*** empty log message ***

diff --git a/makefile b/makefile
index caa73572d0911d5dc8f7ddce2f3b08a88bb47ee3..6ac7e31c49b396397c946010777800a1e29993c2 100644 (file)
--- a/makefile
+++ b/makefile
@@ -9,12 +9,18 @@
 # Macros
 #
 
-# Optimize to level 3:
+USEMPI ?= yes
+64BIT_VERSION ?= yes
+USEREADLINE ?= yes
+CYGWIN_BUILD ?= no
+USECOMPRESSION ?= no
+MOTHUR_FILES = "\"../release\""
+RELEASE_DATE = "\"2/7/2011\""
+VERSION = "\"1.16.0\""
 
+# Optimize to level 3:
 CXXFLAGS += -O3
 
-64BIT_VERSION ?= yes
-
 ifeq  ($(strip $(64BIT_VERSION)),yes)
        #if you are using centos uncomment the following lines
        #CXX = g++44
@@ -28,10 +34,6 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
         CXXFLAGS += -DBIT_VERSION
 endif
 
-MOTHUR_FILES = "\"../release\""
-
-RELEASE_DATE = "\"2/7/2011\""
-VERSION = "\"1.16.0\""
 
 CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
 
@@ -40,7 +42,6 @@ else
        CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
 endif
 
-CYGWIN_BUILD ?= no
 ifeq  ($(strip $(CYGWIN_BUILD)),yes)
     CXXFLAGS += -mno-cygwin
     LDFLAGS += -mno-cygwin 
@@ -49,7 +50,6 @@ endif
 # if you do not want to use the readline library, set this to no.
 # make sure you have the library installed
 
-USEREADLINE ?= yes
 
 ifeq  ($(strip $(USEREADLINE)),yes)
     CXXFLAGS += -DUSE_READLINE
@@ -58,7 +58,6 @@ ifeq  ($(strip $(USEREADLINE)),yes)
       -lncurses
 endif
 
-USEMPI ?= no
 
 ifeq  ($(strip $(USEMPI)),yes)
     CXX = mpic++
@@ -68,7 +67,6 @@ endif
 # if you want to enable reading and writing of compressed files, set to yes.
 # The default is no.  this may only work on unix-like systems, not for windows.
 
-USECOMPRESSION ?= no
 
 ifeq  ($(strip $(USECOMPRESSION)),yes)
   CXXFLAGS += -DUSE_COMPRESSION

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 14eee605880e3dfa61333cc8eb437f23f7c3d6c5..5bf802ef304dde8c9d628db63a9e0915f23f236e 100644 (file)
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -252,11 +252,6 @@ int ShhherCommand::execute(){
 
                double begClock = clock();
                unsigned long int begTime = time(NULL);
-
-               cout.setf(ios::fixed, ios::floatfield);
-               cout.setf(ios::showpoint);
-               cout << setprecision(2);
-               
                
                if(pid == 0){
 
@@ -267,7 +262,7 @@ int ShhherCommand::execute(){
 
                        processors = ncpus;
                        
-                       cout << "\nGetting preliminary data..." << endl;
+                       m->mothurOut("\nGetting preliminary data...\n");
                        getSingleLookUp();
                        getJointLookUp();
                        
@@ -295,13 +290,14 @@ int ShhherCommand::execute(){
                        for(int i=0;i<numFiles;i++){
                                flowFileName = flowFileVector[i];
                        
-                               cout << "\n>>>>>\tProcessing " << flowFileName << " (file " << i+1 << " of " << numFiles << ")\t<<<<<" << endl;
-                               cout << "Reading flowgrams..." << endl;
+                               m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
+                               m->mothurOut("Reading flowgrams...\n");
+                               
                                getFlowData();
-                               cout << "Identifying unique flowgrams..." << endl;
+                               m->mothurOut("Identifying unique flowgrams...\n");
                                getUniques();
 
-                               cout << "Calculating distances between flowgrams..." << endl;
+                               m->mothurOut("Calculating distances between flowgrams...\n");
                                char fileName[1024];
                                strcpy(fileName, flowFileName.c_str());
 
@@ -332,7 +328,7 @@ int ShhherCommand::execute(){
 
                                string namesFileName = createNamesFile();
                                
-                               cout << "\nClustering flowgrams..." << endl;
+                               m->mothurOut("\nClustering flowgrams...\n");
                                string listFileName = cluster(distFileName, namesFileName);
 
                                getOTUData(listFileName);
@@ -351,9 +347,8 @@ int ShhherCommand::execute(){
                                
                                int numOTUsOnCPU = numOTUs / ncpus;
                                int numSeqsOnCPU = numSeqs / ncpus;
-                               
-                               cout << "\nDenoising flowgrams..." << endl;
-                               cout << "iter\tmaxDelta\tnLL\t\tcycletime" << endl;
+                               m->mothurOut("\nDenoising flowgrams...\n");
+                               m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
                                
                                while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 
@@ -454,7 +449,7 @@ int ShhherCommand::execute(){
                                        
                                        iter++;
                                        
-                                       cout << iter << '\t' << maxDelta << '\t' << setprecision(2) << nLL << '\t' << time(NULL) - cycTime << '\t' << setprecision(6) << (clock() - cycClock)/(double)CLOCKS_PER_SEC << endl;                   
+                                       m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');                  
 
                                        if((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
                                                int live = 1;
@@ -471,7 +466,7 @@ int ShhherCommand::execute(){
                                        
                                }       
                                
-                               cout << "\nFinalizing..." << endl;
+                               m->mothurOut("\nFinalizing...\n");
                                fill();
                                setOTUs();
                                vector<int> otuCounts(numOTUs, 0);
@@ -486,10 +481,9 @@ int ShhherCommand::execute(){
                                remove(distFileName.c_str());
                                remove(namesFileName.c_str());
                                remove(listFileName.c_str());
-                               
-                               cout << "Total time to process " << flowFileName << ":\t" << time(NULL) - begTime << '\t' << setprecision(6) << (clock() - begClock)/(double)CLOCKS_PER_SEC << endl;                    
+                                                                
+                               m->mothurOut("Total time to process " + toString(flowFileName) + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');                 
                        }
-
                }
                else{
                        int abort = 1;
@@ -632,10 +626,11 @@ string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
                                }
                        }
                        if(i % 100 == 0){
-                               cout << i << "\t" << (time(NULL) - begTime) << "\t" << (clock()-begClock)/CLOCKS_PER_SEC << endl;
+                               m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
                        }
                }
-               cout << stopSeq << "\t" << (time(NULL) - begTime) << "\t" << (clock()-begClock)/CLOCKS_PER_SEC << endl;
+               
+               m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
                
                string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.dist";
                if(pid != 0){   fDistFileName += ".temp." + toString(pid);      }
@@ -659,9 +654,6 @@ int ShhherCommand::execute(){
        try {
                if (abort == true) { return 0; }
                
-               cout.setf(ios::fixed, ios::floatfield);
-               cout.setf(ios::showpoint);
-               
                getSingleLookUp();
                getJointLookUp();
                                
@@ -686,18 +678,19 @@ int ShhherCommand::execute(){
                for(int i=0;i<numFiles;i++){
                        flowFileName = flowFileVector[i];
 
-                       cout << "\n>>>>>\tProcessing " << flowFileName << " (file " << i+1 << " of " << numFiles << ")\t<<<<<" << endl;
-                       cout << "Reading flowgrams..." << endl;
+                       m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
+                       m->mothurOut("Reading flowgrams...\n");
                        getFlowData();
-                       cout << "Identifying unique flowgrams..." << endl;
+                       
+                       m->mothurOut("Identifying unique flowgrams...\n");
                        getUniques();
                        
                        
-                       cout << "Calculating distances between flowgrams..." << endl;                   
+                       m->mothurOut("Calculating distances between flowgrams...\n");
                        string distFileName = createDistFile(processors);
                        string namesFileName = createNamesFile();
-                       
-                       cout << "\nClustering flowgrams..." << endl;
+                               
+                       m->mothurOut("\nClustering flowgrams...\n");
                        string listFileName = cluster(distFileName, namesFileName);
                        getOTUData(listFileName);
                        
@@ -709,8 +702,8 @@ int ShhherCommand::execute(){
                        double begClock = clock();
                        unsigned long int begTime = time(NULL);
 
-                       cout << "\nDenoising flowgrams..." << endl;
-                       cout << "iter\tmaxDelta\tnLL\t\tcycletime" << endl;
+                       m->mothurOut("\nDenoising flowgrams...\n");
+                       m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
                        
                        while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
                                
@@ -728,10 +721,11 @@ int ShhherCommand::execute(){
 
                                iter++;
                                
-                               cout << iter << '\t' << maxDelta << '\t' << setprecision(2) << nLL << '\t' << time(NULL) - cycTime << '\t' << setprecision(6) << (clock() - cycClock)/(double)CLOCKS_PER_SEC << endl;                   
+                               m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
+
                        }       
                        
-                       cout << "\nFinalizing..." << endl;
+                       m->mothurOut("\nFinalizing...\n");
                        fill();
                        setOTUs();
                        
@@ -749,7 +743,7 @@ int ShhherCommand::execute(){
                        remove(namesFileName.c_str());
                        remove(listFileName.c_str());
                        
-                       cout << "Total time to process " << flowFileName << ":\t" << time(NULL) - begTime << '\t' << setprecision(6) << (clock() - begClock)/(double)CLOCKS_PER_SEC << endl;                    
+                       m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
                }
                return 0;
        }
@@ -903,13 +897,19 @@ void ShhherCommand::getUniques(){
                        int index = 0;
                        
                        vector<short> current(numFlowCells);
-                       for(int j=0;j<numFlowCells;j++){        current[j] = short(((flowDataIntI[i * numFlowCells + j] + 50.0)/100.0));        }
+                       for(int j=0;j<numFlowCells;j++){
+                               current[j] = short(((flowDataIntI[i * numFlowCells + j] + 50.0)/100.0));
+                       }
                                                
                        for(int j=0;j<numUniques;j++){
                                int offset = j * numFlowCells;
                                bool toEnd = 1;
                                
-                               for(int k=0;k<numFlowCells;k++){
+                               int shorterLength;
+                               if(lengths[i] < uniqueLengths[j])       {       shorterLength = lengths[i];                     }
+                               else                                                            {       shorterLength = uniqueLengths[j];       }
+
+                               for(int k=0;k<shorterLength;k++){
                                        if(current[k] != uniqueFlowgrams[offset + k]){
                                                toEnd = 0;
                                                break;
@@ -920,6 +920,7 @@ void ShhherCommand::getUniques(){
                                        mapSeqToUnique[i] = j;
                                        uniqueCount[j]++;
                                        index = j;
+                                       if(lengths[i] > uniqueLengths[j])       {       uniqueLengths[j] = lengths[i];  }
                                        break;
                                }
                                index++;
@@ -1096,7 +1097,8 @@ string ShhherCommand::createDistFile(int processors){
 
                m->mothurOutEndLine();
                
-               cout << "Total time: " << (time(NULL) - begTime) << "\t"  << (clock() - begClock)/CLOCKS_PER_SEC << endl;;
+               m-mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
+               
 
                return fDistFileName;
        }
@@ -1141,9 +1143,6 @@ string ShhherCommand::createNamesFile(){
 string ShhherCommand::cluster(string distFileName, string namesFileName){
        try {
                
-               SparseMatrix* matrix;
-               ListVector* list;
-               RAbundVector* rabund;
                
                globaldata->setNameFile(namesFileName);
                globaldata->setColumnFile(distFileName);
@@ -1156,13 +1155,13 @@ string ShhherCommand::cluster(string distFileName, string namesFileName){
                clusterNameMap->readMap();
                read->read(clusterNameMap);
                
-               list = read->getListVector();
-               matrix = read->getMatrix();
+               ListVector* list = read->getListVector();
+               SparseMatrix* matrix = read->getMatrix();
                
                delete read; 
                delete clusterNameMap; 
                                
-               rabund = new RAbundVector(list->getRAbundVector());
+               RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
                
                Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest"); 
                string tag = cluster->getTag();