added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / listseqscommand.h

diff --git a/listseqscommand.h b/listseqscommand.h
index 391ec9a46b9f09671f79fbc0f895730338570d4c..ea48430e9e0876c1034c344d5688fd64bc0c2bde 100644 (file)
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -16,14 +16,23 @@ 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 getCitation() { return "http://www.mothur.org/wiki/List.seqs"; }
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
-               vector<string> names;
-               string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile;
+               vector<string> names, outputNames;
+               string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
                bool abort;
                
                int readFasta();
@@ -31,6 +40,7 @@ class ListSeqsCommand : public Command {
                int readGroup();
                int readAlign();
                int readList();
+               int readTax();
                
 };