heatmap.cpp

   1 /*
   2  *  heatmap.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 "heatmap.h"
  11
  12 //**********************************************************************************************************************
  13 HeatMap::HeatMap(){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 format = globaldata->getFormat();
  17
  18                 if (format != "list") {  setGroups();  }
  19
  20         }
  21         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. 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 HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 void HeatMap::getPic(OrderVector* order) {
  32         try {
  33                 sabund = order->getSAbundVector();
  34                 string filename = getRootName(globaldata->inputFileName) + order->getLabel();
  35         }
  36         catch(exception& e) {
  37                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  38                 exit(1);
  39         }
  40         catch(...) {
  41                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 void HeatMap::getPic(SharedOrderVector* sharedorder) {
  47         try {
  48                 getSharedVectors(sharedorder);
  49
  50
  51         }
  52         catch(exception& e) {
  53                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  54                 exit(1);
  55         }
  56         catch(...) {
  57                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  58                 exit(1);
  59         }
  60 }
  61 //**********************************************************************************************************************
  62 void HeatMap::getSharedVectors(SharedOrderVector* order){
  63         try {
  64                 lookup.clear();
  65
  66                 vector<SharedRAbundVector*> templookup;
  67
  68                 //create and initialize vector of sharedvectors, one for each group
  69                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  70                         SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
  71                         temp->setLabel(order->getLabel());
  72                         temp->setGroup(globaldata->Groups[i]);
  73                         templookup.push_back(temp);
  74                 }
  75
  76                 int numSeqs = order->size();
  77                 //sample all the members
  78                 for(int i=0;i<numSeqs;i++){
  79                         //get first sample
  80                         individual chosen = order->get(i);
  81                         int abundance;
  82
  83                         //set info for sharedvector in chosens group
  84                         for (int j = 0; j < templookup.size(); j++) {
  85                                 if (chosen.group == templookup[j]->getGroup()) {
  86                                          abundance = templookup[j]->getAbundance(chosen.bin);
  87                                          templookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
  88                                          break;
  89                                 }
  90                         }
  91                 }
  92
  93                 //convert templookups rabunds to lookups sabunds
  94                 for (int j = 0; j < templookup.size(); j++) {
  95                         lookup.push_back(templookup[j]->getSharedSAbundVector());
  96                         delete templookup[j];
  97                 }
  98
  99
 100         }
 101         catch(exception& e) {
 102                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 103                 exit(1);
 104         }
 105         catch(...) {
 106                 cout << "An unknown error has occurred in the HeatMap class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 107                 exit(1);
 108         }
 109
 110 }
 111
 112 //**********************************************************************************************************************
 113 void HeatMap::setGroups() {
 114         try {
 115                 //if the user has not entered specific groups to analyze then do them all
 116                 if (globaldata->Groups.size() != 0) {
 117                         if (globaldata->Groups[0] != "all") {
 118                                 //check that groups are valid
 119                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 120                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 121                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 122                                                 // erase the invalid group from globaldata->Groups
 123                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 124                                         }
 125                                 }
 126
 127                                 //if the user only entered invalid groups
 128                                 if (globaldata->Groups.size() == 0) {
 129                                         cout << "When using the groups parameter you must have at least 1 valid groups. I will run the command using all the groups in your groupfile." << endl;
 130                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 131                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 132                                         }
 133                                 }
 134                         }else{//user has enter "all" and wants the default groups
 135                                 globaldata->Groups.clear();
 136                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 137                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 138                                 }
 139                                 globaldata->setGroups("");
 140                         }
 141                 }else {
 142                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 143                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 144                         }
 145                 }
 146
 147         }
 148         catch(exception& e) {
 149                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 150                 exit(1);
 151         }
 152         catch(...) {
 153                 cout << "An unknown error has occurred in the HeatMap class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 154                 exit(1);
 155         }
 156
 157 }
 158 /***********************************************************/