X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readcluster.cpp;h=0893a146a84c9e71eb95475eabe66c2b80314c93;hb=725a3d4ff2442c79bfde0a75ed3e0904edcf03b7;hp=acbebaeece94faf995cd9d1a26112e40185314b8;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/readcluster.cpp b/readcluster.cpp
index acbebae..0893a14 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;