From: pschloss <pschloss>
Date: Tue, 15 Feb 2011 18:29:26 +0000 (+0000)
Subject: fixed bugg in  shhh.seqs command
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=c8419b3c5f3c9381f4360f1fbdd95e6749827ff7

fixed bugg in  shhh.seqs command
---

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 18266f9..511f0d6 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -16,7 +16,6 @@
 		A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
 		A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; };
 		A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; };
-		A799F6571309C22A00AEEFA0 /* anosimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F6561309C22A00AEEFA0 /* anosimcommand.cpp */; };
 		A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; };
 		A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; };
 		A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; };
@@ -324,8 +323,6 @@
 		A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = "<group>"; };
 		A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = "<group>"; };
 		A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = "<group>"; };
-		A799F6551309C22A00AEEFA0 /* anosimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = anosimcommand.h; sourceTree = "<group>"; };
-		A799F6561309C22A00AEEFA0 /* anosimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = anosimcommand.cpp; sourceTree = "<group>"; };
 		A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = "<group>"; };
 		A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = "<group>"; };
 		A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = "<group>"; };
@@ -1038,8 +1035,6 @@
 				A7E9B65212D37EC300DA6239 /* aligncommand.h */,
 				A7A61F2B130062E000E05B6B /* amovacommand.h */,
 				A7A61F2C130062E000E05B6B /* amovacommand.cpp */,
-				A799F6551309C22A00AEEFA0 /* anosimcommand.h */,
-				A799F6561309C22A00AEEFA0 /* anosimcommand.cpp */,
 				A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
 				A7E9B66112D37EC300DA6239 /* binsequencecommand.h */,
 				A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */,
@@ -1625,7 +1620,7 @@
 			attributes = {
 				ORGANIZATIONNAME = "Schloss Lab";
 			};
-			buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
+			buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
 			compatibilityVersion = "Xcode 3.1";
 			developmentRegion = English;
 			hasScannedForEncodings = 1;
@@ -1932,7 +1927,6 @@
 				A75790591301749D00A30DAB /* homovacommand.cpp in Sources */,
 				A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */,
 				A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */,
-				A799F6571309C22A00AEEFA0 /* anosimcommand.cpp in Sources */,
 			);
 			runOnlyForDeploymentPostprocessing = 0;
 		};
@@ -2048,7 +2042,7 @@
 			defaultConfigurationIsVisible = 0;
 			defaultConfigurationName = Release;
 		};
-		1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
+		1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
 				1DEB928A08733DD80010E9CD /* Debug */,
diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 39a27d5..b2b4de0 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)));
@@ -294,8 +294,8 @@ int ShhherCommand::execute(){
 				
 				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();
 
@@ -704,6 +704,10 @@ int ShhherCommand::execute(){
 			double begClock = clock();
 			unsigned long int begTime = time(NULL);
 
+			
+			cout << numOTUs << endl;
+			
+			
 			m->mothurOut("\nDenoising flowgrams...\n");
 			m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
 			
@@ -1210,7 +1214,7 @@ 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();
@@ -1266,6 +1270,8 @@ 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++){
@@ -1275,6 +1281,13 @@ void ShhherCommand::getOTUData(string listFileName){
 		seqIndex = seqNumber;
 		
 		listFile.close();	
+		
+		for(int i=0;i<seqNumber.size();i++){
+			cout << seqNumber[i] << ' ';
+		}
+		cout << endl;
+		
+		
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ShhherCommand", "getOTUData");
@@ -1295,6 +1308,8 @@ void ShhherCommand::initPyroCluster(){
 		nSeqsBreaks.assign(processors+1, 0);
 		nOTUsBreaks.assign(processors+1, 0);
 
+		cout << numSeqs << '\t' << numOTUs << '\t' << processors << endl;
+		
 		nSeqsBreaks[0] = 0;
 		for(int i=0;i<processors;i++){
 			nSeqsBreaks[i+1] = nSeqsBreaks[i] + (int)((double) numSeqs / (double) processors);
@@ -1393,6 +1408,10 @@ void ShhherCommand::calcCentroidsDriver(int start, int finish){
 	
 	try{
 		
+//		for(int i=0;i<seqNumber.size();i++){
+//			cout << seqNumber[i] << ' ';
+//		}cout << endl;
+		
 		for(int i=start;i<finish;i++){
 			
 			double count = 0;
@@ -1404,7 +1423,7 @@ 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]);