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

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 34dd65e66ee0984d298e68ba0cc587343d191d5b..8322eeedee6721ae333fdcbd6bc0447c9d654c53 100644 (file)
--- 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);
 
 };