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

[mothur.git] / alignmentdb.cpp

diff --git a/alignmentdb.cpp b/alignmentdb.cpp
index bdd3e0325a975dad66c4136d42db9697b3887d95..e2b1dc197eb8d3399156a3ca752bff5da267101f 100644 (file)
--- a/alignmentdb.cpp
+++ b/alignmentdb.cpp
@@ -40,7 +40,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                        MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
                        
                        if (pid == 0) {
-                               positions = setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
+                               positions = m->setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
 
                                //send file positions to all processes
                                for(int i = 1; i < processors; i++) { 
@@ -84,10 +84,10 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                
        #else
                ifstream fastaFile;
-               openInputFile(fastaFileName, fastaFile);
+               m->openInputFile(fastaFileName, fastaFile);
 
                while (!fastaFile.eof()) {
-                       Sequence temp(fastaFile);  gobble(fastaFile);
+                       Sequence temp(fastaFile);  m->gobble(fastaFile);
                        
                        if (m->control_pressed) {  templateSequences.clear(); break;  }
                        
@@ -124,7 +124,7 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
                                ifstream kmerFileTest(kmerDBName.c_str());
                                
                                if(kmerFileTest){       
-                                       bool GoodFile = checkReleaseVersion(kmerFileTest, m->getVersion());
+                                       bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
                                        if (GoodFile) {  needToGenerate = false;        }
                                }
                        #endif