dist.seqs can now use n processors, and only outputs the phylip formatted distance...

[mothur.git] / globaldata.cpp

diff --git a/globaldata.cpp b/globaldata.cpp
index c42969e5ff5b8450a5ae63e9876e0f5bde8d29ad..a3dc757cba2e9adf6aecc051f3a03d9875b92026 100644 (file)
--- a/globaldata.cpp
+++ b/globaldata.cpp
@@ -44,8 +44,8 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                        cutoff = "1.0";
                }
                
-               //set default value for cutoff
-               if(commandName == "dist.seqs") {        cutoff = "1.0";         }
+               //set default value for cutoff and phylip
+               if (commandName == "dist.seqs") {       cutoff = "1.0";   phylipfile = "F";     }
 
                string key, value;              
                //reads in parameters and values
@@ -208,9 +208,12 @@ void GlobalData::parseGlobalData(string commandString, string optionText){
                }
                
                //set format for shared
-               if((listfile != "") && (groupfile != "")) { format = "shared"; }
-               if((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
-                               
+               if ((listfile != "") && (groupfile != "")) { format = "shared"; }
+               if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
+               
+               //set default value for cutoff
+               if (commandName == "dist.seqs") {       format = "fasta";  inputFileName = fastafile;  fileroot = fastafile;    }
+                                               
                //input defaults for calculators
                if(commandName == "collect.single") {