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

[mothur.git] / chimera.cpp

diff --git a/chimera.cpp b/chimera.cpp
index 685d6dbdbb990867dd4e4e49fe9b3aa4e46a270d..ae9ad9a46ef1ce5634c867219904857731bf3d6e 100644 (file)
--- a/chimera.cpp
+++ b/chimera.cpp
@@ -123,7 +123,7 @@ vector<Sequence*> Chimera::readSeqs(string file) {
                        //delete inFileName;
 
                        if (pid == 0) {
-                               positions = setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
+                               positions = m->setFilePosFasta(file, numSeqs); //fills MPIPos, returns numSeqs
 
                                //send file positions to all processes
                                for(int i = 1; i < processors; i++) { 
@@ -167,14 +167,14 @@ vector<Sequence*> Chimera::readSeqs(string file) {
        #else
 
                ifstream in;
-               openInputFile(file, in);
+               m->openInputFile(file, in);
                
                //read in seqs and store in vector
                while(!in.eof()){
                        
                        if (m->control_pressed) { return container; }
                        
-                       Sequence* current = new Sequence(in);  gobble(in);
+                       Sequence* current = new Sequence(in);  m->gobble(in);
                        
                        if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
                        else if (length != current->getAligned().length()) {    unaligned = true;       }
@@ -241,7 +241,7 @@ void Chimera::setMask(string filename) {
        #else
        
                        ifstream infile;
-                       openInputFile(filename, infile);
+                       m->openInputFile(filename, infile);
                        
                        if (!infile.eof()) {
                                Sequence temp(infile);