fixed bug with tree reading

[mothur.git] / clustersplitcommand.h

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index 07ddaf95e72f9f0e8c51baa5e8d55a87fb9a9967..bdefb420de685f6c790deae1589a737ec75c2543 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -16,7 +16,6 @@
 #include "listvector.hpp"
 #include "cluster.hpp"
 #include "sparsematrix.hpp"
-#include "globaldata.hpp"
 
 
 class ClusterSplitCommand : public Command {
@@ -24,20 +23,20 @@ class ClusterSplitCommand : public Command {
 public:
        ClusterSplitCommand(string);
        ClusterSplitCommand();
-       ~ClusterSplitCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~ClusterSplitCommand() {}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "cluster.split";               }
+       string getCommandCategory()             { return "Clustering";                  }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+
 private:
-       GlobalData* globaldata;
        vector<int> processIDS;   //processid
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
-
+       
        string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
        double cutoff, splitcutoff;
        int precision, length, processors, taxLevelCutoff;
@@ -50,6 +49,7 @@ private:
        vector<string> cluster(vector< map<string, string> >, set<string>&);
        int mergeLists(vector<string>, map<float, int>, ListVector*);
        map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
+       int createMergedDistanceFile(vector< map<string, string> >);
 };
 
 #endif