Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / gui / AlignViewport.java

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d6e2ae5..6024cf9 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -39,6 +39,7 @@ import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
 import jalview.renderer.ResidueShader;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
@@ -79,9 +80,9 @@ 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
@@ -208,7 +209,7 @@ public class AlignViewport extends AlignmentViewport
    */
   private void applyViewProperties()
   {
-    antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+    antiAlias = Cache.getDefault("ANTI_ALIAS", true);
 
     viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
     setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
@@ -718,16 +719,20 @@ public void setNormaliseSequenceLogo(boolean state)
     {
       if (AlignmentUtils.isMappable(toAdd, getAlignment()))
       {
-        if (openLinkedAlignment(toAdd, title))
-        {
-          return;
-        }
+        openLinkedAlignment(toAdd, title);
+        return;
       }
     }
+    addDataToAlignment(toAdd);
+  }
 
-    /*
-     * No mappings, or offer declined - add sequences to this alignment
-     */
+  /**
+   * adds sequences to this alignment
+   * 
+   * @param toAdd
+   */
+  void addDataToAlignment(AlignmentI toAdd)
+  {
     // TODO: JAL-407 regardless of above - identical sequences (based on ID and
     // provenance) should share the same dataset sequence
 
@@ -749,7 +754,7 @@ public void setNormaliseSequenceLogo(boolean state)
       }
     }
 
-    ranges.setEndSeq(getAlignment().getHeight());
+    ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
     firePropertyChange("alignment", null, getAlignment().getSequences());
   }
 
@@ -762,30 +767,58 @@ public void setNormaliseSequenceLogo(boolean state)
    * @param al
    * @param title
    */
-  protected boolean openLinkedAlignment(AlignmentI al, String title)
+  protected void openLinkedAlignment(AlignmentI al, String title)
   {
     String[] options = new String[] { MessageManager.getString("action.no"),
         MessageManager.getString("label.split_window"),
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
-    int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+    final AlignViewport us = this;
+    
+    /*
+     * 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.desktop)
+            .setResponseHandler(0, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                  addDataToAlignment(al);
+              }
+            }).setResponseHandler(1, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, true);
+              }
+            }).setResponseHandler(2, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, false);
+              }
+            });
+       dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
             JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
+  }
 
-    if (response != 1 && response != 2)
+  protected void openLinkedAlignmentAs(AlignmentI al, String title,
+          boolean newWindowOrSplitPane)
     {
-      return false;
-    }
-    final boolean openSplitPane = (response == 1);
-    final boolean openInNewWindow = (response == 2);
-
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
      */
-    AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+    AlignmentI thisAlignment = newWindowOrSplitPane
+            ? new Alignment(getAlignment())
             : getAlignment();
     AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
     final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
@@ -817,7 +850,7 @@ public void setNormaliseSequenceLogo(boolean state)
     // alignFrame.setFileName(file, format);
     // }
 
-    if (openInNewWindow)
+    if (!newWindowOrSplitPane)
     {
       Desktop.addInternalFrame(newAlignFrame, title,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -831,13 +864,11 @@ public void setNormaliseSequenceLogo(boolean state)
     {
     }
 
-    if (openSplitPane)
+    if (newWindowOrSplitPane)
     {
       al.alignAs(thisAlignment);
       protein = openSplitFrame(newAlignFrame, thisAlignment);
     }
-
-    return true;
   }
 
   /**
@@ -899,10 +930,9 @@ public void setNormaliseSequenceLogo(boolean state)
     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);
     }
   }
 
@@ -1053,6 +1083,9 @@ public void setNormaliseSequenceLogo(boolean state)
     {
       FeatureColourI preferredColour = featureSettings
               .getFeatureColour(type);
+      FeatureMatcherSetI preferredFilters = featureSettings
+              .getFeatureFilters(type);
+
       FeatureColourI origColour = fr.getFeatureStyle(type);
       if (!mergeOnly || (!origRenderOrder.contains(type)
               || origColour == null
@@ -1067,6 +1100,11 @@ public void setNormaliseSequenceLogo(boolean state)
         {
           fr.setColour(type, preferredColour);
         }
+        if (preferredFilters != null
+                && (!mergeOnly || fr.getFeatureFilter(type) != null))
+        {
+          fr.setFeatureFilter(type, preferredFilters);
+        }
         if (featureSettings.isFeatureDisplayed(type))
         {
           displayed.setVisible(type);