JAL-2588 Check/fix show boxes settings + unit test updates.

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 516dcc1..684701e 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -84,7 +84,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     // TODO replace 8 or so code duplications with calls to this method
     // (refactored as needed)
-    return resColourFinder.getResidueColour(av.getResidueShading(),
+    return resColourFinder.getResidueColour(av.getShowBoxes(),
+            av.getResidueShading(),
             allGroups, seq, position, finder);
   }
 

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 5bb0de7..c27c16b 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -95,7 +95,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public Color getResidueColour(final SequenceI seq, int position,
           FeatureColourFinder finder)
   {
-    return resColourFinder.getResidueColour(av.getResidueShading(),
+    return resColourFinder.getResidueColour(av.getShowBoxes(),
+            av.getResidueShading(),
             allGroups, seq, position,
             finder);
   }

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index 8d9f036..607988f 100644 (file)
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -161,7 +161,8 @@ public class OverviewRenderer
 
     if ((seq != null) && (seq.getLength() > lastcol))
     {
-      color = resColFinder.getResidueColour(shader, allGroups, seq, lastcol,
+      color = resColFinder.getResidueColour(true, shader, allGroups, seq,
+              lastcol,
               fcfinder);
     }
 

diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index 793d349..5ed218b 100644 (file)
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -20,6 +20,7 @@
  */
 package jalview.renderer;
 
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
@@ -33,6 +34,9 @@ public class OverviewResColourFinder extends ResidueColourFinder
     Color resBoxColour = Color.white;
     char currentChar = seq.getCharAt(i);
 
+    // In the overview window, gaps are coloured grey, unless the colour scheme
+    // specifies a gap colour, in which case gaps honour the colour scheme
+    // settings
     if (shader.getColourScheme() != null)
     {
       if (Comparison.isGap(currentChar)
@@ -52,4 +56,28 @@ public class OverviewResColourFinder extends ResidueColourFinder
 
     return resBoxColour;
   }
+
+  /**
+   * {@inheritDoc} In the overview, the showBoxes setting is ignored, as the
+   * overview displays the colours regardless.
+   */
+  @Override
+  protected Color getResidueBoxColour(boolean showBoxes,
+          ResidueShaderI shader,
+          SequenceGroup[] allGroups, SequenceI seq, int i)
+  {
+    ResidueShaderI currentShader;
+    SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
+            i);
+    if (currentSequenceGroup != null)
+    {
+      currentShader = currentSequenceGroup.getGroupColourScheme();
+    }
+    else
+    {
+      currentShader = shader;
+    }
+
+    return getBoxColour(currentShader, seq, i);
+  }
 }

diff --git a/src/jalview/renderer/ResidueColourFinder.java b/src/jalview/renderer/ResidueColourFinder.java
index 99f5107..2da7233 100644 (file)
--- a/src/jalview/renderer/ResidueColourFinder.java
+++ b/src/jalview/renderer/ResidueColourFinder.java
@@ -32,12 +32,32 @@ public class ResidueColourFinder
   {
   }
 
-  public Color getResidueColour(ResidueShaderI shader,
+  /**
+   * Get the colour of a residue in a sequence
+   * 
+   * @param showBoxes
+   *          true if the viewport's Show Boxes setting is true
+   * @param shader
+   *          the viewport's colour scheme
+   * @param allGroups
+   *          all the groups which seq participates in
+   * @param seq
+   *          the sequence containing the residue
+   * @param position
+   *          the position of the residue in the sequence
+   * @param finder
+   *          FeatureColourFinder for the viewport
+   * @return colour of the residue
+   */
+  public Color getResidueColour(boolean showBoxes, ResidueShaderI shader,
           SequenceGroup[] allGroups,
           final SequenceI seq, int position, FeatureColourFinder finder)
   {
-    Color col = getResidueBoxColour(shader, allGroups, seq, position);
+    Color col = getResidueBoxColour(showBoxes, shader, allGroups, seq,
+            position);
 
+    // if there's a FeatureColourFinder we might override the residue colour
+    // here with feature colouring
     if (finder != null)
     {
       col = finder.findFeatureColour(col, seq, position);
@@ -45,27 +65,54 @@ public class ResidueColourFinder
     return col;
   }
 
-  private Color getResidueBoxColour(ResidueShaderI shader,
+  /**
+   * Get the residue colour without accounting for any features
+   * 
+   * @param showBoxes
+   *          true if the viewport's Show Boxes setting is true
+   * @param shader
+   *          the viewport's colour scheme
+   * @param allGroups
+   *          all the groups which seq participates in
+   * @param seq
+   *          the sequence containing the residue
+   * @param i
+   *          the position of the residue in the sequence
+   * @return
+   */
+  protected Color getResidueBoxColour(boolean showBoxes,
+          ResidueShaderI shader,
           SequenceGroup[] allGroups,
           SequenceI seq, int i)
   {
-
-    ResidueShaderI currentShader;
-
     SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
             i);
     if (currentSequenceGroup != null)
     {
-      currentShader = currentSequenceGroup.getGroupColourScheme();
+      if (currentSequenceGroup.getDisplayBoxes())
+      {
+        return getBoxColour(currentSequenceGroup.getGroupColourScheme(),
+                seq, i);
+      }
     }
-    else
+    else if (showBoxes)
     {
-      currentShader = shader;
+      return getBoxColour(shader, seq, i);
     }
-
-    return getBoxColour(currentShader, seq, i);
+  
+    return Color.white;
   }
 
+  /**
+   * Search all the groups for a sequence to find the one which a given res
+   * falls into
+   * 
+   * @param allGroups
+   *          all the groups a sequence participates in
+   * @param res
+   *          the residue to search for
+   * @return a sequence group for res, or null if no sequence group applies
+   */
   public SequenceGroup getCurrentSequenceGroup(SequenceGroup[] allGroups,
           int res)
   {
@@ -90,11 +137,11 @@ public class ResidueColourFinder
    * DOCUMENT ME!
    * 
    * @param shader
-   *          DOCUMENT ME!
+   *          the viewport's colour scheme
    * @param seq
-   *          DOCUMENT ME!
+   *          the sequence containing the residue
    * @param i
-   *          DOCUMENT ME!
+   *          the position of the residue in the sequence
    */
   public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {

diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 900994e..649a0bf 100644 (file)
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -55,10 +55,18 @@ public class OverviewResColourFinderTest
     ResidueColourFinder rcf = new OverviewResColourFinder();
 
     // gaps are grey, residues white
-    assertEquals(Color.white, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(Color.white, rcf.getResidueColour(true,
+            av.getResidueShading(),
             null, seq, 0, null));
     assertEquals(Color.lightGray, rcf
-            .getResidueColour(av.getResidueShading(), null, seq, 2, null));
+            .getResidueColour(true, av.getResidueShading(), null, seq, 2,
+                    null));
+
+    // unaffected by showBoxes setting
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 0, null));
+    assertEquals(Color.lightGray, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 2, null));
   }
 
   @Test(groups = { "Functional" })
@@ -72,22 +80,38 @@ public class OverviewResColourFinderTest
     av.setGlobalColourScheme(new ZappoColourScheme());
 
     // @see ResidueProperties.zappo
-    assertEquals(Color.pink, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(Color.pink,
+            rcf.getResidueColour(true, av.getResidueShading(),
             null, seq, 0, null)); // M
-    assertEquals(Color.green, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(Color.green,
+            rcf.getResidueColour(true, av.getResidueShading(),
             null, seq, 2, null)); // T
-    assertEquals(Color.magenta, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(Color.magenta,
+            rcf.getResidueColour(true, av.getResidueShading(),
             null, seq, 5, null)); // G
-    assertEquals(Color.orange, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(Color.orange,
+            rcf.getResidueColour(true, av.getResidueShading(),
             null, seq, 12, null)); // F
 
     // gap colour not specified so gaps are lightGray
     assertEquals(Color.lightGray, rcf
-            .getResidueColour(av.getResidueShading(), null, seq, 3, null));
+            .getResidueColour(true, av.getResidueShading(), null, seq, 3,
+                    null));
+
+    // unaffected by showBoxes setting
+    assertEquals(Color.pink, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 0, null)); // M
+    assertEquals(Color.green, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 2, null)); // T
+    assertEquals(Color.magenta, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 5, null)); // G
+    assertEquals(Color.orange, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 12, null)); // F
 
     // gap colour not specified so gaps are lightGray
     assertEquals(Color.lightGray, rcf
-            .getResidueColour(av.getResidueShading(), null, seq, 3, null));
+            .getResidueColour(false, av.getResidueShading(), null, seq, 3,
+                    null));
 
   }
 
@@ -110,13 +134,28 @@ public class OverviewResColourFinderTest
 
     // gap colour not specified so gaps are lightGray
     assertEquals(Color.lightGray, rcf
-            .getResidueColour(av.getResidueShading(), null, seq, 3, null));
+            .getResidueColour(true, av.getResidueShading(), null, seq, 3,
+                    null));
 
     newColours[23] = Color.pink;
     av.setGlobalColourScheme(new UserColourScheme(newColours));
 
     // gap colour specified as pink
-    assertEquals(Color.pink, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(Color.pink, rcf.getResidueColour(true,
+            av.getResidueShading(),
             null, seq, 3, null));
+
+    // unaffected by showBoxes setting
+    // gap colour not specified so gaps are lightGray
+    newColours[23] = null;
+    assertEquals(Color.lightGray, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 3, null));
+
+    newColours[23] = Color.pink;
+    av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+    // gap colour specified as pink
+    assertEquals(Color.pink, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 3, null));
   }
 }

diff --git a/test/jalview/renderer/ResidueColourFinderTest.java b/test/jalview/renderer/ResidueColourFinderTest.java
index 175c68e..81fb2c0 100644 (file)
--- a/test/jalview/renderer/ResidueColourFinderTest.java
+++ b/test/jalview/renderer/ResidueColourFinderTest.java
@@ -57,17 +57,28 @@ public class ResidueColourFinderTest
 
     // @see ResidueProperties.zappo
     assertEquals(Color.pink,
-            rcf.getResidueColour(av.getResidueShading(), null, seq, 0,
+            rcf.getResidueColour(true, av.getResidueShading(), null, seq, 0,
                     null)); // M
     assertEquals(Color.green,
-            rcf.getResidueColour(av.getResidueShading(), null, seq, 2,
+            rcf.getResidueColour(true, av.getResidueShading(), null, seq, 2,
                     null)); // T
     assertEquals(Color.magenta,
-            rcf.getResidueColour(av.getResidueShading(), null, seq, 5,
+            rcf.getResidueColour(true, av.getResidueShading(), null, seq, 5,
                     null)); // G
     assertEquals(Color.orange,
-            rcf.getResidueColour(av.getResidueShading(), null, seq, 12,
+            rcf.getResidueColour(true, av.getResidueShading(), null, seq,
+                    12,
                     null)); // F
+
+    // everything is white if showBoxes is false
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 0, null)); // M
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 2, null)); // T
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 5, null)); // G
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 12, null)); // F
   }
 
   @Test(groups = { "Functional" })
@@ -78,10 +89,18 @@ public class ResidueColourFinderTest
     final AlignViewport av = new AlignViewport(al);
     ResidueColourFinder rcf = new ResidueColourFinder();
 
-    assertEquals(Color.white, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(Color.white,
+            rcf.getResidueColour(true, av.getResidueShading(),
             null, seq, 0, null));
-    assertEquals(Color.white, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(Color.white,
+            rcf.getResidueColour(true, av.getResidueShading(),
             null, seq, 2, null));
+
+    // no change if showBoxes is false
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 0, null));
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 2, null));
   }
 
   @Test(groups = { "Functional" })
@@ -103,18 +122,30 @@ public class ResidueColourFinderTest
 
     // gap colour not specified so gap colour is null
     // this is consistent with previous behaviour, but may not be correct?
-    assertEquals(null, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(null, rcf.getResidueColour(true, av.getResidueShading(),
             null, seq, 3, null));
 
     newColours[23] = Color.pink;
     av.setGlobalColourScheme(new UserColourScheme(newColours));
 
     // gap colour specified as pink
-    assertEquals(Color.pink, rcf.getResidueColour(av.getResidueShading(),
+    assertEquals(Color.pink, rcf.getResidueColour(true,
+            av.getResidueShading(),
+            null, seq, 3, null));
+
+    // everything is white if showBoxes is false
+    newColours[23] = null;
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(),
             null, seq, 3, null));
-  }
 
-  // TODO more tests for getResidueColour covering groups, feature rendering,
-  // gaps, overview...
+    newColours[23] = Color.pink;
+    av.setGlobalColourScheme(new UserColourScheme(newColours));
+
+    // gap colour specified as pink
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), null, seq, 3, null));
+  }
 
+  // TODO more tests for getResidueColour covering groups, feature rendering...
 }