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