added namefile to align.check and added seqs from namefile to optimizing piece of...

[mothur.git] / secondarystructurecommand.h

diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h
index dffb4cbd980ff504307465ae64a0f6645fe5e6a5..0b654a4e02bdf42cdf5ebfc9ee419bdbd71eec2f 100644 (file)
--- a/secondarystructurecommand.h
+++ b/secondarystructurecommand.h
@@ -33,15 +33,23 @@ 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, outputDir;
+               string mapfile, fastafile, outputDir, namefile;
                bool abort;
-               int seqLength;
+               int seqLength, haderror;
+               vector<string> outputNames;
+               map<string, vector<string> > outputTypes;
+               map<string, int> nameMap;
                
                void readMap();
                statData getStats(string sequence);