added classify.shared command and random forest files. added count file to pcr.seqs...

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 4561d28614c62686c42e29a9747b84d853537fd0..60e471eebf7865d5924406ef7c720c3bdcdf4648 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -23,7 +23,8 @@ class GetSeqsCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "get.seqs";                            }
                string getCommandCategory()             { return "Sequence Processing";         }
-               string getHelpString(); 
+               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"; }
 
@@ -34,18 +35,24 @@ 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>);
+
                
 };