X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readcluster.cpp;h=af71cbc96f1cca200bb8e5f66258703917f6ac53;hb=2a07f8664a7fd1ef0d572b88e8b5bede24cc0b3c;hp=acbebaeece94faf995cd9d1a26112e40185314b8;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/readcluster.cpp b/readcluster.cpp
index acbebae..af71cbc 100644
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -11,11 +11,14 @@
 
 /***********************************************************************/
 
-ReadCluster::ReadCluster(string distfile, float c){
+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;
 }
 
 /***********************************************************************/
@@ -28,7 +31,8 @@ int ReadCluster::read(NameAssignment* nameMap){
 		
 		if (m->control_pressed) { return 0; }
 		
-		OutPutFile = sortFile(distFile);
+		if (sortWanted) {  OutPutFile = sortFile(distFile, outputDir);  }
+		else {  OutPutFile = distFile;   } //for use by clusters splitMatrix to convert a phylip matrix to column
 		
 		return 0;
 			
@@ -50,7 +54,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 		ofstream out;
 		string tempFile = distFile + ".column.temp";
 		
-		openInputFile(distFile, in);
+		openInputFile(distFile, in);  gobble(in);
 		openOutputFile(tempFile, out);
 		
 		float distance;
@@ -173,7 +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++){
@@ -205,7 +209,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment* nameMap){
 		
 		remove(tempFile.c_str());
 		distFile = outputFile;
-		
+	
 		if (m->control_pressed) {  remove(outputFile.c_str());  }
 
 		return 0;