heatmapcommand.cpp

   1 /*
   2  *  heatmapcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/25/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmapcommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14
  15 HeatMapCommand::HeatMapCommand(){
  16         try {
  17                 globaldata = GlobalData::getInstance();
  18                 heatmap = new HeatMap();
  19                 format = globaldata->getFormat();
  20         }
  21         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  23                 exit(1);
  24         }
  25         catch(...) {
  26                 cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31
  32 HeatMapCommand::~HeatMapCommand(){
  33         delete input;
  34         delete read;
  35         delete heatmap;
  36 }
  37
  38 //**********************************************************************************************************************
  39
  40 int HeatMapCommand::execute(){
  41         try {
  42                 int count = 1;
  43
  44                 if (format == "sharedfile") {
  45                         //you have groups
  46                         read = new ReadOTUFile(globaldata->inputFileName);
  47                         read->read(&*globaldata);
  48
  49                         input = globaldata->ginput;
  50                         lookup = input->getSharedRAbundVectors();
  51                 }else if (format == "list") {
  52                         //you are using just a list file and have only one group
  53                         read = new ReadOTUFile(globaldata->inputFileName);
  54                         read->read(&*globaldata);
  55
  56                         rabund = globaldata->rabund;
  57                         input = globaldata->ginput;
  58                 }
  59
  60                 if (format != "list") {
  61
  62                         while(lookup[0] != NULL){
  63
  64                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
  65
  66                                         cout << lookup[0]->getLabel() << '\t' << count << endl;
  67                                         heatmap->getPic(lookup);
  68                                 }
  69
  70                                 //prevent memory leak
  71                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
  72
  73                                 //get next line to process
  74                                 lookup = input->getSharedRAbundVectors();
  75                                 count++;
  76                         }
  77
  78                         //reset groups parameter
  79                         globaldata->Groups.clear();
  80
  81                 }else{
  82
  83                         while(rabund != NULL){
  84
  85                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){
  86
  87                                         cout << rabund->getLabel() << '\t' << count << endl;
  88                                         heatmap->getPic(rabund);
  89                                 }
  90
  91                                 delete rabund;
  92                                 rabund = input->getRAbundVector();
  93                                 count++;
  94                         }
  95                 }
  96
  97                 globaldata->setGroups("");
  98                 return 0;
  99         }
 100         catch(exception& e) {
 101                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 102                 exit(1);
 103         }
 104         catch(...) {
 105                 cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 106                 exit(1);
 107         }
 108 }
 109
 110 //**********************************************************************************************************************
 111
 112