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

[mothur.git] / fastamap.cpp

diff --git a/fastamap.cpp b/fastamap.cpp
index 36b072121b044490332a8926f0f3f287bf816fab..95d3f3cfe34397f603aecca3dc62bd65dc38c634 100644 (file)
--- a/fastamap.cpp
+++ b/fastamap.cpp
@@ -15,7 +15,7 @@
 void FastaMap::readFastaFile(string inFileName) {
        try {
                ifstream in;
-               openInputFile(inFileName, in);
+               m->openInputFile(inFileName, in);
                string name, sequence, line;
                sequence = "";
                string temp;
@@ -41,7 +41,7 @@ void FastaMap::readFastaFile(string inFileName) {
                                        //                              data[sequence].groupnumber++;
                                }       
                        }
-                       gobble(in);
+                       m->gobble(in);
                }
                in.close();             
        }
@@ -56,7 +56,7 @@ void FastaMap::readFastaFile(string inFileName) {
 void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prints data
        
        ifstream oldNameFile;
-       openInputFile(oldNameFileName, oldNameFile);
+       m->openInputFile(oldNameFileName, oldNameFile);
        
        map<string,string> oldNameMap;
        string name, list;
@@ -65,12 +65,12 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
                
                oldNameFile >> name >> list;
                oldNameMap[name] = list;
-               gobble(oldNameFile);
+               m->gobble(oldNameFile);
        }
        oldNameFile.close();
        
        ifstream inFASTA;
-       openInputFile(inFastaFile, inFASTA);
+       m->openInputFile(inFastaFile, inFASTA);
        string sequence;
        while(!inFASTA.eof()){
                if (m->control_pressed) { break; }
@@ -93,7 +93,7 @@ void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prin
                                //                      data[sequence].groupnumber++;
                        }       
                }
-               gobble(inFASTA);
+               m->gobble(inFASTA);
        }
        
        
@@ -147,7 +147,7 @@ int FastaMap::sizeUnique(){ //returns datas size which is the number of unique s
 void FastaMap::printNamesFile(string outFileName){ //prints data
        try {
                ofstream outFile;
-               openOutputFile(outFileName, outFile);
+               m->openOutputFile(outFileName, outFile);
                
                // two column file created with groupname and them list of identical sequence names
                for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
@@ -167,7 +167,7 @@ void FastaMap::printNamesFile(string outFileName){ //prints data
 void FastaMap::printCondensedFasta(string outFileName){ //prints data
        try {
                ofstream out;
-               openOutputFile(outFileName, out);
+               m->openOutputFile(outFileName, out);
                //creates a fasta file
                for (map<string,group>::iterator it = data.begin(); it != data.end(); it++) {
                        if (m->control_pressed) { break; }