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 == "shared") {
  52                         //you are using a list and a groupfile
  53                         read = new ReadOTUFile(globaldata->inputFileName);
  54                         read->read(&*globaldata);
  55
  56                         input = globaldata->ginput;
  57                         SharedList = globaldata->gSharedList;
  58                         lookup = SharedList->getSharedRAbundVector();
  59                 }else if (format == "list") {
  60                         //you are using just a list file and have only one group
  61                         read = new ReadOTUFile(globaldata->inputFileName);
  62                         read->read(&*globaldata);
  63
  64                         rabund = globaldata->rabund;
  65                         input = globaldata->ginput;
  66                 }
  67
  68                 if (format != "list") {
  69
  70                         while(lookup[0] != NULL){
  71
  72                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
  73
  74                                         cout << lookup[0]->getLabel() << '\t' << count << endl;
  75                                         heatmap->getPic(lookup);
  76                                 }
  77
  78                                 //get next line to process
  79                                 lookup = input->getSharedRAbundVectors();
  80                                 count++;
  81                         }
  82
  83                         //reset groups parameter
  84                         globaldata->Groups.clear();
  85
  86                 }else{
  87
  88                         while(rabund != NULL){
  89
  90                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){
  91
  92                                         cout << rabund->getLabel() << '\t' << count << endl;
  93                                         heatmap->getPic(rabund);
  94                                 }
  95
  96                                 rabund = input->getRAbundVector();
  97                                 count++;
  98                         }
  99                 }
 100
 101                 globaldata->setGroups("");
 102                 return 0;
 103         }
 104         catch(exception& e) {
 105                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 106                 exit(1);
 107         }
 108         catch(...) {
 109                 cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 110                 exit(1);
 111         }
 112 }
 113
 114 //**********************************************************************************************************************
 115
 116