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

[mothur.git] / ccode.cpp

diff --git a/ccode.cpp b/ccode.cpp
index c27644866c1f1d52c14a6f86b9f2002e9342d720..15e482a505494574dddbe56f995d3880e9557ac0 100644 (file)
--- a/ccode.cpp
+++ b/ccode.cpp
@@ -25,7 +25,7 @@ Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int num
        distCalc = new eachGapDist();
        decalc = new DeCalculator();
        
-       mapInfo = outputDir + getRootName(getSimpleName(fastafile)) + "mapinfo";
+       mapInfo = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "mapinfo";
        
        #ifdef USE_MPI
                
@@ -58,7 +58,7 @@ Ccode::Ccode(string filename, string temp, bool f, string mask, int win, int num
        #else
 
                ofstream out2;
-               openOutputFile(mapInfo, out2);
+               m->openOutputFile(mapInfo, out2);
                
                out2 << "Place in masked, filtered and trimmed sequence\tPlace in original alignment" << endl;
                out2.close();
@@ -78,7 +78,7 @@ int Ccode::print(ostream& out, ostream& outAcc) {
        try {
                
                ofstream out2;
-               openOutputFileAppend(mapInfo, out2);
+               m->openOutputFileAppend(mapInfo, out2);
                
                out2 << querySeq->getName() << endl;
                for (it = spotMap.begin(); it!= spotMap.end(); it++) {