X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FPIDColourSchemeTest.java;h=dff19cd65228c4be92aed3937c7d3a830157ee8e;hb=4bc5c1c97bd08007b2ac9ccfd9b3cb29eac10193;hp=1518fb354611deb50418fc04a844dd32a30ec4cd;hpb=8e1be43e250107a4d86898bd554cf03098fa5957;p=jalview.git

diff --git a/test/jalview/schemes/PIDColourSchemeTest.java b/test/jalview/schemes/PIDColourSchemeTest.java
index 1518fb3..dff19cd 100644
--- a/test/jalview/schemes/PIDColourSchemeTest.java
+++ b/test/jalview/schemes/PIDColourSchemeTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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.schemes;
 
 import static org.testng.Assert.assertEquals;
@@ -6,8 +26,22 @@ import java.awt.Color;
 
 import org.testng.annotations.Test;
 
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
 public class PIDColourSchemeTest
 {
+  static final Color white = Color.white;
+
+  static final Color over40 = new Color(204, 204, 255);
+
+  static final Color over60 = new Color(153, 153, 255);
+
+  static final Color over80 = new Color(100, 100, 255);
+
   /**
    * Test findColour for cases:
    * <ul>
@@ -21,31 +55,80 @@ public class PIDColourSchemeTest
    * <li>case insensitive matching</li>
    * <ul>
    */
-  @Test
+  @Test(groups = "Functional")
   public void testFindColour()
   {
     ColourSchemeI scheme = new PIDColourScheme();
 
-    Color over40 = new Color(204, 204, 255);
-    Color over60 = new Color(153, 153, 255);
-    Color over80 = new Color(100, 100, 255);
-
     /*
      * doesn't use column or sequence
+     * we assume consensus residue is computed as upper case
      */
-    assertEquals(scheme.findColour('A', 0, null, "A", 0f), Color.white);
-    assertEquals(scheme.findColour('A', 0, null, "A", 40f), Color.white);
+    assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
+    assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
     assertEquals(scheme.findColour('A', 0, null, "A", 40.1f), over40);
     assertEquals(scheme.findColour('A', 0, null, "A", 60f), over40);
     assertEquals(scheme.findColour('A', 0, null, "A", 60.1f), over60);
     assertEquals(scheme.findColour('A', 0, null, "A", 80f), over60);
     assertEquals(scheme.findColour('A', 0, null, "A", 80.1f), over80);
     assertEquals(scheme.findColour('A', 0, null, "A", 100f), over80);
+    assertEquals(scheme.findColour('A', 0, null, "KFV", 100f), white);
 
     assertEquals(scheme.findColour('a', 0, null, "A", 80f), over60);
-    assertEquals(scheme.findColour('A', 0, null, "a", 80f), over60);
-    assertEquals(scheme.findColour('a', 0, null, "a", 80f), over60);
     assertEquals(scheme.findColour('A', 0, null, "AC", 80f), over60);
     assertEquals(scheme.findColour('A', 0, null, "KCA", 80f), over60);
   }
+
+  /**
+   * Test that changing the 'ignore gaps in consensus' in the viewport (an
+   * option on the annotation label popup menu) results in a change to the
+   * colouring
+   */
+  @Test(groups = "Functional")
+  public void testFindColour_ignoreGaps()
+  {
+    /*
+     * AAAAA
+     * AAAAA
+     * -CCCC
+     * FFFFF
+     * 
+     * first column consensus is A
+     * first column PID is 50%, or 67% ignoring gaps
+     */
+    String seqs = ">seq1\nAAAAA\n>seq2\nAAAAA\n>seq3\n-CCCC\n>seq4\nFFFFF\n";
+
+    /*
+     * load data and wait for consensus to be computed
+     */
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqs,
+            DataSourceType.PASTE);
+    AlignViewport viewport = af.getViewport();
+    viewport.setIgnoreGapsConsensus(false, af.alignPanel);
+    do
+    {
+      try
+      {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+      }
+    } while (af.getViewport().getCalcManager().isWorking());
+    af.changeColour_actionPerformed(JalviewColourScheme.PID.toString());
+
+    SequenceI seq = viewport.getAlignment().getSequenceAt(0);
+
+    /*
+     * including gaps, A should be coloured for 50% consensus
+     */
+    Color c = viewport.getResidueShading().findColour('A', 0, seq);
+    assertEquals(c, over40);
+
+    /*
+     * now choose to ignore gaps; colour should be for 67%
+     */
+    viewport.setIgnoreGapsConsensus(true, af.alignPanel);
+    c = viewport.getResidueShading().findColour('A', 0, seq);
+    assertEquals(c, over60);
+  }
 }