added processors to pre.cluster for mac and windows. Fixed bug in reNameFile function...

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 678912c2076a10af0580f9b778238e3134542c44..47f55311cc6037a7dca827338d51ab903027fc40 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -11,6 +11,7 @@
 #include "readphylip.h"
 #include "readcolumn.h"
 #include "readmatrix.hpp"
+#include "clusterdoturcommand.h"
 
 //**********************************************************************************************************************
 vector<string> ClusterCommand::setParameters(){        
@@ -207,7 +208,7 @@ ClusterCommand::ClusterCommand(string option)  {
                        timing = validParameter.validFile(parameters, "timing", false);
                        if (timing == "not found") { timing = "F"; }
                        
-                       }
+               }
        }
        catch(exception& e) {
                m->errorOut(e, "ClusterCommand", "ClusterCommand");
@@ -223,6 +224,34 @@ int ClusterCommand::execute(){
        
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
+               //phylip file given and cutoff not given - use cluster.classic because it uses less memory and is faster
+               if ((format == "phylip") && (cutoff > 10.0)) {
+                       m->mothurOutEndLine(); m->mothurOut("You are using a phylip file and no cutoff.  I will run cluster.classic to save memory and time."); m->mothurOutEndLine();
+                       
+                       //run unique.seqs for deconvolute results
+                       string inputString = "phylip=" + distfile;
+                       if (namefile != "") { inputString += ", name=" + namefile; }
+                       inputString += ", precision=" + toString(precision);
+                       inputString += ", method=" + method;
+                       if (hard)       { inputString += ", hard=T";    }
+                       else            { inputString += ", hard=F";    }
+                       if (sim)        { inputString += ", sim=T";             }
+                       else            { inputString += ", sim=F";             }
+
+                       
+                       m->mothurOutEndLine(); 
+                       m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine(); 
+                       m->mothurOut("Running command: cluster.classic(" + inputString + ")"); m->mothurOutEndLine(); 
+                       
+                       Command* clusterClassicCommand = new ClusterDoturCommand(inputString);
+                       clusterClassicCommand->execute();
+                       delete clusterClassicCommand;
+                       
+                       m->mothurOut("/------------------------------------------------------------/"); m->mothurOutEndLine();  
+
+                       return 0;
+               }
+               
                ReadMatrix* read;
                if (format == "column") { read = new ReadColumnMatrix(columnfile, sim); }       //sim indicates whether its a similarity matrix
                else if (format == "phylip") { read = new ReadPhylipMatrix(phylipfile, sim); }