X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2FResidueShaderTest.java;h=78f00c80ce16a07a3f6009050f785c0a4d69db5e;hb=e9a1c2c372f4bbf6cf658de3dba73ef326b20c20;hp=76fd9b42c3ffe5e07d87d3a96ca1137a5f989180;hpb=b2b7e99113e1f0962140fc72d989cc826799a2d4;p=jalview.git

diff --git a/test/jalview/renderer/ResidueShaderTest.java b/test/jalview/renderer/ResidueShaderTest.java
index 76fd9b4..78f00c8 100644
--- a/test/jalview/renderer/ResidueShaderTest.java
+++ b/test/jalview/renderer/ResidueShaderTest.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.renderer;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -8,9 +28,15 @@ import jalview.analysis.Conservation;
 import jalview.datamodel.Profile;
 import jalview.datamodel.ProfileI;
 import jalview.datamodel.Profiles;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.ResidueCount;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
 
 import java.awt.Color;
 import java.util.Collections;
@@ -155,12 +181,179 @@ public class ResidueShaderTest
     assertEquals(Color.WHITE, ccs.applyConservation(colour, 4));
     assertEquals(Color.WHITE, ccs.applyConservation(colour, 5));
     assertEquals(Color.WHITE, ccs.applyConservation(colour, 6));
-    assertEquals(new Color(235, 225, 215), ccs.applyConservation(colour, 7));
-    assertEquals(new Color(215, 195, 175), ccs.applyConservation(colour, 8));
-    assertEquals(new Color(195, 165, 135), ccs.applyConservation(colour, 9));
+    assertEquals(new Color(235, 225, 215),
+            ccs.applyConservation(colour, 7));
+    assertEquals(new Color(215, 195, 175),
+            ccs.applyConservation(colour, 8));
+    assertEquals(new Color(195, 165, 135),
+            ccs.applyConservation(colour, 9));
     assertEquals(colour, ccs.applyConservation(colour, 10));
     assertEquals(colour, ccs.applyConservation(colour, 11));
     assertEquals(Color.WHITE, ccs.applyConservation(colour, 12));
   }
 
+  @Test(groups = "Functional")
+  public void testFindColour_gapColour()
+  {
+    /*
+     * normally, a gap is coloured white
+     */
+    ResidueShader rs = new ResidueShader(new ZappoColourScheme());
+    assertEquals(Color.white, rs.findColour(' ', 7, null));
+
+    /*
+     * a User Colour Scheme may specify a bespoke gap colour
+     */
+    Color[] colours = new Color[ResidueProperties.maxProteinIndex + 1];
+    colours[5] = Color.blue; // Q colour
+    colours[23] = Color.red; // gap colour
+    ColourSchemeI cs = new UserColourScheme(colours);
+    rs = new ResidueShader(cs);
+
+    assertEquals(Color.red, rs.findColour(' ', 7, null));
+    assertEquals(Color.blue, rs.findColour('Q', 7, null));
+
+    /*
+     * stub Conservation to return a given consensus string
+     */
+    final String consSequence = "0123456789+*-";
+    Conservation cons = new Conservation(null,
+            Collections.<SequenceI> emptyList(), 0, 0)
+    {
+      @Override
+      public SequenceI getConsSequence()
+      {
+        return new Sequence("seq", consSequence);
+      }
+    };
+    rs.setConservation(cons);
+
+    /*
+     * with 0% threshold, there should be no fading
+     */
+    rs.setConservationInc(0);
+    assertEquals(Color.red, rs.findColour(' ', 7, null));
+    assertEquals(Color.blue, rs.findColour('Q', 7, null));
+
+    /*
+     * with 40% threshold, 'fade factor' is 
+     * (11-score)/10 * 40/20 = (11-score)/5
+     * so position 7, score 7 fades 80% of the way to white (255, 255, 255)
+     */
+    rs.setConservationInc(40);
+
+    /*
+     * gap colour is unchanged for Conservation
+     */
+    assertEquals(Color.red, rs.findColour(' ', 7, null));
+    assertEquals(Color.red, rs.findColour('-', 7, null));
+    assertEquals(Color.red, rs.findColour('.', 7, null));
+
+    /*
+     * residue colour is faded 80% of the way from
+     * blue(0, 0, 255) to white(255, 255, 255)
+     * making (204, 204, 255)
+     */
+    assertEquals(new Color(204, 204, 255), rs.findColour('Q', 7, null));
+
+    /*
+     * turn off By Conservation, apply Above Identity Threshold
+     * providing a stub Consensus that has modal residue "Q" with pid 60%
+     */
+    rs.setConservationApplied(false);
+    ProfilesI consensus = getStubConsensus("Q", 60f);
+    rs.setConsensus(consensus);
+
+    // with consensus pid (60) above threshold (50), colours are unchanged
+    rs.setThreshold(50, false);
+    assertEquals(Color.blue, rs.findColour('Q', 7, null));
+    assertEquals(Color.red, rs.findColour('-', 7, null));
+
+    // with consensus pid (60) below threshold (70),
+    // residue colour becomes white, gap colour is unchanged
+    rs.setThreshold(70, false);
+    assertEquals(Color.white, rs.findColour('Q', 7, null));
+    assertEquals(Color.red, rs.findColour('-', 7, null));
+  }
+
+  /**
+   * @param modalResidue
+   * @param pid
+   * @return
+   */
+  protected ProfilesI getStubConsensus(final String modalResidue,
+          final float pid)
+  {
+    ProfilesI consensus = new ProfilesI()
+    {
+
+      @Override
+      public ProfileI get(int i)
+      {
+        return new ProfileI()
+        {
+          @Override
+          public void setCounts(ResidueCount residueCounts)
+          {
+          }
+
+          @Override
+          public float getPercentageIdentity(boolean ignoreGaps)
+          {
+            return pid;
+          }
+
+          @Override
+          public ResidueCount getCounts()
+          {
+            return null;
+          }
+
+          @Override
+          public int getHeight()
+          {
+            return 0;
+          }
+
+          @Override
+          public int getGapped()
+          {
+            return 0;
+          }
+
+          @Override
+          public int getMaxCount()
+          {
+            return 0;
+          }
+
+          @Override
+          public String getModalResidue()
+          {
+            return modalResidue;
+          }
+
+          @Override
+          public int getNonGapped()
+          {
+            return 0;
+          }
+        };
+      }
+
+      @Override
+      public int getStartColumn()
+      {
+        return 0;
+      }
+
+      @Override
+      public int getEndColumn()
+      {
+        return 0;
+      }
+
+    };
+    return consensus;
+  }
 }