JAL-1270 more fix for failing Functional test

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

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 44a19f3..999d158 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.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.structure;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -8,15 +28,14 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.FormatAdapter;
+import jalview.io.StructureFile;
 
-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;
@@ -24,6 +43,7 @@ public class StructureSelectionManagerTest
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
+    StructureViewSettings.setShowSeqFeatures(true);
     ssm = new StructureSelectionManager();
   }
 
@@ -34,21 +54,21 @@ public class StructureSelectionManagerTest
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
 
     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" })
@@ -58,10 +78,10 @@ public class StructureSelectionManagerTest
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
 
-    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);
 
@@ -73,10 +93,10 @@ 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));
   }
 
   /**
@@ -92,7 +112,7 @@ 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);