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

[mothur.git] / readcluster.cpp

diff --git a/readcluster.cpp b/readcluster.cpp
index af71cbc96f1cca200bb8e5f66258703917f6ac53..205581c72ab26bd767a0a4c47fdfcb3d73e124d5 100644 (file)
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -31,7 +31,7 @@ int ReadCluster::read(NameAssignment* nameMap){
                
                if (m->control_pressed) { return 0; }
                
-               if (sortWanted) {  OutPutFile = sortFile(distFile, outputDir);  }
+               if (sortWanted) {  OutPutFile = m->sortFile(distFile, outputDir);  }
                else {  OutPutFile = distFile;   } //for use by clusters splitMatrix to convert a phylip matrix to column
                
                return 0;
@@ -54,8 +54,8 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                ofstream out;
                string tempFile = distFile + ".column.temp";
                
-               openInputFile(distFile, in);  gobble(in);
-               openOutputFile(tempFile, out);
+               m->openInputFile(distFile, in);  m->gobble(in);
+               m->openOutputFile(tempFile, out);
                
                float distance;
                int square, nseqs;
@@ -190,9 +190,9 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                ifstream in2;
                ofstream out2;
                
-               string outputFile = getRootName(distFile) + "column.dist";
-               openInputFile(tempFile, in2);
-               openOutputFile(outputFile, out2);
+               string outputFile = m->getRootName(distFile) + "column.dist";
+               m->openInputFile(tempFile, in2);
+               m->openOutputFile(outputFile, out2);
                
                int first, second;
                float dist;
@@ -202,7 +202,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
                        
                        in2 >> first >> second >> dist;
                        out2 << rowToName[first] << '\t' << rowToName[second] << '\t' << dist << endl;
-                       gobble(in2);
+                       m->gobble(in2);
                }
                in2.close();
                out2.close();