X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.h;h=2da134e4660202410c86f86d6c1ef1e1139bff5e;hb=62568a297aaf939ab753334f17abde82ec8e8531;hp=5d8d6c4a87223dd1ec5573563f64b0b658cfcc1d;hpb=b8f3e71c8a0310e25261464d27e6fcfe891483b0;p=mothur.git

diff --git a/chopseqscommand.h b/chopseqscommand.h
index 5d8d6c4..2da134e 100644
--- 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