added screen.seqs command - pds

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index fffa45770cde70da74792b6bab1feb105b0bd1d5..af4c03a950a0f42ad4fd9d7453ad698423381bd0 100644 (file)
--- 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
+#endif