added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / countseqscommand.h

diff --git a/countseqscommand.h b/countseqscommand.h
index 89549a9ac0b0c74e6cdd18372ac4cdb834b5e8be..555d6a74fa36fa034b6d0aafeb5f07bd0c4e7bbc 100644 (file)
--- a/countseqscommand.h
+++ b/countseqscommand.h
@@ -23,6 +23,7 @@ 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"; }
@@ -33,8 +34,14 @@ public:
        
 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