X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=954cfcc64f880da7b1e412956c8f5fc3d8a29668;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=fb3ec3a22c6be2578c2e63ac721c258d66762cd9;hpb=4b1c969e87feaefd4fb9c49ba3d6b828b3ce1a9c;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fb3ec3a..954cfcc 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -47,6 +47,7 @@ import jalview.schemes.UserColourScheme;
 import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
+import jalview.util.ColorUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
@@ -56,6 +57,7 @@ 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.Iterator;
 import java.util.List;
@@ -77,9 +79,9 @@ public class AlignViewport extends AlignmentViewport
 
   boolean antiAlias = false;
 
-  private Rectangle explodedGeometry;
+  private Rectangle explodedGeometry = null;
 
-  private String viewName;
+  private String viewName = null;
 
   /*
    * Flag set true on the view that should 'gather' multiple views of the same
@@ -206,7 +208,10 @@ public class AlignViewport extends AlignmentViewport
    */
   private void applyViewProperties()
   {
-    antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, false);
+	  // BH! using final static strings here because we also use these in 
+	  // JS version startup api
+	  // BH was false
+    antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, true);
 
     viewStyle.setShowJVSuffix(
             Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
@@ -297,8 +302,8 @@ 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)
@@ -823,10 +828,10 @@ public class AlignViewport extends AlignmentViewport
   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
-     * in a new split pane.
-     */
+     // BH: thisAlignment is already a copy if mode == SPLIT_FRAME
+     // Identify protein and dna alignments. Make a copy of this one if opening
+     // in a new split pane.
+     
     AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
     AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
 
@@ -865,8 +870,7 @@ public class AlignViewport extends AlignmentViewport
 
     try
     {
-      newAlignFrame.setMaximum(jalview.bin.Cache
-              .getDefault(Preferences.SHOW_FULLSCREEN, false));
+      newAlignFrame.setMaximum(Cache.getDefault(Preferences.SHOW_FULLSCREEN, false));
     } catch (java.beans.PropertyVetoException ex)
     {
     }
@@ -937,10 +941,9 @@ public class AlignViewport extends AlignmentViewport
     if (ap != null)
     {
       // modify GUI elements to reflect geometry change
-      Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
-              .getPreferredSize();
+      Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
       idw.width = i;
-      getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+      ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
     }
   }
 
@@ -1029,6 +1032,35 @@ public class AlignViewport extends AlignmentViewport
   @Override
   public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
   {
+    transferFeaturesStyles(featureSettings, false);
+  }
+
+  /**
+   * 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
+   */
+  @Override
+  public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+  {
+    transferFeaturesStyles(featureSettings, true);
+  }
+
+  /**
+   * 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.
+   * 
+   * @param featureSettings
+   * @param mergeOnly
+   */
+  private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
+          boolean mergeOnly)
+  {
     if (featureSettings == null)
     {
       return;
@@ -1036,12 +1068,24 @@ public class AlignViewport extends AlignmentViewport
 
     FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
             .getFeatureRenderer();
+    List<String> origRenderOrder = new ArrayList<>(),
+            origGroups = new ArrayList<>();
+    // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+    origRenderOrder.addAll(fr.getRenderOrder());
+    origGroups.addAll(fr.getFeatureGroups());
+
     fr.findAllFeatures(true);
     List<String> renderOrder = fr.getRenderOrder();
     FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
+    if (!mergeOnly)
+    {
+      // only clear displayed features if we are merging
     displayed.clear();
+    }
     // TODO this clears displayed.featuresRegistered - do we care?
-
+    //
+    // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
+    // feature visibility has already been configured is not very friendly
     /*
      * set feature colour if specified by feature settings
      * set visibility of all features
@@ -1050,6 +1094,16 @@ public class AlignViewport extends AlignmentViewport
     {
       FeatureColourI preferredColour = featureSettings
               .getFeatureColour(type);
+      FeatureColourI origColour = fr.getFeatureStyle(type);
+      if (!mergeOnly || (!origRenderOrder.contains(type)
+              || origColour == null
+              || (!origColour.isGraduatedColour()
+                      && origColour.getColour() != null
+                      && origColour.getColour().equals(
+                              ColorUtils.createColourFromName(type)))))
+      {
+        // if we are merging, only update if there wasn't already a colour defined for
+        // this type
       if (preferredColour != null)
       {
         fr.setColour(type, preferredColour);
@@ -1059,13 +1113,19 @@ public class AlignViewport extends AlignmentViewport
         displayed.setVisible(type);
       }
     }
+    }
 
     /*
      * set visibility of feature groups
      */
     for (String group : fr.getFeatureGroups())
     {
-      fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+      if (!mergeOnly || !origGroups.contains(group))
+      {
+        // when merging, display groups only if the aren't already marked as not visible
+        fr.setGroupVisibility(group,
+                featureSettings.isGroupDisplayed(group));
+      }
     }
 
     /*