JAL-3010 option to apply colour to all ontology sub-types

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index fe905c0..0c90646 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -1759,9 +1759,9 @@ public class FeatureSettings extends JPanel
 
       for (int r = 0; r < data.length; r++)
       {
-        String type2 = (String) data[r][TYPE_COLUMN];
-        if (!type2.equals(type))
+        if (r != row)
         {
+          String type2 = (String) data[r][TYPE_COLUMN];
           if (so.isA(type2, type))
           {
             data[r][SHOW_COLUMN] = value;

diff --git a/src/jalview/gui/FeatureTypeSettings.java b/src/jalview/gui/FeatureTypeSettings.java
index 201ec44..e412274 100644 (file)
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@ -228,7 +228,7 @@ public class FeatureTypeSettings extends JalviewDialog
    * if selected, colour settings are also applied to any 
    * feature sub-types in the Sequence Ontology
    */
-  private JCheckBox applyColourToChildren;
+  private JCheckBox applyColourToSubtypes;
 
   /**
    * Constructor
@@ -783,6 +783,19 @@ public class FeatureTypeSettings extends JalviewDialog
     colourByPanel.setLayout(new BoxLayout(colourByPanel, BoxLayout.Y_AXIS));
 
     /*
+     * option to apply colour to sub-types as well (if there are any)
+     */
+    if (!subTypes.isEmpty())
+    {
+      JPanel toSubtypes = new JPanel(new FlowLayout(FlowLayout.RIGHT));
+      toSubtypes.setBackground(Color.WHITE);
+      applyColourToSubtypes = new JCheckBox("Apply also to child terms");
+      applyColourToSubtypes.setToolTipText(getSubtypesTooltip());
+      toSubtypes.add(applyColourToSubtypes);
+      colourByPanel.add(toSubtypes);
+    }
+
+    /*
      * simple colour radio button and colour picker
      */
     JPanel simpleColourPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
@@ -918,9 +931,16 @@ public class FeatureTypeSettings extends JalviewDialog
     FeatureColourI acg = makeColourFromInputs();
 
     /*
-     * save the colour, and repaint stuff
+     * save the colour, and set on subtypes if selected
      */
     fr.setColour(featureType, acg);
+    if (applyColourToSubtypes.isSelected())
+    {
+      for (String child : subTypes)
+      {
+        fr.setColour(child, acg);
+      }
+    }
     refreshFeatureSettings();
     ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
 
@@ -1281,13 +1301,7 @@ public class FeatureTypeSettings extends JalviewDialog
       JPanel panel2 = new JPanel(new FlowLayout(FlowLayout.RIGHT));
       panel2.setBackground(Color.white);
       andOrPanel.add(panel2, BorderLayout.EAST);
-      StringBuilder sb = new StringBuilder(20 * subTypes.size());
-      sb.append("Apply filters also to child terms" + ":"); // todo i18n
-      for (String child : subTypes)
-      {
-        sb.append("<br>").append(child);
-      }
-      String tooltip = JvSwingUtils.wrapTooltip(true, sb.toString());
+      String tooltip = getSubtypesTooltip();
       applyFiltersToSubtypes.setToolTipText(tooltip);
       panel2.add(applyFiltersToSubtypes);
     }
@@ -1296,6 +1310,24 @@ public class FeatureTypeSettings extends JalviewDialog
   }
 
   /**
+   * Builds a tooltip for the 'Apply to subtypes' checkbox with a list of
+   * subtypes of this feature type
+   * 
+   * @return
+   */
+  protected String getSubtypesTooltip()
+  {
+    StringBuilder sb = new StringBuilder(20 * subTypes.size());
+    sb.append("Apply filters also to child terms" + ":"); // todo i18n
+    for (String child : subTypes)
+    {
+      sb.append("<br>").append(child);
+    }
+    String tooltip = JvSwingUtils.wrapTooltip(true, sb.toString());
+    return tooltip;
+  }
+
+  /**
    * Refreshes the display to show any filters currently configured for the
    * selected feature type (editable, with 'remove' option), plus one extra row
    * for adding a condition. This should be called after a filter has been