X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=aligncommand.h;h=f7d59b0206c989558f0e11163d1f7abddcf9a784;hb=648ec37228eb16075ace911dd5a5773cdfe683da;hp=c3c244138a7b2457dd20ba5bedc152b88f0e0e2b;hpb=5ca05ed0a8311b2943c1c0a1fad825785db484d6;p=mothur.git

diff --git a/aligncommand.h b/aligncommand.h
index c3c2441..f7d59b0 100644
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -36,16 +36,16 @@ private:
 	AlignmentDB* templateDB;
 	Alignment* alignment;
 	
-	int driver(linePair*, string, string);
-	void createProcesses(string, string);
+	int driver(linePair*, string, string, string);
+	void createProcesses(string, string, string);
 	void appendAlignFiles(string, string); 
 	void appendReportFiles(string, string);
 	
 	string candidateFileName, templateFileName, distanceFileName, search, align;
-	float match, misMatch, gapOpen, gapExtend;
+	float match, misMatch, gapOpen, gapExtend, threshold;
 	int processors, kmerSize;
 	
-	bool abort;
+	bool abort, flip;
 };
 
 #endif