JAL-2808 pass FeatureSettings to controller as array of data bean

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 39a2747..7db1fbe 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -20,15 +20,12 @@
  */
 package jalview.appletgui;
 
-import static jalview.viewmodel.seqfeatures.FeatureRendererModel.COLOUR_COLUMN;
-import static jalview.viewmodel.seqfeatures.FeatureRendererModel.SHOW_COLUMN;
-import static jalview.viewmodel.seqfeatures.FeatureRendererModel.TYPE_COLUMN;
-
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 
 import java.awt.BorderLayout;
 import java.awt.Button;
@@ -71,6 +68,12 @@ public class FeatureSettings extends Panel
         implements ItemListener, MouseListener, MouseMotionListener,
         ActionListener, AdjustmentListener, FeatureSettingsControllerI
 {
+  private static final int TYPE_COLUMN = 0;
+
+  private static final int COLOUR_COLUMN = 1;
+
+  private static final int SHOW_COLUMN = 2;
+
   FeatureRenderer fr;
 
   AlignmentPanel ap;
@@ -607,11 +610,27 @@ public class FeatureSettings extends Panel
     Object[][] data = new Object[tmpSize][columnCount];
     System.arraycopy(tmp, 0, data, 0, tmpSize);
 
-    fr.setFeaturePriority(data);
+    fr.setFeaturePriority(getTableAsBeans(data));
 
     ap.paintAlignment(updateOverview, updateOverview);
   }
 
+  /**
+   * Converts table data into an array of data beans
+   */
+  private FeatureSettingsBean[] getTableAsBeans(Object[][] data)
+  {
+    FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length];
+    for (int i = 0; i < data.length; i++)
+    {
+      String type = (String) data[i][TYPE_COLUMN];
+      FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN];
+      Boolean isShown = (Boolean) data[i][SHOW_COLUMN];
+      // feature filter set to null as not (yet) offered in applet
+      rowData[i] = new FeatureSettingsBean(type, colour, null, isShown);
+    }
+    return rowData;
+  }
   MyCheckbox selectedCheck;
 
   boolean dragging = false;

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index fedfe3f..2b3688f 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -20,10 +20,10 @@
  */
 package jalview.gui;
 
-import static jalview.viewmodel.seqfeatures.FeatureRendererModel.COLOUR_COLUMN;
-import static jalview.viewmodel.seqfeatures.FeatureRendererModel.FILTER_COLUMN;
-import static jalview.viewmodel.seqfeatures.FeatureRendererModel.SHOW_COLUMN;
-import static jalview.viewmodel.seqfeatures.FeatureRendererModel.TYPE_COLUMN;
+import static jalview.gui.FeatureSettings.FeatureTableModel.COLOUR_COLUMN;
+import static jalview.gui.FeatureSettings.FeatureTableModel.FILTER_COLUMN;
+import static jalview.gui.FeatureSettings.FeatureTableModel.SHOW_COLUMN;
+import static jalview.gui.FeatureSettings.FeatureTableModel.TYPE_COLUMN;
 
 import jalview.api.FeatureColourI;
 import jalview.api.FeatureSettingsControllerI;
@@ -42,6 +42,7 @@ import jalview.util.QuickSort;
 import jalview.util.matcher.KeyedMatcherSet;
 import jalview.util.matcher.KeyedMatcherSetI;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 import jalview.ws.DasSequenceFeatureFetcher;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 
@@ -111,14 +112,10 @@ public class FeatureSettings extends JPanel
 {
   private static final int COLUMN_COUNT = 4;
 
-  private static final String COLON = ":";
-
   private static final int MIN_WIDTH = 400;
 
   private static final int MIN_HEIGHT = 400;
 
-  private static final int MAX_TOOLTIP_LENGTH = 50;
-
   DasSourceBrowser dassourceBrowser;
 
   DasSequenceFeatureFetcher dasFeatureFetcher;
@@ -1105,12 +1102,32 @@ public class FeatureSettings extends JPanel
    */
   private void updateFeatureRenderer(Object[][] data, boolean visibleNew)
   {
-    if (fr.setFeaturePriority(data, visibleNew))
+    FeatureSettingsBean[] rowData = getTableAsBeans(data);
+
+    if (fr.setFeaturePriority(rowData, visibleNew))
     {
       af.alignPanel.paintAlignment(true, true);
     }
   }
 
+  /**
+   * Converts table data into an array of data beans
+   */
+  private FeatureSettingsBean[] getTableAsBeans(Object[][] data)
+  {
+    FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length];
+    for (int i = 0; i < data.length; i++)
+    {
+      String type = (String) data[i][TYPE_COLUMN];
+      FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN];
+      KeyedMatcherSetI theFilter = (KeyedMatcherSetI) data[i][FILTER_COLUMN];
+      Boolean isShown = (Boolean) data[i][SHOW_COLUMN];
+      rowData[i] = new FeatureSettingsBean(type, colour, theFilter,
+              isShown);
+    }
+    return rowData;
+  }
+
   private void jbInit() throws Exception
   {
     this.setLayout(new BorderLayout());
@@ -1492,6 +1509,16 @@ public class FeatureSettings extends JPanel
   // ///////////////////////////////////////////////////////////////////////
   class FeatureTableModel extends AbstractTableModel
   {
+    /*
+     * column indices of fields in Feature Settings table
+     */
+    static final int TYPE_COLUMN = 0;
+
+    static final int COLOUR_COLUMN = 1;
+
+    static final int FILTER_COLUMN = 2;
+
+    static final int SHOW_COLUMN = 3;
 
     private String[] columnNames = {
         MessageManager.getString("label.feature_type"),

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 4797675..8bdcad4 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -50,16 +50,27 @@ public abstract class FeatureRendererModel
         implements jalview.api.FeatureRenderer
 {
   /*
-   * column indices of fields in Feature Settings table
-   * todo: transfer valuers as data beans instead of Object[][]
+   * a data bean to hold one row of feature settings from the gui
    */
-  public static final int TYPE_COLUMN = 0;
+  public static class FeatureSettingsBean
+  {
+    public final String featureType;
+
+    public final FeatureColourI featureColour;
 
-  public static final int COLOUR_COLUMN = 1;
+    public final KeyedMatcherSetI filter;
 
-  public static final int FILTER_COLUMN = 2;
+    public final Boolean show;
 
-  public static final int SHOW_COLUMN = 3;
+    public FeatureSettingsBean(String type, FeatureColourI colour,
+            KeyedMatcherSetI theFilter, Boolean isShown)
+    {
+      featureType = type;
+      featureColour = colour;
+      filter = theFilter;
+      show = isShown;
+    }
+  }
 
   /*
    * global transparency for feature
@@ -673,26 +684,27 @@ public abstract class FeatureRendererModel
    * Replace current ordering with new ordering
    * 
    * @param data
-   *          { String(Type), Colour(Type), Boolean(Displayed) }
+   *          an array of { Type, Colour, Filter, Boolean }
    * @return true if any visible features have been reordered, else false
    */
-  public boolean setFeaturePriority(Object[][] data)
+  public boolean setFeaturePriority(FeatureSettingsBean[] data)
   {
     return setFeaturePriority(data, true);
   }
 
   /**
-   * Sets the priority order for features, with the highest priority (displayed
-   * on top) at the start of the data array
+   * Sets the priority order for features, with the highest priority (displayed on
+   * top) at the start of the data array
    * 
    * @param data
-   *          { String(Type), Colour(Type), Boolean(Displayed) }
+   *          an array of { Type, Colour, Filter, Boolean }
    * @param visibleNew
    *          when true current featureDisplay list will be cleared
-   * @return true if any visible features have been reordered or recoloured,
-   *         else false (i.e. no need to repaint)
+   * @return true if any visible features have been reordered or recoloured, else
+   *         false (i.e. no need to repaint)
    */
-  public boolean setFeaturePriority(Object[][] data, boolean visibleNew)
+  public boolean setFeaturePriority(FeatureSettingsBean[] data,
+          boolean visibleNew)
   {
     /*
      * note visible feature ordering and colours before update
@@ -731,9 +743,9 @@ public abstract class FeatureRendererModel
     {
       for (int i = 0; i < data.length; i++)
       {
-        String type = data[i][TYPE_COLUMN].toString();
-        setColour(type, (FeatureColourI) data[i][COLOUR_COLUMN]);
-        if (((Boolean) data[i][SHOW_COLUMN]).booleanValue())
+        String type = data[i].featureType;
+        setColour(type, data[i].featureColour);
+        if (data[i].show)
         {
           av_featuresdisplayed.setVisible(type);
         }

diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index f6dfed6..d8b905e 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -15,6 +15,7 @@ import jalview.gui.FeatureRenderer;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.schemes.FeatureColour;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 
 import java.awt.Color;
 import java.util.List;
@@ -172,9 +173,9 @@ public class FeatureColourFinderTest
      * - currently no way other than mimicking reordering of
      * table in Feature Settings
      */
-    Object[][] data = new Object[2][];
-    data[0] = new Object[] { "Metal", red, true };
-    data[1] = new Object[] { "Domain", green, true };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[2];
+    data[0] = new FeatureSettingsBean("Metal", red, null, true);
+    data[1] = new FeatureSettingsBean("Domain", green, null, true);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.blue, seq, 10);
     assertEquals(c, Color.red);
@@ -182,7 +183,7 @@ public class FeatureColourFinderTest
     /*
      * ..and turn off display of Metal
      */
-    data[0][2] = false;
+    data[0] = new FeatureSettingsBean("Metal", red, null, false);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.blue, seq, 10);
     assertEquals(c, Color.green);
@@ -216,8 +217,8 @@ public class FeatureColourFinderTest
     /*
      * turn off display of Metal - is this the easiest way to do it??
      */
-    Object[][] data = new Object[1][];
-    data[0] = new Object[] { "Metal", red, false };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[1];
+    data[0] = new FeatureSettingsBean("Metal", red, null, false);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.blue, seq, 10);
     assertEquals(c, Color.blue);
@@ -225,7 +226,7 @@ public class FeatureColourFinderTest
     /*
      * turn display of Metal back on
      */
-    data[0] = new Object[] { "Metal", red, true };
+    data[0] = new FeatureSettingsBean("Metal", red, null, true);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.blue, seq, 10);
     assertEquals(c, Color.red);
@@ -399,9 +400,9 @@ public class FeatureColourFinderTest
      * 1) 0.6 * green(0, 255, 0) + 0.4 * cyan(0, 255, 255) = (0, 255, 102)
      * 2) 0.6* red(255, 0, 0) + 0.4 * (0, 255, 102) = (153, 102, 41) rounded
      */
-    Object[][] data = new Object[2][];
-    data[0] = new Object[] { "Metal", red, true };
-    data[1] = new Object[] { "Domain", green, true };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[2];
+    data[0] = new FeatureSettingsBean("Metal", red, null, true);
+    data[1] = new FeatureSettingsBean("Domain", green, null, true);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.cyan, seq, 10);
     assertEquals(c, new Color(153, 102, 41));
@@ -411,7 +412,7 @@ public class FeatureColourFinderTest
      * Domain (green) above background (pink)
      * 0.6 * green(0, 255, 0) + 0.4 * pink(255, 175, 175) = (102, 223, 70)
      */
-    data[0][2] = false;
+    data[0] = new FeatureSettingsBean("Metal", red, null, false);
     fr.setFeaturePriority(data);
     c = finder.findFeatureColour(Color.pink, seq, 10);
     assertEquals(c, new Color(102, 223, 70));
@@ -447,8 +448,8 @@ public class FeatureColourFinderTest
     /*
      * turn off display of Metal
      */
-    Object[][] data = new Object[1][];
-    data[0] = new Object[] { "Metal", red, false };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[1];
+    data[0] = new FeatureSettingsBean("Metal", red, null, false);
     fr.setFeaturePriority(data);
     assertTrue(finder.noFeaturesDisplayed());
 
@@ -503,9 +504,9 @@ public class FeatureColourFinderTest
     /*
      * render order is kd above Metal
      */
-    Object[][] data = new Object[2][];
-    data[0] = new Object[] { kdFeature, fc, true };
-    data[1] = new Object[] { metalFeature, green, true };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[2];
+    data[0] = new FeatureSettingsBean(kdFeature, fc, null, true);
+    data[1] = new FeatureSettingsBean(metalFeature, green, null, true);
     fr.setFeaturePriority(data);
 
     av.setShowSequenceFeatures(true);

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index 745eec3..73ae9d7 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -17,6 +17,7 @@ import jalview.util.matcher.Condition;
 import jalview.util.matcher.KeyedMatcher;
 import jalview.util.matcher.KeyedMatcherSet;
 import jalview.util.matcher.KeyedMatcherSetI;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 
 import java.awt.Color;
 import java.util.ArrayList;
@@ -122,11 +123,11 @@ public class FeatureRendererTest
      * change render order (todo: an easier way)
      * nb here last comes first in the data array
      */
-    Object[][] data = new Object[3][];
+    FeatureSettingsBean[] data = new FeatureSettingsBean[3];
     FeatureColourI colour = new FeatureColour(Color.RED);
-    data[0] = new Object[] { "Rfam", colour, true };
-    data[1] = new Object[] { "Pfam", colour, false };
-    data[2] = new Object[] { "Scop", colour, false };
+    data[0] = new FeatureSettingsBean("Rfam", colour, null, true);
+    data[1] = new FeatureSettingsBean("Pfam", colour, null, false);
+    data[2] = new FeatureSettingsBean("Scop", colour, null, false);
     fr.setFeaturePriority(data);
     assertEquals(fr.getRenderOrder(), Arrays.asList("Scop", "Pfam", "Rfam"));
     assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
@@ -223,12 +224,13 @@ public class FeatureRendererTest
     /*
      * make "Type2" not displayed
      */
-    Object[][] data = new Object[4][];
     FeatureColourI colour = new FeatureColour(Color.RED);
-    data[0] = new Object[] { "Type1", colour, true };
-    data[1] = new Object[] { "Type2", colour, false };
-    data[2] = new Object[] { "Type3", colour, true };
-    data[3] = new Object[] { "Disulphide Bond", colour, true };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[4];
+    data[0] = new FeatureSettingsBean("Type1", colour, null, true);
+    data[1] = new FeatureSettingsBean("Type2", colour, null, false);
+    data[2] = new FeatureSettingsBean("Type3", colour, null, true);
+    data[3] = new FeatureSettingsBean("Disulphide Bond", colour, null,
+            true);
     fr.setFeaturePriority(data);
 
     features = fr.findFeaturesAtColumn(seq, 15);
@@ -377,11 +379,11 @@ public class FeatureRendererTest
     /*
      * hide feature type, then unhide
      */
-    Object[][] data = new Object[1][];
-    data[0] = new Object[] { "Cath", fc, false };
+    FeatureSettingsBean[] data = new FeatureSettingsBean[1];
+    data[0] = new FeatureSettingsBean("Cath", fc, null, false);
     fr.setFeaturePriority(data);
     assertNull(fr.getColour(sf1));
-    data[0] = new Object[] { "Cath", fc, true };
+    data[0] = new FeatureSettingsBean("Cath", fc, null, true);
     fr.setFeaturePriority(data);
     assertEquals(fr.getColour(sf1), Color.red);