fixes while testing 1.33.0

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index b249072e41aba8b7ff0501c1fc946b90c48dfd22..9895432b7c25d6016bbf6b38ced773487aeb0201 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -18,29 +18,43 @@ class GetSeqsCommand : public Command {
        
                GetSeqsCommand(string);
                GetSeqsCommand();
-               ~GetSeqsCommand(){};
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
+               ~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, qualfile, outputDir;
+               string accnosfile, accnosfile2, fastafile, fastqfile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
                bool abort, dups;
-               map<string, vector<string> > outputTypes;
+        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>);
+
                
 };