X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=readcluster.cpp;h=205581c72ab26bd767a0a4c47fdfcb3d73e124d5;hb=a537fefa3bd2c2eba7d532249375b6a11b295e25;hp=c8a8bc7b5074bf91ea46e2c30f2364a509d2c5ff;hpb=e189982e0a9b7352ad57cc38ccee675f128be22e;p=mothur.git

diff --git a/readcluster.cpp b/readcluster.cpp
index c8a8bc7..205581c 100644
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -11,12 +11,14 @@
 
 /***********************************************************************/
 
-ReadCluster::ReadCluster(string distfile, float c, string o){
+ReadCluster::ReadCluster(string distfile, float c, string o, bool s){
 		globaldata = GlobalData::getInstance();
 		m = MothurOut::getInstance();
         distFile = distfile;
 		cutoff = c;
 		outputDir = o;
+		sortWanted = s;
+		list = NULL;
 }
 
 /***********************************************************************/
@@ -29,7 +31,8 @@ int ReadCluster::read(NameAssignment* nameMap){
 		
 		if (m->control_pressed) { return 0; }
 		
-		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;
 			
@@ -51,8 +54,8 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 		ofstream out;
 		string tempFile = distFile + ".column.temp";
 		
-		openInputFile(distFile, in);
-		openOutputFile(tempFile, out);
+		m->openInputFile(distFile, in);  m->gobble(in);
+		m->openOutputFile(tempFile, out);
 		
 		float distance;
 		int square, nseqs;
@@ -174,7 +177,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 		list->setLabel("0");
 		in.close();
 		out.close();
-		
+	
 		if(nameMap == NULL){
 			nameMap = new NameAssignment();
 			for(int i=0;i<matrixNames.size();i++){
@@ -187,9 +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;
@@ -199,14 +202,14 @@ 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();
 		
 		remove(tempFile.c_str());
 		distFile = outputFile;
-		
+	
 		if (m->control_pressed) {  remove(outputFile.c_str());  }
 
 		return 0;