some changes to trim.flows

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index ceea8988a2bc0963abaa4d18d898729d88c8960a..7a17c9de22a4c08b8d44a6e59ea3c6f07f18430a 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -39,7 +39,12 @@ class GetOTURepCommand : public Command {
 
 public:
        GetOTURepCommand(string);
+       GetOTURepCommand();
        ~GetOTURepCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
 
@@ -53,24 +58,29 @@ private:
        ReadMatrix* readMatrix;
        FormatMatrix* formatMatrix;
        NameAssignment* nameMap;
-       string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir;
+       string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir, groups;
        ofstream out;
        ifstream in, inNames, inRow;
-       bool abort, allLines, groupError, large;
+       bool abort, allLines, groupError, large, weighted;
        set<string> labels; //holds labels to be used
        map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
+       map<string, string> nameFileMap;
+       vector<string> outputNames, Groups;
+       map<string, string> outputNameFiles;
        float cutoff;
        int precision;
        vector<SeqMap> seqVec;                  // contains maps with sequence index and distance
                                                                        // for all distances related to a certain sequence
        vector<int> rowPositions;
+       map<string, vector<string> > outputTypes;
 
        void readNamesFile();
+       void readNamesFile(bool);
        int process(ListVector*);
        SeqMap getMap(int);
-       string findRep(int, string&, ListVector*, int&);        // returns the name of the "representative" sequence of given bin, 
-                                                                       // fills a string containing the groups in that bin if a groupfile is given,
-                                                                       // and returns the number of sequences in the given bin
+       string findRep(vector<string>);         // returns the name of the "representative" sequence of given bin or subset of a bin, for groups
+       int processNames(string, string);
+                                                                                               
 
 };