working on pam

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 2e6191ca67f47f92f38bb8c030a8ad3e32920af6..ce97a2243c2b9da797e5a34da3454050b5002396 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -33,15 +33,29 @@ class AlignCheckCommand : public Command {
        public:
        
                AlignCheckCommand(string);      
-               ~AlignCheckCommand(){};
-               int execute();
-               void help();    
+               AlignCheckCommand();
+               ~AlignCheckCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "align.check";                         }
+               string getCommandCategory()             { return "Sequence Processing";         }
                
+       string getHelpString(); 
+    string getOutputPattern(string);   
+               string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
+               string getDescription()         { return "calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment"; }
+
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
        private:
                vector<int> structMap;
-               string mapfile, fastafile, outputDir;
+               string mapfile, fastafile, outputDir, namefile, countfile;
                bool abort;
                int seqLength, haderror;
+               vector<string> outputNames;
+               map<string, int> nameMap;
                
                void readMap();
                statData getStats(string sequence);