+/*
+ * heatmap.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 3/25/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "heatmap.h"
+
+//**********************************************************************************************************************
+HeatMap::HeatMap(){
+ try {
+ globaldata = GlobalData::getInstance();
+ format = globaldata->getFormat();
+
+ if (format != "list") { setGroups(); }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void HeatMap::getPic(OrderVector* order) {
+ try {
+ sabund = order->getSAbundVector();
+ string filename = getRootName(globaldata->inputFileName) + order->getLabel();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void HeatMap::getPic(SharedOrderVector* sharedorder) {
+ try {
+ getSharedVectors(sharedorder);
+
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void HeatMap::getSharedVectors(SharedOrderVector* order){
+ try {
+ lookup.clear();
+
+ vector<SharedRAbundVector*> templookup;
+
+ //create and initialize vector of sharedvectors, one for each group
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
+ temp->setLabel(order->getLabel());
+ temp->setGroup(globaldata->Groups[i]);
+ templookup.push_back(temp);
+ }
+
+ int numSeqs = order->size();
+ //sample all the members
+ for(int i=0;i<numSeqs;i++){
+ //get first sample
+ individual chosen = order->get(i);
+ int abundance;
+
+ //set info for sharedvector in chosens group
+ for (int j = 0; j < templookup.size(); j++) {
+ if (chosen.group == templookup[j]->getGroup()) {
+ abundance = templookup[j]->getAbundance(chosen.bin);
+ templookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
+ break;
+ }
+ }
+ }
+
+ //convert templookups rabunds to lookups sabunds
+ for (int j = 0; j < templookup.size(); j++) {
+ lookup.push_back(templookup[j]->getSharedSAbundVector());
+ delete templookup[j];
+ }
+
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMap class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+
+//**********************************************************************************************************************
+void HeatMap::setGroups() {
+ try {
+ //if the user has not entered specific groups to analyze then do them all
+ if (globaldata->Groups.size() != 0) {
+ if (globaldata->Groups[0] != "all") {
+ //check that groups are valid
+ for (int i = 0; i < globaldata->Groups.size(); i++) {
+ if (globaldata->gGroupmap->isValidGroup(globaldata->Groups[i]) != true) {
+ cout << globaldata->Groups[i] << " is not a valid group, and will be disregarded." << endl;
+ // erase the invalid group from globaldata->Groups
+ globaldata->Groups.erase(globaldata->Groups.begin()+i);
+ }
+ }
+
+ //if the user only entered invalid groups
+ if (globaldata->Groups.size() == 0) {
+ 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;
+ for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ }
+ }
+ }else{//user has enter "all" and wants the default groups
+ globaldata->Groups.clear();
+ for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ }
+ globaldata->setGroups("");
+ }
+ }else {
+ for (int i = 0; i < globaldata->gGroupmap->namesOfGroups.size(); i++) {
+ globaldata->Groups.push_back(globaldata->gGroupmap->namesOfGroups[i]);
+ }
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the HeatMap class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/***********************************************************/