added versioning info to all shortcut files mothur makes.

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 7f451261550a949b3a1cbb7ab72fd374122597bb..59a615881418f25ace4a0db84b1a0d35f9d9fcd5 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();
                }
 
@@ -108,7 +108,10 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        
                        kmerDBName = tempFile.substr(0,tempFile.find_last_of(".")+1) + char('0'+ kmerSize) + "mer";
                        ifstream kmerFileTest(kmerDBName.c_str());
-                       if(kmerFileTest){       needToGenerate = false;         }
+                       if(kmerFileTest){       
+                               bool GoodFile = checkReleaseVersion(kmerFileTest, m->getVersion());
+                               if (GoodFile) {  needToGenerate = false;        }
+                       }
                }
                else if(method == "suffix")             {       database = new SuffixDB(numSeqs);                                                               }
                else if(method == "blast")              {       database = new BlastDB(gapOpen, gapExtend, match, misMatch);    }
@@ -138,7 +141,7 @@ 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 +153,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        }
                        fastaFile.close();
                }
-#endif         
+#endif 
+       
                database->setNumSeqs(names.size());
                
                //sanity check
@@ -182,7 +186,7 @@ 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; 
@@ -253,7 +257,7 @@ int Classify::readTaxonomy(string file) {
                phyloTree->assignHeirarchyIDs(0);
                
                phyloTree->setUp(file);
-               
+       
                m->mothurOut("DONE.");
                m->mothurOutEndLine();  cout.flush();