JAL-2929 unit test, tidy unused/unneeded fields/parameters

diff --git a/src/jalview/appletgui/OverviewCanvas.java b/src/jalview/appletgui/OverviewCanvas.java
index 9597b44..a556bdb 100644 (file)
--- a/src/jalview/appletgui/OverviewCanvas.java
+++ b/src/jalview/appletgui/OverviewCanvas.java
@@ -128,8 +128,7 @@ public class OverviewCanvas extends Component
     {
       mg.translate(0, od.getSequencesHeight());
       or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
-              av.getCharWidth(), od.getGraphHeight(),
-              od.getColumns(av.getAlignment()));
+              od.getGraphHeight(), od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
     System.gc();

diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 9df0d82..1f55ea6 100644 (file)
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -157,8 +157,7 @@ public class OverviewCanvas extends JComponent
     {
       mg.translate(0, od.getSequencesHeight());
       or.drawGraph(mg, av.getAlignmentConservationAnnotation(),
-              av.getCharWidth(), od.getGraphHeight(),
-              od.getColumns(av.getAlignment()));
+              od.getGraphHeight(), od.getColumns(av.getAlignment()));
       mg.translate(0, -od.getSequencesHeight());
     }
     System.gc();

diff --git a/src/jalview/renderer/OverviewRenderer.java b/src/jalview/renderer/OverviewRenderer.java
index f36461a..e9b4de4 100644 (file)
--- a/src/jalview/renderer/OverviewRenderer.java
+++ b/src/jalview/renderer/OverviewRenderer.java
@@ -44,8 +44,6 @@ public class OverviewRenderer
   // transparency of hidden cols/seqs overlay
   private final float TRANSPARENCY = 0.5f;
 
-  private final Color HIDDEN_COLOUR = Color.DARK_GRAY.darker();
-
   public static final String UPDATE = "OverviewUpdate";
 
   private static final int MAX_PROGRESS = 100;
@@ -152,7 +150,7 @@ public class OverviewRenderer
         if (pixelCol <= endCol)
         {
           rgbcolor = getColumnColourFromSequence(allGroups, seq,
-                  alignmentCol, finder);
+                  alignmentCol);
     
           // fill in the appropriate number of pixels
           for (int row = pixelRow; row <= endRow; ++row)
@@ -216,26 +214,23 @@ public class OverviewRenderer
   }
 
   /*
-   * Find the colour of a sequence at a specified column position
+   * Find the RGB value of the colour of a sequence at a specified column position
    * 
    * @param seq
    *          sequence to get colour for
    * @param lastcol
    *          column position to get colour for
-   * @param fcfinder
-   *          FeatureColourFinder to use
    * @return colour of sequence at this position, as RGB
    */
-  private int getColumnColourFromSequence(SequenceGroup[] allGroups,
-          jalview.datamodel.SequenceI seq,
-          int lastcol, FeatureColourFinder fcfinder)
+  int getColumnColourFromSequence(SequenceGroup[] allGroups,
+          SequenceI seq, int lastcol)
   {
     Color color = resColFinder.GAP_COLOUR;
 
     if ((seq != null) && (seq.getLength() > lastcol))
     {
       color = resColFinder.getResidueColour(true, shader, allGroups, seq,
-              lastcol, fcfinder);
+              lastcol, finder);
     }
 
     return color.getRGB();
@@ -358,15 +353,13 @@ public class OverviewRenderer
    *          the graphics object to draw on
    * @param anno
    *          alignment annotation information
-   * @param charWidth
-   *          alignment character width value
    * @param y
    *          y-position for the annotation graph
    * @param cols
    *          the collection of columns used in the overview panel
    */
-  public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth,
-          int y, AlignmentColsCollectionI cols)
+  public void drawGraph(Graphics g, AlignmentAnnotation anno, int y,
+          AlignmentColsCollectionI cols)
   {
     Annotation[] annotations = anno.annotations;
     g.setColor(Color.white);

diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java
new file mode 100644 (file)
index 0000000..bc9c2e4
--- /dev/null
+++ b/test/jalview/renderer/OverviewRendererTest.java
@@ -0,0 +1,73 @@
+package jalview.renderer;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.schemes.FeatureColour;
+import jalview.schemes.ZappoColourScheme;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.OverviewDimensions;
+import jalview.viewmodel.OverviewDimensionsShowHidden;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.Color;
+
+import org.testng.annotations.Test;
+public class OverviewRendererTest
+{
+
+  @Test
+  public void testGetColumnColourFromSequence()
+  {
+    OverviewResColourFinder cf = new OverviewResColourFinder(false,
+            Color.PINK, Color.green); // gapColour, hiddenColour
+    Sequence seq1 = new Sequence("seq1", "PQ-RL-");
+    Sequence seq2 = new Sequence("seq2", "FVE");
+    AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+    AlignmentViewport av = new AlignViewport(al);
+    OverviewDimensions od = new OverviewDimensionsShowHidden(new ViewportRanges(al), false);
+    ResidueShaderI rs = new ResidueShader(new ZappoColourScheme());
+    FeatureRenderer fr = new FeatureRenderer(av);
+    OverviewRenderer or = new OverviewRenderer(fr, od, al, rs, cf);
+
+    // P is magenta (see ResidueProperties.zappo)
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 0), Color.magenta.getRGB());
+    // Q is green
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 1),
+            Color.green.getRGB());
+    // gap is pink (specified in OverviewResColourFinder constructor above)
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 2),
+            Color.pink.getRGB());
+    // F is orange
+    assertEquals(or.getColumnColourFromSequence(null, seq2, 0),
+            Color.orange.getRGB());
+    // E is red
+    assertEquals(or.getColumnColourFromSequence(null, seq2, 2),
+            Color.red.getRGB());
+    // past end of sequence colour as gap (JAL-2929)
+    assertEquals(or.getColumnColourFromSequence(null, seq2, 3),
+            Color.pink.getRGB());
+
+    /*
+     * now add a feature on seq1
+     */
+    seq1.addSequenceFeature(
+            new SequenceFeature("Pfam", "desc", 1, 4, null));
+    fr.findAllFeatures(true);
+    av.setShowSequenceFeatures(true);
+    fr.setColour("Pfam", new FeatureColour(Color.yellow));
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 0),
+            Color.yellow.getRGB());
+
+    // don't show sequence features
+    av.setShowSequenceFeatures(false);
+    assertEquals(or.getColumnColourFromSequence(null, seq1, 0),
+            Color.magenta.getRGB());
+  }
+}