took cout's from shhh.seqs

[mothur.git] / shhhercommand.cpp

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 5bf802ef304dde8c9d628db63a9e0915f23f236e..6833f5d4c1cae8f4ee0e3b6f3da3bd2474b31285 100644 (file)
--- 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();