some changes while testing 1.9

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index a9f0a36a2a440e17e8f4f433954c766abba041ed..26df57ffbb56d6ddd0cc3532013c2be65fe5e3f8 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -313,6 +313,7 @@ int ClassifySeqsCommand::execute(){
                        for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                        
 #ifdef USE_MPI 
+
                                int pid, end, numSeqsPerProcessor; 
                                int tag = 2001;
                                vector<long> MPIPos;
@@ -392,6 +393,7 @@ int ClassifySeqsCommand::execute(){
                                MPI_File_close(&outMPITempTax);
                                
 #else
+
                        //read namefile
                        if(namefile != "") {
                                nameMap.clear(); //remove old names
@@ -469,7 +471,9 @@ int ClassifySeqsCommand::execute(){
                        driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
        #endif  
 #endif
-
+               
+               delete classify;
+               
                #ifdef USE_MPI  
                        if (pid == 0) {  //this part does not need to be paralellized
                #endif
@@ -484,6 +488,7 @@ int ClassifySeqsCommand::execute(){
                
                        //read in users taxonomy file and add sequences to tree
                        string name, taxon;
+
                        while(!in.eof()){
                                in >> name >> taxon; gobble(in);
                                
@@ -561,7 +566,6 @@ int ClassifySeqsCommand::execute(){
                        m->mothurOut("It took " + toString(time(NULL) - start) + " secs to classify " + toString(numFastaSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
                }
                
-               delete classify;
                return 0;
        }
        catch(exception& e) {
@@ -677,13 +681,13 @@ int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFNa
                        if (m->control_pressed) { return 0; }
                        
                        Sequence* candidateSeq = new Sequence(inFASTA);
-                       
+       
                        if (candidateSeq->getName() != "") {
                                taxonomy = classify->getTaxonomy(candidateSeq);
                                
                                if (m->control_pressed) { delete candidateSeq; return 0; }
 
-                               if (taxonomy != "bad seq") {
+                               if ((taxonomy != "bad seq") && (taxonomy != "")) {
                                        //output confidence scores or not
                                        if (probs) {
                                                outTax << candidateSeq->getName() << '\t' << taxonomy << endl;
@@ -692,7 +696,7 @@ int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFNa
                                        }
                                        
                                        outTaxSimple << candidateSeq->getName() << '\t' << classify->getSimpleTax() << endl;
-                               }
+                               }else{  m->mothurOut("Sequence: " + candidateSeq->getName() + " is bad."); m->mothurOutEndLine();  }
                        }                               
                        delete candidateSeq;
                        
@@ -744,7 +748,7 @@ int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
                        if (candidateSeq->getName() != "") {
                                taxonomy = classify->getTaxonomy(candidateSeq);
                                
-                               if (taxonomy != "bad seq") {
+                               if ((taxonomy != "bad seq") && (taxonomy != ""))  {
                                        //output confidence scores or not
                                        if (probs) {
                                                outputString =  candidateSeq->getName() + "\t" + taxonomy + "\n";
@@ -764,7 +768,7 @@ int ClassifySeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
                                        strcpy(buf, outputString.c_str()); 
                                
                                        MPI_File_write_shared(tempFile, buf, length, MPI_CHAR, &statusTemp);
-                               }
+                               }else{  cout << "Sequence: " << candidateSeq->getName() << " is bad." << endl;  }
                        }                               
                        delete candidateSeq;