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                 abort = true;
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["sabund"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> GetSAbundCommand::getRequiredParameters(){
  39         try {
  40                 vector<string> myArray;
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "GetSAbundCommand", "getRequiredParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 vector<string> GetSAbundCommand::getRequiredFiles(){
  50         try {
  51                 string Array[] =  {"list","rabund"};
  52                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "GetSAbundCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61 GetSAbundCommand::GetSAbundCommand(string option)  {
  62         try {
  63                 globaldata = GlobalData::getInstance();
  64                 abort = false;
  65                 allLines = 1;
  66                 labels.clear();
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string Array[] =  {"label","outputdir","inputdir"};
  74                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string,string> parameters = parser.getParameters();
  78
  79                         ValidParameters validParameter;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (map<string,string>::iterator 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 output directory command factory will send this info to us in the output parameter
  91                         string outputDir = validParameter.validFile(parameters, "outputdir", false);            if (outputDir == "not found"){
  92                                 outputDir = "";
  93                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  94                         }
  95
  96                         //make sure the user has already run the read.otu command
  97                         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; }
  98
  99                         //check for optional parameter and set defaults
 100                         // ...at some point should added some additional type checking...
 101                         label = validParameter.validFile(parameters, "label", false);
 102                         if (label == "not found") { label = ""; }
 103                         else {
 104                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 105                                 else { allLines = 1;  }
 106                         }
 107
 108                         //if the user has not specified any labels use the ones from read.otu
 109                         if(label == "") {
 110                                 allLines = globaldata->allLines;
 111                                 labels = globaldata->labels;
 112                         }
 113
 114                         if (abort == false) {
 115                                 filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund";
 116                                 m->openOutputFile(filename, out);
 117                         }
 118                 }
 119
 120         }
 121         catch(exception& e) {
 122                 m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
 123                 exit(1);
 124         }
 125 }
 126 //**********************************************************************************************************************
 127
 128 void GetSAbundCommand::help(){
 129         try {
 130                 m->mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
 131                 m->mothurOut("The get.sabund command parameters is label.  No parameters are required.\n");
 132                 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");
 133                 m->mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n");
 134                 m->mothurOut("Example get.sabund().\n");
 135                 m->mothurOut("The default value for label is all labels in your inputfile.\n");
 136                 m->mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
 137                 m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
 138         }
 139         catch(exception& e) {
 140                 m->errorOut(e, "GetSAbundCommand", "help");
 141                 exit(1);
 142         }
 143 }
 144
 145 //**********************************************************************************************************************
 146
 147 GetSAbundCommand::~GetSAbundCommand(){
 148 }
 149
 150 //**********************************************************************************************************************
 151
 152 int GetSAbundCommand::execute(){
 153         try {
 154
 155                 if (abort == true) { return 0; }
 156
 157                 //using order vector so you don't have to distinguish between the list and rabund files
 158                 read = new ReadOTUFile(globaldata->inputFileName);
 159                 read->read(&*globaldata);
 160
 161                 order = globaldata->gorder;
 162                 string lastLabel = order->getLabel();
 163                 input = globaldata->ginput;
 164
 165                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 166                 set<string> processedLabels;
 167                 set<string> userLabels = labels;
 168
 169                 if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 170
 171
 172                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 173
 174                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 175                                         m->mothurOut(order->getLabel());  m->mothurOutEndLine();
 176                                         sabund = new SAbundVector();
 177                                         *sabund = (order->getSAbundVector());
 178                                         sabund->print(out);
 179                                         delete sabund;
 180
 181                                         if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 182
 183                                         processedLabels.insert(order->getLabel());
 184                                         userLabels.erase(order->getLabel());
 185                         }
 186
 187                         if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 188                                         string saveLabel = order->getLabel();
 189
 190                                         delete order;
 191                                         order = (input->getOrderVector(lastLabel));
 192
 193                                         m->mothurOut(order->getLabel());  m->mothurOutEndLine();
 194                                         sabund = new SAbundVector();
 195                                         *sabund = (order->getSAbundVector());
 196                                         sabund->print(out);
 197                                         delete sabund;
 198
 199                                         if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 200
 201                                         processedLabels.insert(order->getLabel());
 202                                         userLabels.erase(order->getLabel());
 203
 204                                         //restore real lastlabel to save below
 205                                         order->setLabel(saveLabel);
 206                         }
 207
 208
 209                         lastLabel = order->getLabel();
 210
 211                         delete order;
 212                         order = (input->getOrderVector());
 213                 }
 214
 215                 //output error messages about any remaining user labels
 216                 set<string>::iterator it;
 217                 bool needToRun = false;
 218                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 219                         m->mothurOut("Your file does not include the label " + *it);
 220                         if (processedLabels.count(lastLabel) != 1) {
 221                                 m->mothurOut(". I will use " + lastLabel + ".");  m->mothurOutEndLine();
 222                                 needToRun = true;
 223                         }else {
 224                                 m->mothurOut(". Please refer to " + lastLabel + ".");  m->mothurOutEndLine();
 225                         }
 226                 }
 227
 228                 //run last label if you need to
 229                 if (needToRun == true)  {
 230                         if (order != NULL) {    delete order;   }
 231                         order = (input->getOrderVector(lastLabel));
 232
 233                         m->mothurOut(order->getLabel());  m->mothurOutEndLine();
 234                         sabund = new SAbundVector();
 235                         *sabund = (order->getSAbundVector());
 236                         sabund->print(out);
 237                         delete sabund;
 238
 239                         if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete order; globaldata->gorder = NULL;  return 0; }
 240
 241                         delete order;
 242                 }
 243                 globaldata->gorder = NULL;
 244
 245                 out.close();
 246
 247                 m->mothurOutEndLine();
 248                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 249                 m->mothurOut(filename); m->mothurOutEndLine();  outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
 250                 m->mothurOutEndLine();
 251
 252                 return 0;
 253         }
 254
 255         catch(exception& e) {
 256                 m->errorOut(e, "GetSAbundCommand", "execute");
 257                 exit(1);
 258         }
 259 }
 260
 261 //**********************************************************************************************************************
 262
 263