X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Frenderer%2FOverviewResColourFinderTest.java;h=76beab80e27d0c58c1ed6c532815f035c9dddb6c;hb=447c5c1b22bd12a78730640321264fb38c39ec7b;hp=d7ce4a897d906a1f2ac6077a93b132a5c67377ec;hpb=6fba772f85971a17ec141fe27aed669db209f976;p=jalview.git

diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index d7ce4a8..76beab8 100644
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -26,14 +26,16 @@ import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignViewport;
 import jalview.gui.JvOptionPane;
-import jalview.gui.Preferences;
+import jalview.schemes.ColourSchemeI;
 import jalview.schemes.UserColourScheme;
 import jalview.schemes.ZappoColourScheme;
 
 import java.awt.Color;
+import java.util.ArrayList;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -46,6 +48,7 @@ public class OverviewResColourFinderTest
   {
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
   }
 
   @Test(groups = { "Functional" })
@@ -56,19 +59,20 @@ public class OverviewResColourFinderTest
     final AlignViewport av = new AlignViewport(al);
     ResidueColourFinder rcf = new OverviewResColourFinder();
 
+    ResidueShaderI sh = av.getResidueShading();
+
     // gaps are grey, residues white
-    assertEquals(Color.white, rcf.getResidueColour(true,
-            av.getResidueShading(),
-            null, seq, 0, null));
-    assertEquals(Color.lightGray, rcf
-            .getResidueColour(true, av.getResidueShading(), null, seq, 2,
-                    null));
+    assertEquals(Color.white,
+            rcf.getResidueColour(true, sh, null, seq, 0, null));
+    System.out.println(rcf.getResidueColour(true, sh, null, seq, 2, null));
+    assertEquals(Color.lightGray, rcf.getResidueColour(true,
+            sh, null, seq, 2, null));
 
     // unaffected by showBoxes setting
     assertEquals(Color.white, rcf.getResidueColour(false,
-            av.getResidueShading(), null, seq, 0, null));
+            sh, null, seq, 0, null));
     assertEquals(Color.lightGray, rcf.getResidueColour(false,
-            av.getResidueShading(), null, seq, 2, null));
+            sh, null, seq, 2, null));
   }
 
   @Test(groups = { "Functional" })
@@ -150,6 +154,7 @@ public class OverviewResColourFinderTest
     // unaffected by showBoxes setting
     // gap colour not specified so gaps are lightGray
     newColours[23] = null;
+
     assertEquals(Color.lightGray, rcf.getResidueColour(false,
             av.getResidueShading(), null, seq, 3, null));
 
@@ -161,11 +166,70 @@ public class OverviewResColourFinderTest
             av.getResidueShading(), null, seq, 3, null));
   }
 
-  @Test
-  public void testGetBoxColour()
+  @Test(groups = "Functional")
+  public void testGetResidueBoxColour_group()
   {
-    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
+    AlignmentI al = new Alignment(new SequenceI[] { seq });
+    
+    ColourSchemeI cs = new ZappoColourScheme();
+    ArrayList<SequenceI> seqlist = new ArrayList<>();
+    seqlist.add(seq);
+    SequenceGroup sg = new SequenceGroup(seqlist, "testgroup", cs, true,
+            true, true, 5, 9);
+    al.addGroup(sg);
+    SequenceGroup[] groups = new SequenceGroup[1];
+    groups[0] = sg;
+    
+    final AlignViewport av = new AlignViewport(al);
+    ResidueColourFinder rcf = new OverviewResColourFinder();
+    
+    // G in group specified as magenta in Zappo
+    assertEquals(Color.magenta, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 7, null));
+
+    // Residue outside group coloured white
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 0, null));
+
+    // Gap outside group coloured lightgray
+    assertEquals(Color.lightGray, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 2, null));
 
+    // use legacy colouring
+    rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
+  
+    // G in group specified as magenta in Zappo
+    assertEquals(Color.magenta, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 7, null));
+
+    // Residue outside group coloured lightgray
+    assertEquals(Color.lightGray, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 0, null));
+
+    // Gap outside group coloured white
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 2, null));
+
+    // use new colouring
+    rcf = new OverviewResColourFinder(false, Color.blue, Color.red);
+
+    // G in group specified as magenta in Zappo
+    assertEquals(Color.magenta, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 7, null));
+
+    // Residue outside group coloured white
+    assertEquals(Color.white, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 0, null));
+
+    // Gap outside group coloured blue
+    assertEquals(Color.blue, rcf.getResidueColour(false,
+            av.getResidueShading(), groups, seq, 2, null));
+  }
+
+  @Test(groups = "Functional")
+  public void testGetBoxColour()
+  {
     SequenceI seq = new Sequence("name", "MAT--GSPRAPAFF"); // FER1_MAIZE... + a
                                                             // gap
     AlignmentI al = new Alignment(new SequenceI[] { seq });
@@ -181,7 +245,9 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+    assertEquals(
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
+            c);
 
     // legacy colouring set explicitly via constructor
     rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
@@ -205,7 +271,9 @@ public class OverviewResColourFinderTest
 
     // gaps gap colour
     c = rcf.getBoxColour(shader, seq, 3);
-    assertEquals(Preferences.OVERVIEW_DEFAULT_GAP, c);
+    assertEquals(
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP,
+            c);
 
     // non legacy colouring with colour scheme
     rcf = new OverviewResColourFinder(false, Color.blue, Color.red);