Merge branch 'JAL-1445' into develop

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index afbd223..c3dfdf1 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,21 +14,13 @@
  * 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/>.
+ * 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.*;
@@ -68,26 +60,13 @@ public class FeaturesFile extends AlignFile
    * 
    * @throws IOException
    *           DOCUMENT ME!
-   * @throws SAXException
-   * @throws ParserConfigurationException
-   * @throws ExceptionFileFormatOrSyntax
-   * @throws ExceptionLoadingFailed
-   * @throws ExceptionPermissionDenied
-   * @throws InterruptedException
-   * @throws ExceptionUnmatchedClosingParentheses
    */
-  public FeaturesFile(String inFile, String type) throws IOException,
-          ExceptionFileFormatOrSyntax, ParserConfigurationException,
-          SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
-          InterruptedException, ExceptionUnmatchedClosingParentheses
+  public FeaturesFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
 
-  public FeaturesFile(FileParse source) throws IOException,
-          ExceptionFileFormatOrSyntax, ParserConfigurationException,
-          SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed,
-          InterruptedException, ExceptionUnmatchedClosingParentheses
+  public FeaturesFile(FileParse source) throws IOException
   {
     super(source);
   }
@@ -151,7 +130,7 @@ 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
@@ -628,7 +607,6 @@ 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();