X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=distancecommand.h;h=8322eeedee6721ae333fdcbd6bc0447c9d654c53;hb=e7fe6dd9db877b98c362f9524c3130bbbd037200;hp=34dd65e66ee0984d298e68ba0cc587343d191d5b;hpb=d5d2761f88b41f1006d0b700e0ab51e2ce48b875;p=mothur.git

diff --git a/distancecommand.h b/distancecommand.h
index 34dd65e..8322eee 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -16,13 +16,11 @@
 #include "validcalculator.h"
 #include "dist.h"
 #include "sequencedb.h"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
 
-
-using namespace std;
+struct linePair {
+	int start;
+	int end;
+};
 
 class DistanceCommand : public Command {
 
@@ -36,15 +34,19 @@ private:
 	ValidCalculators* validCalculator;
 	Dist* distCalculator;
 	SequenceDB* seqDB;
-	ReadSeqs* readSeqs;
-	ofstream out;
+	ofstream out, phylipOut;
+	ifstream in;
 	string outputFileName;
-	string ends;
+	string countends, phylip;
 	int processors;
 	float cutoff;
+	map<int, int> processIDS;   //end line, processid
+	map<int, int>::iterator it;
+	vector<linePair*> lines;
 	
 	void appendFiles(string, string);
-	int driver(Dist*, SequenceDB*, int, int, string, float);
+	void createProcesses(string, string);
+	int driver(Dist*, SequenceDB*, int, int, string, string, float);
 
 };