changes while testing

[mothur.git] / listseqscommand.h

diff --git a/listseqscommand.h b/listseqscommand.h
index 4e0febd9c6dc84a7b49589e614c076493638c913..b8a79c06035825fd92050a1e0c610ac6b77bd122 100644 (file)
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -16,20 +16,35 @@ class ListSeqsCommand : public Command {
        
        public:
        
-               ListSeqsCommand(string);        
-               ~ListSeqsCommand(){};
-               int execute();
-               void help();    
+               ListSeqsCommand(string);
+               ListSeqsCommand();      
+               ~ListSeqsCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "list.seqs";                           }
+               string getCommandCategory()             { return "Sequence Processing";         }
                
+       string getHelpString(); 
+    string getOutputPattern(string);   
+               string getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
+               string getDescription()         { return "lists sequences from a list, fasta, name, group, alignreport or taxonomy file"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
-               vector<string> names;
-               string fastafile, namefile, groupfile, alignfile, inputFileName;
+               vector<string> names, outputNames;
+               string fastafile, namefile, groupfile, countfile, alignfile, inputFileName, outputDir, listfile, taxfile;
                bool abort;
                
-               void readFasta();
-               void readName();
-               void readGroup();
-               void readAlign();
+               int readFasta();
+               int readName();
+               int readGroup();
+               int readAlign();
+               int readList();
+               int readTax();
+        int readCount();
                
 };