line and label no longer persist between commands. Added phylip formated output...

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 8bdf845e372a9dfc25c8700b14afaa9f6802c8b8..1f43856f43a033473a62c420e5c0bfce191fb182 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -16,11 +16,6 @@
 #include "validcalculator.h"
 #include "dist.h"
 #include "sequencedb.h"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
 
 class DistanceCommand : public Command {
 
@@ -34,15 +29,15 @@ private:
        ValidCalculators* validCalculator;
        Dist* distCalculator;
        SequenceDB* seqDB;
-       ReadSeqs* readSeqs;
-       ofstream out;
+       ofstream out, phylipOut;
+       ifstream in;
        string outputFileName;
        string countends;
        int processors;
        float cutoff;
        
        void appendFiles(string, string);
-       int driver(Dist*, SequenceDB*, int, int, string, float);
+       int driver(Dist*, SequenceDB*, int, int, string, string, float);
 
 };