X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=readcluster.cpp;fp=readcluster.cpp;h=205581c72ab26bd767a0a4c47fdfcb3d73e124d5;hp=af71cbc96f1cca200bb8e5f66258703917f6ac53;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hpb=d84bb41d7dadcfa2c67ce5edb9b94060e5659fa7

diff --git a/readcluster.cpp b/readcluster.cpp
index af71cbc..205581c 100644
--- 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();