5 * Created by Sarah Westcott on 11/18/08.
6 * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
11 //#include "ordervector.hpp"
13 /***********************************************************************/
15 int Rarefact::getCurve(float percentFreq = 0.01, int nIters = 1000){
17 RarefactionCurveData* rcd = new RarefactionCurveData();
18 for(int i=0;i<displays.size();i++){
19 rcd->registerDisplay(displays[i]);
22 //convert freq percentage to number
23 int increment = numSeqs * percentFreq;
25 for(int iter=0;iter<nIters;iter++){
27 for(int i=0;i<displays.size();i++){
28 displays[i]->init(label);
31 RAbundVector* lookup = new RAbundVector(order->getNumBins());
32 SAbundVector* rank = new SAbundVector(order->getMaxRank()+1);
33 random_shuffle(order->begin(), order->end());
35 for(int i=0;i<numSeqs;i++){
37 if (m->control_pressed) { delete lookup; delete rank; delete rcd; return 0; }
39 int binNumber = order->get(i);
40 int abundance = lookup->get(binNumber);
42 rank->set(abundance, rank->get(abundance)-1);
45 lookup->set(binNumber, abundance);
46 rank->set(abundance, rank->get(abundance)+1);
48 if((i == 0) || (i+1) % increment == 0){
49 rcd->updateRankData(rank);
53 if(numSeqs % increment != 0){
54 rcd->updateRankData(rank);
57 for(int i=0;i<displays.size();i++){
65 for(int i=0;i<displays.size();i++){
72 m->errorOut(e, "Rarefact", "getCurve");
77 /***********************************************************************/
79 int Rarefact::getSharedCurve(float percentFreq = 0.01, int nIters = 1000){
81 SharedRarefactionCurveData* rcd = new SharedRarefactionCurveData();
83 label = lookup[0]->getLabel();
85 //register the displays
86 for(int i=0;i<displays.size();i++){
87 rcd->registerDisplay(displays[i]);
90 //if jumble is false all iters will be the same
91 if (globaldata->jumble == false) { nIters = 1; }
93 //convert freq percentage to number
94 int increment = numSeqs * percentFreq;
96 for(int iter=0;iter<nIters;iter++){
98 for(int i=0;i<displays.size();i++){
99 displays[i]->init(label);
102 if (globaldata->jumble == true) {
103 //randomize the groups
104 random_shuffle(lookup.begin(), lookup.end());
107 //make merge the size of lookup[0]
108 SharedRAbundVector* merge = new SharedRAbundVector(lookup[0]->size());
110 //make copy of lookup zero
111 for(int i = 0; i<lookup[0]->size(); i++) {
112 merge->set(i, lookup[0]->getAbundance(i), "merge");
115 vector<SharedRAbundVector*> subset;
116 //send each group one at a time
117 for (int k = 0; k < lookup.size(); k++) {
118 if (m->control_pressed) { delete merge; delete rcd; return 0; }
120 subset.clear(); //clears out old pair of sharedrabunds
121 //add in new pair of sharedrabunds
122 subset.push_back(merge); subset.push_back(lookup[k]);
124 rcd->updateSharedData(subset, k+1, numGroupComb);
125 mergeVectors(merge, lookup[k]);
128 //resets output files
129 for(int i=0;i<displays.size();i++){
130 displays[i]->reset();
136 for(int i=0;i<displays.size();i++){
137 displays[i]->close();
143 catch(exception& e) {
144 m->errorOut(e, "Rarefact", "getSharedCurve");
149 /**************************************************************************************/
150 void Rarefact::mergeVectors(SharedRAbundVector* shared1, SharedRAbundVector* shared2) {
152 for (int k = 0; k < shared1->size(); k++) {
153 //merge new species into shared1
154 shared1->set(k, (shared1->getAbundance(k) + shared2->getAbundance(k)), "combo"); //set to 'combo' since this vector now contains multiple groups
157 catch(exception& e) {
158 m->errorOut(e, "Rarefact", "mergeVectors");