Merge remote-tracking branch 'origin/master'

[mothur.git] / countseqscommand.h

diff --git a/countseqscommand.h b/countseqscommand.h
index 385cd13536e0ed395bed74d875e620bc131e87c4..555d6a74fa36fa034b6d0aafeb5f07bd0c4e7bbc 100644 (file)
--- a/countseqscommand.h
+++ b/countseqscommand.h
@@ -23,17 +23,25 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "count.seqs";                          }
        string getCommandCategory()             { return "Sequence Processing";         }
+       string getOutputFileNameTag(string, string);
        string getHelpString(); 
        string getCitation() { return "http://www.mothur.org/wiki/Count.seqs"; }
-       
+       string getDescription()         { return "counts the number of sequences represented by each unique sequence in a namesfile"; }
+
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
        
 private:
        string namefile, groupfile, outputDir, groups;
-       bool abort;
-       vector<string> Groups;
+       bool abort, large;
+       vector<string> Groups, outputNames;
+    
+    int processSmall(string);
+    int processLarge(string);
+    map<int, string> processNameFile(string);
+    map<int, string> getGroupNames(string, set<string>&);
+    
 };
 
 #endif