changed tags on temp blast db to include template name

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 9a2de1fa46d78e99f8909abd729fb6f24e00bdf0..8ea9e4bcf050ce505b3913e4038fc75e1b052272 100644 (file)
--- a/classify.cpp
+++ b/classify.cpp
@@ -46,7 +46,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        //delete inFileName;
 
                        if (pid == 0) { //only one process needs to scan file
-                               positions = setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs
+                               positions = m->setFilePosFasta(tempFile, numSeqs); //fills MPIPos, returns numSeqs
 
                                //send file positions to all processes
                                for(int i = 1; i < processors; i++) { 
@@ -96,8 +96,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                //need to know number of template seqs for suffixdb
                if (method == "suffix") {
                        ifstream inFASTA;
-                       openInputFile(tempFile, inFASTA);
-                       getNumSeqs(inFASTA, numSeqs);
+                       m->openInputFile(tempFile, inFASTA);
+                       m->getNumSeqs(inFASTA, numSeqs);
                        inFASTA.close();
                }
 
@@ -108,10 +108,13 @@ 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 = m->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);    }
+               else if(method == "blast")              {       database = new BlastDB(tempFile.substr(0,tempFile.find_last_of(".")+1), gapOpen, gapExtend, match, misMatch);   }
                else if(method == "distance")   {       database = new DistanceDB();    }
                else {
                        m->mothurOut(method + " is not a valid search option. I will run the command using kmer, ksize=8.");
@@ -121,11 +124,11 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                
                if (needToGenerate) {
                        ifstream fastaFile;
-                       openInputFile(tempFile, fastaFile);
+                       m->openInputFile(tempFile, fastaFile);
                        
                        while (!fastaFile.eof()) {
                                Sequence temp(fastaFile);
-                               gobble(fastaFile);
+                               m->gobble(fastaFile);
                        
                                names.push_back(temp.getName());
                                                        
@@ -140,11 +143,11 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
                        database->readKmerDB(kmerFileTest);     
                
                        ifstream fastaFile;
-                       openInputFile(tempFile, fastaFile);
+                       m->openInputFile(tempFile, fastaFile);
                        
                        while (!fastaFile.eof()) {
                                Sequence temp(fastaFile);
-                               gobble(fastaFile);
+                               m->gobble(fastaFile);
 
                                names.push_back(temp.getName());
                        }
@@ -201,7 +204,7 @@ int Classify::readTaxonomy(string file) {
                //delete inFileName;
 
                if (pid == 0) {
-                       positions = setFilePosEachLine(file, num);
+                       positions = m->setFilePosEachLine(file, num);
                        
                        //send file positions to all processes
                        for(int i = 1; i < processors; i++) { 
@@ -236,7 +239,7 @@ int Classify::readTaxonomy(string file) {
                MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else                          
                ifstream inTax;
-               openInputFile(file, inTax);
+               m->openInputFile(file, inTax);
        
                //read template seqs and save
                while (!inTax.eof()) {
@@ -246,7 +249,7 @@ int Classify::readTaxonomy(string file) {
                        
                        phyloTree->addSeqToTree(name, taxInfo);
                
-                       gobble(inTax);
+                       m->gobble(inTax);
                }
                inTax.close();
 #endif 
@@ -254,7 +257,7 @@ int Classify::readTaxonomy(string file) {
                phyloTree->assignHeirarchyIDs(0);
                
                phyloTree->setUp(file);
-               
+       
                m->mothurOut("DONE.");
                m->mothurOutEndLine();  cout.flush();