modified seqerror and qualscores

[mothur.git] / readtreecommand.h

diff --git a/readtreecommand.h b/readtreecommand.h
index ca9f3b8c581d7b72f277332a1b70936d9f095854..464a825d002e7e1ac3cfe7f43af91142d2a6aeb9 100644 (file)
--- a/readtreecommand.h
+++ b/readtreecommand.h
@@ -19,7 +19,12 @@ class GlobalData;
 class ReadTreeCommand : public Command {
 public:
        ReadTreeCommand(string);
+       ReadTreeCommand() { abort = true; calledHelp = true; }
        ~ReadTreeCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -27,11 +32,14 @@ private:
        GlobalData* globaldata;
        ReadTree* read;
        TreeMap* treeMap;
-       string filename, treefile, groupfile;
-       OptionParser* parser;
-       map<string, string> parameters;
-       map<string, string>::iterator it;
+       string filename, treefile, groupfile, namefile;
        bool abort;
+       map<string, string> nameMap;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       
+       int readNamesFile();
+       int numUniquesInName;
 
 };