JAL-2488 remove finalize methods

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index b07666e..36cb185 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -62,15 +62,6 @@ public class AlignViewport extends AlignmentViewport
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
-  @Override
-  public void finalize()
-  {
-    applet = null;
-    quality = null;
-    alignment = null;
-    colSel = null;
-  }
-
   public AlignViewport(AlignmentI al, JalviewLite applet)
   {
     super(al);

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 8e333ba..bb26caa 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -73,23 +73,6 @@ public class AlignmentPanel extends Panel
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
-  @Override
-  public void finalize() throws Throwable
-  {
-    alignFrame = null;
-    av = null;
-    vpRanges = null;
-    seqPanel = null;
-    seqPanelHolder = null;
-    sequenceHolderPanel = null;
-    scalePanel = null;
-    scalePanelHolder = null;
-    annotationPanel = null;
-    annotationPanelHolder = null;
-    annotationSpaceFillerHolder = null;
-    super.finalize();
-  }
-
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     try

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index dd05843..e44c32d 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -52,14 +52,6 @@ public class AlignViewController implements AlignViewControllerI
    */
   private AlignViewControllerGuiI avcg;
 
-  @Override
-  protected void finalize() throws Throwable
-  {
-    viewport = null;
-    alignPanel = null;
-    avcg = null;
-  };
-
   public AlignViewController(AlignViewControllerGuiI alignFrame,
           AlignViewportI viewport, AlignmentViewPanel alignPanel)
   {

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index c464af2..09facbf 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -241,19 +241,6 @@ public class AlignmentAnnotation
 
   private boolean isrna;
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#finalize()
-   */
-  @Override
-  protected void finalize() throws Throwable
-  {
-    sequenceRef = null;
-    groupRef = null;
-    super.finalize();
-  }
-
   public static int getGraphValueFromString(String string)
   {
     if (string.equalsIgnoreCase("BAR_GRAPH"))

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index 328b96a..b5184fb 100644 (file)
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -693,19 +693,6 @@ public class Mapping
     to = tto;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#finalize()
-   */
-  @Override
-  protected void finalize() throws Throwable
-  {
-    map = null;
-    to = null;
-    super.finalize();
-  }
-
   /**
    * Returns an iterator which can serve up the aligned codon column positions
    * and their corresponding peptide products

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 13b715e..fd640cf 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2713,8 +2713,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     /*
      * Create a new AlignmentPanel (with its own, new Viewport)
      */
-    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
-            true);
+    AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
     if (!copyAnnotation)
     {
       /*

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 1658f0f..a64a475 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -216,34 +216,6 @@ public class Jalview2XML
     }
   }
 
-  void clearSeqRefs()
-  {
-    if (_cleartables)
-    {
-      if (seqRefIds != null)
-      {
-        seqRefIds.clear();
-      }
-      if (seqsToIds != null)
-      {
-        seqsToIds.clear();
-      }
-      if (incompleteSeqs != null)
-      {
-        incompleteSeqs.clear();
-      }
-      // seqRefIds = null;
-      // seqsToIds = null;
-    }
-    else
-    {
-      // do nothing
-      warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
-      // seqRefIds = new Hashtable();
-      // seqsToIds = new IdentityHashMap();
-    }
-  }
-
   void initSeqRefs()
   {
     if (seqsToIds == null)
@@ -5341,28 +5313,25 @@ public class Jalview2XML
 
   }
 
-  public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
-          boolean keepSeqRefs)
+  /**
+   * Provides a 'copy' of an alignment view (on action New View) by 'saving' the
+   * view as XML (but not to file), and then reloading it
+   * 
+   * @param ap
+   * @return
+   */
+  public AlignmentPanel copyAlignPanel(AlignmentPanel ap)
   {
     initSeqRefs();
     JalviewModel jm = saveState(ap, null, null, null);
 
-    if (!keepSeqRefs)
-    {
-      clearSeqRefs();
-      jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
-    }
-    else
-    {
-      uniqueSetSuffix = "";
-      jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
-      // overwrite the
-      // view we just
-      // copied
-    }
+    uniqueSetSuffix = "";
+    jm.getJalviewModelSequence().getViewport(0).setId(null);
+    // we don't overwrite the view we just copied
+
     if (this.frefedSequence == null)
     {
-      frefedSequence = new Vector();
+      frefedSequence = new Vector<SeqFref>();
     }
 
     viewportsAdded.clear();
@@ -5382,32 +5351,8 @@ public class Jalview2XML
     return af.alignPanel;
   }
 
-  /**
-   * flag indicating if hashtables should be cleared on finalization TODO this
-   * flag may not be necessary
-   */
-  private final boolean _cleartables = true;
-
   private Hashtable jvids2vobj;
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#finalize()
-   */
-  @Override
-  protected void finalize() throws Throwable
-  {
-    // really make sure we have no buried refs left.
-    if (_cleartables)
-    {
-      clearSeqRefs();
-    }
-    this.seqRefIds = null;
-    this.seqsToIds = null;
-    super.finalize();
-  }
-
   private void warn(String msg)
   {
     warn(msg, null);

diff --git a/src/jalview/gui/ViewSelectionMenu.java b/src/jalview/gui/ViewSelectionMenu.java
index cdbb4fa..2a7743a 100644 (file)
--- a/src/jalview/gui/ViewSelectionMenu.java
+++ b/src/jalview/gui/ViewSelectionMenu.java
@@ -60,15 +60,6 @@ public class ViewSelectionMenu extends JMenu
 
   private ItemListener _handler;
 
-  @Override
-  protected void finalize() throws Throwable
-  {
-    _selectedviews = null;
-    _handler = null;
-    _allviews = null;
-    super.finalize();
-  }
-
   /**
    * create a new view selection menu. This menu has some standard entries
    * (select all, invert selection), and a checkbox for every view. Mousing over

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 26641b1..f26d6da 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -606,18 +606,4 @@ public class FileLoader implements Runnable
     return tempStructFile.toString();
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see java.lang.Object#finalize()
-   */
-  @Override
-  protected void finalize() throws Throwable
-  {
-    source = null;
-    alignFrame = null;
-    viewport = null;
-    super.finalize();
-  }
-
 }

diff --git a/src/jalview/io/InputStreamParser.java b/src/jalview/io/InputStreamParser.java
index d269e97..65ba74a 100644 (file)
--- a/src/jalview/io/InputStreamParser.java
+++ b/src/jalview/io/InputStreamParser.java
@@ -47,11 +47,4 @@ public class InputStreamParser extends FileParse
     error = false;
   }
 
-  @Override
-  protected void finalize() throws Throwable
-  {
-    dataIn = null;
-    super.finalize();
-  }
-
 }

diff --git a/src/jalview/javascript/JSFunctionExec.java b/src/jalview/javascript/JSFunctionExec.java
index 083cd26..29f3fa9 100644 (file)
--- a/src/jalview/javascript/JSFunctionExec.java
+++ b/src/jalview/javascript/JSFunctionExec.java
@@ -39,19 +39,6 @@ public class JSFunctionExec implements Runnable
     jvlite.setExecutor(this);
   }
 
-  @Override
-  protected void finalize() throws Throwable
-  {
-    jvlite = null;
-    executor = null;
-    if (jsExecQueue != null)
-    {
-      jsExecQueue.clear();
-    }
-    jsExecQueue = null;
-    super.finalize();
-  }
-
   private Vector jsExecQueue;
 
   private Thread executor = null;

diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java
index 874bfd3..6071933 100644 (file)
--- a/src/jalview/javascript/MouseOverStructureListener.java
+++ b/src/jalview/javascript/MouseOverStructureListener.java
@@ -299,13 +299,6 @@ public class MouseOverStructureListener extends JSFunctionExec
   }
 
   @Override
-  public void finalize() throws Throwable
-  {
-    jvlite = null;
-    super.finalize();
-  }
-
-  @Override
   public void releaseReferences(Object svl)
   {
 

diff --git a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
index cb8f75a..2f3c298 100644 (file)
--- a/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
+++ b/src/jalview/ws/jws2/jabaws2/Jws2Instance.java
@@ -170,13 +170,11 @@ public class Jws2Instance
     {
       try
       {
-        Closeable svc = (Closeable) service;
-        service = null;
-        svc.close();
-      } catch (Exception e)
+        ((Closeable) service).close();
+      } catch (Throwable t)
       {
+        // ignore
       }
-      ;
     }
     super.finalize();
   }