changes while testing

[mothur.git] / listseqscommand.h

diff --git a/listseqscommand.h b/listseqscommand.h
index bd7beae73360da9453911e7d5b755135a00f4d54..b8a79c06035825fd92050a1e0c610ac6b77bd122 100644 (file)
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -21,17 +21,21 @@ class ListSeqsCommand : public Command {
                ~ListSeqsCommand(){}
        
                vector<string> setParameters();
-               string getCommandName()                 { return "get.seqs";                            }
+               string getCommandName()                 { return "list.seqs";                           }
                string getCommandCategory()             { return "Sequence Processing";         }
-               string getHelpString(); 
-       
+               
+       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, outputNames;
-               string fastafile, namefile, groupfile, alignfile, inputFileName, outputDir, listfile, taxfile;
+               string fastafile, namefile, groupfile, countfile, alignfile, inputFileName, outputDir, listfile, taxfile;
                bool abort;
                
                int readFasta();
@@ -40,6 +44,7 @@ class ListSeqsCommand : public Command {
                int readAlign();
                int readList();
                int readTax();
+        int readCount();
                
 };