fixed subsample name file name issue. added count parameter to cluster command....

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 5d8d6c4a87223dd1ec5573563f64b0b658cfcc1d..cc22c751483a75f246f69e4955985f158d041638 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -12,20 +12,34 @@
 
 
 #include "command.hpp"
+#include "sequence.hpp"
 
 class ChopSeqsCommand : public Command {
        
        public:
        
-               ChopSeqsCommand(string);        
+               ChopSeqsCommand(string);
+               ChopSeqsCommand();      
                ~ChopSeqsCommand(){};
-               int execute();
-               void help();    
-               
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "chop.seqs";           }
+               string getCommandCategory()             { return "Sequence Processing"; }
+               string getOutputFileNameTag(string, string);
+        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;
-               bool abort;
-               int end;
+               string fastafile, outputDir, keep;
+               bool abort, countGaps, Short;
+               int numbases;
+               vector<string> outputNames;
+               
+               string getChopped(Sequence);
 };
 
 #endif