working on pam

[mothur.git] / listseqscommand.h

diff --git a/listseqscommand.h b/listseqscommand.h
index 6a210a180e5bc9453005c7aefb8613fa45d52c03..9d320d9e9a94ad031826bc547d42a03b30e8ec30 100644 (file)
--- a/listseqscommand.h
+++ b/listseqscommand.h
@@ -16,14 +16,26 @@ 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, outputDir, listfile, taxfile;
+               vector<string> names, outputNames;
+               string fastafile, namefile, groupfile, countfile, alignfile, inputFileName, outputDir, listfile, taxfile, fastqfile;
                bool abort;
                
                int readFasta();
@@ -32,7 +44,8 @@ class ListSeqsCommand : public Command {
                int readAlign();
                int readList();
                int readTax();
-               
+        int readCount();
+        int readFastq();
 };
 
 #endif