fixes while testing 1.12.0

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 7f451261550a949b3a1cbb7ab72fd374122597bb..9a2de1fa46d78e99f8909abd729fb6f24e00bdf0 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -28,7 +28,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                m->mothurOut("Generating search database...    "); cout.flush();
 #ifdef USE_MPI 
                        int pid, processors;
-                       vector<long> positions;
+                       vector<unsigned long int> positions;
                        int tag = 2001;
                
                        MPI_Status status; 
@@ -97,7 +97,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                if (method == "suffix") {
                        ifstream inFASTA;
                        openInputFile(tempFile, inFASTA);
-                       numSeqs = count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+                       getNumSeqs(inFASTA, numSeqs);
                        inFASTA.close();
                }
 
@@ -138,7 +138,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                }else if ((method == "kmer") && (!needToGenerate)) {    
                        ifstream kmerFileTest(kmerDBName.c_str());
                        database->readKmerDB(kmerFileTest);     
-                       
+               
                        ifstream fastaFile;
                        openInputFile(tempFile, fastaFile);
                        
@@ -150,7 +150,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        }
                        fastaFile.close();
                }
-#endif         
+#endif 
+       
                database->setNumSeqs(names.size());
                
                //sanity check
@@ -182,7 +183,7 @@ int Classify::readTaxonomy(string file) {
 
 #ifdef USE_MPI 
                int pid, num, processors;
-               vector<long> positions;
+               vector<unsigned long int> positions;
                int tag = 2001;
                
                MPI_Status status;