removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / degapseqscommand.h

diff --git a/degapseqscommand.h b/degapseqscommand.h
index 5501d49b6affcdfe7e24fb8b444f837800d08ff5..db93b02a299aae60666b1993469f7e00cdc31a58 100644 (file)
--- a/degapseqscommand.h
+++ b/degapseqscommand.h
@@ -17,13 +17,15 @@ class DegapSeqsCommand : public Command {
 public:
        DegapSeqsCommand(string);
        DegapSeqsCommand();
-       ~DegapSeqsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~DegapSeqsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "degap.seqs";          }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
 
@@ -31,7 +33,7 @@ private:
        string fastafile, outputDir;
        vector<string> outputNames;
        vector<string> fastaFileNames;
-       map<string, vector<string> > outputTypes;
+       
 };
 
 #endif