From 5890a0d1e8f3a549652abc18a2f34d65b3ce7075 Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Tue, 15 Feb 2011 11:41:28 +0000
Subject: [PATCH] mods to shhh.seqs command

---
 shhhercommand.cpp | 21 ++++++++++++++++-----
 shhhercommand.h   | 13 +++++++------
 2 files changed, 23 insertions(+), 11 deletions(-)

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 6a19618..39a27d5 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -289,7 +289,9 @@ int ShhherCommand::execute(){
 			
 			for(int i=0;i<numFiles;i++){
 				flowFileName = flowFileVector[i];
-			
+
+				
+				
 				m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
 				m->mothurOut("Reading flowgrams...\n");
 				
@@ -761,6 +763,11 @@ void ShhherCommand::getFlowData(){
 		m->openInputFile(flowFileName, flowFile);
 		
 		string seqName;
+		seqNameVector.clear();
+		lengths.clear();
+		flowDataIntI.clear();
+		nameMap.clear();
+		
 		
 		int currentNumFlowCells;
 		
@@ -943,7 +950,7 @@ void ShhherCommand::getUniques(){
 		uniqueFlowDataIntI.resize(numFlowCells * numUniques);
 		uniqueLengths.resize(numUniques);	
 		
-		flowDataPrI.assign(numSeqs * numFlowCells, 0);
+		flowDataPrI.resize(numSeqs * numFlowCells, 0);
 		for(int i=0;i<flowDataPrI.size();i++)	{	flowDataPrI[i] = getProbIntensity(flowDataIntI[i]);		}
 	}
 	catch(exception& e) {
@@ -1205,6 +1212,10 @@ void ShhherCommand::getOTUData(string listFileName){
 		nSeqsPerOTU.assign(numOTUs, 0);
 		aaP.resize(numOTUs);
 		
+		seqNumber.clear();
+		aaI.clear();
+		seqIndex.clear();
+		
 		string singleOTU = "";
 		
 		for(int i=0;i<numOTUs;i++){
@@ -1673,9 +1684,9 @@ void ShhherCommand::calcNewDistancesChildMPI(int startSeq, int stopSeq, vector<i
 	try{
 		vector<double> newTau(numOTUs,0);
 		vector<double> norms(numSeqs, 0);
-		otuIndex.resize(0);
-		seqIndex.resize(0);
-		singleTau.resize(0);
+		otuIndex.clear();
+		seqIndex.clear();
+		singleTau.clear();
 		
 		
 		
diff --git a/shhhercommand.h b/shhhercommand.h
index 9e50824..acceb7f 100644
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -40,19 +40,20 @@ private:
 	
 	vector<int> nSeqsBreaks;
 	vector<int> nOTUsBreaks;
-	vector<double> flowDataPrI;
-	vector<short> flowDataIntI;
-	vector<int> lengths;
-	vector<string> seqNameVector;
 	vector<double> singleLookUp;
 	vector<double> jointLookUp;
+	
+	vector<string> seqNameVector;
+	vector<int> lengths;
+	vector<short> flowDataIntI;
+	vector<double> flowDataPrI;
 	map<string, int> nameMap;
 	vector<int> otuData;
 	vector<int> cumNumSeqs;
 	vector<int> nSeqsPerOTU;
 	vector<vector<int> > aaP;	//tMaster->aanP:	each row is a different otu / each col contains the sequence indices
-	vector<int> seqNumber;		//tMaster->anP:		the sequence id number sorted by OTU
 	vector<vector<int> > aaI;	//tMaster->aanI:	that are in each otu - can't differentiate between aaP and aaI 
+	vector<int> seqNumber;		//tMaster->anP:		the sequence id number sorted by OTU
 	vector<int> seqIndex;		//tMaster->anI;		the index that corresponds to seqNumber
 	vector<double> dist;		//adDist - distance of sequences to centroids
 	vector<short> change;		//did the centroid sequence change? 0 = no; 1 = yes
@@ -61,9 +62,9 @@ private:
 	vector<double> singleTau;	//tMaster->adTau:	1-D Tau vector (1xnumSeqs)
 	vector<short> uniqueFlowgrams;
 	vector<int> uniqueCount;
-	vector<int> uniqueLengths;
 	vector<int> mapSeqToUnique;
 	vector<int> mapUniqueToSeq;
+	vector<int> uniqueLengths;
 	
 	int numSeqs, numUniques, numOTUs, numFlowCells;
 	
-- 
2.39.2