removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 0b654a4e02bdf42cdf5ebfc9ee419bdbd71eec2f..2e04936a8eea682d1f8511de11a16a601c9e9d1c 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -35,20 +35,21 @@ 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(); 
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
        private:
                vector<int> structMap;
                string mapfile, fastafile, outputDir, namefile;
                bool abort;
                int seqLength, haderror;
                vector<string> outputNames;
-               map<string, vector<string> > outputTypes;
                map<string, int> nameMap;
                
                void readMap();