Merge remote-tracking branch 'origin/bug/JAL-2722' into portforward/JAL-2675_2102b1to2103

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 5be7f55..0a1e8ef 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -95,6 +95,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   public Color getResidueColour(final SequenceI seq, int position,
           FeatureColourFinder finder)
   {
+    allGroups = av.getAlignment().findAllGroups(seq);
     return resColourFinder.getResidueColour(av.getShowBoxes(),
             av.getResidueShading(),
             allGroups, seq, position,

diff --git a/test/jalview/gui/SequenceRendererTest.java b/test/jalview/gui/SequenceRendererTest.java
new file mode 100644 (file)
index 0000000..359377a
--- /dev/null
+++ b/test/jalview/gui/SequenceRendererTest.java
@@ -0,0 +1,89 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.ZappoColourScheme;
+
+import java.awt.Color;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+public class SequenceRendererTest
+{
+  AlignmentI al;
+  AlignViewport av;
+
+  SequenceI seq1;
+
+  @BeforeClass(alwaysRun = true)
+  public static void setUpBeforeClass() throws Exception
+  {
+    Jalview.main(
+            new String[]
+    { "-nonews", "-props", "test/jalview/testProps.jvprops" });
+  }
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    seq1 = new Sequence("Seq1", "ABCEEEABCABC");
+    SequenceI seq2 = new Sequence("Seq2", "ABCABCABCABC");
+    SequenceI seq3 = new Sequence("Seq3", "ABCABCABCABC");
+    SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
+    al = new Alignment(seqs);
+    al.setDataset(null);
+    av = new AlignViewport(al);
+  }
+
+  @Test(groups = "Functional")
+  public void testGetResidueColour_WithGroup()
+  {
+    SequenceRenderer sr = new SequenceRenderer(av);
+    SequenceGroup sg = new SequenceGroup();
+    sg.addSequence(seq1, false);
+    sg.setStartRes(3);
+    sg.setEndRes(5);
+
+    ResidueShaderI rs = new ResidueShader();
+    rs.setColourScheme(new ZappoColourScheme());
+    sg.setGroupColourScheme(rs);
+
+    av.getAlignment().addGroup(sg);
+
+    // outside group residues are white
+    assertEquals(Color.white, sr.getResidueColour(seq1, 1, null));
+
+    // within group use Zappo scheme - E = red
+    assertEquals(Color.red, sr.getResidueColour(seq1, 3, null));
+  }
+}