made make.table alias to count.seqs command. added large parameter to count.seqs...

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 4f4c809e51e7f9308ae4f372bdd2195eb964f6c3..c71b5f2804a71190c6919f0dc80bf80d32f15508 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,23 +17,41 @@ class GetSeqsCommand : public Command {
        public:
        
                GetSeqsCommand(string);
-               ~GetSeqsCommand(){};
-               int execute();
-               void help();    
-               
+               GetSeqsCommand();
+               ~GetSeqsCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.seqs";                            }
+               string getCommandCategory()             { return "Sequence Processing";         }
+               string getOutputFileNameTag(string, string);
+       string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
+               string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
        private:
                set<string> names;
                vector<string> outputNames;
-               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
+               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
+    
+        //for debug
+        map<string, set<string> > sanity; //maps file type to names chosen for file. something like "fasta" -> vector<string>. If running in debug mode this is filled and we check to make sure all the files have the same names. If they don't we output the differences for the user.
                
                int readFasta();
                int readName();
                int readGroup();
                int readAlign();
-               int readAccnos();
                int readList();
                int readTax();
+               int readQual();
+               int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
                
 };