sens.spec changes

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 7d015a85aed7e084926a918888f6e5ee761228cc..6c5d827d6553eac7f8ca8696091dd3ab7c87e4f3 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -320,7 +320,7 @@ void ClassifySeqsCommand::help(){
                m->mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
                m->mothurOut("The numwanted parameter allows you to specify the number of sequence matches you want with the knn method.  The default is 10.\n");
                m->mothurOut("The cutoff parameter allows you to specify a bootstrap confidence threshold for your taxonomy.  The default is 0.\n");
-               m->mothurOut("The probs parameter shut off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be run.\n");
+               m->mothurOut("The probs parameter shuts off the bootstrapping results for the bayesian method. The default is true, meaning you want the bootstrapping to be shown.\n");
                m->mothurOut("The iters parameter allows you to specify how many iterations to do when calculating the bootstrap confidence score for your taxonomy with the bayesian method.  The default is 100.\n");
                m->mothurOut("The classify.seqs command should be in the following format: \n");
                m->mothurOut("classify.seqs(template=yourTemplateFile, fasta=yourFastaFile, method=yourClassificationMethod, search=yourSearchmethod, ksize=yourKmerSize, taxonomy=yourTaxonomyFile, processors=yourProcessors) \n");
@@ -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));
@@ -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));