added set.dir command and modified commands to redirect input and output, removed...

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index fffa45770cde70da74792b6bab1feb105b0bd1d5..0946396e3a0fe6623f3501feed5fc6e7b4ba239a 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -6,43 +6,35 @@
  *  Mothur
  *
  *  Created by Thomas Ryabin on 5/4/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
 
 #include "command.hpp"
-#include "mothur.h"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
+#include "filters.h"
 
+class Sequence;
 class FilterSeqsCommand : public Command {
 
 public:
-       FilterSeqsCommand() {};
+       FilterSeqsCommand(string);
        ~FilterSeqsCommand() {};
        int execute();  
+       void help();
        
 private:
-       void doTrump();
-       void doSoft();
-       void doFilter();
-       
-       GlobalData* globaldata;
-       string filename, trump, filter;
-       
-       ReadFasta* readFasta;
-       ReadNexus* readNexus;
-       ReadClustal* readClustal;
-       ReadPhylip* readPhylip;
+       string vertical, filter, fastafile, hard, outputDir;    
+       int alignmentLength;
+
+       char trump;
+       bool abort;
+       float soft;
+       int numSeqs;
        
-       vector<bool> columnsToRemove;
-       SequenceDB* db;
-       double soft;
+       Filters F;
+               
+       vector<int> a, t, g, c, gap;
+
 };
 
-#endif
\ No newline at end of file
+#endif