added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 8e007ff7513e62df1dd32e7fe192628c02e48425..e73714d2e98406da2a05e54bb34f61398bd0143c 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -21,23 +21,24 @@ class ChopSeqsCommand : public Command {
                ChopSeqsCommand(string);
                ChopSeqsCommand();      
                ~ChopSeqsCommand(){};
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
-               
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "chop.seqs";           }
+               string getCommandCategory()             { return "Sequence Processing"; }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Chops.seqs"; }
+               string getDescription()         { return "trim sequence length"; }
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }          
+       
        private:
                string fastafile, outputDir, keep;
-               bool abort, countGaps;
+               bool abort, countGaps, Short;
                int numbases;
                vector<string> outputNames;
-               map<string, vector<string> > outputTypes;
                
                string getChopped(Sequence);
-               
-               
 };
 
 #endif