added pipeline commands which involved change to command factory and command class...

[mothur.git] / splitmatrix.cpp

diff --git a/splitmatrix.cpp b/splitmatrix.cpp
index b7a3b49362dbd7c67f54649ba1b846a5c7cf6c79..dcc5b50ef8b396d9186c755c3ba949f9c789cf64 100644 (file)
--- a/splitmatrix.cpp
+++ b/splitmatrix.cpp
@@ -24,12 +24,13 @@ SplitMatrix::SplitMatrix(string distfile, string name, string tax, float c, stri
 }
 /***********************************************************************/
 
-SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, string t, int p, string output){
+SplitMatrix::SplitMatrix(string ffile, string name, string tax, float c, float cu, string t, int p, string output){
        m = MothurOut::getInstance();
        fastafile = ffile;
        namefile = name;
        taxFile = tax;
-       cutoff = c;
+       cutoff = c;  //tax level cutoff
+       distCutoff = cu; //for fasta method if you are creating distance matrix you need a cutoff for that
        method = t;
        processors = p;
        outputDir = output;
@@ -181,7 +182,7 @@ int SplitMatrix::createDistanceFilesFromTax(map<string, int>& seqGroup, int numG
                //process each distance file
                for (int i = 0; i < numGroups; i++) { 
                        
-                       string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(cutoff);
+                       string options = "fasta=" + (fastafile + "." + toString(i) + ".temp") + ", processors=" + toString(processors) + ", cutoff=" + toString(distCutoff);
                        
                        Command* command = new DistanceCommand(options);
                        command->execute();