fixed bug with aligner and longest base. added deunique.seqs command.

[mothur.git] / readdistcommand.h

diff --git a/readdistcommand.h b/readdistcommand.h
index 4f38d034f1f14e320da5495ac79a04d4deff16b3..984b4a78ec40fc5b9d643cd51434ef4255d3e239 100644 (file)
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -9,10 +9,10 @@
  *
  */
 
-#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. 
@@ -26,17 +26,31 @@ class GlobalData;
 
 class ReadDistCommand : public Command {
 public:
-       ReadDistCommand();
+       ReadDistCommand(string);
+       ReadDistCommand() {}
        ~ReadDistCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
+       void help();
        
 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;
+       map<string, vector<string> > outputTypes;
+
+       bool abort, sim;
+
 };
 
 #endif