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 string GetSAbundCommand::getOutputFileNameTag(string type, string inputName=""){
  50         try {
  51         string outputFileName = "";
  52                 map<string, vector<string> >::iterator it;
  53
  54         //is this a type this command creates
  55         it = outputTypes.find(type);
  56         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  57         else {
  58             if (type == "sabund")            {   outputFileName = "sabund";  }
  59             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  60         }
  61         return outputFileName;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "GetSAbundCommand", "getOutputFileNameTag");
  65                 exit(1);
  66         }
  67 }
  68 //**********************************************************************************************************************
  69 GetSAbundCommand::GetSAbundCommand(){
  70         try {
  71                 abort = true; calledHelp = true;
  72                 setParameters();
  73                 vector<string> tempOutNames;
  74                 outputTypes["sabund"] = tempOutNames;
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82 GetSAbundCommand::GetSAbundCommand(string option)  {
  83         try {
  84                 abort = false; calledHelp = false;
  85                 allLines = 1;
  86
  87                 //allow user to run help
  88                 if(option == "help") { help(); abort = true; calledHelp = true; }
  89                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  90
  91                 else {
  92                         vector<string> myArray = setParameters();
  93
  94                         OptionParser parser(option);
  95                         map<string,string> parameters = parser.getParameters();
  96                         map<string,string>::iterator it;
  97
  98                         ValidParameters validParameter;
  99
 100                         //check to make sure all parameters are valid for command
 101                         for (it = parameters.begin(); it != parameters.end(); it++) {
 102                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 103                         }
 104
 105                         //initialize outputTypes
 106                         vector<string> tempOutNames;
 107                         outputTypes["sabund"] = tempOutNames;
 108
 109                         //if the user changes the input directory command factory will send this info to us in the output parameter
 110                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 111                         if (inputDir == "not found"){   inputDir = "";          }
 112                         else {
 113                                 string path;
 114                                 it = parameters.find("list");
 115                                 //user has given a template file
 116                                 if(it != parameters.end()){
 117                                         path = m->hasPath(it->second);
 118                                         //if the user has not given a path then, add inputdir. else leave path alone.
 119                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 120                                 }
 121
 122                                 it = parameters.find("rabund");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 128                                 }
 129                         }
 130
 131
 132                         //check for required parameters
 133                         listfile = validParameter.validFile(parameters, "list", true);
 134                         if (listfile == "not open") { listfile = ""; abort = true; }
 135                         else if (listfile == "not found") { listfile = ""; }
 136                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 137
 138                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 139                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 140                         else if (rabundfile == "not found") { rabundfile = ""; }
 141                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 142
 143
 144                                                 //check for optional parameter and set defaults
 145                         // ...at some point should added some additional type checking...
 146                         label = validParameter.validFile(parameters, "label", false);
 147                         if (label == "not found") { label = ""; }
 148                         else {
 149                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 150                                 else { allLines = 1;  }
 151                         }
 152
 153                         if ((listfile == "") && (rabundfile == "")) {
 154                                 //is there are current file available for any of these?
 155                                 //give priority to shared, then list, then rabund, then sabund
 156                                 //if there is a current shared file, use it
 157                                 listfile = m->getListFile();
 158                                 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 159                                 else {
 160                                         rabundfile = m->getRabundFile();
 161                                         if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 162                                         else {
 163                                                 m->mothurOut("No valid current files. You must provide a list or rabund file."); m->mothurOutEndLine();
 164                                                 abort = true;
 165                                         }
 166                                 }
 167                         }
 168
 169
 170                         //if the user changes the output directory command factory will send this info to us in the output parameter
 171                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);      }
 172
 173
 174                 }
 175
 176         }
 177         catch(exception& e) {
 178                 m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
 179                 exit(1);
 180         }
 181 }
 182 //**********************************************************************************************************************
 183
 184 int GetSAbundCommand::execute(){
 185         try {
 186
 187                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 188                 filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("sabund");
 189                 m->openOutputFile(filename, out);
 190
 191                 input = new InputData(inputfile, format);
 192                 sabund = input->getSAbundVector();
 193                 string lastLabel = sabund->getLabel();
 194
 195
 196                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 197                 set<string> processedLabels;
 198                 set<string> userLabels = labels;
 199
 200                 if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input; return 0; }
 201
 202
 203                 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 204
 205                         if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 206                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 207
 208                                         sabund->print(out);
 209
 210                                 if (m->control_pressed) { outputTypes.clear();  out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 211
 212                                         processedLabels.insert(sabund->getLabel());
 213                                         userLabels.erase(sabund->getLabel());
 214                         }
 215
 216                         if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 217                                         string saveLabel = sabund->getLabel();
 218
 219                                         delete sabund;
 220                                         sabund = (input->getSAbundVector(lastLabel));
 221
 222                                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 223                                         sabund->print(out);
 224
 225                                         if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 226
 227                                         processedLabels.insert(sabund->getLabel());
 228                                         userLabels.erase(sabund->getLabel());
 229
 230                                         //restore real lastlabel to save below
 231                                         sabund->setLabel(saveLabel);
 232                         }
 233
 234
 235                         lastLabel = sabund->getLabel();
 236
 237                         delete sabund;
 238                         sabund = (input->getSAbundVector());
 239                 }
 240
 241                 //output error messages about any remaining user labels
 242                 set<string>::iterator it;
 243                 bool needToRun = false;
 244                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 245                         m->mothurOut("Your file does not include the label " + *it);
 246                         if (processedLabels.count(lastLabel) != 1) {
 247                                 m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 248                                 needToRun = true;
 249                         }else {
 250                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 251                         }
 252                 }
 253
 254                 //run last label if you need to
 255                 if (needToRun == true)  {
 256                         if (sabund != NULL) {   delete sabund;  }
 257                         sabund = (input->getSAbundVector(lastLabel));
 258
 259                         m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
 260                         sabund->print(out);
 261                         delete sabund;
 262
 263                         if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; return 0; }
 264
 265                 }
 266
 267                 out.close();
 268                 delete input;
 269
 270                 m->mothurOutEndLine();
 271                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 272                 m->mothurOut(filename); m->mothurOutEndLine();  outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
 273                 m->mothurOutEndLine();
 274
 275                 //set sabund file as new current sabundfile
 276                 string current = "";
 277                 itTypes = outputTypes.find("sabund");
 278                 if (itTypes != outputTypes.end()) {
 279                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
 280                 }
 281
 282                 return 0;
 283         }
 284
 285         catch(exception& e) {
 286                 m->errorOut(e, "GetSAbundCommand", "execute");
 287                 exit(1);
 288         }
 289 }
 290
 291 //**********************************************************************************************************************
 292
 293