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

[mothur.git] / readdistcommand.h

diff --git a/readdistcommand.h b/readdistcommand.h
index b6e3ae44de298a115ce9a72de193b51ff951ea34..984b4a78ec40fc5b9d643cd51434ef4255d3e239 100644 (file)
--- a/readdistcommand.h
+++ b/readdistcommand.h
@@ -27,7 +27,12 @@ class GlobalData;
 class ReadDistCommand : public Command {
 public:
        ReadDistCommand(string);
+       ReadDistCommand() {}
        ~ReadDistCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -38,13 +43,13 @@ private:
        ReadMatrix* read;
        FullMatrix* matrix;
        GroupMap* groupMap;
-       string filename, format, method;
-       string phylipfile, columnfile, namefile, groupfile;
+       string distFileName, format, method;
+       string phylipfile, columnfile, namefile, groupfile, outputDir;
        NameAssignment* nameMap;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
-       bool abort;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+
+       bool abort, sim;
 
 };