X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;fp=test%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModelTest.java;h=c92daea38158af0362acb10a166b3656e7c1ee46;hb=33cd496c5d0b474f3e9fce004c0558eaaa5c738c;hp=0422537722575020f5c13c840998729dbd07c9eb;hpb=74aef94780598806be39c9c63b85c67d0b01a6e3;p=jalview.git

diff --git a/test/jalview/structures/models/AAStructureBindingModelTest.java b/test/jalview/structures/models/AAStructureBindingModelTest.java
index 0422537..c92daea 100644
--- a/test/jalview/structures/models/AAStructureBindingModelTest.java
+++ b/test/jalview/structures/models/AAStructureBindingModelTest.java
@@ -24,6 +24,7 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
@@ -44,6 +45,7 @@ import jalview.structures.models.AAStructureBindingModel.SuperposeData;
 
 import java.awt.Color;
 import java.util.Arrays;
+import java.util.BitSet;
 import java.util.List;
 
 import org.testng.annotations.BeforeClass;
@@ -169,9 +171,10 @@ public class AAStructureBindingModelTest
       }
 
       @Override
-      public void superposeStructures(AlignmentI[] als, int[] alm,
+      public String superposeStructures(AlignmentI[] als, int[] alm,
               ColumnSelection[] alc)
       {
+        return null;
       }
 
       @Override
@@ -182,7 +185,7 @@ public class AAStructureBindingModelTest
       @Override
       protected StructureMappingcommandSet[] getColourBySequenceCommands(
               String[] files, SequenceRenderer sr, FeatureRenderer fr,
-              AlignmentI alignment)
+              AlignViewportI viewport)
       {
         return null;
       }
@@ -234,11 +237,14 @@ public class AAStructureBindingModelTest
       structs[i] = testee.new SuperposeData(al.getWidth());
     }
     /*
-     * initialise array of 'superposable columns' to true (would be false for
+     * initialise BitSet of 'superposable columns' to true (would be false for
      * hidden columns)
      */
-    boolean[] matched = new boolean[al.getWidth()];
-    Arrays.fill(matched, true);
+    BitSet matched = new BitSet();
+    for (int i = 0; i < al.getWidth(); i++)
+    {
+      matched.set(i);
+    }
 
     int refStructure = testee
             .findSuperposableResidues(al, matched, structs);
@@ -248,12 +254,12 @@ public class AAStructureBindingModelTest
     /*
      * only ungapped, structure-mapped columns are superposable
      */
-    assertFalse(matched[0]); // gap in first sequence
-    assertTrue(matched[1]);
-    assertFalse(matched[2]); // gap in third sequence
-    assertFalse(matched[3]); // gap in fourth sequence
-    assertTrue(matched[4]);
-    assertTrue(matched[5]); // gap in second sequence
+    assertFalse(matched.get(0)); // gap in first sequence
+    assertTrue(matched.get(1));
+    assertFalse(matched.get(2)); // gap in third sequence
+    assertFalse(matched.get(3)); // gap in fourth sequence
+    assertTrue(matched.get(4));
+    assertTrue(matched.get(5)); // gap in second sequence
 
     assertEquals("1YCS", structs[0].pdbId);
     assertEquals("3A6S", structs[1].pdbId);
@@ -278,13 +284,17 @@ public class AAStructureBindingModelTest
       structs[i] = testee.new SuperposeData(al.getWidth());
     }
     /*
-     * initialise array of 'superposable columns' to true (would be false for
+     * initialise BitSet of 'superposable columns' to true (would be false for
      * hidden columns)
      */
-    boolean[] matched = new boolean[al.getWidth()];
-    Arrays.fill(matched, true);
+    BitSet matched = new BitSet();
+    for (int i = 0; i < al.getWidth(); i++)
+    {
+      matched.set(i);
+    }
+
     // treat column 5 of the alignment as hidden
-    matched[4] = false;
+    matched.clear(4);
 
     int refStructure = testee
             .findSuperposableResidues(al, matched, structs);
@@ -292,21 +302,11 @@ public class AAStructureBindingModelTest
     assertEquals(0, refStructure);
 
     // only ungapped, structure-mapped columns are not superposable
-    assertFalse(matched[0]);
-    assertTrue(matched[1]);
-    assertFalse(matched[2]);
-    assertFalse(matched[3]);
-    assertFalse(matched[4]); // superposable, but hidden, column
-    assertTrue(matched[5]);
-  }
-
-  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
-  {
-    return null;
-  }
-
-  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
-  {
-    return null;
+    assertFalse(matched.get(0));
+    assertTrue(matched.get(1));
+    assertFalse(matched.get(2));
+    assertFalse(matched.get(3));
+    assertFalse(matched.get(4)); // superposable, but hidden, column
+    assertTrue(matched.get(5));
   }
 }