added pairwise.seqs

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 5d8d6c4a87223dd1ec5573563f64b0b658cfcc1d..dbf4d23b71ebc1302672e66bc65472331117713f 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -12,20 +12,32 @@
 
 
 #include "command.hpp"
+#include "sequence.hpp"
 
 class ChopSeqsCommand : public Command {
        
        public:
        
-               ChopSeqsCommand(string);        
+               ChopSeqsCommand(string);
+               ChopSeqsCommand();      
                ~ChopSeqsCommand(){};
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();
                void help();    
                
        private:
-               string fastafile, outputDir;
-               bool abort;
-               int end;
+               string fastafile, outputDir, keep;
+               bool abort, countGaps, Short;
+               int numbases;
+               vector<string> outputNames;
+               map<string, vector<string> > outputTypes;
+               
+               string getChopped(Sequence);
+               
+               
 };
 
 #endif