X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.h;h=2279689d4671d5a7fae99204d0ab5421b5070ed6;hb=31c6076fe649829d9b8f773f6f12b627d3ef5d9b;hp=fffa45770cde70da74792b6bab1feb105b0bd1d5;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/filterseqscommand.h b/filterseqscommand.h
index fffa457..2279689 100644
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -6,7 +6,7 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 5/4/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
@@ -23,26 +23,25 @@ using namespace std;
 class FilterSeqsCommand : public Command {
 
 public:
-	FilterSeqsCommand() {};
+	FilterSeqsCommand();
 	~FilterSeqsCommand() {};
 	int execute();	
 	
 private:
 	void doTrump();
 	void doSoft();
-	void doFilter();
+	void doHard();
+	void doVertical();
 	
-	GlobalData* globaldata;
-	string filename, trump, filter;
+	int alignmentLength;
+	int numSeqs;
 	
-	ReadFasta* readFasta;
-	ReadNexus* readNexus;
-	ReadClustal* readClustal;
-	ReadPhylip* readPhylip;
-	
-	vector<bool> columnsToRemove;
+	GlobalData* globaldata;	
+	ReadSeqs* readSeqs;
 	SequenceDB* db;
-	double soft;
+	
+	string filter;
+
 };
 
 #endif
\ No newline at end of file