Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

[jalview.git] / src / jalview / io / FeaturesFile.java

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 7b45600..804cefc 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,34 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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;
 
 import java.io.*;
 import java.util.*;
 
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
 import jalview.analysis.SequenceIdMatcher;
 import jalview.datamodel.*;
 import jalview.schemes.*;
@@ -65,14 +59,16 @@ public class FeaturesFile extends AlignFile
    *          DOCUMENT ME!
    * @param type
    *          DOCUMENT ME!
- * @throws Exception 
+   * 
+   * @throws IOException
+   *           DOCUMENT ME!
    */
-  public FeaturesFile(String inFile, String type) throws Exception
+  public FeaturesFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
 
-  public FeaturesFile(FileParse source) throws Exception
+  public FeaturesFile(FileParse source) throws IOException
   {
     super(source);
   }
@@ -682,7 +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);
   }
@@ -701,7 +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();
@@ -718,11 +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)
         {
@@ -930,12 +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();