sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 809109c486de9f00b39091b863da8a23dfc95a96..c5b6ca4141afc00c12b646ea34604b898b1c4131 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -17,22 +17,43 @@ 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, outputDir;
-               bool abort;
+               string accnosfile, accnosfile2, fastafile, 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.
                
-               void readFasta();
-               void readName();
-               void readGroup();
-               void readAlign();
-               void readAccnos();
-               void readList();
+               int readFasta();
+               int readName();
+               int readGroup();
+        int readCount();
+               int readAlign();
+               int readList();
+               int readTax();
+               int readQual();
+               int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
                
 };