changes while testing

[mothur.git] / degapseqscommand.h

diff --git a/degapseqscommand.h b/degapseqscommand.h
index 5501d49b6affcdfe7e24fb8b444f837800d08ff5..3b03c9b0ca1d8a61704dd3c13885d12d8204100a 100644 (file)
--- a/degapseqscommand.h
+++ b/degapseqscommand.h
@@ -17,13 +17,19 @@ 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(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Degap.seqs"; }
+       string getDescription()         { return "removes gap characters from sequences"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
 
@@ -31,7 +37,7 @@ private:
        string fastafile, outputDir;
        vector<string> outputNames;
        vector<string> fastaFileNames;
-       map<string, vector<string> > outputTypes;
+       
 };
 
 #endif