working on sffinfo

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index e5c04949905d7edd6ba5ec45f4fd5a8214053471..2a210b01ad3a8fb0812c1877595028a851bdbee7 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -470,7 +470,7 @@ int ClassifySeqsCommand::execute(){
                        if(processors == 1){
                                ifstream inFASTA;
                                openInputFile(fastaFileNames[s], inFASTA);
-                               numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numFastaSeqs);
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numFastaSeqs));
@@ -478,7 +478,7 @@ int ClassifySeqsCommand::execute(){
                                driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
                        }
                        else{
-                               vector<int> positions;
+                               vector<unsigned long int> positions;
                                processIDS.resize(0);
                                
                                ifstream inFASTA;
@@ -488,7 +488,7 @@ int ClassifySeqsCommand::execute(){
                                while(!inFASTA.eof()){
                                        input = getline(inFASTA);
                                        if (input.length() != 0) {
-                                               if(input[0] == '>'){    int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);       }
+                                               if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
                                        }
                                }
                                inFASTA.close();
@@ -496,9 +496,9 @@ int ClassifySeqsCommand::execute(){
                                numFastaSeqs = positions.size();
                                
                                int numSeqsPerProcessor = numFastaSeqs / processors;
-                               
+       
                                for (int i = 0; i < processors; i++) {
-                                       int startPos = positions[ i * numSeqsPerProcessor ];
+                                       unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
                                        if(i == processors - 1){
                                                numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
                                        }
@@ -520,7 +520,7 @@ int ClassifySeqsCommand::execute(){
        #else
                        ifstream inFASTA;
                        openInputFile(fastaFileNames[s], inFASTA);
-                       numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                       getNumSeqs(inFASTA, numFastaSeqs);
                        inFASTA.close();
                        
                        lines.push_back(new linePair(0, numFastaSeqs));
@@ -761,9 +761,9 @@ int ClassifySeqsCommand::driver(linePair* line, string taxFName, string tempTFNa
 
                for(int i=0;i<line->numSeqs;i++){
                        if (m->control_pressed) { return 0; }
-                       
-                       Sequence* candidateSeq = new Sequence(inFASTA);
-                       
+               
+                       Sequence* candidateSeq = new Sequence(inFASTA); gobble(inFASTA);
+               
                        if (candidateSeq->getName() != "") {
                                taxonomy = classify->getTaxonomy(candidateSeq);