added check to make sure shhh.flows child processes finish properly. added subsamplin...

[mothur.git] / readtreecommand.h

diff --git a/readtreecommand.h b/readtreecommand.h
index 2ee72a15e591374d1df21a4aed7ff2f6a0457cde..cbf376909ff998531ed959f34edb5d72e8b72fcd 100644 (file)
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -14,19 +14,34 @@
 #include "readtree.h"
 #include "treemap.h"
 
-class GlobalData;
 
 class ReadTreeCommand : public Command {
 public:
-       ReadTreeCommand();
-       ~ReadTreeCommand();
-       int execute();
+       ReadTreeCommand(string);
+       ReadTreeCommand() { abort = true; calledHelp = true; }
+       ~ReadTreeCommand() {}
+       
+       vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
+       string getCommandName()                 { return "read.tree";   }
+       string getCommandCategory()             { return "Hidden";      }
+       string getHelpString() { return "This command is no longer available. You can provide your files directly to the downstream commands like unifrac.unweighted."; }       
+       string getCitation() { return "http://www.mothur.org/wiki/Read.tree"; }
+       string getDescription()         { return "read.tree"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
        ReadTree* read;
        TreeMap* treeMap;
-       string filename;
+       string filename, treefile, groupfile, namefile;
+       bool abort;
+       map<string, string> nameMap;
+       vector<string> outputNames;
+       
+       int readNamesFile();
+       int numUniquesInName;
+
 };