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

[mothur.git] / consensusseqscommand.h

diff --git a/consensusseqscommand.h b/consensusseqscommand.h
index 555b62c63f263526917a388a6e03b62359cc1db3..07a4c0816020ee0c9678f81dbdafe108c0f0f92d 100644 (file)
--- a/consensusseqscommand.h
+++ b/consensusseqscommand.h
@@ -18,13 +18,15 @@ class ConsensusSeqsCommand : public Command {
 public:
        ConsensusSeqsCommand(string);
        ConsensusSeqsCommand();
-       ~ConsensusSeqsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~ConsensusSeqsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "consensus.seqs";              }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        
@@ -32,7 +34,6 @@ private:
        string fastafile, listfile, namefile, label, outputDir;
        set<string> labels;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        map<string, string> fastaMap;
        map<string, string> nameMap;
        map<string, string> nameFileMap;