X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=countseqscommand.h;h=b4170a8867897b96e13f7483f6053b960f7629b4;hb=767c2ab76d70664af19b1afca8e1fd5233962698;hp=385cd13536e0ed395bed74d875e620bc131e87c4;hpb=75962c819c16814e5c2340d99af1aa62e564dc20;p=mothur.git

diff --git a/countseqscommand.h b/countseqscommand.h
index 385cd13..b4170a8 100644
--- a/countseqscommand.h
+++ b/countseqscommand.h
@@ -23,17 +23,26 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "count.seqs";				}
 	string getCommandCategory()		{ return "Sequence Processing";		}
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	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