fixed bug with tree reading

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index d43eaa484aad5be4403d7967a6abda1e066a127c..2d0eabc1aa5a1504d23d1fc146f525504f3213f9 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -20,13 +20,15 @@ class TrimSeqsCommand : public Command {
 public:
        TrimSeqsCommand(string);
        TrimSeqsCommand();
-       ~TrimSeqsCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~TrimSeqsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "trim.seqs";   }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        
@@ -51,7 +53,6 @@ private:
        bool cullAmbigs(Sequence&);
        bool compareDNASeq(string, string);
        int countDiffs(string, string);
-       map<string, vector<string> > outputTypes;
 
        bool abort;
        string fastaFile, oligoFile, qFileName, groupfile, outputDir;
@@ -69,6 +70,7 @@ private:
        map<string, int> groupToIndex;
        vector<string> primerNameVector;        //needed here?
        vector<string> barcodeNameVector;       //needed here?
+       map<string, int> groupCounts;  
 
        vector<int> processIDS;   //processid
        vector<linePair*> lines;