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

[mothur.git] / blastdb.cpp

diff --git a/blastdb.cpp b/blastdb.cpp
index d8a04da762b65406af2d43062460de9324d41f61..979d507c23d61b4537d62a1a4736721624616fb2 100644 (file)
--- a/blastdb.cpp
+++ b/blastdb.cpp
@@ -69,7 +69,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                vector<int> topMatches;
                
                ofstream queryFile;
-               openOutputFile((queryFileName+seq->getName()), queryFile);
+               m->openOutputFile((queryFileName+seq->getName()), queryFile);
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
@@ -84,11 +84,11 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                system(blastCommand.c_str());
                
                ifstream m8FileHandle;
-               openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+               m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
                
                string dummy;
                int templateAccession;
-               gobble(m8FileHandle);
+               m->gobble(m8FileHandle);
                
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore;
@@ -96,7 +96,7 @@ vector<int> BlastDB::findClosestSequences(Sequence* seq, int n) {
                        //get rest of junk in line
                        while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       } 
                        
-                       gobble(m8FileHandle);
+                       m->gobble(m8FileHandle);
                        topMatches.push_back(templateAccession);
                }
                m8FileHandle.close();
@@ -118,7 +118,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                vector<int> topMatches;
                
                ofstream queryFile;
-               openOutputFile((queryFileName+seq->getName()), queryFile);
+               m->openOutputFile((queryFileName+seq->getName()), queryFile);
                queryFile << '>' << seq->getName() << endl;
                queryFile << seq->getUnaligned() << endl;
                queryFile.close();
@@ -132,11 +132,11 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                system(blastCommand.c_str());
 
                ifstream m8FileHandle;
-               openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
+               m->openInputFile(blastFileName+seq->getName(), m8FileHandle, "no error");
        
                string dummy;
                int templateAccession;
-               gobble(m8FileHandle);
+               m->gobble(m8FileHandle);
                
                while(!m8FileHandle.eof()){
                        m8FileHandle >> dummy >> templateAccession >> searchScore;
@@ -144,7 +144,7 @@ vector<int> BlastDB::findClosestMegaBlast(Sequence* seq, int n) {
                        //get rest of junk in line
                        while (!m8FileHandle.eof())     {       char c = m8FileHandle.get(); if (c == 10 || c == 13){   break;  }       } 
                        
-                       gobble(m8FileHandle);
+                       m->gobble(m8FileHandle);
                        topMatches.push_back(templateAccession);
 //cout << templateAccession << endl;
                }
@@ -164,7 +164,7 @@ void BlastDB::addSequence(Sequence seq) {
        try {
        
                ofstream unalignedFastaFile;
-               openOutputFileAppend(dbFileName, unalignedFastaFile);                           
+               m->openOutputFileAppend(dbFileName, unalignedFastaFile);                                
        
                //      generating a fasta file with unaligned template
                unalignedFastaFile << '>' << count << endl;                                     //      sequences, which will be input to formatdb