fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / readdistcommand.h

diff --git a/readdistcommand.h b/readdistcommand.h
index 3dfda1ba5cb5960642c0891570290fa9ae0d01a1..afe077d4e0e16c7763dc8304130242d2e0af1d4e 100644 (file)
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -9,11 +9,10 @@
  *
  */
 
-#include <Carbon/Carbon.h>
-#include <iostream>
-#include <fstream>
 #include "command.hpp"
 #include "readmatrix.hpp"
+#include "fullmatrix.h"
+#include "groupmap.h"
 
 /* The read.dist command is used to read a distance matrix file.  
 The read.dist command parameter options are phylipfile, columnfile, namefile, cutoff and precision. 
@@ -22,22 +21,36 @@ namefile=yourNameFile, cutoff=yourCutoff, precision=yourPrecision). The phylipfi
 If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.  */
 
 class NameAssignment;
-class GlobalData;
-
 
 class ReadDistCommand : public Command {
 public:
-       ReadDistCommand();
-       ~ReadDistCommand();
-       int execute();
+       ReadDistCommand(string);
+       ReadDistCommand() { abort = true; calledHelp = true; }
+       ~ReadDistCommand() {}
+       
+       vector<string> setParameters() {  return outputNames; } //dummy doesn't really do anything
+       string getCommandName()                 { return "read.dist";   }
+       string getCommandCategory()             { return "Hidden";      }
+       string getHelpString() { return "This command is no longer available. You can provide your distance files directly to the downstream commands like cluster."; } 
+       string getCitation() { return "http://www.mothur.org/wiki/Read.dist"; }
+       string getDescription()         { return "read.dist"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
        double cutoff;
        int precision;
        ReadMatrix* read;
-       string filename, format, method;
+       FullMatrix* matrix;
+       GroupMap* groupMap;
+       string distFileName, format, method;
+       string phylipfile, columnfile, namefile, groupfile, outputDir;
        NameAssignment* nameMap;
+       vector<string> outputNames;
+
+       bool abort, sim;
+
 };
 
-#endif
\ No newline at end of file
+#endif