added shared file to make.table

[mothur.git] / countseqscommand.h

diff --git a/countseqscommand.h b/countseqscommand.h
index a5326d401e870c1878b5d8e7f4c2708bc0c48f04..e91ed08fc1be2200ae85b01a9284419730dbf8c8 100644 (file)
--- a/countseqscommand.h
+++ b/countseqscommand.h
@@ -12,6 +12,7 @@
 
 #include "command.hpp"
 #include "groupmap.h"
+#include "sharedrabundvector.h"
 
 class CountSeqsCommand : public Command {
        
@@ -28,7 +29,7 @@ public:
        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"; }
+       string getDescription()         { return "makes a count file from a names or shared file"; }
 
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
@@ -42,10 +43,11 @@ private:
                linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
        };
     
-       string namefile, groupfile, outputDir, groups;
-       bool abort, large;
+       string namefile, groupfile, outputDir, groups, sharedfile;
+       bool abort, large, allLines;
        vector<string> Groups, outputNames;
     int processors;
+    set<string> labels;
     
     int processSmall(string);
     int processLarge(string);
@@ -54,6 +56,8 @@ private:
     
     int createProcesses(GroupMap*&, string);
     int driver(unsigned long long, unsigned long long, string, GroupMap*&);
+    int processShared(vector<SharedRAbundVector*>& lookup, map<string, string> variables);
+
     
 };