changes to chop.seqs

[mothur.git] / chopseqscommand.h

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 5d8d6c4a87223dd1ec5573563f64b0b658cfcc1d..2da134e4660202410c86f86d6c1ef1e1139bff5e 100644 (file)
--- a/chopseqscommand.h
+++ b/chopseqscommand.h
@@ -12,6 +12,7 @@
 
 
 #include "command.hpp"
+#include "sequence.hpp"
 
 class ChopSeqsCommand : public Command {
        
@@ -25,7 +26,10 @@ class ChopSeqsCommand : public Command {
        private:
                string fastafile, outputDir;
                bool abort;
-               int end;
+               int end, fromend;
+               
+               string getChoppedAligned(Sequence);
+               string getChoppedUnaligned(Sequence);
 };
 
 #endif