trim.seqs fix of gobble

[mothur.git] / seqerrorcommand.h

diff --git a/seqerrorcommand.h b/seqerrorcommand.h
index 00b536771ca730945324a3674d2a34646cddf25d..19fcd4731d22edc39383003b62c796242b7a4363 100644 (file)
--- a/seqerrorcommand.h
+++ b/seqerrorcommand.h
@@ -43,13 +43,15 @@ class SeqErrorCommand : public Command {
 public:
        SeqErrorCommand(string);
        SeqErrorCommand();
-       ~SeqErrorCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SeqErrorCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "seq.error";                           }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        bool abort;
@@ -68,13 +70,12 @@ private:
        double threshold;
        bool ignoreChimeras;
        int numRefs;
+       int maxLength;
        ofstream errorSummaryFile, errorSeqFile;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        
        vector<Sequence> referenceSeqs;
        vector<vector<int> > substitutionMatrix;
-       int a,t,g,c,gap,n;
 };
 
 #endif