removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / readdistcommand.h

diff --git a/readdistcommand.h b/readdistcommand.h
index 2f05ddbd3169d4cd4f204245ca2a0dd88571cb8e..8c248cd0af21ff65cb6eab139f11e56f6bc74e83 100644 (file)
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -21,23 +21,22 @@ 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(string);
        ReadDistCommand() { abort = true; calledHelp = true; }
-       ~ReadDistCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~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."; } 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       GlobalData* globaldata;
        double cutoff;
        int precision;
        ReadMatrix* read;
@@ -47,7 +46,6 @@ private:
        string phylipfile, columnfile, namefile, groupfile, outputDir;
        NameAssignment* nameMap;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 
        bool abort, sim;