changes to dist.seqs and pairwise.seqs and cluster.classic no longer resizes

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 64eac8d57affc1090bbc324bb76ccb6f7fa5648d..595483d2b3e84aef55478a78bd84906771949e5d 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -21,27 +21,35 @@ class DistanceCommand : public Command {
 
 public:
        DistanceCommand(string);
+       DistanceCommand();
        ~DistanceCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
 private:
-       struct linePair {
+       struct distlinePair {
                int start;
                int end;
+               
        };
        
        Dist* distCalculator;
        SequenceDB alignDB;
 
-       string countends, output, fastafile, calc, outputDir, oldfastafile, column;
+       string countends, output, fastafile, calc, outputDir, oldfastafile, column, compress;
+
        int processors, numNewFasta;
        float cutoff;
-       map<int, int> processIDS;   //end line, processid
-       vector<linePair*> lines;
+       vector<int> processIDS;   //end line, processid
+       vector<distlinePair> lines;
        
        bool abort;
-       vector<string>  Estimators; //holds estimators to be used
+       vector<string>  Estimators, outputNames; //holds estimators to be used
+       map<string, vector<string> > outputTypes;
        
        //void m->appendFiles(string, string);
        void createProcesses(string);