Merge branch 'releases/Release_2_11_1_Branch' into task/JAL-3608_and_JAL-3609_merged_...

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

diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index a2194f4..5b77dfc 100644 (file)
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@ -20,8 +20,10 @@
  */
 package jalview.gui;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
+import jalview.bin.Cache;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.features.FeatureAttributes;
 import jalview.datamodel.features.FeatureAttributes.Datatype;
@@ -165,7 +167,7 @@ public class FeatureTypeSettings extends JalviewDialog
 
   private JPanel maxColour = new JPanel();
 
-  private JComboBox<String> threshold = new JComboBox<>();
+  private JComboBox<Object> threshold = new JComboBox<>();
 
   private JSlider slider = new JSlider();
 
@@ -182,17 +184,17 @@ public class FeatureTypeSettings extends JalviewDialog
   /*
    * choice of option for 'colour for no value'
    */
-  private JComboBox<String> noValueCombo;
+  private JComboBox<Object> noValueCombo;
 
   /*
    * choice of what to colour by text (Label or attribute)
    */
-  private JComboBox<String> colourByTextCombo;
+  private JComboBox<Object> colourByTextCombo;
 
   /*
    * choice of what to colour by range (Score or attribute)
    */
-  private JComboBox<String> colourByRangeCombo;
+  private JComboBox<Object> colourByRangeCombo;
 
   private JRadioButton andFilters;
 
@@ -673,7 +675,7 @@ public class FeatureTypeSettings extends JalviewDialog
          */
         if (ap != null)
         {
-          ap.paintAlignment(true, true);
+          refreshDisplay(true);
         }
       }
     });
@@ -874,7 +876,7 @@ public class FeatureTypeSettings extends JalviewDialog
      * save the colour, and repaint stuff
      */
     fr.setColour(featureType, acg);
-    ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
+    refreshDisplay(updateStructsAndOverview);
 
     updateColoursTab();
   }
@@ -1013,7 +1015,7 @@ public class FeatureTypeSettings extends JalviewDialog
   {
     fr.setColour(featureType, originalColour);
     fr.setFeatureFilter(featureType, originalFilter);
-    ap.paintAlignment(true, true);
+    refreshDisplay(true);
   }
 
   /**
@@ -1104,7 +1106,7 @@ public class FeatureTypeSettings extends JalviewDialog
    * @param withRange
    * @param withText
    */
-  protected JComboBox<String> populateAttributesDropdown(
+  protected JComboBox<Object> populateAttributesDropdown(
           List<String[]> attNames, boolean withRange, boolean withText)
   {
     List<String> displayAtts = new ArrayList<>();
@@ -1143,9 +1145,11 @@ public class FeatureTypeSettings extends JalviewDialog
       tooltips.add(desc == null ? "" : desc);
     }
 
-    JComboBox<String> attCombo = JvSwingUtils
-            .buildComboWithTooltips(displayAtts, tooltips);
-
+    // now convert String List to Object List for buildComboWithTooltips
+    List<Object> displayAttsObjects = new ArrayList<>(displayAtts);
+    JComboBox<Object> attCombo = JvSwingUtils
+            .buildComboWithTooltips(displayAttsObjects, tooltips);
+    
     return attCombo;
   }
 
@@ -1316,7 +1320,7 @@ public class FeatureTypeSettings extends JalviewDialog
      * drop-down choice of attribute, with description as a tooltip 
      * if we can obtain it
      */
-    final JComboBox<String> attCombo = populateAttributesDropdown(attNames,
+    final JComboBox<Object> attCombo = populateAttributesDropdown(attNames,
             true, true);
     String filterBy = setSelectedAttribute(attCombo, filter);
 
@@ -1444,7 +1448,7 @@ public class FeatureTypeSettings extends JalviewDialog
    * @param attCombo
    * @param filter
    */
-  private String setSelectedAttribute(JComboBox<String> attCombo,
+  private String setSelectedAttribute(JComboBox<Object> attCombo,
           FeatureMatcherI filter)
   {
     String item = null;
@@ -1661,11 +1665,19 @@ public class FeatureTypeSettings extends JalviewDialog
    * @param valueField
    * @param filterIndex
    */
-  protected boolean updateFilter(JComboBox<String> attCombo,
+  protected boolean updateFilter(JComboBox<Object> attCombo,
           JComboBox<Condition> condCombo, JTextField valueField,
           int filterIndex)
   {
-    String attName = (String) attCombo.getSelectedItem();
+    String attName;
+    try
+    {
+      attName = (String) attCombo.getSelectedItem();
+    } catch (Exception e)
+    {
+      Cache.log.error("Problem casting Combo box entry to String");
+      attName = attCombo.getSelectedItem().toString();
+    }
     Condition cond = (Condition) condCombo.getSelectedItem();
     String pattern = valueField.getText().trim();
 
@@ -1742,8 +1754,26 @@ public class FeatureTypeSettings extends JalviewDialog
      * (note this might now be an empty filter with no conditions)
      */
     fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
-    ap.paintAlignment(true, true);
+    refreshDisplay(true);
 
     updateFiltersTab();
   }
+
+  /**
+   * Repaints alignment, structure and overview (if shown). If there is a
+   * complementary view which is showing this view's features, then also
+   * repaints that.
+   * 
+   * @param updateStructsAndOverview
+   */
+  void refreshDisplay(boolean updateStructsAndOverview)
+  {
+    ap.paintAlignment(true, updateStructsAndOverview);
+    AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
+    if (complement != null && complement.isShowComplementFeatures())
+    {
+      AlignFrame af2 = Desktop.getAlignFrameFor(complement);
+      af2.alignPanel.paintAlignment(true, updateStructsAndOverview);
+    }
+  }
 }