X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=1f43856f43a033473a62c420e5c0bfce191fb182;hb=4f4070ac3fbb5da75f834b48062e9123364b006e;hp=8bdf845e372a9dfc25c8700b14afaa9f6802c8b8;hpb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 8bdf845..1f43856 100644
--- 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);
 
 };