From 5eca3348fe3962b8965236ca877ef6f52e8fb104 Mon Sep 17 00:00:00 2001
From: pschloss <pschloss>
Date: Fri, 23 Dec 2011 16:15:16 +0000
Subject: [PATCH] *** empty log message ***

---
 bayesian.cpp      | 26 +++++++++++++-------------
 classify.cpp      | 10 +++++-----
 makefile          |  6 +++---
 shhhercommand.cpp |  3 +--
 4 files changed, 22 insertions(+), 23 deletions(-)

diff --git a/bayesian.cpp b/bayesian.cpp
index d62bb23..b1f2c4c 100644
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -111,8 +111,8 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
 			//cout << numKmers << '\t' << genusNodes.size() << endl;
 				for (int j = 0; j < wordGenusProb.size(); j++) {	wordGenusProb[j].resize(genusNodes.size());		}
 			//cout << numKmers << '\t' << genusNodes.size() << endl;	
-				ofstream out;
-				ofstream out2;
+				//ofstream out;
+				//ofstream out2;
 				
 				#ifdef USE_MPI
 					int pid;
@@ -122,17 +122,17 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
 				#endif
 
 				
-				m->openOutputFile(probFileName, out);
+				//m->openOutputFile(probFileName, out);
 				
 				//output mothur version
-				out << "#" << m->getVersion() << endl;
+				//out << "#" << m->getVersion() << endl;
 				
-				out << numKmers << endl;
+				//out << numKmers << endl;
 				
-				m->openOutputFile(probFileName2, out2);
+				//m->openOutputFile(probFileName2, out2);
 				
 				//output mothur version
-				out2 << "#" << m->getVersion() << endl;
+				//out2 << "#" << m->getVersion() << endl;
 				
 				#ifdef USE_MPI
 					}
@@ -149,7 +149,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
 						if (pid == 0) {  
 					#endif
 
-					out << i << '\t';
+					//out << i << '\t';
 					
 					#ifdef USE_MPI
 						}
@@ -184,7 +184,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
 								if (pid == 0) {  
 							#endif
 
-							out << k << '\t' << wordGenusProb[i][k] << '\t'; 
+							//out << k << '\t' << wordGenusProb[i][k] << '\t'; 
 							
 							#ifdef USE_MPI
 								}
@@ -200,8 +200,8 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
 						if (pid == 0) {  
 					#endif
 					
-					out << endl;
-					out2 << probabilityInTemplate << '\t' << numNotZero << endl;
+					//out << endl;
+					//out2 << probabilityInTemplate << '\t' << numNotZero << endl;
 					
 					#ifdef USE_MPI
 						}
@@ -214,8 +214,8 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
 					if (pid == 0) {  
 				#endif
 				
-				out.close();
-				out2.close();
+				//out.close();
+				//out2.close();
 				
 				#ifdef USE_MPI
 					}
diff --git a/classify.cpp b/classify.cpp
index 25aa2dd..c92d9fd 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -61,7 +61,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 					names.push_back(temp.getName());
 					database->addSequence(temp);	
 				}
-				database->generateDB();
+//				database->generateDB();
 			}else if ((method == "kmer") && (!needToGenerate)) {	
 				ifstream kmerFileTest(kmerDBName.c_str());
 				database->readKmerDB(kmerFileTest);	
@@ -150,7 +150,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 					}
 				}
 				
-				database->generateDB();
+//				database->generateDB();
 				MPI_File_close(&inMPI);
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 		#else
@@ -200,7 +200,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 				}
 				fastaFile.close();
 
-				database->generateDB();
+//				database->generateDB();
 				
 			}else if ((method == "kmer") && (!needToGenerate)) {	
 				ifstream kmerFileTest(kmerDBName.c_str());
@@ -223,9 +223,9 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 			database->setNumSeqs(names.size());
 			
 			//sanity check
-			bool okay = phyloTree->ErrorCheck(names);
+			//bool okay = phyloTree->ErrorCheck(names);
 			
-			if (!okay) { m->control_pressed = true; }
+			//if (!okay) { m->control_pressed = true; }
 			
 			m->mothurOut("DONE."); m->mothurOutEndLine();
 			m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
diff --git a/makefile b/makefile
index 90e4957..c7dc1fd 100644
--- a/makefile
+++ b/makefile
@@ -24,10 +24,10 @@ CXXFLAGS += -O3
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
 	#if you are using centos uncomment the following lines
-	#CXX = g++44
+	CXX = g++44
 	
 	#if you are a mac user use the following line
-	TARGET_ARCH += -arch x86_64
+#	TARGET_ARCH += -arch x86_64
 	
 	#if you using cygwin to build Windows the following line
 	#CXX = x86_64-w64-mingw32-g++
@@ -35,7 +35,7 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
  	#TARGET_ARCH += -m64 -static
 
 	#if you are a linux user use the following line
-	#CXXFLAGS += -mtune=native -march=native -m64
+	CXXFLAGS += -mtune=native -march=native -m64
 	
 	 CXXFLAGS += -DBIT_VERSION
 endif
diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 3c46793..13e7ccf 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -1501,9 +1501,8 @@ void ShhherCommand::getOTUData(string listFileName){
 
 void ShhherCommand::initPyroCluster(){                          
 	try{
-		
 		if (numOTUs < processors) { processors = 1; }
-		
+
 		dist.assign(numSeqs * numOTUs, 0);
 		change.assign(numOTUs, 1);
 		centroids.assign(numOTUs, -1);
-- 
2.39.2