added cluster.split command

[mothur.git] / readcluster.cpp

diff --git a/readcluster.cpp b/readcluster.cpp
index c8a8bc7b5074bf91ea46e2c30f2364a509d2c5ff..0893a146a84c9e71eb95475eabe66c2b80314c93 100644 (file)
--- 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 = sortFile(distFile, outputDir);  }
+               else {  OutPutFile = distFile;   } //for use by clusters splitMatrix to convert a phylip matrix to column
                
                return 0;