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
  14 GetSAbundCommand::GetSAbundCommand(string option){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17                 abort = false;
  18                 allLines = 1;
  19                 labels.clear();
  20
  21                 //allow user to run help
  22                 if(option == "help") { help(); abort = true; }
  23
  24                 else {
  25                         //valid paramters for this command
  26                         string Array[] =  {"label"};
  27                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  28
  29                         OptionParser parser(option);
  30                         map<string,string> parameters = parser.getParameters();
  31
  32                         ValidParameters validParameter;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         //make sure the user has already run the read.otu command
  40                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund command."); mothurOutEndLine(); abort = true; }
  41
  42                         //check for optional parameter and set defaults
  43                         // ...at some point should added some additional type checking...
  44                         label = validParameter.validFile(parameters, "label", false);
  45                         if (label == "not found") { label = ""; }
  46                         else {
  47                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  48                                 else { allLines = 1;  }
  49                         }
  50
  51                         //if the user has not specified any labels use the ones from read.otu
  52                         if(label == "") {
  53                                 allLines = globaldata->allLines;
  54                                 labels = globaldata->labels;
  55                         }
  56
  57                         if (abort == false) {
  58                                 filename = getRootName(globaldata->inputFileName) + "sabund";
  59                                 openOutputFile(filename, out);
  60                         }
  61                 }
  62
  63         }
  64         catch(exception& e) {
  65                 errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 void GetSAbundCommand::help(){
  72         try {
  73                 mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
  74                 mothurOut("The get.sabund command parameters is label.  No parameters are required.\n");
  75                 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");
  76                 mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n");
  77                 mothurOut("Example get.sabund().\n");
  78                 mothurOut("The default value for label is all labels in your inputfile.\n");
  79                 mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
  80                 mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
  81         }
  82         catch(exception& e) {
  83                 errorOut(e, "GetSAbundCommand", "help");
  84                 exit(1);
  85         }
  86 }
  87
  88 //**********************************************************************************************************************
  89
  90 GetSAbundCommand::~GetSAbundCommand(){
  91 }
  92
  93 //**********************************************************************************************************************
  94
  95 int GetSAbundCommand::execute(){
  96         try {
  97
  98                 if (abort == true) { return 0; }
  99
 100                 //using order vector so you don't have to distinguish between the list and rabund files
 101                 read = new ReadOTUFile(globaldata->inputFileName);
 102                 read->read(&*globaldata);
 103
 104                 order = globaldata->gorder;
 105                 string lastLabel = order->getLabel();
 106                 input = globaldata->ginput;
 107
 108                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 109                 set<string> processedLabels;
 110                 set<string> userLabels = labels;
 111
 112                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 113
 114                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 115                                         mothurOut(order->getLabel());  mothurOutEndLine();
 116                                         sabund = new SAbundVector();
 117                                         *sabund = (order->getSAbundVector());
 118                                         sabund->print(out);
 119                                         delete sabund;
 120
 121                                         processedLabels.insert(order->getLabel());
 122                                         userLabels.erase(order->getLabel());
 123                         }
 124
 125                         if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 126                                         string saveLabel = order->getLabel();
 127
 128                                         delete order;
 129                                         order = (input->getOrderVector(lastLabel));
 130
 131                                         mothurOut(order->getLabel());  mothurOutEndLine();
 132                                         sabund = new SAbundVector();
 133                                         *sabund = (order->getSAbundVector());
 134                                         sabund->print(out);
 135                                         delete sabund;
 136
 137                                         processedLabels.insert(order->getLabel());
 138                                         userLabels.erase(order->getLabel());
 139
 140                                         //restore real lastlabel to save below
 141                                         order->setLabel(saveLabel);
 142                         }
 143
 144
 145                         lastLabel = order->getLabel();
 146
 147                         delete order;
 148                         order = (input->getOrderVector());
 149                 }
 150
 151                 //output error messages about any remaining user labels
 152                 set<string>::iterator it;
 153                 bool needToRun = false;
 154                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 155                         mothurOut("Your file does not include the label " + *it);
 156                         if (processedLabels.count(lastLabel) != 1) {
 157                                 mothurOut(". I will use " + lastLabel + ".");  mothurOutEndLine();
 158                                 needToRun = true;
 159                         }else {
 160                                 mothurOut(". Please refer to " + lastLabel + ".");  mothurOutEndLine();
 161                         }
 162                 }
 163
 164                 //run last label if you need to
 165                 if (needToRun == true)  {
 166                         if (order != NULL) {    delete order;   }
 167                         order = (input->getOrderVector(lastLabel));
 168
 169                         mothurOut(order->getLabel());  mothurOutEndLine();
 170                         sabund = new SAbundVector();
 171                         *sabund = (order->getSAbundVector());
 172                         sabund->print(out);
 173                         delete sabund;
 174                         delete order;
 175                 }
 176                 globaldata->gorder = NULL;
 177
 178                 out.close();
 179                 return 0;
 180         }
 181
 182         catch(exception& e) {
 183                 errorOut(e, "GetSAbundCommand", "execute");
 184                 exit(1);
 185         }
 186 }
 187
 188 //**********************************************************************************************************************
 189
 190