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                 util = new SharedUtil();
  21
  22         }
  23         catch(exception& e) {
  24                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  25                 exit(1);
  26         }
  27         catch(...) {
  28                 cout << "An unknown error has occurred in the HeatMapCommand class function HeatMapCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  29                 exit(1);
  30         }
  31 }
  32 //**********************************************************************************************************************
  33
  34 HeatMapCommand::~HeatMapCommand(){
  35         delete input;
  36         delete read;
  37         delete heatmap;
  38         delete util;
  39 }
  40
  41 //**********************************************************************************************************************
  42
  43 int HeatMapCommand::execute(){
  44         try {
  45                 int count = 1;
  46
  47                 if (format == "sharedfile") {
  48                         //you have groups
  49                         read = new ReadPhilFile(globaldata->inputFileName);
  50                         read->read(&*globaldata);
  51
  52                         input = globaldata->ginput;
  53                         order = input->getSharedOrderVector();
  54                 }else if (format == "shared") {
  55                         //you are using a list and a groupfile
  56                         read = new ReadPhilFile(globaldata->inputFileName);
  57                         read->read(&*globaldata);
  58
  59                         input = globaldata->ginput;
  60                         SharedList = globaldata->gSharedList;
  61                         order = SharedList->getSharedOrderVector();
  62                 }else if (format == "list") {
  63                         //you are using just a list file and have only one group
  64                         read = new ReadPhilFile(globaldata->inputFileName);
  65                         read->read(&*globaldata);
  66
  67                         ordersingle = globaldata->gorder;
  68                         input = globaldata->ginput;
  69                 }
  70
  71                 if (format != "list") {
  72
  73                         util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "heat");
  74                         globaldata->setGroups("");
  75
  76
  77                         while(order != NULL){
  78
  79                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
  80
  81                                         cout << order->getLabel() << '\t' << count << endl;
  82                                         heatmap->getPic(order);
  83
  84                                 }
  85
  86                                 //get next line to process
  87                                 if (format == "sharedfile") {
  88                                         order = input->getSharedOrderVector();
  89                                 }else {
  90                                         //you are using a list and a groupfile
  91                                         SharedList = input->getSharedListVector(); //get new list vector to process
  92                                         if (SharedList != NULL) {
  93                                                 order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
  94                                         }else {
  95                                                 break;
  96                                         }
  97                                 }
  98                                 count++;
  99                         }
 100
 101                         //reset groups parameter
 102                         globaldata->Groups.clear();
 103
 104                 }else{
 105                         while(ordersingle != NULL){
 106
 107                                 if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(ordersingle->getLabel()) == 1){
 108
 109                                         cout << ordersingle->getLabel() << '\t' << count << endl;
 110                                         heatmap->getPic(ordersingle);
 111
 112                                 }
 113
 114                                 ordersingle = (input->getOrderVector());
 115                                 count++;
 116                         }
 117                 }
 118
 119                 return 0;
 120         }
 121         catch(exception& e) {
 122                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 123                 exit(1);
 124         }
 125         catch(...) {
 126                 cout << "An unknown error has occurred in the HeatMapCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 127                 exit(1);
 128         }
 129 }
 130
 131 //**********************************************************************************************************************
 132
 133