got rid of extra temp files in dist.seqs

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 6bd7572629f1ada2b372127110cadb1fce943f76..2cb653f790aeb970f2a8f9ba7e1122d2f8ef4c57 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 {
 
@@ -36,14 +34,17 @@ private:
        ValidCalculators* validCalculator;
        Dist* distCalculator;
        SequenceDB* seqDB;
-       ReadSeqs* readSeqs;
-       ofstream out;
-       string outputFileName;
-       string countends;
+       ofstream out, outFile;
+       ifstream in;
+       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);
+       void createProcesses(string);
        int driver(Dist*, SequenceDB*, int, int, string, float);
 
 };