fixed a bug in calculating the # of ambig bases

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 9e703ceeb62c2d610776c7f245980de651ab28a1..af4c03a950a0f42ad4fd9d7453ad698423381bd0 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -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