X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhercommand.cpp;h=6833f5d4c1cae8f4ee0e3b6f3da3bd2474b31285;hb=83bf613d5a7ffb4dcc75b3cad106d1eed1f9e498;hp=5bf802ef304dde8c9d628db63a9e0915f23f236e;hpb=502a5ed3b2c5798b390ece3595efa3a714ad3f75;p=mothur.git

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 5bf802e..6833f5d 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -32,7 +32,7 @@
 vector<string> ShhherCommand::getValidParameters(){	
 	try {
 		string Array[] =  {	
-			"file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors"	
+			"file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"	
 		};
 		
 		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
@@ -111,7 +111,7 @@ ShhherCommand::ShhherCommand(string option) {
 			
 			//valid paramters for this command
 			string AlignArray[] =  {
-				"file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors"	
+				"file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"	
 			};
 			
 			vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
@@ -289,11 +289,13 @@ 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");
-				
 				getFlowData();
+
 				m->mothurOut("Identifying unique flowgrams...\n");
 				getUniques();
 
@@ -702,6 +704,7 @@ int ShhherCommand::execute(){
 			double begClock = clock();
 			unsigned long int begTime = time(NULL);
 
+			
 			m->mothurOut("\nDenoising flowgrams...\n");
 			m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
 			
@@ -761,6 +764,11 @@ void ShhherCommand::getFlowData(){
 		m->openInputFile(flowFileName, flowFile);
 		
 		string seqName;
+		seqNameVector.clear();
+		lengths.clear();
+		flowDataIntI.clear();
+		nameMap.clear();
+		
 		
 		int currentNumFlowCells;
 		
@@ -943,7 +951,7 @@ 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) {
@@ -1097,7 +1105,7 @@ string ShhherCommand::createDistFile(int processors){
 
 		m->mothurOutEndLine();
 		
-		m-mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
+		m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
 		
 
 		return fDistFileName;
@@ -1203,7 +1211,11 @@ void ShhherCommand::getOTUData(string listFileName){
 		otuData.assign(numSeqs, 0);
 		cumNumSeqs.assign(numOTUs, 0);
 		nSeqsPerOTU.assign(numOTUs, 0);
-		aaP.resize(numOTUs);
+		aaP.clear();aaP.resize(numOTUs);
+		
+		seqNumber.clear();
+		aaI.clear();
+		seqIndex.clear();
 		
 		string singleOTU = "";
 		
@@ -1255,6 +1267,8 @@ void ShhherCommand::getOTUData(string listFileName){
 			for(int j=nSeqsPerOTU[i];j<numSeqs;j++){
 				aaP[i].push_back(0);
 			}
+			
+			
 		}
 		
 		for(int i=1;i<numOTUs;i++){
@@ -1264,6 +1278,7 @@ void ShhherCommand::getOTUData(string listFileName){
 		seqIndex = seqNumber;
 		
 		listFile.close();	
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ShhherCommand", "getOTUData");
@@ -1382,6 +1397,7 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){
 	
 	try{
 		
+	
 		for(int i=start;i<finish;i++){
 			
 			double count = 0;
@@ -1393,7 +1409,7 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){
 			for(int j=0;j<nSeqsPerOTU[i];j++){
 				count += singleTau[seqNumber[cumNumSeqs[i] + j]];
 			}
-			
+
 			if(nSeqsPerOTU[i] > 0 && count > MIN_COUNT){
 				vector<double> adF(nSeqsPerOTU[i]);
 				vector<int> anL(nSeqsPerOTU[i]);
@@ -1673,9 +1689,9 @@ 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();