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

[mothur.git] / pairwiseseqscommand.h

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index cf73f3e82a2c0bd59bfff9fad48ee4628a2b1917..52ba63db10adf51e10e6440e5df7b92b78c4c894 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -23,13 +23,15 @@ class PairwiseSeqsCommand : public Command {
 public:
        PairwiseSeqsCommand(string);    
        PairwiseSeqsCommand();
-       ~PairwiseSeqsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       ~PairwiseSeqsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "pairwise.seqs";               }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       
        int execute(); 
-       void help();    
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        struct distlinePair {
@@ -37,10 +39,8 @@ private:
                int end;
        };
        
-       
        vector<int> processIDS;   //end line, processid
        vector<distlinePair> lines;
-       map<string, vector<string> > outputTypes;
        
        Alignment* alignment;
        Dist* distCalculator;