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JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...
[jalview.git] / src / jalview / gui / AlignViewport.java
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 4edb580..fb3ec3a 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -206,25 +206,26 @@ public class AlignViewport extends AlignmentViewport
    */
   private void applyViewProperties()
   {
-    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+    antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, false);
 
-    viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
+    viewStyle.setShowJVSuffix(
+            Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
     setShowAnnotation(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
 
-    setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
-    setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
-    autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+    setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false));
+    setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false));
+    autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
 
-    setPadGaps(Cache.getDefault("PAD_GAPS", true));
-    setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
-    setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
-    viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+    setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true));
+    setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true));
+    setShowDBRefs(Cache.getDefault(Preferences.SHOW_DBREFS_TOOLTIP, true));
+    viewStyle.setSeqNameItalics(Cache.getDefault(Preferences.ID_ITALICS, true));
     viewStyle.setWrapAlignment(
             Cache.getDefault(Preferences.WRAP_ALIGNMENT, false));
     viewStyle.setShowUnconserved(
             Cache.getDefault(Preferences.SHOW_UNCONSERVED, false));
     sortByTree = Cache.getDefault(Preferences.SORT_BY_TREE, false);
-    followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+    followSelection = Cache.getDefault(Preferences.FOLLOW_SELECTIONS, true);
     sortAnnotationsBy = SequenceAnnotationOrder
             .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
                     SequenceAnnotationOrder.NONE.name()));
@@ -238,9 +239,10 @@ public class AlignViewport extends AlignmentViewport
   {
     applyViewProperties();
 
-    String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
-    String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
-    String fontSize = Cache.getDefault("FONT_SIZE", "10");
+    String fontName = Cache.getDefault(Preferences.FONT_NAME, "SansSerif");
+    String fontStyle = Cache.getDefault(Preferences.FONT_STYLE,
+            Font.PLAIN + "");
+    String fontSize = Cache.getDefault(Preferences.FONT_SIZE, "10");
 
     int style = 0;
 
@@ -256,7 +258,8 @@ public class AlignViewport extends AlignmentViewport
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
     alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+            .setGapCharacter(Cache.getDefault(Preferences.GAP_SYMBOL, "-")
+                    .charAt(0));
 
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
@@ -264,21 +267,22 @@ public class AlignViewport extends AlignmentViewport
     {
       if (!alignment.isNucleotide())
       {
-        showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION, true);
+        showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION,
+                true);
         showQuality = Cache.getDefault(Preferences.SHOW_QUALITY, true);
-        showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
-                false);
+        showGroupConservation = Cache
+                .getDefault(Preferences.SHOW_GROUP_CONSERVATION, false);
       }
-      showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
-              true);
-      showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO, false);
-
-      normaliseSequenceLogo = Cache.getDefault(
-              Preferences.NORMALISE_CONSENSUS_LOGO,
+      showConsensusHistogram = Cache
+              .getDefault(Preferences.SHOW_CONSENSUS_HISTOGRAM, true);
+      showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO,
               false);
+
+      normaliseSequenceLogo = Cache
+              .getDefault(Preferences.NORMALISE_CONSENSUS_LOGO, false);
       showGroupConsensus = Cache
               .getDefault(Preferences.SHOW_GROUP_CONSENSUS, false);
-      showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+      showConsensus = Cache.getDefault(Preferences.SHOW_IDENTITY, true);
 
       showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
     }
@@ -293,8 +297,8 @@ public class AlignViewport extends AlignmentViewport
       schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
               ResidueColourScheme.NONE);
     }
-    ColourSchemeI colourScheme = ColourSchemeProperty
-            .getColourScheme(this, alignment, schemeName);
+    ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
+            alignment, schemeName);
     residueShading = new ResidueShader(colourScheme);
 
     if (colourScheme instanceof UserColourScheme)
@@ -387,7 +391,7 @@ public class AlignViewport extends AlignmentViewport
      */
     if (align != null)
     {
-      Desktop.getInstance().getStructureSelectionManager()
+      Desktop.getStructureSelectionManager()
               .registerMappings(align.getCodonFrames());
     }
 
@@ -408,7 +412,7 @@ public class AlignViewport extends AlignmentViewport
       List<AlignedCodonFrame> mappings = al.getCodonFrames();
       if (mappings != null)
       {
-        StructureSelectionManager ssm = Desktop.getInstance()
+        StructureSelectionManager ssm = Desktop
                 .getStructureSelectionManager();
         for (AlignedCodonFrame acf : mappings)
         {
@@ -534,7 +538,7 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public void sendSelection()
   {
-    Desktop.getInstance().getStructureSelectionManager().sendSelection(
+    Desktop.getStructureSelectionManager().sendSelection(
             new SequenceGroup(getSelectionGroup()),
             new ColumnSelection(getColumnSelection()),
             new HiddenColumns(getAlignment().getHiddenColumns()), this);
@@ -578,7 +582,7 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public StructureSelectionManager getStructureSelectionManager()
   {
-    return Desktop.getInstance().getStructureSelectionManager();
+    return Desktop.getStructureSelectionManager();
   }
 
   @Override
@@ -769,20 +773,20 @@ public class AlignViewport extends AlignmentViewport
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
-    
 
     /*
      * options No, Split Window, New Window correspond to
      * dialog responses 0, 1, 2 (even though JOptionPane shows them
      * in reverse order)
      */
-    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.getDesktopPane())
+    JvOptionPane dialog = JvOptionPane
+            .newOptionDialog(Desktop.getDesktopPane())
             .setResponseHandler(NO_SPLIT, new Runnable()
             {
               @Override
               public void run()
               {
-                  addDataToAlignment(al);
+                addDataToAlignment(al);
               }
             }).setResponseHandler(SPLIT_FRAME, new Runnable()
             {
@@ -790,8 +794,8 @@ public class AlignViewport extends AlignmentViewport
               public void run()
               {
                 openLinkedAlignmentAs(getAlignPanel().alignFrame,
-                        new Alignment(getAlignment()), al,
-                        title, SPLIT_FRAME);
+                        new Alignment(getAlignment()), al, title,
+                        SPLIT_FRAME);
               }
             }).setResponseHandler(NEW_WINDOW, new Runnable()
             {
@@ -816,9 +820,8 @@ public class AlignViewport extends AlignmentViewport
    * @param mode
    *          SPLIT_FRAME or NEW_WINDOW
    */
-  public static void openLinkedAlignmentAs(AlignFrame thisFrame, AlignmentI thisAlignment,
-          AlignmentI al, String title,
-          int mode)
+  public static void openLinkedAlignmentAs(AlignFrame thisFrame,
+          AlignmentI thisAlignment, AlignmentI al, String title, int mode)
   {
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
@@ -862,8 +865,8 @@ public class AlignViewport extends AlignmentViewport
 
     try
     {
-      newAlignFrame.setMaximum(
-              jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+      newAlignFrame.setMaximum(jalview.bin.Cache
+              .getDefault(Preferences.SHOW_FULLSCREEN, false));
     } catch (java.beans.PropertyVetoException ex)
     {
     }
@@ -886,8 +889,7 @@ public class AlignViewport extends AlignmentViewport
    * @return the protein alignment in the split frame
    */
   static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
-          AlignFrame newAlignFrame,
-          AlignmentI complement)
+          AlignFrame newAlignFrame, AlignmentI complement)
   {
     /*
      * Make a new frame with a copy of the alignment we are adding to. If this