removed parse.sff command and made its functionality part of sffinfo command. fixed...

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index d94cc95582f8d1482233a3cac0aee4b418dcc925..c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -33,17 +33,25 @@ class AlignCheckCommand : public Command {
        public:
        
                AlignCheckCommand(string);      
-               ~AlignCheckCommand(){};
+               AlignCheckCommand();
+               ~AlignCheckCommand(){}
+               vector<string> getRequiredParameters();
+               vector<string> getValidParameters();
+               vector<string> getRequiredFiles();
+               map<string, vector<string> > getOutputFiles() { return outputTypes; }
                int execute();
                void help();    
                
        private:
                vector<int> structMap;
-               string mapfile, fastafile;
+               string mapfile, fastafile, outputDir;
                bool abort;
-               int seqLength;
+               int seqLength, haderror;
+               vector<string> outputNames;
+               map<string, vector<string> > outputTypes;
                
                void readMap();
+               statData getStats(string sequence);
 };
 
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