broke up globaldata and moved error checking and help into commands

[mothur.git] / filterseqscommand.h

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 17f1b3387ee1279a3b44e6ef3d34b732fc88834d..3f1e4c46d349d9da15837466502bd06a2f243883 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -17,9 +17,10 @@
 class FilterSeqsCommand : public Command {
 
 public:
-       FilterSeqsCommand();
+       FilterSeqsCommand(string);
        ~FilterSeqsCommand() {};
        int execute();  
+       void help();
        
 private:
        void doHard();
@@ -27,13 +28,16 @@ private:
        void doVertical();
        void doSoft();
        void getFreqs(Sequence);
-       string filter;  
+       string vertical, filter, fastafile, hard;       
        int alignmentLength;
 
        char trump;
-       bool vertical;
+       bool abort;
        float soft;
        int numSeqs;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
        
        GlobalData* globaldata; 
        vector<int> a, t, g, c, gap;