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 a43e3955c9ec8184040653389b6a2f61ad2e94ba..1f43856f43a033473a62c420e5c0bfce191fb182 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -17,9 +17,6 @@
 #include "dist.h"
 #include "sequencedb.h"
 
-
-using namespace std;
-
 class DistanceCommand : public Command {
 
 public:
@@ -32,13 +29,15 @@ private:
        ValidCalculators* validCalculator;
        Dist* distCalculator;
        SequenceDB* seqDB;
-       ofstream out;
+       ofstream out, phylipOut;
+       ifstream in;
        string outputFileName;
-       string ends, distFile;
+       string countends;
        int processors;
        float cutoff;
        
-       int driver(Dist*, SequenceDB*, int, int, string, float);
+       void appendFiles(string, string);
+       int driver(Dist*, SequenceDB*, int, int, string, string, float);
 
 };