X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fschemes%2FColourSchemesTest.java;h=58e272dfc4cf02fea027b486580fdf8b842d525f;hb=7023502056283eef1bfde1efa577fa1e0c2aeb5f;hp=4618ed7be9b4bb605ccbb9fe6cd5b31620c86ef1;hpb=b0832234b2a89510d715951d94ae213e449ca6b2;p=jalview.git

diff --git a/test/jalview/schemes/ColourSchemesTest.java b/test/jalview/schemes/ColourSchemesTest.java
index 4618ed7..58e272d 100644
--- a/test/jalview/schemes/ColourSchemesTest.java
+++ b/test/jalview/schemes/ColourSchemesTest.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;
@@ -5,6 +25,7 @@ import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AnnotatedCollectionI;
@@ -54,15 +75,15 @@ public class ColourSchemesTest
     }
 
     @Override
-    public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-            Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+    public ColourSchemeI getInstance(AlignViewportI view,
+            AnnotatedCollectionI sg)
     {
-      final ColourSchemeI cs1 = ColourSchemes.getInstance()
-              .getColourScheme(JalviewColourScheme.Taylor.toString(),
-                      (AnnotatedCollectionI) null);
-      final ColourSchemeI cs2 = ColourSchemes.getInstance()
-              .getColourScheme(JalviewColourScheme.Zappo.toString(),
-                      (AnnotatedCollectionI) null);
+      final ColourSchemeI cs1 = ColourSchemes.getInstance().getColourScheme(
+              JalviewColourScheme.Taylor.toString(),
+              (AnnotatedCollectionI) null);
+      final ColourSchemeI cs2 = ColourSchemes.getInstance().getColourScheme(
+              JalviewColourScheme.Zappo.toString(),
+              (AnnotatedCollectionI) null);
       return new Stripy(cs1, cs2);
     }
 
@@ -85,7 +106,7 @@ public class ColourSchemesTest
       return "stripy";
     }
   };
-  
+
   /*
    * a colour scheme that is Clustal but using AWT colour equivalents
    */
@@ -144,10 +165,10 @@ public class ColourSchemesTest
     }
 
     @Override
-    public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-            Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+    public ColourSchemeI getInstance(AlignViewportI view,
+            AnnotatedCollectionI sg)
     {
-      return new MyClustal(sg,              hiddenRepSequences);
+      return new MyClustal(sg, view.getHiddenRepSequences());
     }
 
     @Override
@@ -182,7 +203,8 @@ public class ColourSchemesTest
      * in the order in which they are declared in the JalviewColourScheme enum
      * (this also determines their order in Colour menus)
      */
-    Iterator<ColourSchemeI> schemes = ColourSchemes.getInstance().getColourSchemes().iterator();
+    Iterator<ColourSchemeI> schemes = ColourSchemes.getInstance()
+            .getColourSchemes().iterator();
     JalviewColourScheme[] jalviewSchemes = JalviewColourScheme.values();
     int i = 0;
     while (schemes.hasNext() && i < jalviewSchemes.length)
@@ -209,7 +231,7 @@ public class ColourSchemesTest
     }
     af.closeMenuItem_actionPerformed(true);
   }
-  
+
   @Test(groups = "Functional")
   public void testRegisterColourScheme()
   {
@@ -228,9 +250,9 @@ public class ColourSchemesTest
      * set and check Taylor colours
      */
     af.changeColour_actionPerformed(JalviewColourScheme.Taylor.toString());
-    Color taylor1 = sr.getResidueBoxColour(seq, 88); // E 255,0,102
-    Color taylor2 = sr.getResidueBoxColour(seq, 89); // A 204,255,0
-    Color taylor3 = sr.getResidueBoxColour(seq, 90); // G 255,153,0
+    Color taylor1 = sr.getResidueColour(seq, 88, null); // E 255,0,102
+    Color taylor2 = sr.getResidueColour(seq, 89, null); // A 204,255,0
+    Color taylor3 = sr.getResidueColour(seq, 90, null); // G 255,153,0
     assertEquals(taylor1, new Color(255, 0, 102));
     assertEquals(taylor2, new Color(204, 255, 0));
     assertEquals(taylor3, new Color(255, 153, 0));
@@ -239,9 +261,9 @@ public class ColourSchemesTest
      * set and check Zappo colours
      */
     af.changeColour_actionPerformed(JalviewColourScheme.Zappo.toString());
-    Color zappo1 = sr.getResidueBoxColour(seq, 88); // E red
-    Color zappo2 = sr.getResidueBoxColour(seq, 89); // A pink
-    Color zappo3 = sr.getResidueBoxColour(seq, 90); // G magenta
+    Color zappo1 = sr.getResidueColour(seq, 88, null); // E red
+    Color zappo2 = sr.getResidueColour(seq, 89, null); // A pink
+    Color zappo3 = sr.getResidueColour(seq, 90, null); // G magenta
     assertEquals(zappo1, Color.red);
     assertEquals(zappo2, Color.pink);
     assertEquals(zappo3, Color.magenta);
@@ -250,9 +272,9 @@ public class ColourSchemesTest
      * set 'stripy' colours - odd columns are Taylor and even are Zappo 
      */
     af.changeColour_actionPerformed("stripy");
-    Color stripy1 = sr.getResidueBoxColour(seq, 88);
-    Color stripy2 = sr.getResidueBoxColour(seq, 89);
-    Color stripy3 = sr.getResidueBoxColour(seq, 90);
+    Color stripy1 = sr.getResidueColour(seq, 88, null);
+    Color stripy2 = sr.getResidueColour(seq, 89, null);
+    Color stripy3 = sr.getResidueColour(seq, 90, null);
     assertEquals(stripy1, zappo1);
     assertEquals(stripy2, taylor2);
     assertEquals(stripy3, zappo3);
@@ -261,9 +283,9 @@ public class ColourSchemesTest
      * set and check Clustal colours
      */
     af.changeColour_actionPerformed(JalviewColourScheme.Clustal.toString());
-    Color clustal1 = sr.getResidueBoxColour(seq, 88);
-    Color clustal2 = sr.getResidueBoxColour(seq, 89);
-    Color clustal3 = sr.getResidueBoxColour(seq, 90);
+    Color clustal1 = sr.getResidueColour(seq, 88, null);
+    Color clustal2 = sr.getResidueColour(seq, 89, null);
+    Color clustal3 = sr.getResidueColour(seq, 90, null);
     assertEquals(clustal1, ClustalColour.MAGENTA.colour);
     assertEquals(clustal2, ClustalColour.BLUE.colour);
     assertEquals(clustal3, ClustalColour.ORANGE.colour);
@@ -272,9 +294,9 @@ public class ColourSchemesTest
      * set 'MyClustal' colours - uses AWT colour equivalents
      */
     af.changeColour_actionPerformed("MyClustal");
-    Color myclustal1 = sr.getResidueBoxColour(seq, 88);
-    Color myclustal2 = sr.getResidueBoxColour(seq, 89);
-    Color myclustal3 = sr.getResidueBoxColour(seq, 90);
+    Color myclustal1 = sr.getResidueColour(seq, 88, null);
+    Color myclustal2 = sr.getResidueColour(seq, 89, null);
+    Color myclustal3 = sr.getResidueColour(seq, 90, null);
     assertEquals(myclustal1, Color.MAGENTA);
     assertEquals(myclustal2, Color.BLUE);
     assertEquals(myclustal3, Color.ORANGE);