added pipeline commands which involved change to command factory and command class...

[mothur.git] / clustersplitcommand.h

diff --git a/clustersplitcommand.h b/clustersplitcommand.h
index e838bc41ee1b3616d3f0f95e6a512c5bde136d33..07ddaf95e72f9f0e8c51baa5e8d55a87fb9a9967 100644 (file)
--- a/clustersplitcommand.h
+++ b/clustersplitcommand.h
@@ -23,7 +23,12 @@ 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();
        
@@ -31,18 +36,20 @@ 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;
+       string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
        double cutoff, splitcutoff;
        int precision, length, processors, taxLevelCutoff;
-       bool print_start, abort, hard;
+       bool print_start, abort, hard, large;
        time_t start;
        ofstream outList, outRabund, outSabund;
        
        void printData(ListVector*);
        int createProcesses(vector < vector < map<string, string> > >);
        vector<string> cluster(vector< map<string, string> >, set<string>&);
-       int mergeLists(vector<string>, string, set<string>);
+       int mergeLists(vector<string>, map<float, int>, ListVector*);
+       map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
 };
 
 #endif