added topdown parameter to pre.cluster. added more debugging output to bayesian...

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 07d13d6703426e1990fab1a1bc9afdb82124c801..42070e53a57cf05c6d5674e022c602636fa374bf 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -23,8 +23,12 @@ class GetSeqsCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "get.seqs";                            }
                string getCommandCategory()             { return "Sequence Processing";         }
-               string getHelpString(); 
-       
+               
+       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()); }  
        
@@ -32,18 +36,24 @@ class GetSeqsCommand : public Command {
        private:
                set<string> names;
                vector<string> outputNames;
-               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               string accnosfile, accnosfile2, fastafile, namefile, countfile, 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 readCount();
                int readAlign();
-               int readAccnos();
                int readList();
                int readTax();
                int readQual();
                int compareAccnos();
+        int runSanityCheck();
+        int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
+
                
 };