--- /dev/null
+//
+// subsample.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 4/2/12.
+// Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "subsample.h"
+
+//**********************************************************************************************************************
+vector<SharedRAbundVector*> SubSample::getSamplePreserve(vector<SharedRAbundVector*>& thislookup, vector<string>& newLabels, int size) {
+ try {
+
+ vector<SharedRAbundVector*> newlookup; newlookup.resize(thislookup.size(), NULL);
+
+ //save mothurOut's binLabels to restore for next label
+ vector<string> saveBinLabels = m->currentBinLabels;
+
+ int numBins = thislookup[0]->getNumBins();
+ for (int i = 0; i < thislookup.size(); i++) {
+ int thisSize = thislookup[i]->getNumSeqs();
+
+ if (thisSize != size) {
+
+ string thisgroup = thislookup[i]->getGroup();
+
+ OrderVector order;
+ for(int p=0;p<numBins;p++){
+ for(int j=0;j<thislookup[i]->getAbundance(p);j++){
+ order.push_back(p);
+ }
+ }
+ random_shuffle(order.begin(), order.end());
+
+ SharedRAbundVector* temp = new SharedRAbundVector(numBins);
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+
+ newlookup[i] = temp;
+
+ for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { return newlookup; }
+
+ int bin = order.get(j);
+
+ int abund = newlookup[i]->getAbundance(bin);
+ newlookup[i]->set(bin, (abund+1), thisgroup);
+ }
+ }
+ }
+
+ //subsampling may have created some otus with no sequences in them
+ eliminateZeroOTUS(newlookup);
+
+ if (m->control_pressed) { return newlookup; }
+
+ //save mothurOut's binLabels to restore for next label
+ newLabels = m->currentBinLabels;
+ m->currentBinLabels = saveBinLabels;
+
+ return newlookup;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "getSamplePreserve");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> SubSample::getSample(vector<SharedRAbundVector*>& thislookup, int size) {
+ try {
+
+ //save mothurOut's binLabels to restore for next label
+ vector<string> saveBinLabels = m->currentBinLabels;
+
+ int numBins = thislookup[0]->getNumBins();
+ for (int i = 0; i < thislookup.size(); i++) {
+ int thisSize = thislookup[i]->getNumSeqs();
+
+ if (thisSize != size) {
+
+ string thisgroup = thislookup[i]->getGroup();
+
+ OrderVector order;
+ for(int p=0;p<numBins;p++){
+ for(int j=0;j<thislookup[i]->getAbundance(p);j++){
+ order.push_back(p);
+ }
+ }
+ random_shuffle(order.begin(), order.end());
+
+ SharedRAbundVector* temp = new SharedRAbundVector(numBins);
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+
+ delete thislookup[i];
+ thislookup[i] = temp;
+
+
+ for (int j = 0; j < size; j++) {
+
+ if (m->control_pressed) { return m->currentBinLabels; }
+
+ int bin = order.get(j);
+
+ int abund = thislookup[i]->getAbundance(bin);
+ thislookup[i]->set(bin, (abund+1), thisgroup);
+ }
+ }
+ }
+
+ //subsampling may have created some otus with no sequences in them
+ eliminateZeroOTUS(thislookup);
+
+ if (m->control_pressed) { return m->currentBinLabels; }
+
+ //save mothurOut's binLabels to restore for next label
+ vector<string> subsampleBinLabels = m->currentBinLabels;
+ m->currentBinLabels = saveBinLabels;
+
+ return subsampleBinLabels;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "getSample");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int SubSample::eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup) {
+ try {
+
+ vector<SharedRAbundVector*> newLookup;
+ for (int i = 0; i < thislookup.size(); i++) {
+ SharedRAbundVector* temp = new SharedRAbundVector();
+ temp->setLabel(thislookup[i]->getLabel());
+ temp->setGroup(thislookup[i]->getGroup());
+ newLookup.push_back(temp);
+ }
+
+ //for each bin
+ vector<string> newBinLabels;
+ string snumBins = toString(thislookup[0]->getNumBins());
+ for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
+ if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
+
+ //look at each sharedRabund and make sure they are not all zero
+ bool allZero = true;
+ for (int j = 0; j < thislookup.size(); j++) {
+ if (thislookup[j]->getAbundance(i) != 0) { allZero = false; break; }
+ }
+
+ //if they are not all zero add this bin
+ if (!allZero) {
+ for (int j = 0; j < thislookup.size(); j++) {
+ newLookup[j]->push_back(thislookup[j]->getAbundance(i), thislookup[j]->getGroup());
+ }
+ //if there is a bin label use it otherwise make one
+ string binLabel = "Otu";
+ string sbinNumber = toString(i+1);
+ if (sbinNumber.length() < snumBins.length()) {
+ int diff = snumBins.length() - sbinNumber.length();
+ for (int h = 0; h < diff; h++) { binLabel += "0"; }
+ }
+ binLabel += sbinNumber;
+ if (i < m->currentBinLabels.size()) { binLabel = m->currentBinLabels[i]; }
+
+ newBinLabels.push_back(binLabel);
+ }
+ }
+
+ for (int j = 0; j < thislookup.size(); j++) { delete thislookup[j]; }
+ thislookup.clear();
+
+ thislookup = newLookup;
+ m->currentBinLabels = newBinLabels;
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SubSample", "eliminateZeroOTUS");
+ exit(1);
+ }
+}
+
+
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff