JAL-3130 Some automatically fixed deprecated calls. Mostly constructors converted...

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index b15c3cc..b0b5d37 100644 (file)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -37,12 +37,12 @@ import jalview.util.MessageManager;
 
 import java.awt.Color;
 import java.awt.Dimension;
-import java.awt.Event;
 import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.Image;
 // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
 import java.awt.Panel;
+import java.awt.event.InputEvent;
 import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseEvent;
@@ -295,7 +295,7 @@ public class AppletPDBCanvas extends Panel
   {
     seqColoursReady = false;
     // Sort the bonds by z coord
-    visiblebonds = new Vector<Bond>();
+    visiblebonds = new Vector<>();
 
     for (int ii = 0; ii < pdb.getChains().size(); ii++)
     {
@@ -799,7 +799,7 @@ public class AppletPDBCanvas extends Panel
           {
             if (highlightRes == null)
             {
-              highlightRes = new Vector<String>();
+              highlightRes = new Vector<>();
             }
 
             final String atomString = Integer
@@ -893,7 +893,7 @@ public class AppletPDBCanvas extends Panel
     MCMatrix objmat = new MCMatrix(3, 3);
     objmat.setIdentity();
 
-    if ((evt.getModifiers() & Event.META_MASK) != 0)
+    if ((evt.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
     {
       objmat.rotatez(((mx - omx)));
     }

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 904e307..a2ce2ae 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -83,14 +83,14 @@ public class Atom
     resNumber = Integer.parseInt(str.substring(22, 26).trim());
     resNumIns = str.substring(22, 27).trim();
     insCode = str.substring(26, 27).charAt(0);
-    this.x = (new Float(str.substring(30, 38).trim()).floatValue());
-    this.y = (new Float(str.substring(38, 46).trim()).floatValue());
-    this.z = (new Float(str.substring(47, 55).trim()).floatValue());
+    this.x = (Float.valueOf(str.substring(30, 38).trim()).floatValue());
+    this.y = (Float.valueOf(str.substring(38, 46).trim()).floatValue());
+    this.z = (Float.valueOf(str.substring(47, 55).trim()).floatValue());
     // optional entries - see JAL-730
     String tm = str.substring(54, 60).trim();
     if (tm.length() > 0)
     {
-      occupancy = (new Float(tm)).floatValue();
+      occupancy = (Float.valueOf(tm)).floatValue();
     }
     else
     {
@@ -100,7 +100,7 @@ public class Atom
     tm = str.substring(60, 66).trim();
     if (tm.length() > 0)
     {
-      tfactor = (new Float(tm).floatValue());
+      tfactor = (Float.valueOf(tm).floatValue());
     }
     else
     {

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index ab172f2..cc9f85c 100644 (file)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -36,13 +36,13 @@ import jalview.structure.StructureSelectionManager;
 
 import java.awt.Color;
 import java.awt.Dimension;
-import java.awt.Event;
 import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
 import java.awt.Image;
 import java.awt.RenderingHints;
+import java.awt.event.InputEvent;
 import java.awt.event.KeyAdapter;
 import java.awt.event.KeyEvent;
 import java.awt.event.MouseEvent;
@@ -277,7 +277,7 @@ public class PDBCanvas extends JPanel
   {
     seqColoursReady = false;
     // Sort the bonds by z coord
-    visiblebonds = new Vector<Bond>();
+    visiblebonds = new Vector<>();
 
     for (PDBChain chain : pdb.getChains())
     {
@@ -771,7 +771,7 @@ public class PDBCanvas extends JPanel
           {
             if (highlightRes == null)
             {
-              highlightRes = new Vector<String>();
+              highlightRes = new Vector<>();
             }
 
             final String atomString = Integer
@@ -858,7 +858,7 @@ public class PDBCanvas extends JPanel
     MCMatrix objmat = new MCMatrix(3, 3);
     objmat.setIdentity();
 
-    if ((evt.getModifiers() & Event.META_MASK) != 0)
+    if ((evt.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
     {
       objmat.rotatez(((mx - omx)));
     }

diff --git a/src/com/stevesoft/pat/RegOpt.java b/src/com/stevesoft/pat/RegOpt.java
index 50d799f..d5f62de 100755 (executable)
--- a/src/com/stevesoft/pat/RegOpt.java
+++ b/src/com/stevesoft/pat/RegOpt.java
@@ -138,16 +138,16 @@ class Branch extends Pattern
       n = RegOpt.opt(n, ignoreCase, dontMinQ);
     }
     n.setParent(this);
-    set(new Character(o.c), n, ignoreCase, dontMinQ);
+    set(Character.valueOf(o.c), n, ignoreCase, dontMinQ);
     if (ignoreCase)
     {
       if (o.c != o.altc)
       {
-        set(new Character(o.altc), n, ignoreCase, dontMinQ);
+        set(Character.valueOf(o.altc), n, ignoreCase, dontMinQ);
       }
       if (o.c != o.altc2 && o.altc != o.altc2)
       {
-        set(new Character(o.altc2), n, ignoreCase, dontMinQ);
+        set(Character.valueOf(o.altc2), n, ignoreCase, dontMinQ);
       }
     }
   }
@@ -250,7 +250,7 @@ class Branch extends Pattern
     {
       return -1;
     }
-    Pattern n = (Pattern) h.get(new Character(pt.src.charAt(pos)));
+    Pattern n = (Pattern) h.get(Character.valueOf(pt.src.charAt(pos)));
     if (n == null)
     {
       return -1;

diff --git a/src/com/stevesoft/pat/RegexTokenizer.java b/src/com/stevesoft/pat/RegexTokenizer.java
index 31fa2ba..c99bfea 100755 (executable)
--- a/src/com/stevesoft/pat/RegexTokenizer.java
+++ b/src/com/stevesoft/pat/RegexTokenizer.java
@@ -43,13 +43,13 @@ public class RegexTokenizer implements Enumeration
     if (r.searchFrom(toParse, pos))
     {
       v.addElement(r.left().substring(pos));
-      vi.addElement(new Integer(r.matchFrom() + r.charsMatched()));
+      vi.addElement(Integer.valueOf(r.matchFrom() + r.charsMatched()));
       for (int i = 0; i < r.numSubs(); i++)
       {
         if (r.substring() != null)
         {
           v.addElement(r.substring(i + offset));
-          vi.addElement(new Integer(r.matchFrom(i + offset)
+          vi.addElement(Integer.valueOf(r.matchFrom(i + offset)
                   + r.charsMatched(i + offset)));
         }
       }

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
index 1d57a31..6b5e36c 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimUtils.java
@@ -173,7 +173,7 @@ public abstract class ChimUtils
       float[] rgbValues = new float[4];
       for (int i = 0; i < rgbStrings.length; i++)
       {
-        Float f = new Float(rgbStrings[i]);
+        Float f = Float.valueOf(rgbStrings[i]);
         rgbValues[i] = f.floatValue();
       }
       if (rgbStrings.length == 4)
@@ -203,7 +203,7 @@ public abstract class ChimUtils
    */
   public static Integer makeModelKey(int model, int subModel)
   {
-    return new Integer(model * MAX_SUB_MODELS + subModel);
+    return Integer.valueOf(model * MAX_SUB_MODELS + subModel);
   }
 
   // invoked by the getResdiue (parseConnectivityReplies in

diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
index 9a29a99..4f871d3 100644 (file)
--- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
+++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraChain.java
@@ -200,7 +200,7 @@ public class ChimeraChain implements ChimeraStructuralObject
    */
   public ChimeraResidue getResidue(String index)
   {
-    // Integer index = new Integer(residueIndex);
+    // Integer index = Integer.valueOf(residueIndex);
     if (residueMap.containsKey(index))
       return residueMap.get(index);
     return null;

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index b5cefe0..8473904 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -586,7 +586,7 @@ public class AlignmentSorter
 
     for (int i = 0; i < alignment.length; i++)
     {
-      ids[i] = (new Float(alignment[i].getName().substring(8)))
+      ids[i] = (Float.valueOf(alignment[i].getName().substring(8)))
               .floatValue();
     }
 

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 0af5d20..c3de19b 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -695,7 +695,7 @@ public class Conservation
 
       max = Math.max(max, bigtot);
 
-      quality.addElement(new Double(bigtot));
+      quality.addElement(Double.valueOf(bigtot));
     }
 
     double newmax = -Double.MAX_VALUE;
@@ -707,7 +707,7 @@ public class Conservation
       tmp = ((max - tmp) * (size - cons2GapCounts[j])) / size;
 
       // System.out.println(tmp+ " " + j);
-      quality.setElementAt(new Double(tmp), j);
+      quality.setElementAt(Double.valueOf(tmp), j);
 
       if (tmp > newmax)
       {

diff --git a/src/jalview/analysis/ParseProperties.java b/src/jalview/analysis/ParseProperties.java
index 629a8a3..4b68d93 100644 (file)
--- a/src/jalview/analysis/ParseProperties.java
+++ b/src/jalview/analysis/ParseProperties.java
@@ -134,7 +134,7 @@ public class ParseProperties
           double score = Double.NaN;
           try
           {
-            score = new Double(sstring).doubleValue();
+            score = Double.valueOf(sstring).doubleValue();
           } catch (Exception e)
           {
             // don't try very hard to parse if regex was wrong.

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index fabd0c6..fdca89d 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -45,8 +45,8 @@ public class SeqsetUtils
   {
     Hashtable sqinfo = new Hashtable();
     sqinfo.put("Name", seq.getName());
-    sqinfo.put("Start", new Integer(seq.getStart()));
-    sqinfo.put("End", new Integer(seq.getEnd()));
+    sqinfo.put("Start", Integer.valueOf(seq.getStart()));
+    sqinfo.put("End", Integer.valueOf(seq.getEnd()));
     if (seq.getDescription() != null)
     {
       sqinfo.put("Description", seq.getDescription());

diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java
index b681aa6..1342bb2 100644 (file)
--- a/src/jalview/analysis/StructureFrequency.java
+++ b/src/jalview/analysis/StructureFrequency.java
@@ -227,14 +227,14 @@ public class StructureFrequency
           maxResidue = "{";
         }
       }
-      residueHash.put(MAXCOUNT, new Integer(count));
+      residueHash.put(MAXCOUNT, Integer.valueOf(count));
       residueHash.put(MAXRESIDUE, maxResidue);
 
       percentage = ((float) count * 100) / jSize;
-      residueHash.put(PID_GAPS, new Float(percentage));
+      residueHash.put(PID_GAPS, Float.valueOf(percentage));
 
       percentage = ((float) count * 100) / nongap;
-      residueHash.put(PID_NOGAPS, new Float(percentage));
+      residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
 
       if (result[i] == null)
       {
@@ -261,14 +261,14 @@ public class StructureFrequency
           residueHash.put(PAIRPROFILE, pairs);
         }
 
-        residueHash.put(MAXCOUNT, new Integer(count));
+        residueHash.put(MAXCOUNT, Integer.valueOf(count));
         residueHash.put(MAXRESIDUE, maxResidue);
 
         percentage = ((float) count * 100) / jSize;
-        residueHash.put(PID_GAPS, new Float(percentage));
+        residueHash.put(PID_GAPS, Float.valueOf(percentage));
 
         percentage = ((float) count * 100) / nongap;
-        residueHash.put(PID_NOGAPS, new Float(percentage));
+        residueHash.put(PID_NOGAPS, Float.valueOf(percentage));
 
         result[bpEnd] = residueHash;
       }

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 262948d..246f77a 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -76,7 +76,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          widthScale = new Float(param).floatValue();
+          widthScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }
@@ -99,7 +99,7 @@ public class AlignViewport extends AlignmentViewport
       {
         try
         {
-          heightScale = new Float(param).floatValue();
+          heightScale = Float.valueOf(param).floatValue();
         } catch (Exception e)
         {
         }

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 533226e..9456986 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -350,7 +350,7 @@ public class AnnotationColourChooser extends Panel implements
     {
       try
       {
-        float f = new Float(thresholdValue.getText()).floatValue();
+        float f = Float.valueOf(thresholdValue.getText()).floatValue();
         slider.setValue((int) (f * 1000));
         adjustmentValueChanged(null);
       } catch (NumberFormatException ex)

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 1366f31..a0102b9 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -457,8 +457,8 @@ public class AnnotationLabels extends Panel
             .getAlignmentAnnotation();
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
 
       PopupMenu popup = new PopupMenu(

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 50bc184..2b50c32 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -354,8 +354,8 @@ public class AnnotationPanel extends Panel
       }
     }
 
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK
             && activeRow != -1)
     {
       if (av.getColumnSelection() == null

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index d9eae11..19f6eec 100644 (file)
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -309,7 +309,7 @@ public class FeatureColourChooser extends Panel implements ActionListener,
   {
     try
     {
-      float f = new Float(thresholdValue.getText()).floatValue();
+      float f = Float.valueOf(thresholdValue.getText()).floatValue();
       slider.setValue((int) (f * SCALE_FACTOR_1K));
       adjustmentValueChanged(null);
 

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index a60aacd..489cbb1 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -703,7 +703,7 @@ public class FeatureSettings extends Panel
   public void mouseClicked(MouseEvent evt)
   {
     MyCheckbox check = (MyCheckbox) evt.getSource();
-    if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) != 0)
+    if ((evt.getModifiersEx() & InputEvent.BUTTON3_DOWN_MASK) != 0)
     {
       this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY());
     }

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 15e269c..041b2df 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -279,8 +279,8 @@ public class IdPanel extends Panel
 
     int seq = alignPanel.seqPanel.findSeq(e);
 
-    if ((e.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((e.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
       SequenceI sq = av.getAlignment().getSequenceAt(seq);
 

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 3bbbe95..703f8ac 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -114,8 +114,8 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mouseClicked(MouseEvent evt)
   {
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
       showPopupMenu(evt);
     }
@@ -139,8 +139,8 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mousePressed(MouseEvent evt)
   {
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
       if (!Platform.isAMac())
       {
@@ -182,8 +182,8 @@ public class OverviewPanel extends Panel implements Runnable,
   @Override
   public void mouseDragged(MouseEvent evt)
   {
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
       if (!Platform.isAMac())
       {

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index c91449f..d3f4a69 100755 (executable)
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -96,8 +96,8 @@ public class ScalePanel extends Panel
 
     min = res;
     max = res;
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
       rightMouseButtonPressed(evt, res);
     }

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index e07dae6..fee68c8 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -499,8 +499,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     // For now, ignore the mouseWheel font resizing on Macs
     // As the Button2_mask always seems to be true
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON2_DOWN_MASK) == InputEvent.BUTTON2_DOWN_MASK
             && !av.MAC)
     {
       mouseWheelPressed = true;
@@ -1432,8 +1432,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    if ((evt.getModifiers()
-            & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ((evt.getModifiersEx()
+            & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
     {
       List<SequenceFeature> allFeatures = findFeaturesAtColumn(sequence,
               sequence.findPosition(column + 1));

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index a60496c..8873cc9 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -198,7 +198,7 @@ public class JalviewLite extends Applet
       int apos = -1;
       try
       {
-        apos = new Integer(position).intValue();
+        apos = Integer.valueOf(position).intValue();
         apos--;
       } catch (NumberFormatException ex)
       {
@@ -337,7 +337,7 @@ public class JalviewLite extends Applet
           int from = -1, to = -1;
           try
           {
-            from = new Integer(cl.substring(0, p)).intValue();
+            from = Integer.valueOf(cl.substring(0, p)).intValue();
             from--;
           } catch (NumberFormatException ex)
           {
@@ -348,7 +348,7 @@ public class JalviewLite extends Applet
           }
           try
           {
-            to = new Integer(cl.substring(p + 1)).intValue();
+            to = Integer.valueOf(cl.substring(p + 1)).intValue();
             to--;
           } catch (NumberFormatException ex)
           {
@@ -408,7 +408,7 @@ public class JalviewLite extends Applet
           int r = -1;
           try
           {
-            r = new Integer(cl).intValue();
+            r = Integer.valueOf(cl).intValue();
             r--;
           } catch (NumberFormatException ex)
           {
@@ -1176,7 +1176,7 @@ public class JalviewLite extends Applet
         try
         {
           StructureSelectionManager.getStructureSelectionManager(me)
-                  .mouseOverStructure(new Integer(pdbResNum).intValue(),
+                  .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(),
                           chain, pdbfile);
           if (debug)
           {
@@ -1212,8 +1212,8 @@ public class JalviewLite extends Applet
       {
         try
         {
-          alf.scrollTo(new Integer(topRow).intValue(),
-                  new Integer(leftHandColumn).intValue());
+          alf.scrollTo(Integer.valueOf(topRow).intValue(),
+                  Integer.valueOf(leftHandColumn).intValue());
 
         } catch (Exception ex)
         {
@@ -1244,7 +1244,7 @@ public class JalviewLite extends Applet
       {
         try
         {
-          alf.scrollToRow(new Integer(topRow).intValue());
+          alf.scrollToRow(Integer.valueOf(topRow).intValue());
 
         } catch (Exception ex)
         {
@@ -1276,7 +1276,7 @@ public class JalviewLite extends Applet
       {
         try
         {
-          alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+          alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
 
         } catch (Exception ex)
         {

diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index ee9389c..2ee4503 100755 (executable)
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -991,7 +991,7 @@ public class AlignmentAnnotation
           seqPos = i + startRes;
         }
 
-        sequenceMapping.put(new Integer(seqPos), annotations[i]);
+        sequenceMapping.put(Integer.valueOf(seqPos), annotations[i]);
       }
     }
 
@@ -1030,7 +1030,7 @@ public class AlignmentAnnotation
     {
       for (a = sequenceRef.getStart(); a <= sequenceRef.getEnd(); a++)
       {
-        index = new Integer(a);
+        index = Integer.valueOf(a);
         Annotation annot = sequenceMapping.get(index);
         if (annot != null)
         {

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index c33abb3..cea9de7 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -169,7 +169,7 @@ public class BinarySequence extends Sequence
 
     for (int i = 0; i < binary.length; i++)
     {
-      out += (new Integer(binary[i])).toString();
+      out += (Integer.valueOf(binary[i])).toString();
 
       if (i < (binary.length - 1))
       {

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 6d620b4..916011b 100644 (file)
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -105,7 +105,7 @@ public class ColumnSelection
     void remove(int col)
     {
 
-      Integer colInt = new Integer(col);
+      Integer colInt = Integer.valueOf(col);
 
       if (selected.get(col))
       {
@@ -203,7 +203,7 @@ public class ColumnSelection
           // clear shifted bits and update List of selected columns
           selected.clear(temp);
           mask.set(temp - change);
-          order.set(i, new Integer(temp - change));
+          order.set(i, Integer.valueOf(temp - change));
         }
       }
       // lastly update the bitfield all at once
@@ -308,7 +308,7 @@ public class ColumnSelection
     Integer colInt;
     for (int i = start; i < end; i++)
     {
-      colInt = new Integer(i);
+      colInt = Integer.valueOf(i);
       if (selection.contains(colInt))
       {
         selection.remove(colInt);

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 8832278..06817f2 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -876,7 +876,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       try
       {
         // recover PDB filename for the model hovered over.
-        int mnumber = new Integer(mdlId).intValue() - 1;
+        int mnumber = Integer.valueOf(mdlId).intValue() - 1;
         if (_modelFileNameMap != null)
         {
           int _mp = _modelFileNameMap.length - 1;

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2b6d868..0ea488b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2092,7 +2092,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();
@@ -2139,7 +2139,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                     newGraphGroups.add(q, null);
                   }
                   newGraphGroups.set(newann.graphGroup,
-                          new Integer(++fgroup));
+                          Integer.valueOf(++fgroup));
                 }
                 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
                         .intValue();

diff --git a/src/jalview/gui/BlogReader.java b/src/jalview/gui/BlogReader.java
index 9d68af1..65c8b5a 100644 (file)
--- a/src/jalview/gui/BlogReader.java
+++ b/src/jalview/gui/BlogReader.java
@@ -538,7 +538,7 @@ public class BlogReader extends JPanel
     public LaunchJvBrowserOnItem(JList listItems)
     {
       super("Open in Browser");
-      this.putValue(MNEMONIC_KEY, new Integer(KeyEvent.VK_O));
+      this.putValue(MNEMONIC_KEY, Integer.valueOf(KeyEvent.VK_O));
       this.putValue(Action.LONG_DESCRIPTION, "Open in Browser");
       _listItems = listItems;
     }

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 874c619..9d379fe 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1107,7 +1107,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
             InputEvent.CTRL_DOWN_MASK);
     KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask());
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx());
 
     InputMap inputMap = frame
             .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
@@ -2822,7 +2822,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   {
     getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW)
             .put(KeyStroke.getKeyStroke(KeyEvent.VK_Q,
-                    Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()),
+                    Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()),
                     "Quit");
     getRootPane().getActionMap().put("Quit", new AbstractAction()
     {
@@ -2879,18 +2879,18 @@ public class Desktop extends jalview.jbgui.GDesktop
       progressBarHandlers = new Hashtable<>();
     }
 
-    if (progressBars.get(new Long(id)) != null)
+    if (progressBars.get(Long.valueOf(id)) != null)
     {
-      JPanel panel = progressBars.remove(new Long(id));
-      if (progressBarHandlers.contains(new Long(id)))
+      JPanel panel = progressBars.remove(Long.valueOf(id));
+      if (progressBarHandlers.contains(Long.valueOf(id)))
       {
-        progressBarHandlers.remove(new Long(id));
+        progressBarHandlers.remove(Long.valueOf(id));
       }
       removeProgressPanel(panel);
     }
     else
     {
-      progressBars.put(new Long(id), addProgressPanel(message));
+      progressBars.put(Long.valueOf(id), addProgressPanel(message));
     }
   }
 
@@ -2905,13 +2905,13 @@ public class Desktop extends jalview.jbgui.GDesktop
           final IProgressIndicatorHandler handler)
   {
     if (progressBarHandlers == null
-            || !progressBars.containsKey(new Long(id)))
+            || !progressBars.containsKey(Long.valueOf(id)))
     {
       throw new Error(MessageManager.getString(
               "error.call_setprogressbar_before_registering_handler"));
     }
-    progressBarHandlers.put(new Long(id), handler);
-    final JPanel progressPanel = progressBars.get(new Long(id));
+    progressBarHandlers.put(Long.valueOf(id), handler);
+    final JPanel progressPanel = progressBars.get(Long.valueOf(id));
     if (handler.canCancel())
     {
       JButton cancel = new JButton(

diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
index 46f574e..e22f506 100644 (file)
--- a/src/jalview/gui/FeatureRenderer.java
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -269,8 +269,8 @@ public class FeatureRenderer
             name.setText(sf.getType());
             description.setText(sf.getDescription());
             group.setText(sf.getFeatureGroup());
-            start.setValue(new Integer(sf.getBegin()));
-            end.setValue(new Integer(sf.getEnd()));
+            start.setValue(Integer.valueOf(sf.getBegin()));
+            end.setValue(Integer.valueOf(sf.getEnd()));
 
             SearchResultsI highlight = new SearchResults();
             highlight.addResult(sequences.get(0), sf.getBegin(),
@@ -357,8 +357,8 @@ public class FeatureRenderer
     name.setText(featureType);
     group.setText(featureGroup);
 
-    start.setValue(new Integer(firstFeature.getBegin()));
-    end.setValue(new Integer(firstFeature.getEnd()));
+    start.setValue(Integer.valueOf(firstFeature.getBegin()));
+    end.setValue(Integer.valueOf(firstFeature.getEnd()));
     description.setText(firstFeature.getDescription());
     updateColourButton(mainPanel, colour,
             (oldcol = fcol = getFeatureStyle(featureType)));

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index a135785..a6c3451 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -679,7 +679,7 @@ public class FeatureSettings extends JPanel
         data[dataIndex][FILTER_COLUMN] = featureFilter == null
                 ? new FeatureMatcherSet()
                 : featureFilter;
-        data[dataIndex][SHOW_COLUMN] = new Boolean(
+        data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(
                 af.getViewport().getFeaturesDisplayed().isVisible(type));
         dataIndex++;
         displayableTypes.remove(type);
@@ -706,7 +706,7 @@ public class FeatureSettings extends JPanel
       data[dataIndex][FILTER_COLUMN] = featureFilter == null
               ? new FeatureMatcherSet()
               : featureFilter;
-      data[dataIndex][SHOW_COLUMN] = new Boolean(true);
+      data[dataIndex][SHOW_COLUMN] = Boolean.valueOf(true);
       dataIndex++;
       displayableTypes.remove(type);
     }

diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java
index c1e935a..e4c8f78 100644 (file)
--- a/src/jalview/gui/PCAPanel.java
+++ b/src/jalview/gui/PCAPanel.java
@@ -712,11 +712,11 @@ public class PCAPanel extends GPCAPanel
     // }
     //
     // JPanel progressPanel;
-    // Long lId = new Long(id);
+    // Long lId = Long.valueOf(id);
     // GridLayout layout = (GridLayout) statusPanel.getLayout();
     // if (progressBars.get(lId) != null)
     // {
-    // progressPanel = (JPanel) progressBars.get(new Long(id));
+    // progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
     // statusPanel.remove(progressPanel);
     // progressBars.remove(lId);
     // progressPanel = null;
@@ -755,13 +755,13 @@ public class PCAPanel extends GPCAPanel
           final IProgressIndicatorHandler handler)
   {
     progressBar.registerHandler(id, handler);
-    // if (progressBarHandlers == null || !progressBars.contains(new Long(id)))
+    // if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(id)))
     // {
     // throw new
     // Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
     // }
-    // progressBarHandlers.put(new Long(id), handler);
-    // final JPanel progressPanel = (JPanel) progressBars.get(new Long(id));
+    // progressBarHandlers.put(Long.valueOf(id), handler);
+    // final JPanel progressPanel = (JPanel) progressBars.get(Long.valueOf(id));
     // if (handler.canCancel())
     // {
     // JButton cancel = new JButton(

diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java
index 02368df..5e68d16 100755 (executable)
--- a/src/jalview/gui/RotatableCanvas.java
+++ b/src/jalview/gui/RotatableCanvas.java
@@ -736,7 +736,7 @@ public class RotatableCanvas extends JPanel implements MouseListener,
     my = evt.getY();
 
     // Check if this is a rectangle drawing drag
-    if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) != 0)
+    if ((evt.getModifiersEx() & InputEvent.BUTTON2_DOWN_MASK) != 0)
     {
       // rectx2 = evt.getX();
       // recty2 = evt.getY();

diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index a0d31cf..98a8251 100644 (file)
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -412,7 +412,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
      * Ctrl-W / Cmd-W - close view or window
      */
     KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     action = new AbstractAction()
     {
       @Override
@@ -433,7 +433,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
      * Ctrl-T / Cmd-T open new view
      */
     KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     AbstractAction action = new AbstractAction()
     {
       @Override
@@ -773,7 +773,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
      * Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
      */
     KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     AbstractAction action = new AbstractAction()
     {
       @Override

diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java
index 850ef21..5186a26 100644 (file)
--- a/src/jalview/gui/WsPreferences.java
+++ b/src/jalview/gui/WsPreferences.java
@@ -123,7 +123,7 @@ public class WsPreferences extends GWsPreferences
     for (String url : wsUrls)
     {
       int status = Jws2Discoverer.getDiscoverer().getServerStatusFor(url);
-      tdat[r][1] = new Integer(status);
+      tdat[r][1] = Integer.valueOf(status);
       tdat[r++][0] = url;
     }
 

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index e578a45..fd515d5 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -274,7 +274,7 @@ public class AnnotationFile
           if (row.graphGroup > -1)
           {
             graphGroupSeen.set(row.graphGroup);
-            Integer key = new Integer(row.graphGroup);
+            Integer key = Integer.valueOf(row.graphGroup);
             if (graphGroup.containsKey(key))
             {
               graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
@@ -762,7 +762,7 @@ public class AnnotationFile
                       autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
                               (aa[aai].groupRef == null ? null
                                       : aa[aai].groupRef.getName())),
-                      new Integer(1));
+                      Integer.valueOf(1));
             }
           }
         }
@@ -1271,7 +1271,7 @@ public class AnnotationFile
         {
           displayChar = token;
           // foo
-          value = new Float(token).floatValue();
+          value = Float.valueOf(token).floatValue();
           parsedValue = true;
           continue;
         } catch (NumberFormatException ex)

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 169da5a..8d1b4b2 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -440,7 +440,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       float score = Float.NaN;
       try
       {
-        score = new Float(gffColumns[6]).floatValue();
+        score = Float.valueOf(gffColumns[6]).floatValue();
       } catch (NumberFormatException ex)
       {
         sf = new SequenceFeature(ft, desc, startPos, endPos, featureGroup);

diff --git a/src/jalview/io/JPredFile.java b/src/jalview/io/JPredFile.java
index 026c879..6732e82 100755 (executable)
--- a/src/jalview/io/JPredFile.java
+++ b/src/jalview/io/JPredFile.java
@@ -207,7 +207,7 @@ public class JPredFile extends AlignFile
           {
             ascore = symbols.nextToken();
 
-            Float score = new Float(ascore);
+            Float score = Float.valueOf(ascore);
             scores.addElement(score);
           }
 
@@ -283,7 +283,7 @@ public class JPredFile extends AlignFile
 
           seq_entries.addElement(newseq.toString());
           ids.addElement(id);
-          Symscores.put(id, new Integer(ids.size() - 1));
+          Symscores.put(id, Integer.valueOf(ids.size() - 1));
         }
       }
     }

diff --git a/src/jalview/io/JnetAnnotationMaker.java b/src/jalview/io/JnetAnnotationMaker.java
index c9f1fcf..6828202 100755 (executable)
--- a/src/jalview/io/JnetAnnotationMaker.java
+++ b/src/jalview/io/JnetAnnotationMaker.java
@@ -148,7 +148,7 @@ public class JnetAnnotationMaker
             {
               for (int j = 0; j < width; j++)
               {
-                float value = new Float(preds[i].getCharAt(j) + "")
+                float value = Float.valueOf(preds[i].getCharAt(j) + "")
                         .floatValue();
                 annotations[gapmap[j]] = new Annotation(
                         preds[i].getCharAt(j) + "", "",
@@ -159,7 +159,7 @@ public class JnetAnnotationMaker
             {
               for (int j = 0; j < width; j++)
               {
-                float value = new Float(preds[i].getCharAt(j) + "")
+                float value = Float.valueOf(preds[i].getCharAt(j) + "")
                         .floatValue();
                 annotations[gapmap[delMap[j]]] = new Annotation(
                         preds[i].getCharAt(j) + "", "",

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 442278d..c1849fc 100755 (executable)
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -85,7 +85,7 @@ public class ModellerDescription
 
     resCode(int v)
     {
-      val = new Integer(v);
+      val = Integer.valueOf(v);
       field = val.toString();
     }
   };

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index c414145..2221f00 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -477,7 +477,7 @@ public class NewickFile extends FileParse
           {
             try
             {
-              bootstrap = (new Integer(nbootstrap.stringMatched(1)))
+              bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
                       .intValue();
               HasBootstrap = true;
             } catch (Exception e)
@@ -494,7 +494,7 @@ public class NewickFile extends FileParse
         {
           try
           {
-            distance = (new Float(ndist.stringMatched(1))).floatValue();
+            distance = (Float.valueOf(ndist.stringMatched(1))).floatValue();
             HasDistances = true;
             nodehasdistance = true;
           } catch (Exception e)
@@ -661,7 +661,7 @@ public class NewickFile extends FileParse
             if (code.toLowerCase().equals("b"))
             {
               int v = -1;
-              Float iv = new Float(value);
+              Float iv = Float.valueOf(value);
               v = iv.intValue(); // jalview only does integer bootstraps
               // currently
               c.setBootstrap(v);

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index adf4447..387dbfa 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -2248,7 +2248,7 @@ public class VamsasAppDatastore
           Float val = null;
           try
           {
-            val = new Float(props[p].getContent());
+            val = Float.valueOf(props[p].getContent());
           } catch (Exception e)
           {
             Cache.log.warn("Failed to parse threshold property");
@@ -2537,7 +2537,7 @@ public class VamsasAppDatastore
           int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
           for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
           {
-            posList.add(new Integer(p));
+            posList.add(Integer.valueOf(p));
           }
         }
       }
@@ -2548,7 +2548,7 @@ public class VamsasAppDatastore
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
-          posList.add(new Integer(pos));
+          posList.add(Integer.valueOf(pos));
         }
       }
     }

diff --git a/src/jalview/io/vamsas/Rangetype.java b/src/jalview/io/vamsas/Rangetype.java
index ee4fa83..b4580f0 100644 (file)
--- a/src/jalview/io/vamsas/Rangetype.java
+++ b/src/jalview/io/vamsas/Rangetype.java
@@ -148,7 +148,7 @@ public abstract class Rangetype extends DatastoreItem
           int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
           for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
           {
-            posList.add(new Integer(p));
+            posList.add(Integer.valueOf(p));
           }
         }
       }
@@ -159,7 +159,7 @@ public abstract class Rangetype extends DatastoreItem
         for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
         {
           pos = dseta.getPos(p).getI();
-          posList.add(new Integer(pos));
+          posList.add(Integer.valueOf(pos));
         }
       }
     }
@@ -193,8 +193,8 @@ public abstract class Rangetype extends DatastoreItem
         for (int s = 0, sSize = range.getSegCount(); s < sSize; s++)
         {
           se = getSegRange(range.getSeg(s), false);
-          posList.addElement(new Integer(se[0]));
-          posList.addElement(new Integer(se[1]));
+          posList.addElement(Integer.valueOf(se[0]));
+          posList.addElement(Integer.valueOf(se[1]));
         }
       }
       else if (range.getPosCount() > 0)
@@ -204,8 +204,8 @@ public abstract class Rangetype extends DatastoreItem
         for (int p = 0, pSize = range.getPosCount(); p < pSize; p++)
         {
           pos = range.getPos(p).getI();
-          posList.add(new Integer(pos));
-          posList.add(new Integer(pos));
+          posList.add(Integer.valueOf(pos));
+          posList.add(Integer.valueOf(pos));
         }
       }
     }

diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index 74f73d4..f8d86d5 100644 (file)
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -351,7 +351,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Boolean(p.getContent());
+            val = Boolean.valueOf(p.getContent());
           } catch (Exception e)
           {
           }
@@ -360,7 +360,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Float(p.getContent());
+            val = Float.valueOf(p.getContent());
 
           } catch (Exception e)
           {
@@ -370,7 +370,7 @@ public class Sequencefeature extends Rangetype
         {
           try
           {
-            val = new Integer(p.getContent());
+            val = Integer.valueOf(p.getContent());
           } catch (Exception e)
           {
           }

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index aa130cc..9c1f5ea 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -443,7 +443,7 @@ public class Tree extends DatastoreItem
     Integer nindx = (Integer) nodespecs.get(nname);
     if (nindx == null)
     {
-      nindx = new Integer(1);
+      nindx = Integer.valueOf(1);
     }
     nname = nindx.toString() + " " + nname;
     return nname;
@@ -465,7 +465,7 @@ public class Tree extends DatastoreItem
     String oval = nodespec.substring(0, nodespec.indexOf(' '));
     try
     {
-      occurence = new Integer(oval).intValue();
+      occurence = Integer.valueOf(oval).intValue();
     } catch (Exception e)
     {
       System.err.println("Invalid nodespec '" + nodespec + "'");

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 1cf482d..2d46033 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -201,7 +201,7 @@ public class GAlignFrame extends JInternalFrame
 
   private boolean showAutoCalculatedAbove = false;
 
-  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<KeyStroke, JMenuItem>();
+  private Map<KeyStroke, JMenuItem> accelerators = new HashMap<>();
 
   private SplitContainerI splitFrame;
 
@@ -263,14 +263,14 @@ public class GAlignFrame extends JInternalFrame
 
     // FIXME getDefaultToolkit throws an exception in Headless mode
     KeyStroke keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()
+                    | KeyEvent.SHIFT_DOWN_MASK,
             false);
     addMenuActionAndAccelerator(keyStroke, saveAs, al);
 
     closeMenuItem.setText(MessageManager.getString("action.close"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -293,7 +293,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem selectAllSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.select_all"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -320,7 +320,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertSequenceMenuItem = new JMenuItem(
             MessageManager.getString("action.invert_sequence_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -356,7 +356,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2LeftMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_left"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -370,7 +370,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem remove2RightMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_right"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -384,7 +384,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeGappedColumnMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_empty_columns"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -398,8 +398,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeAllGapsMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_all_gaps"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()
+                    | KeyEvent.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -506,7 +506,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem removeRedundancyMenuItem = new JMenuItem(
             MessageManager.getString("action.remove_redundancy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -681,7 +681,7 @@ public class GAlignFrame extends JInternalFrame
     undoMenuItem.setEnabled(false);
     undoMenuItem.setText(MessageManager.getString("action.undo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -695,7 +695,7 @@ public class GAlignFrame extends JInternalFrame
     redoMenuItem.setEnabled(false);
     redoMenuItem.setText(MessageManager.getString("action.redo"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -719,7 +719,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem printMenuItem = new JMenuItem(
             MessageManager.getString("action.print"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -745,7 +745,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem findMenuItem = new JMenuItem(
             MessageManager.getString("action.find"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.find_tip")));
     al = new ActionListener()
@@ -906,7 +906,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem deleteGroups = new JMenuItem(
             MessageManager.getString("action.undefine_groups"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -931,7 +931,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem createGroup = new JMenuItem(
             MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -945,8 +945,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem unGroup = new JMenuItem(
             MessageManager.getString("action.remove_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()
+                    | KeyEvent.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -960,7 +960,7 @@ public class GAlignFrame extends JInternalFrame
 
     copy.setText(MessageManager.getString("action.copy"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
 
     al = new ActionListener()
     {
@@ -974,7 +974,7 @@ public class GAlignFrame extends JInternalFrame
 
     cut.setText(MessageManager.getString("action.cut"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1000,8 +1000,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteNew = new JMenuItem(
             MessageManager.getString("label.to_new_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.SHIFT_MASK,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()
+                    | KeyEvent.SHIFT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1016,7 +1016,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem pasteThis = new JMenuItem(
             MessageManager.getString("label.to_this_alignment"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1511,8 +1511,8 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem invertColSel = new JMenuItem(
             MessageManager.getString("action.invert_column_selection"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask()
-                    | KeyEvent.ALT_MASK,
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx()
+                    | KeyEvent.ALT_DOWN_MASK,
             false);
     al = new ActionListener()
     {
@@ -1575,7 +1575,7 @@ public class GAlignFrame extends JInternalFrame
 
     JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override
@@ -1600,7 +1600,7 @@ public class GAlignFrame extends JInternalFrame
     JMenuItem newView = new JMenuItem(
             MessageManager.getString("action.new_view"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false);
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false);
     al = new ActionListener()
     {
       @Override

diff --git a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
index a6e0ace..389a030 100644 (file)
--- a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
@@ -136,11 +136,11 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
     });
     close.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_W,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false));
     selectAll.setText(MessageManager.getString("action.select_all"));
     selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_A,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false));
     selectAll.addActionListener(new ActionListener()
     {
       @Override
@@ -153,7 +153,7 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
     save.setText(MessageManager.getString("action.save"));
     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false));
     save.addActionListener(new ActionListener()
     {
       @Override
@@ -164,7 +164,7 @@ public class GCutAndPasteHtmlTransfer extends JInternalFrame
     });
     copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_C,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false));
 
     editMenubar.add(jMenu1);
     editMenubar.add(editMenu);

diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index 97ac840..2e4d733 100755 (executable)
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -123,7 +123,7 @@ public class GCutAndPasteTransfer extends JInternalFrame
     selectAll.setText(MessageManager.getString("action.select_all"));
     selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_A,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false));
     selectAll.addActionListener(new ActionListener()
     {
       @Override
@@ -136,7 +136,7 @@ public class GCutAndPasteTransfer extends JInternalFrame
     save.setText(MessageManager.getString("action.save"));
     save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_S,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false));
     save.addActionListener(new ActionListener()
     {
       @Override
@@ -147,10 +147,10 @@ public class GCutAndPasteTransfer extends JInternalFrame
     });
     copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_C,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false));
     pasteMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_V,
-            Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));
+            Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(), false));
     editMenubar.add(jMenu1);
     editMenubar.add(editMenu);
     textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));

diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index d200d06..fe6a6f8 100755 (executable)
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -159,7 +159,7 @@ public class GDesktop extends JFrame
             .setText(MessageManager.getString("label.load_tree_from_file"));
     inputLocalFileMenuItem.setAccelerator(
             javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O,
-                    Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(),
+                    Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx(),
                     false));
     inputLocalFileMenuItem
             .addActionListener(new java.awt.event.ActionListener()

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index b153d9f..12ff223 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -4839,7 +4839,7 @@ public class Jalview2XML
         }
         else
         {
-          featureOrder.put(featureType, new Float(
+          featureOrder.put(featureType, Float.valueOf(
                   fs / jm.getFeatureSettings().getSetting().size()));
         }
         if (safeBoolean(setting.isDisplay()))
@@ -4851,7 +4851,7 @@ public class Jalview2XML
       for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
       {
         Group grp = jm.getFeatureSettings().getGroup().get(gs);
-        fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
+        fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
       }
       // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
       // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?

diff --git a/src/jalview/schemes/FeatureColour.java b/src/jalview/schemes/FeatureColour.java
index 51e7645..aaf89e3 100644 (file)
--- a/src/jalview/schemes/FeatureColour.java
+++ b/src/jalview/schemes/FeatureColour.java
@@ -316,7 +316,7 @@ public class FeatureColour implements FeatureColourI
       {
         if (minval.length() > 0)
         {
-          min = new Float(minval).floatValue();
+          min = Float.valueOf(minval).floatValue();
         }
       } catch (Exception e)
       {
@@ -328,7 +328,7 @@ public class FeatureColour implements FeatureColourI
       {
         if (maxval.length() > 0)
         {
-          max = new Float(maxval).floatValue();
+          max = Float.valueOf(maxval).floatValue();
         }
       } catch (Exception e)
       {
@@ -396,7 +396,7 @@ public class FeatureColour implements FeatureColourI
         {
           gcol.nextToken();
           tval = gcol.nextToken();
-          featureColour.setThreshold(new Float(tval).floatValue());
+          featureColour.setThreshold(Float.valueOf(tval).floatValue());
         } catch (Exception e)
         {
           System.err.println("Couldn't parse threshold value as a float: ("

diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index 4625055..1be6086 100644 (file)
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -140,7 +140,7 @@ public class Platform
       {
         return false;
       }
-      return (Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMask()
+      return (Toolkit.getDefaultToolkit().getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
               & e.getModifiersEx()) != 0; // getModifiers()) != 0;
     }
     return e.isControlDown();

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 553f813..f9fa1ba 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -652,7 +652,7 @@ public abstract class FeatureRendererModel
     {
       featureOrder = new Hashtable<>();
     }
-    featureOrder.put(type, new Float(position));
+    featureOrder.put(type, Float.valueOf(position));
     return position;
   }
 
@@ -852,7 +852,7 @@ public abstract class FeatureRendererModel
     }
     if (newGroupsVisible)
     {
-      featureGroups.put(group, new Boolean(true));
+      featureGroups.put(group, Boolean.valueOf(true));
       return true;
     }
     return false;
@@ -888,7 +888,7 @@ public abstract class FeatureRendererModel
   @Override
   public void setGroupVisibility(String group, boolean visible)
   {
-    featureGroups.put(group, new Boolean(visible));
+    featureGroups.put(group, Boolean.valueOf(visible));
   }
 
   @Override
@@ -900,7 +900,7 @@ public abstract class FeatureRendererModel
       for (String gst : toset)
       {
         Boolean st = featureGroups.get(gst);
-        featureGroups.put(gst, new Boolean(visible));
+        featureGroups.put(gst, Boolean.valueOf(visible));
         if (st != null)
         {
           rdrw = rdrw || (visible != st.booleanValue());

diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java
index 80c9ce9..f9e597f 100644 (file)
--- a/src/jalview/ws/jws2/RNAalifoldClient.java
+++ b/src/jalview/ws/jws2/RNAalifoldClient.java
@@ -237,7 +237,7 @@ public class RNAalifoldClient extends JabawsCalcWorker
         // The Score objects contain a set of size one containing the range and
         // an ArrayList<float> of size one containing the probabilty
         basePairs.put(score.getRanges().first(),
-                new Float(score.getScores().get(0)));
+                Float.valueOf(score.getScores().get(0)));
       }
 
       for (int i = 0, ri = 0, iEnd = struct.length(); i < iEnd; i++, ri++)

diff --git a/src/uk/ac/ebi/www/InputParams.java b/src/uk/ac/ebi/www/InputParams.java
index fe1c70c..ba8f8b0 100755 (executable)
--- a/src/uk/ac/ebi/www/InputParams.java
+++ b/src/uk/ac/ebi/www/InputParams.java
@@ -296,8 +296,8 @@ public class InputParams implements java.io.Serializable
     {
       _hashCode += getMatrix().hashCode();
     }
-    _hashCode += new Float(getExp()).hashCode();
-    _hashCode += new Boolean(isEchofilter()).hashCode();
+    _hashCode += Float.valueOf(getExp()).hashCode();
+    _hashCode += Boolean.valueOf(isEchofilter()).hashCode();
     if (getFilter() != null)
     {
       _hashCode += getFilter().hashCode();
@@ -325,7 +325,7 @@ public class InputParams implements java.io.Serializable
       _hashCode += getOutformat().hashCode();
     }
     _hashCode += getTopcombon();
-    _hashCode += new Boolean(isAsync()).hashCode();
+    _hashCode += Boolean.valueOf(isAsync()).hashCode();
     if (getEmail() != null)
     {
       _hashCode += getEmail().hashCode();

diff --git a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
index 5391221..666ebd3 100644 (file)
--- a/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
+++ b/src/uk/ac/ebi/www/picr/AccessionMappingService/AccessionMapperBindingStub.java
@@ -258,6 +258,7 @@ public class AccessionMapperBindingStub extends org.apache.axis.client.Stub
     }
   }
 
+  @Override
   public uk.ac.ebi.picr.model.UPEntry getUPIForSequence(
           java.lang.String sequence, java.lang.String[] searchDatabases,
           java.lang.String taxonId, boolean onlyActive)
@@ -285,7 +286,7 @@ public class AccessionMapperBindingStub extends org.apache.axis.client.Stub
     setAttachments(_call);
     java.lang.Object _resp = _call.invoke(new java.lang.Object[] {
         sequence, searchDatabases, taxonId,
-        new java.lang.Boolean(onlyActive) });
+        java.lang.Boolean.valueOf(onlyActive) });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -305,6 +306,7 @@ public class AccessionMapperBindingStub extends org.apache.axis.client.Stub
     }
   }
 
+  @Override
   public uk.ac.ebi.picr.model.UPEntry[] getUPIForAccession(
           java.lang.String accession, java.lang.String ac_version,
           java.lang.String[] searchDatabases, java.lang.String taxonId,
@@ -332,7 +334,7 @@ public class AccessionMapperBindingStub extends org.apache.axis.client.Stub
     setAttachments(_call);
     java.lang.Object _resp = _call.invoke(new java.lang.Object[] {
         accession, ac_version, searchDatabases, taxonId,
-        new java.lang.Boolean(onlyActive) });
+        java.lang.Boolean.valueOf(onlyActive) });
 
     if (_resp instanceof java.rmi.RemoteException)
     {
@@ -352,6 +354,7 @@ public class AccessionMapperBindingStub extends org.apache.axis.client.Stub
     }
   }
 
+  @Override
   public java.lang.String[] getMappedDatabaseNames()
           throws java.rmi.RemoteException
   {

diff --git a/test/jalview/datamodel/ColumnSelectionTest.java b/test/jalview/datamodel/ColumnSelectionTest.java
index 8709961..a6782c6 100644 (file)
--- a/test/jalview/datamodel/ColumnSelectionTest.java
+++ b/test/jalview/datamodel/ColumnSelectionTest.java
@@ -100,8 +100,8 @@ public class ColumnSelectionTest
     cs.removeElement(1);
     List<Integer> sel = cs.getSelected();
     assertEquals(2, sel.size());
-    assertEquals(new Integer(2), sel.get(0));
-    assertEquals(new Integer(5), sel.get(1));
+    assertEquals(Integer.valueOf(2), sel.get(0));
+    assertEquals(Integer.valueOf(5), sel.get(1));
 
     // removing an element in the list removes it
     cs.removeElement(2);
@@ -109,7 +109,7 @@ public class ColumnSelectionTest
     assertEquals(1, sel.size());
     sel = cs.getSelected();
     assertEquals(1, sel.size());
-    assertEquals(new Integer(5), sel.get(0));
+    assertEquals(Integer.valueOf(5), sel.get(0));
   }
 
   /**

diff --git a/test/jalview/datamodel/SequenceFeatureTest.java b/test/jalview/datamodel/SequenceFeatureTest.java
index c955979..9111e5a 100644 (file)
--- a/test/jalview/datamodel/SequenceFeatureTest.java
+++ b/test/jalview/datamodel/SequenceFeatureTest.java
@@ -48,7 +48,7 @@ public class SequenceFeatureTest
             12.5f, "group");
     sf1.setValue("STRAND", "+");
     sf1.setValue("Note", "Testing");
-    Integer count = new Integer(7);
+    Integer count = Integer.valueOf(7);
     sf1.setValue("Count", count);
 
     SequenceFeature sf2 = new SequenceFeature(sf1);
@@ -106,7 +106,7 @@ public class SequenceFeatureTest
     assertEquals("+", sf1.getValue("STRAND"));
     assertNull(sf1.getValue("strand")); // case-sensitive
     assertEquals(".", sf1.getValue("unknown", "."));
-    Integer i = new Integer(27);
+    Integer i = Integer.valueOf(27);
     assertSame(i, sf1.getValue("Unknown", i));
   }
 

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index e86c8ad..ba4312a 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -257,8 +257,8 @@ public class StockholmFileTest
           assertEquals("Threshold line not identical.",
                   aa_original[i].threshold, aa_new[i].threshold);
           // graphGroup may differ, but pattern should be the same
-          Integer o_ggrp = new Integer(aa_original[i].graphGroup + 2);
-          Integer n_ggrp = new Integer(aa_new[i].graphGroup + 2);
+          Integer o_ggrp = Integer.valueOf(aa_original[i].graphGroup + 2);
+          Integer n_ggrp = Integer.valueOf(aa_new[i].graphGroup + 2);
           BitSet orig_g = orig_groups.get(o_ggrp);
           BitSet new_g = new_groups.get(n_ggrp);
           if (orig_g == null)

diff --git a/utils/deprecation_auto_fixes.sh b/utils/deprecation_auto_fixes.sh
new file mode 100644 (file)
index 0000000..559d016
--- /dev/null
+++ b/utils/deprecation_auto_fixes.sh
@@ -0,0 +1,11 @@
+#!/usr/bin/env bash
+
+TYPES="Boolean|Character|Double|Float|Long|Integer" find src test -type f -name "*.java" -exec perl -p -i -e 's/\bnew\s+(java\.lang\.)?($ENV{TYPES})\(/${1}${2}.valueOf(/;' {} +
+
+find src test -type f -name "*.java" -exec perl -p -i -e 's/InputEvent\s*\.\s*([A-Z0-9]+)_MASK\b/InputEvent.${1}_DOWN_MASK/g;' {} +
+
+find src test -type f -name "*.java" -exec perl -p -i -e 's/\b(e|evt)\.getModifiers\b/${1}.getModifiersEx/g;' {} +
+
+find src test -type f -name "*.java" -exec perl -p -i -e 's/\.getMenuShortcutKeyMask\b/\.getMenuShortcutKeyMaskEx/g;' {} +
+
+