fixed bug with trim.seqs allfiles=t

[mothur.git] / pairwiseseqscommand.h

diff --git a/pairwiseseqscommand.h b/pairwiseseqscommand.h
index b40d6c97ea10bbc708ddc2c4985be7b960843fab..cbd5aa402e7c61d624671590313bb32cb974dc11 100644 (file)
--- a/pairwiseseqscommand.h
+++ b/pairwiseseqscommand.h
@@ -23,22 +23,25 @@ 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(); 
+       string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
+       
        int execute(); 
-       void help();    
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       struct linePair {
+       struct distlinePair {
                int start;
                int end;
        };
-       map<int, int> processIDS;   //end line, processid
-       vector<linePair*> lines;
-       map<string, vector<string> > outputTypes;
+       
+       vector<int> processIDS;   //end line, processid
+       vector<distlinePair> lines;
        
        Alignment* alignment;
        Dist* distCalculator;