moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / classify.cpp

diff --git a/classify.cpp b/classify.cpp
index 59a615881418f25ace4a0db84b1a0d35f9d9fcd5..875628d85d8dbcb4caf6d712b41be517eefef733 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();
                }
 
@@ -109,7 +109,7 @@ 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){       
-                               bool GoodFile = checkReleaseVersion(kmerFileTest, m->getVersion());
+                               bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
                                if (GoodFile) {  needToGenerate = false;        }
                        }
                }
@@ -124,11 +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());
                                                        
@@ -143,11 +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());
                        }
@@ -204,7 +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++) { 
@@ -239,7 +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()) {
@@ -249,7 +249,7 @@ int Classify::readTaxonomy(string file) {
                        
                        phyloTree->addSeqToTree(name, taxInfo);
                
-                       gobble(inTax);
+                       m->gobble(inTax);
                }
                inTax.close();
 #endif