X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFeaturesFile.java;h=260b32d7de38f32da1cf65a70faa366ebc9e5fb7;hb=61c62b2455f3e25a14587aa37e4a2949184041a2;hp=a87fd60c4634a8bb3e7153bb696e4b8aba38babf;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index a87fd60..260b32d 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
@@ -130,7 +132,7 @@ public class FeaturesFile extends AlignFile
   }
 
   /**
-   * /** Parse GFF or sequence features file
+   * Parse GFF or sequence features file
    * 
    * @param align
    *          - alignment/dataset containing sequences that are to be annotated
@@ -607,7 +609,6 @@ public class FeaturesFile extends AlignFile
       resetMatcher();
     } catch (Exception ex)
     {
-      System.out.println(line);
       System.out.println("Error parsing feature file: " + ex + "\n" + line);
       ex.printStackTrace(System.err);
       resetMatcher();
@@ -677,7 +678,7 @@ public class FeaturesFile extends AlignFile
    *          hash of feature types and colours
    * @return features file contents
    */
-  public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)
+  public String printJalviewFormat(SequenceI[] seqs, Map<String,Object> visible)
   {
     return printJalviewFormat(seqs, visible, true, true);
   }
@@ -696,7 +697,7 @@ public class FeaturesFile extends AlignFile
    *          of group or type)
    * @return features file contents
    */
-  public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,
+  public String printJalviewFormat(SequenceI[] seqs, Map visible,
           boolean visOnly, boolean nonpos)
   {
     StringBuffer out = new StringBuffer();
@@ -713,11 +714,11 @@ public class FeaturesFile extends AlignFile
       // write feature colours only if we're given them and we are generating
       // viewed features
       // TODO: decide if feature links should also be written here ?
-      Enumeration en = visible.keys();
+      Iterator en = visible.keySet().iterator();
       String type, color;
-      while (en.hasMoreElements())
+      while (en.hasNext())
       {
-        type = en.nextElement().toString();
+        type = en.next().toString();
 
         if (visible.get(type) instanceof GraduatedColor)
         {
@@ -925,12 +926,12 @@ public class FeaturesFile extends AlignFile
    * @param visible
    * @return
    */
-  public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
+  public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible)
   {
     return printGFFFormat(seqs, visible, true, true);
   }
 
-  public String printGFFFormat(SequenceI[] seqs, Hashtable visible,
+  public String printGFFFormat(SequenceI[] seqs, Map<String,Object> visible,
           boolean visOnly, boolean nonpos)
   {
     StringBuffer out = new StringBuffer();