JAL-2089 Merge branch releases/Release_2_10_Branch to master

[jalview.git] / test / jalview / structure / StructureSelectionManagerTest.java

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 52b1323..2556ab1 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -28,15 +28,15 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.FormatAdapter;
+import jalview.io.StructureFile;
+import jalview.util.MapList;
 
-import java.util.HashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import MCview.PDBfile;
-
 public class StructureSelectionManagerTest
 {
   private StructureSelectionManager ssm;
@@ -44,6 +44,7 @@ public class StructureSelectionManagerTest
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
+    StructureImportSettings.setShowSeqFeatures(true);
     ssm = new StructureSelectionManager();
   }
 
@@ -51,37 +52,47 @@ public class StructureSelectionManagerTest
   public void testRegisterMapping()
   {
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
 
     ssm.registerMapping(acf1);
-    assertEquals(1, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
+    assertEquals(1, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
 
     ssm.registerMapping(acf2);
-    assertEquals(2, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertTrue(ssm.seqmappings.contains(acf2));
+    assertEquals(2, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
+    assertTrue(ssm.getSequenceMappings().contains(acf2));
 
     /*
      * Re-adding the first mapping does nothing
      */
     ssm.registerMapping(acf1);
-    assertEquals(2, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertTrue(ssm.seqmappings.contains(acf2));
+    assertEquals(2, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
+    assertTrue(ssm.getSequenceMappings().contains(acf2));
   }
 
   @Test(groups = { "Functional" })
   public void testRegisterMappings()
   {
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
+    acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
+            new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
 
-    Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
     set1.add(acf1);
     set1.add(acf2);
-    Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> set2 = new ArrayList<AlignedCodonFrame>();
     set2.add(acf2);
     set2.add(acf3);
 
@@ -93,10 +104,10 @@ public class StructureSelectionManagerTest
     ssm.registerMappings(set2);
     ssm.registerMappings(set2);
 
-    assertEquals(3, ssm.seqmappings.size());
-    assertTrue(ssm.seqmappings.contains(acf1));
-    assertTrue(ssm.seqmappings.contains(acf2));
-    assertTrue(ssm.seqmappings.contains(acf3));
+    assertEquals(3, ssm.getSequenceMappings().size());
+    assertTrue(ssm.getSequenceMappings().contains(acf1));
+    assertTrue(ssm.getSequenceMappings().contains(acf2));
+    assertTrue(ssm.getSequenceMappings().contains(acf3));
   }
 
   /**
@@ -112,7 +123,7 @@ public class StructureSelectionManagerTest
     StructureSelectionManager sm = new StructureSelectionManager();
     sm.setProcessSecondaryStructure(true);
     sm.setAddTempFacAnnot(true);
-    PDBfile pmap = sm.setMapping(true, new SequenceI[] { seq },
+    StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
             new String[] { null }, "examples/1gaq.txt", FormatAdapter.FILE);
     assertTrue(pmap != null);