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

[mothur.git] / preclustercommand.h

diff --git a/preclustercommand.h b/preclustercommand.h
index 3a1157d1979935e990f45e1f3202d4fe74525574..7bbb5a7f448351d1bf72616e3c40f7f10b41eda4 100644 (file)
--- a/preclustercommand.h
+++ b/preclustercommand.h
@@ -30,8 +30,13 @@ struct seqPNode {
 class PreClusterCommand : public Command {
        
 public:
-       PreClusterCommand(string);      
+       PreClusterCommand(string);
+       PreClusterCommand();
        ~PreClusterCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -40,12 +45,16 @@ private:
        bool abort;
        string fastafile, namefile, outputDir;
        vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
-//     map<string, string> names; //represents the names file first column maps to second column
-//     map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
+       map<string, string> names; //represents the names file first column maps to second column
+       map<string, int> sizes;  //this map a seq name to the number of identical seqs in the names file
+       map<string, int>::iterator itSize; 
 //     map<string, bool> active; //maps sequence name to whether it has already been merged or not.
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
        
        int readFASTA();
-       int readNamesFASTA();
+       void readNameFile();
+       //int readNamesFASTA();
        int calcMisMatches(string, string);
        void printData(string, string); //fasta filename, names file name
 };