This contains Pat's bug fixes and updates. It represents mothur v.1.3.0

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 06eaa6db7e2deb8b74344d7f408f09734cbf43cf..2279689d4671d5a7fae99204d0ab5421b5070ed6 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -23,23 +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;
        
+       GlobalData* globaldata; 
        ReadSeqs* readSeqs;
-       
-       vector<bool> columnsToRemove;
        SequenceDB* db;
-       double soft;
+       
+       string filter;
+
 };
 
 #endif
\ No newline at end of file