changed how we count sequences in a fastafile to allow for '>' in sequence names

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 1c70b3e493fd2c3bf407746f8f97ddb276b801ea..a6290a6afe55a28001e5e229e518a7c03c6a1c28 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -336,8 +336,9 @@ int FilterSeqsCommand::filterSequences() {
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                if(processors == 1){
                                        ifstream inFASTA;
+                                       int numFastaSeqs;
                                        openInputFile(fastafileNames[s], inFASTA);
-                                       int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                                       getNumSeqs(inFASTA, numFastaSeqs);
                                        inFASTA.close();
                                        
                                        lines.push_back(new linePair(0, numFastaSeqs));
@@ -361,8 +362,9 @@ int FilterSeqsCommand::filterSequences() {
                                if (m->control_pressed) {  return 1; }
                #else
                                ifstream inFASTA;
+                               int numFastaSeqs;
                                openInputFile(fastafileNames[s], inFASTA);
-                               int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numFastaSeqs);
                                inFASTA.close();
                                        
                                lines.push_back(new linePair(0, numFastaSeqs));
@@ -625,8 +627,9 @@ string FilterSeqsCommand::createFilter() {
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                if(processors == 1){
                                        ifstream inFASTA;
+                                       int numFastaSeqs;
                                        openInputFile(fastafileNames[s], inFASTA);
-                                       int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                                       getNumSeqs(inFASTA, numFastaSeqs);
                                        inFASTA.close();
                                        
                                        numSeqs += numFastaSeqs;
@@ -642,8 +645,9 @@ string FilterSeqsCommand::createFilter() {
                                if (m->control_pressed) {  return filterString; }
                #else
                                ifstream inFASTA;
+                               int numFastaSeqs;
                                openInputFile(fastafileNames[s], inFASTA);
-                               int numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                               getNumSeqs(inFASTA, numFastaSeqs);
                                inFASTA.close();
                                
                                numSeqs += numFastaSeqs;