fixes while testing 1.33.0

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 4f4c809e51e7f9308ae4f372bdd2195eb964f6c3..9895432b7c25d6016bbf6b38ced773487aeb0201 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,23 +17,44 @@ 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 getHelpString(); 
+    string getOutputPattern(string);   
+               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, fastqfile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
+        map<string, string> uniqueMap;
+        //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 readFastq();
                int readName();
                int readGroup();
+        int readCount();
                int readAlign();
-               int readAccnos();
                int readList();
                int readTax();
+               int readQual();
+               int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
                
 };