fixed read.tree so that it can read trees generated by fasttree

[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
index 47f56f75c52f6ec3bf11128fa06ea14295571649..4f4c809e51e7f9308ae4f372bdd2195eb964f6c3 100644 (file)
--- a/getseqscommand.h
+++ b/getseqscommand.h
@@ -6,7 +6,7 @@
  *  Mothur
  *
  *  Created by Sarah Westcott on 7/8/09.
- *  Copyright 2009 __MyCompanyName__. All rights reserved.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
  
@@ -16,21 +16,24 @@ class GetSeqsCommand : public Command {
        
        public:
        
-               GetSeqsCommand(string); 
+               GetSeqsCommand(string);
                ~GetSeqsCommand(){};
                int execute();
                void help();    
                
        private:
                set<string> names;
-               string accnosfile, fastafile, namefile, groupfile, alignfile;
-               bool abort;
+               vector<string> outputNames;
+               string accnosfile, fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir;
+               bool abort, dups;
                
-               void readFasta();
-               void readName();
-               void readGroup();
-               void readAlign();
-               void readAccnos();
+               int readFasta();
+               int readName();
+               int readGroup();
+               int readAlign();
+               int readAccnos();
+               int readList();
+               int readTax();
                
 };