added pipeline commands which involved change to command factory and command class...

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index 2e6191ca67f47f92f38bb8c030a8ad3e32920af6..c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -33,7 +33,12 @@ 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();    
                
@@ -42,6 +47,8 @@ class AlignCheckCommand : public Command {
                string mapfile, fastafile, outputDir;
                bool abort;
                int seqLength, haderror;
+               vector<string> outputNames;
+               map<string, vector<string> > outputTypes;
                
                void readMap();
                statData getStats(string sequence);