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) + "heatmap" + 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                 //fills vector of sharedsabunds - lookup
  49                 getSharedVectors(sharedorder);
  50
  51                 string filename = getRootName(globaldata->inputFileName) + "heatmap" + sharedorder->getLabel();
  52
  53
  54         }
  55         catch(exception& e) {
  56                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  57                 exit(1);
  58         }
  59         catch(...) {
  60                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  61                 exit(1);
  62         }
  63 }
  64 //**********************************************************************************************************************
  65 void HeatMap::getSharedVectors(SharedOrderVector* order){
  66         try {
  67                 lookup.clear();
  68
  69                 vector<SharedRAbundVector*> templookup;
  70
  71                 //create and initialize vector of sharedvectors, one for each group
  72                 for (int i = 0; i < globaldata->Groups.size(); i++) {
  73                         SharedRAbundVector* temp = new SharedRAbundVector(order->getMaxRank());
  74                         temp->setLabel(order->getLabel());
  75                         temp->setGroup(globaldata->Groups[i]);
  76                         templookup.push_back(temp);
  77                 }
  78
  79                 int numSeqs = order->size();
  80                 //sample all the members
  81                 for(int i=0;i<numSeqs;i++){
  82                         //get first sample
  83                         individual chosen = order->get(i);
  84                         int abundance;
  85
  86                         //set info for sharedvector in chosens group
  87                         for (int j = 0; j < templookup.size(); j++) {
  88                                 if (chosen.group == templookup[j]->getGroup()) {
  89                                          abundance = templookup[j]->getAbundance(chosen.bin);
  90                                          templookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
  91                                          break;
  92                                 }
  93                         }
  94                 }
  95
  96                 //convert templookups rabunds to lookups sabunds
  97                 for (int j = 0; j < templookup.size(); j++) {
  98                         lookup.push_back(templookup[j]->getSharedSAbundVector());
  99                         delete templookup[j];
 100                 }
 101
 102
 103         }
 104         catch(exception& e) {
 105                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getSharedVectors. 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 HeatMap class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 110                 exit(1);
 111         }
 112
 113 }
 114
 115 //**********************************************************************************************************************
 116 void HeatMap::setGroups() {
 117         try {
 118                 //if the user has not entered specific groups to analyze then do them all
 119                 if (globaldata->Groups.size() != 0) {
 120                         if (globaldata->Groups[0] != "all") {
 121                                 //check that groups are valid
 122                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 123                                         if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
 124                                                 cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
 125                                                 // erase the invalid group from globaldata->Groups
 126                                                 globaldata->Groups.erase(globaldata->Groups.begin()+i);
 127                                         }
 128                                 }
 129
 130                                 //if the user only entered invalid groups
 131                                 if (globaldata->Groups.size() == 0) {
 132                                         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;
 133                                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 134                                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 135                                         }
 136                                 }
 137                         }else{//user has enter "all" and wants the default groups
 138                                 globaldata->Groups.clear();
 139                                 for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 140                                         globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 141                                 }
 142                                 globaldata->setGroups("");
 143                         }
 144                 }else {
 145                         for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
 146                                 globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
 147                         }
 148                 }
 149
 150         }
 151         catch(exception& e) {
 152                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 153                 exit(1);
 154         }
 155         catch(...) {
 156                 cout << "An unknown error has occurred in the HeatMap class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 157                 exit(1);
 158         }
 159
 160 }
 161 /***********************************************************/