X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2FOverviewRendererTest.java;fp=test%2Fjalview%2Frenderer%2FOverviewRendererTest.java;h=1d532f78ced4148b125f134631761ddff6ba8ba4;hb=b83eff8c672cede0305da3c76823dab414749dde;hp=0000000000000000000000000000000000000000;hpb=d943fcd0dc04fd4974344eddd13902c89fb595b2;p=jalview.git

diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java
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+/*
+ * 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.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());
+  }
+}