changes while testing

[mothur.git] / removeseqscommand.h

diff --git a/removeseqscommand.h b/removeseqscommand.h
index de1e3d9d6aff8595a098cf8bf2fd6c1d5c79ec9f..1a6365dac35b9e18669f8827c4054268b9123d9e 100644 (file)
--- a/removeseqscommand.h
+++ b/removeseqscommand.h
@@ -19,25 +19,32 @@ class RemoveSeqsCommand : public Command {
                RemoveSeqsCommand(string);      
                RemoveSeqsCommand();
                ~RemoveSeqsCommand(){}
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "remove.seqs";                         }
+               string getCommandCategory()             { return "Sequence Processing";         }
                
+       string getHelpString(); 
+    string getOutputPattern(string);   
+               string getCitation() { return "http://www.mothur.org/wiki/Remove.seqs"; }
+               string getDescription()         { return "removes sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
                set<string> names;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               string accnosfile, fastafile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
                vector<string> outputNames;
-               map<string, vector<string> > outputTypes;
+        map<string, string> uniqueMap;
                
                int readFasta();
                int readName();
                int readGroup();
+        int readCount();
                int readAlign();
-               void readAccnos();
                int readList();
                int readTax();
                int readQual();