X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FPIDColourSchemeTest.java;h=dff19cd65228c4be92aed3937c7d3a830157ee8e;hb=d5bd34eb49f43735e240058f8875ab0bfcae4441;hp=6f60e50245194d6a5cfa6708256ae04d1a7e64d7;hpb=9270bd30c65a1304c4228b2f07734bc8461cd531;p=jalview.git

diff --git a/test/jalview/schemes/PIDColourSchemeTest.java b/test/jalview/schemes/PIDColourSchemeTest.java
index 6f60e50..dff19cd 100644
--- a/test/jalview/schemes/PIDColourSchemeTest.java
+++ b/test/jalview/schemes/PIDColourSchemeTest.java
@@ -1,17 +1,37 @@
+/*
+ * 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;
 
+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;
 
-import java.awt.Color;
-
-import org.testng.annotations.Test;
-
 public class PIDColourSchemeTest
 {
   static final Color white = Color.white;
@@ -35,13 +55,14 @@ public class PIDColourSchemeTest
    * <li>case insensitive matching</li>
    * <ul>
    */
-  @Test
+  @Test(groups = "Functional")
   public void testFindColour()
   {
     ColourSchemeI scheme = new PIDColourScheme();
 
     /*
      * doesn't use column or sequence
+     * we assume consensus residue is computed as upper case
      */
     assertEquals(scheme.findColour('A', 0, null, "A", 0f), white);
     assertEquals(scheme.findColour('A', 0, null, "A", 40f), white);
@@ -54,8 +75,6 @@ public class PIDColourSchemeTest
     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);
   }
@@ -65,7 +84,7 @@ public class PIDColourSchemeTest
    * option on the annotation label popup menu) results in a change to the
    * colouring
    */
-  @Test
+  @Test(groups = "Functional")
   public void testFindColour_ignoreGaps()
   {
     /*
@@ -78,10 +97,23 @@ public class PIDColourSchemeTest
      * 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);
@@ -89,16 +121,14 @@ public class PIDColourSchemeTest
     /*
      * including gaps, A should be coloured for 50% consensus
      */
-    Color c = viewport
-            .getViewportColourScheme().findColour('A', 0, seq);
+    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
-            .getViewportColourScheme().findColour('A', 0, seq);
+    c = viewport.getResidueShading().findColour('A', 0, seq);
     assertEquals(c, over60);
   }
 }