getsabundcommand.cpp

   1 /*
   2  *  getsabundcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getsabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> GetSAbundCommand::setParameters(){
  14         try {
  15                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
  16                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
  17                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  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, "GetSAbundCommand", "setParameters");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 string GetSAbundCommand::getHelpString(){
  32         try {
  33                 string helpString = "";
  34                 helpString += "The get.sabund command parameters is list, rabund and label.  list or rabund is required unless a valid current file exists.\n";
  35                 helpString += "The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n";
  36                 helpString += "The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n";
  37                 helpString += "Example get.sabund().\n";
  38                 helpString += "The default value for label is all labels in your inputfile.\n";
  39                 helpString += "The get.sabund command outputs a .sabund file containing the labels you selected.\n";
  40                 helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n";
  41                 return helpString;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "GetSAbundCommand", "getHelpString");
  45                 exit(1);
  46         }
  47 }
  48
  49 //**********************************************************************************************************************
  50 GetSAbundCommand::GetSAbundCommand(){
  51         try {
  52                 abort = true; calledHelp = true;
  53                 setParameters();
  54                 vector<string> tempOutNames;
  55                 outputTypes["sabund"] = tempOutNames;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63 GetSAbundCommand::GetSAbundCommand(string option)  {
  64         try {
  65                 abort = false; calledHelp = false;
  66                 allLines = 1;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; calledHelp = true; }
  70                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  71
  72                 else {
  73                         vector<string> myArray = setParameters();
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77                         map<string,string>::iterator it;
  78
  79                         ValidParameters validParameter;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //initialize outputTypes
  87                         vector<string> tempOutNames;
  88                         outputTypes["sabund"] = tempOutNames;
  89
  90                         //if the user changes the input directory command factory will send this info to us in the output parameter
  91                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  92                         if (inputDir == "not found"){   inputDir = "";          }
  93                         else {
  94                                 string path;
  95                                 it = parameters.find("list");
  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["list"] = inputDir + it->second;             }
 101                                 }
 102
 103                                 it = parameters.find("rabund");
 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["rabund"] = inputDir + it->second;           }
 109                                 }
 110                         }
 111
 112
 113                         //check for required parameters
 114                         listfile = validParameter.validFile(parameters, "list", true);
 115                         if (listfile == "not open") { listfile = ""; abort = true; }
 116                         else if (listfile == "not found") { listfile = ""; }
 117                         else {  format = "list"; inputfile = listfile; }
 118
 119                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 120                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 121                         else if (rabundfile == "not found") { rabundfile = ""; }
 122                         else {  format = "rabund"; inputfile = rabundfile; }
 123
 124
 125                                                 //check for optional parameter and set defaults
 126                         // ...at some point should added some additional type checking...
 127                         label = validParameter.validFile(parameters, "label", false);
 128                         if (label == "not found") { label = ""; }
 129                         else {
 130                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 131                                 else { allLines = 1;  }
 132                         }
 133
 134                         if ((listfile == "") && (rabundfile == "")) {
 135                                 //is there are current file available for any of these?
 136                                 //give priority to shared, then list, then rabund, then sabund
 137                                 //if there is a current shared file, use it
 138                                 listfile = m->getListFile();
 139                                 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 140                                 else {
 141                                         rabundfile = m->getRabundFile();
 142                                         if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 143                                         else {
 144                                                 m->mothurOut("No valid current files. You must provide a list or rabund file."); m->mothurOutEndLine();
 145                                                 abort = true;
 146                                         }
 147                                 }
 148                         }
 149
 150
 151                         //if the user changes the output directory command factory will send this info to us in the output parameter
 152                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);      }
 153
 154
 155                 }
 156
 157         }
 158         catch(exception& e) {
 159                 m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
 160                 exit(1);
 161         }
 162 }
 163 //**********************************************************************************************************************
 164
 165 int GetSAbundCommand::execute(){
 166         try {
 167
 168                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 169                 filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "sabund";
 170                 m->openOutputFile(filename, out);
 171
 172                 input = new InputData(inputfile, format);
 173                 sabund = input->getSAbundVector();
 174                 string lastLabel = sabund->getLabel();
 175
 176
 177                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 178                 set<string> processedLabels;
 179                 set<string> userLabels = labels;
 180
 181                 if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input; return 0; }
 182
 183
 184                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 185
 186                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 187                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 188
 189                                         sabund->print(out);
 190
 191                                 if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
 192
 193                                         processedLabels.insert(sabund->getLabel());
 194                                         userLabels.erase(sabund->getLabel());
 195                         }
 196
 197                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 198                                         string saveLabel = sabund->getLabel();
 199
 200                                         delete sabund;
 201                                         sabund = (input->getSAbundVector(lastLabel));
 202
 203                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 204                                         sabund->print(out);
 205
 206                                         if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
 207
 208                                         processedLabels.insert(sabund->getLabel());
 209                                         userLabels.erase(sabund->getLabel());
 210
 211                                         //restore real lastlabel to save below
 212                                         sabund->setLabel(saveLabel);
 213                         }
 214
 215
 216                         lastLabel = sabund->getLabel();
 217
 218                         delete sabund;
 219                         sabund = (input->getSAbundVector());
 220                 }
 221
 222                 //output error messages about any remaining user labels
 223                 set<string>::iterator it;
 224                 bool needToRun = false;
 225                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 226                         m->mothurOut("Your file does not include the label " + *it);
 227                         if (processedLabels.count(lastLabel) != 1) {
 228                                 m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 229                                 needToRun = true;
 230                         }else {
 231                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 232                         }
 233                 }
 234
 235                 //run last label if you need to
 236                 if (needToRun == true)  {
 237                         if (sabund != NULL) {   delete sabund;  }
 238                         sabund = (input->getSAbundVector(lastLabel));
 239
 240                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 241                         sabund->print(out);
 242                         delete sabund;
 243
 244                         if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; return 0; }
 245
 246                 }
 247
 248                 out.close();
 249                 delete input;
 250
 251                 m->mothurOutEndLine();
 252                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 253                 m->mothurOut(filename); m->mothurOutEndLine();  outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
 254                 m->mothurOutEndLine();
 255
 256                 //set sabund file as new current sabundfile
 257                 string current = "";
 258                 itTypes = outputTypes.find("sabund");
 259                 if (itTypes != outputTypes.end()) {
 260                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 261                 }
 262
 263                 return 0;
 264         }
 265
 266         catch(exception& e) {
 267                 m->errorOut(e, "GetSAbundCommand", "execute");
 268                 exit(1);
 269         }
 270 }
 271
 272 //**********************************************************************************************************************
 273
 274