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::getValidParameters(){
  14         try {
  15                 string Array[] =  {"label","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "GetSAbundCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 GetSAbundCommand::GetSAbundCommand(){
  26         try {
  27                 //initialize outputTypes
  28                 vector<string> tempOutNames;
  29                 outputTypes["sabund"] = tempOutNames;
  30         }
  31         catch(exception& e) {
  32                 m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37 vector<string> GetSAbundCommand::getRequiredParameters(){
  38         try {
  39                 vector<string> myArray;
  40                 return myArray;
  41         }
  42         catch(exception& e) {
  43                 m->errorOut(e, "GetSAbundCommand", "getRequiredParameters");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48 vector<string> GetSAbundCommand::getRequiredFiles(){
  49         try {
  50                 string Array[] =  {"list","rabund"};
  51                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  52                 return myArray;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "GetSAbundCommand", "getRequiredFiles");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 GetSAbundCommand::GetSAbundCommand(string option)  {
  61         try {
  62                 globaldata = GlobalData::getInstance();
  63                 abort = false;
  64                 allLines = 1;
  65                 labels.clear();
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; }
  69
  70                 else {
  71                         //valid paramters for this command
  72                         string Array[] =  {"label","outputdir","inputdir"};
  73                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter;
  79
  80                         //check to make sure all parameters are valid for command
  81                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  82                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  83                         }
  84
  85                         //initialize outputTypes
  86                         vector<string> tempOutNames;
  87                         outputTypes["sabund"] = tempOutNames;
  88
  89                         //if the user changes the output directory command factory will send this info to us in the output parameter
  90                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){
  91                                 outputDir = "";
  92                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  93                         }
  94
  95                         //make sure the user has already run the read.otu command
  96                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { m->mothurOut("You must read a list or rabund before you can use the get.sabund command."); m->mothurOutEndLine(); abort = true; }
  97
  98                         //check for optional parameter and set defaults
  99                         // ...at some point should added some additional type checking...
 100                         label = validParameter.validFile(parameters, "label", false);
 101                         if (label == "not found") { label = ""; }
 102                         else {
 103                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 104                                 else { allLines = 1;  }
 105                         }
 106
 107                         //if the user has not specified any labels use the ones from read.otu
 108                         if(label == "") {
 109                                 allLines = globaldata->allLines;
 110                                 labels = globaldata->labels;
 111                         }
 112
 113                         if (abort == false) {
 114                                 filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund";
 115                                 m->openOutputFile(filename, out);
 116                         }
 117                 }
 118
 119         }
 120         catch(exception& e) {
 121                 m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
 122                 exit(1);
 123         }
 124 }
 125 //**********************************************************************************************************************
 126
 127 void GetSAbundCommand::help(){
 128         try {
 129                 m->mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
 130                 m->mothurOut("The get.sabund command parameters is label.  No parameters are required.\n");
 131                 m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n");
 132                 m->mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n");
 133                 m->mothurOut("Example get.sabund().\n");
 134                 m->mothurOut("The default value for label is all labels in your inputfile.\n");
 135                 m->mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
 136                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
 137         }
 138         catch(exception& e) {
 139                 m->errorOut(e, "GetSAbundCommand", "help");
 140                 exit(1);
 141         }
 142 }
 143
 144 //**********************************************************************************************************************
 145
 146 GetSAbundCommand::~GetSAbundCommand(){
 147 }
 148
 149 //**********************************************************************************************************************
 150
 151 int GetSAbundCommand::execute(){
 152         try {
 153
 154                 if (abort == true) { return 0; }
 155
 156                 //using order vector so you don't have to distinguish between the list and rabund files
 157                 read = new ReadOTUFile(globaldata->inputFileName);
 158                 read->read(&*globaldata);
 159
 160                 order = globaldata->gorder;
 161                 string lastLabel = order->getLabel();
 162                 input = globaldata->ginput;
 163
 164                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 165                 set<string> processedLabels;
 166                 set<string> userLabels = labels;
 167
 168                 if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 169
 170
 171                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 172
 173                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 174                                         m->mothurOut(order->getLabel());  m->mothurOutEndLine();
 175                                         sabund = new SAbundVector();
 176                                         *sabund = (order->getSAbundVector());
 177                                         sabund->print(out);
 178                                         delete sabund;
 179
 180                                         if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 181
 182                                         processedLabels.insert(order->getLabel());
 183                                         userLabels.erase(order->getLabel());
 184                         }
 185
 186                         if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 187                                         string saveLabel = order->getLabel();
 188
 189                                         delete order;
 190                                         order = (input->getOrderVector(lastLabel));
 191
 192                                         m->mothurOut(order->getLabel());  m->mothurOutEndLine();
 193                                         sabund = new SAbundVector();
 194                                         *sabund = (order->getSAbundVector());
 195                                         sabund->print(out);
 196                                         delete sabund;
 197
 198                                         if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 199
 200                                         processedLabels.insert(order->getLabel());
 201                                         userLabels.erase(order->getLabel());
 202
 203                                         //restore real lastlabel to save below
 204                                         order->setLabel(saveLabel);
 205                         }
 206
 207
 208                         lastLabel = order->getLabel();
 209
 210                         delete order;
 211                         order = (input->getOrderVector());
 212                 }
 213
 214                 //output error messages about any remaining user labels
 215                 set<string>::iterator it;
 216                 bool needToRun = false;
 217                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 218                         m->mothurOut("Your file does not include the label " + *it);
 219                         if (processedLabels.count(lastLabel) != 1) {
 220                                 m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 221                                 needToRun = true;
 222                         }else {
 223                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 224                         }
 225                 }
 226
 227                 //run last label if you need to
 228                 if (needToRun == true)  {
 229                         if (order != NULL) {    delete order;   }
 230                         order = (input->getOrderVector(lastLabel));
 231
 232                         m->mothurOut(order->getLabel());  m->mothurOutEndLine();
 233                         sabund = new SAbundVector();
 234                         *sabund = (order->getSAbundVector());
 235                         sabund->print(out);
 236                         delete sabund;
 237
 238                         if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 239
 240                         delete order;
 241                 }
 242                 globaldata->gorder = NULL;
 243
 244                 out.close();
 245
 246                 m->mothurOutEndLine();
 247                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 248                 m->mothurOut(filename); m->mothurOutEndLine();  outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
 249                 m->mothurOutEndLine();
 250
 251                 return 0;
 252         }
 253
 254         catch(exception& e) {
 255                 m->errorOut(e, "GetSAbundCommand", "execute");
 256                 exit(1);
 257         }
 258 }
 259
 260 //**********************************************************************************************************************
 261
 262