fixed cluster.classic and added weighted method to hcluster

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 090c9f4ef9ed40287040bec733f0e5d8802ff23d..077181220a836f6b118f68008996b411f81822fa 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -23,25 +23,37 @@ class SummarySharedCommand : public Command {
 
 public:
        SummarySharedCommand(string);
+       SummarySharedCommand();
        ~SummarySharedCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
 private:
+       struct linePair {
+               int start;
+               int end;
+       };
+       vector<linePair> lines;
        GlobalData* globaldata;
        ReadOTUFile* read;
        vector<Calculator*> sumCalculators;     
        InputData* input;
        ValidCalculators* validCalculator;
        
-       bool abort, allLines, mult, all;
+       bool abort, allLines, mult, all, createPhylip;
        set<string> labels; //holds labels to be used
        string label, calc, groups;
-       vector<string>  Estimators, Groups;
+       vector<string>  Estimators, Groups, outputNames;
+       map<string, vector<string> > outputTypes;
        vector<SharedRAbundVector*> lookup;
-       string outputFileName, format, outAllFileName;
-       ofstream outputFileHandle, outAll;
-       void process(vector<SharedRAbundVector*>);
+       string format, outputDir;
+       int numGroups, processors;
+       int process(vector<SharedRAbundVector*>, string, string);
+       int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
 
 };