broke up globaldata and moved error checking and help into commands

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 800ec3d047fac0221edde0dec47fb130058519ad..03ee1f5745222a1e3fb154c22b4099d26e77d029 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -17,9 +17,10 @@
 
 class TrimSeqsCommand : public Command {
 public:
-       TrimSeqsCommand();
+       TrimSeqsCommand(string);
        ~TrimSeqsCommand();
        int execute();
+       void help();
        
 private:
        void getOligos();
@@ -31,7 +32,11 @@ private:
        bool cullAmbigs(Sequence&);
        
        GlobalData* globaldata;
-
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort;
+       string fastafile;
        bool oligos, flip;
        int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength;
        vector<string> forPrimer, revPrimer;