added clearcut source to mothur, fixed mislabeled sharedcalcs

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 2da134e4660202410c86f86d6c1ef1e1139bff5e..604906425997010d3cfcde2b41b9cdeb6b5a1ae7 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -24,12 +24,12 @@ class ChopSeqsCommand : public Command {
                void help();    
                
        private:
-               string fastafile, outputDir;
-               bool abort;
-               int end, fromend;
+               string fastafile, outputDir, keep;
+               bool abort, countGaps;
+               int numbases;
+               
+               string getChopped(Sequence);
                
-               string getChoppedAligned(Sequence);
-               string getChoppedUnaligned(Sequence);
 };
 
 #endif