merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index b59d0a4b4cfa1ce7f7d86deb48b90515f5cc965a..cfa56b39df6a4001014e1bc42048bed50bede8fa 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -11,37 +11,31 @@
  */
 
 #include "command.hpp"
-#include "mothur.h"
-#include "globaldata.hpp"
-#include "readfasta.h"
-#include "readnexus.h"
-#include "readclustal.h"
-#include "readseqsphylip.h"
-
-using namespace std;
 
+class Sequence;
 class FilterSeqsCommand : public Command {
 
 public:
-       FilterSeqsCommand();
+       FilterSeqsCommand(string);
        ~FilterSeqsCommand() {};
        int execute();  
+       void help();
        
 private:
-       void doTrump();
-       void doSoft();
        void doHard();
+       void doTrump(Sequence);
        void doVertical();
-       string filter;  
+       void doSoft();
+       void getFreqs(Sequence);
+       string vertical, filter, fastafile, hard;       
        int alignmentLength;
 
        char trump;
-       bool vertical;
-       
-       GlobalData* globaldata; 
-//     ReadSeqs* readSeqs;
-//     SequenceDB* db;
+       bool abort;
+       float soft;
+       int numSeqs;
        
+       vector<int> a, t, g, c, gap;
 
 };