, sabund, rabund and shared file. \n";
  48                 helpString += "The get.label command should be in the following format: \n";
  49                 helpString += "get.label()\n";
  50                 helpString += "Example get.label().\n";
  51                 return helpString;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "GetlabelCommand", "getHelpString");
  55                 exit(1);
  56         }
  57 }
  58 //**********************************************************************************************************************
  59
  60 GetlabelCommand::GetlabelCommand(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
  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                                 it = parameters.find("shared");
  87                                 //user has given a template file
  88                                 if(it != parameters.end()){
  89                                         path = m->hasPath(it->second);
  90                                         //if the user has not given a path then, add inputdir. else leave path alone.
  91                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
  92                                 }
  93
  94                                 it = parameters.find("rabund");
  95                                 //user has given a template file
  96                                 if(it != parameters.end()){
  97                                         path = m->hasPath(it->second);
  98                                         //if the user has not given a path then, add inputdir. else leave path alone.
  99                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 100                                 }
 101
 102                                 it = parameters.find("sabund");
 103                                 //user has given a template file
 104                                 if(it != parameters.end()){
 105                                         path = m->hasPath(it->second);
 106                                         //if the user has not given a path then, add inputdir. else leave path alone.
 107                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 108                                 }
 109
 110                                 it = parameters.find("list");
 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["list"] = inputDir + it->second;             }
 116                                 }
 117                         }
 118
 119                         //check for required parameters
 120                         listfile = validParameter.validFile(parameters, "list", true);
 121                         if (listfile == "not open") { listfile = ""; abort = true; }
 122                         else if (listfile == "not found") { listfile = ""; }
 123                         else {  format = "list"; inputfile = listfile; }
 124
 125                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 126                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 127                         else if (sabundfile == "not found") { sabundfile = ""; }
 128                         else {  format = "sabund"; inputfile = sabundfile; }
 129
 130                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 131                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 132                         else if (rabundfile == "not found") { rabundfile = ""; }
 133                         else {  format = "rabund"; inputfile = rabundfile; }
 134
 135                         sharedfile = validParameter.validFile(parameters, "shared", true);
 136                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 137                         else if (sharedfile == "not found") { sharedfile = ""; }
 138                         else {  format = "sharedfile"; inputfile = sharedfile; }
 139
 140                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
 141                                 //is there are current file available for any of these?
 142                                 //give priority to shared, then list, then rabund, then sabund
 143                                 //if there is a current shared file, use it
 144                                 sharedfile = m->getSharedFile();
 145                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 146                                 else {
 147                                         listfile = m->getListFile();
 148                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 149                                         else {
 150                                                 rabundfile = m->getRabundFile();
 151                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 152                                                 else {
 153                                                         sabundfile = m->getSabundFile();
 154                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 155                                                         else {
 156                                                                 m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine();
 157                                                                 abort = true;
 158                                                         }
 159                                                 }
 160                                         }
 161                                 }
 162                         }
 163
 164                 }
 165
 166         }
 167         catch(exception& e) {
 168                 m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
 169                 exit(1);
 170         }
 171 }
 172 //**********************************************************************************************************************
 173
 174 int GetlabelCommand::execute(){
 175         try {
 176
 177                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 178
 179                 InputData* input = new InputData(inputfile, format);
 180                 OrderVector* order = input->getOrderVector();
 181                 string label = order->getLabel();
 182
 183                 while (order != NULL) {
 184
 185                         if (m->control_pressed) { delete input;  delete order; return 0; }
 186
 187                         m->mothurOut(label); m->mothurOutEndLine();
 188
 189                         label = order->getLabel();
 190
 191                         delete order;
 192                         order = input->getOrderVector();
 193                 }
 194
 195                 delete input;
 196
 197                 return 0;
 198         }
 199
 200         catch(exception& e) {
 201                 m->errorOut(e, "GetlabelCommand", "execute");
 202                 exit(1);
 203         }
 204 }
 205 //**********************************************************************************************************************
 206
 207