changes while testing

[mothur.git] / clusterfragmentscommand.h

diff --git a/clusterfragmentscommand.h b/clusterfragmentscommand.h
index 01f38e45ff55518238894a79503928759124679c..ee25fb30da91c4ab338b0b173bcf05a6f1689c81 100644 (file)
--- a/clusterfragmentscommand.h
+++ b/clusterfragmentscommand.h
@@ -13,6 +13,7 @@
 
 #include "command.hpp"
 #include "sequence.hpp"
+#include "counttable.h"
 
 /************************************************************/
 struct seqRNode {
@@ -32,24 +33,30 @@ class ClusterFragmentsCommand : public Command {
 public:
        ClusterFragmentsCommand(string);
        ClusterFragmentsCommand();
-       ~ClusterFragmentsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();  
-       void help();
+       ~ClusterFragmentsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "cluster.fragments";           }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
+       string getDescription()         { return "creates a namesfile with sequences that are a fragment of a larger sequence"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
+    CountTable ct;
        bool abort;
-       string fastafile, namefile, outputDir;
+       string fastafile, namefile, countfile, outputDir;
        int diffs, percent;
        vector<seqRNode> alignSeqs; 
        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; 
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        int readFASTA();
        void readNameFile();