sens.spec changes

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index c5407ca345a2ff7bdec2ed47089f7e10d1df1fc3..16006f72e602e37270d3f2f8396245f921bd064f 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -267,26 +267,14 @@ int AlignCommand::execute(){
                                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                                int inMode=MPI_MODE_RDONLY; 
                                
-                               //char* outAlignFilename = new char[alignFileName.length()];
-                               //memcpy(outAlignFilename, alignFileName.c_str(), alignFileName.length());
-                               
                                char outAlignFilename[1024];
                                strcpy(outAlignFilename, alignFileName.c_str());
-
-                               //char* outReportFilename = new char[reportFileName.length()];
-                               //memcpy(outReportFilename, reportFileName.c_str(), reportFileName.length());
                                
                                char outReportFilename[1024];
                                strcpy(outReportFilename, reportFileName.c_str());
-
-                               //char* outAccnosFilename = new char[accnosFileName.length()];
-                               //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
                                
                                char outAccnosFilename[1024];
                                strcpy(outAccnosFilename, accnosFileName.c_str());
-
-                               //char* inFileName = new char[candidateFileNames[s].length()];
-                               //memcpy(inFileName, candidateFileNames[s].c_str(), candidateFileNames[s].length());
                                
                                char inFileName[1024];
                                strcpy(inFileName, candidateFileNames[s].c_str());
@@ -373,7 +361,7 @@ int AlignCommand::execute(){
                        if(processors == 1){
                                ifstream inFASTA;
                                openInputFile(candidateFileNames[s], inFASTA);
-                               numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numFastaSeqs);
                                inFASTA.close();
                                
                                lines.push_back(new linePair(0, numFastaSeqs));
@@ -472,7 +460,7 @@ int AlignCommand::execute(){
        #else
                        ifstream inFASTA;
                        openInputFile(candidateFileNames[s], inFASTA);
-                       numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                       getNumSeqs(inFASTA, numFastaSeqs);
                        inFASTA.close();
                        
                        lines.push_back(new linePair(0, numFastaSeqs));