added citation function to commands

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4..daee85a37fd4e13df952ea363da36227dde85143 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -35,20 +35,23 @@ class AlignCheckCommand : public Command {
                AlignCheckCommand(string);      
                AlignCheckCommand();
                ~AlignCheckCommand(){}
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
-               
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "align.check";                         }
+               string getCommandCategory()             { return "Sequence Processing";         }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Align.check"; }
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
        private:
                vector<int> structMap;
-               string mapfile, fastafile, outputDir;
+               string mapfile, fastafile, outputDir, namefile;
                bool abort;
                int seqLength, haderror;
                vector<string> outputNames;
-               map<string, vector<string> > outputTypes;
+               map<string, int> nameMap;
                
                void readMap();
                statData getStats(string sequence);