5 * Created by Sarah Westcott on 11/18/08.
6 * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
12 /***********************************************************************/
14 void Collect::getCurve(int increment = 1){
16 RAbundVector* lookup = new RAbundVector(order->getNumBins());
17 SAbundVector* rank = new SAbundVector(order->getMaxRank()+1);
19 CollectorsCurveData* ccd = new CollectorsCurveData();
21 for(int i=0;i<displays.size();i++){
22 ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
23 displays[i]->init(label); //sets displays label
25 for(int i=0;i<numSeqs;i++){
27 int binNumber = order->get(i);
28 int abundance = lookup->get(binNumber);
30 rank->set(abundance, rank->get(abundance)-1);
34 lookup->set(binNumber, abundance);
35 rank->set(abundance, rank->get(abundance)+1); //increment rank(abundance)
37 if((i == 0) || (i+1) % increment == 0){
38 ccd->updateRankData(rank);
42 if(numSeqs % increment != 0){
43 ccd->updateRankData(rank);
46 for(int i=0;i<displays.size();i++){
51 cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
55 cout << "An unknown error has occurred in the Collect class function getCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
61 /***********************************************************************/
62 void Collect::getSharedCurve(int increment = 1){
64 globaldata = GlobalData::getInstance();
65 vector<SharedRAbundVector*> lookup;
67 //create and initialize vector of sharedvectors, one for each group
68 for (int i = 0; i < globaldata->Groups.size(); i++) {
69 SharedRAbundVector* temp = new SharedRAbundVector(sharedorder->getNumBins());
70 temp->setLabel(sharedorder->getLabel());
71 temp->setGroup(globaldata->Groups[i]);
72 temp->setGroupIndex(globaldata->gGroupmap->groupIndex[globaldata->Groups[i]]);
73 lookup.push_back(temp);
76 SharedCollectorsCurveData* ccd = new SharedCollectorsCurveData();
78 //initialize labels for output
79 //makes 'uniqueAB uniqueAC uniqueBC' if your groups are A, B, C
82 for (int s = 0; s < groupComb.size(); s++) {
83 groupLabel = groupLabel + label + groupComb[s] + "\t";
86 for(int i=0;i<displays.size();i++){
87 ccd->registerDisplay(displays[i]); //adds a display[i] to cdd
88 displays[i]->init(groupLabel);
91 //sample all the members
92 for(int i=0;i<numSeqs;i++){
94 individual chosen = sharedorder->get(i);
97 //set info for sharedvector in chosens group
98 for (int j = 0; j < lookup.size(); j++) {
99 if (chosen.group == lookup[j]->getGroup()) {
100 abundance = lookup[j]->getAbundance(chosen.bin);
101 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
107 //calculate at 0 and the given increment
108 if((i == 0) || (i+1) % increment == 0){
109 //randomize group order
110 if (globaldata->getJumble() == "1") { random_shuffle(lookup.begin(), lookup.end()); }
111 //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
113 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
114 for (int l = n; l < lookup.size(); l++) {
115 ccd->updateSharedData(lookup[k], lookup[l], i+1, globaldata->Groups.size());
123 //calculate last line if you haven't already
124 if(numSeqs % increment != 0){
125 //how many comparisons to make i.e. for group a, b, c = ab, ac, bc.
127 for (int k = 0; k < (lookup.size() - 1); k++) { // pass cdd each set of groups to commpare
128 for (int l = n; l < lookup.size(); l++) {
129 ccd->updateSharedData(lookup[k], lookup[l], totalNumSeq, globaldata->Groups.size());
135 //resets output files
136 for(int i=0;i<displays.size();i++){
137 displays[i]->reset();
140 catch(exception& e) {
141 cout << "Standard Error: " << e.what() << " has occurred in the Collect class Function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
145 cout << "An unknown error has occurred in the Collect class function getSharedCurve. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
151 /**************************************************************************************/
153 void Collect::getGroupComb() {
159 for (int i = 0; i < (globaldata->Groups.size() - 1); i++) {
160 for (int l = n; l < globaldata->Groups.size(); l++) {
161 group = globaldata->Groups[i] + globaldata->Groups[l];
162 groupComb.push_back(group);
170 /**************************************************************************************/