X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;fp=src%2Fjalview%2Fgui%2FAlignViewport.java;h=a43b89b321a5336ed04e91f322338330919ccf80;hb=3459a8a691cb22508d7067f240b7254e588e77d3;hp=092d7e7504b3e6868d3338e23658ba14b128b4ea;hpb=5b27f1062b2203c4c31702e205f4c78e1992063e;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 092d7e7..a43b89b 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -20,6 +20,17 @@
  */
 package jalview.gui;
 
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewportI;
@@ -53,17 +64,6 @@ import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
 
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-
-import javax.swing.JInternalFrame;
-
 /**
  * DOCUMENT ME!
  * 
@@ -291,8 +291,8 @@ 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)
@@ -741,7 +741,7 @@ public class AlignViewport extends AlignmentViewport
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
     final AlignViewport us = this;
-    
+
     /*
      * options No, Split Window, New Window correspond to
      * dialog responses 0, 1, 2 (even though JOptionPane shows them
@@ -753,7 +753,7 @@ public class AlignViewport extends AlignmentViewport
               @Override
               public void run()
               {
-                  addDataToAlignment(al);
+                addDataToAlignment(al);
               }
             }).setResponseHandler(1, new Runnable()
             {
@@ -770,7 +770,7 @@ public class AlignViewport extends AlignmentViewport
                 us.openLinkedAlignmentAs(al, title, false);
               }
             });
-	dialog.showDialog(question,
+    dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
             JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
@@ -778,7 +778,7 @@ public class AlignViewport extends AlignmentViewport
 
   protected void openLinkedAlignmentAs(AlignmentI al, String title,
           boolean newWindowOrSplitPane)
-    {
+  {
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
@@ -824,8 +824,7 @@ public class AlignViewport extends AlignmentViewport
 
     try
     {
-      newAlignFrame.setMaximum(
-              Cache.getDefault("SHOW_FULLSCREEN", false));
+      newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
     } catch (java.beans.PropertyVetoException ex)
     {
     }
@@ -991,10 +990,10 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * Applies the supplied feature settings descriptor to currently known features.
-   * This supports an 'initial configuration' of feature colouring based on a
-   * preset or user favourite. This may then be modified in the usual way using
-   * the Feature Settings dialogue.
+   * Applies the supplied feature settings descriptor to currently known
+   * features. This supports an 'initial configuration' of feature colouring
+   * based on a preset or user favourite. This may then be modified in the usual
+   * way using the Feature Settings dialogue.
    * 
    * @param featureSettings
    */
@@ -1007,8 +1006,8 @@ public class AlignViewport extends AlignmentViewport
   /**
    * when mergeOnly is set, then group and feature visibility or feature colours
    * are not modified for features and groups already known to the feature
-   * renderer. Feature ordering is always adjusted, and transparency is always set
-   * regardless.
+   * renderer. Feature ordering is always adjusted, and transparency is always
+   * set regardless.
    * 
    * @param featureSettings
    * @param mergeOnly
@@ -1020,12 +1019,13 @@ public class AlignViewport extends AlignmentViewport
     {
       return;
     }
-    
+
     FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
             .getFeatureRenderer();
     List<String> origRenderOrder = new ArrayList<>();
     List<String> origGroups = new ArrayList<>();
-    // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+    // preserve original render order - allows differentiation between user
+    // configured colours and autogenerated ones
     origRenderOrder.addAll(fr.getRenderOrder());
     origGroups.addAll(fr.getFeatureGroups());
 
@@ -1057,7 +1057,8 @@ public class AlignViewport extends AlignmentViewport
                       && origColour.getColour().equals(
                               ColorUtils.createColourFromName(type)))))
       {
-        // if we are merging, only update if there wasn't already a colour defined for
+        // if we are merging, only update if there wasn't already a colour
+        // defined for
         // this type
         if (preferredColour != null)
         {
@@ -1081,7 +1082,8 @@ public class AlignViewport extends AlignmentViewport
     {
       if (!mergeOnly || !origGroups.contains(group))
       {
-        // when merging, display groups only if the aren't already marked as not visible
+        // when merging, display groups only if the aren't already marked as not
+        // visible
         fr.setGroupVisibility(group,
                 featureSettings.isGroupDisplayed(group));
       }