X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=subsample.cpp;fp=subsample.cpp;h=d5b4e3ecf19f2114855426350e1ecfbe57780736;hb=53171f07cc0c0e560e2b4ba2946f690d59fc2dc4;hp=0000000000000000000000000000000000000000;hpb=8da8321bc4d705f6c156248d6229c60a0204f750;p=mothur.git

diff --git a/subsample.cpp b/subsample.cpp
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+++ b/subsample.cpp
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+//
+//  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);
+	}
+}
+
+
+//**********************************************************************************************************************
+
+