JAL-3253 ApplicationSingletonProvider replaces Instance

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

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index a882bce..d8f7314 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -46,6 +47,7 @@ import jalview.io.FileLoader;
 import jalview.io.Jalview2xmlBase;
 import jalview.io.StructureFile;
 import jalview.util.MapList;
+import jalview.ws.DBRefFetcher;
 import jalview.ws.sifts.SiftsSettings;
 
 import java.util.ArrayList;
@@ -78,7 +80,8 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
   public void setUp()
   {
     StructureImportSettings.setShowSeqFeatures(true);
-    ssm = new StructureSelectionManager();
+    StructureSelectionManager.release(null);
+    ssm = StructureSelectionManager.getStructureSelectionManager(null);
   }
 
   @Test(groups = { "Functional" })
@@ -122,10 +125,10 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
     acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
             new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
 
-    List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> set1 = new ArrayList<>();
     set1.add(acf1);
     set1.add(acf2);
-    List<AlignedCodonFrame> set2 = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> set2 = new ArrayList<>();
     set2.add(acf2);
     set2.add(acf3);
 
@@ -153,7 +156,8 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
     SequenceI seq = new Sequence(
             "1GAQ|B",
             "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
-    StructureSelectionManager sm = new StructureSelectionManager();
+    StructureSelectionManager sm = StructureSelectionManager
+            .getStructureSelectionManager(null);
     sm.setProcessSecondaryStructure(true);
     sm.setAddTempFacAnnot(true);
     StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
@@ -197,14 +201,15 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
   {
     // for some reason 'BeforeMethod' (which should be inherited from
     // Jalview2XmlBase isn't always called)...
-    Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.getInstance().closeAll_actionPerformed(null);
     try { 
       Thread.sleep(200);
-    } catch (Exception foo) {}; 
+    } catch (Exception foo) {} 
     SequenceI seq = new Sequence("4IM2|A",
             "LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE");
     String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb";
-    StructureSelectionManager sm = new StructureSelectionManager();
+    StructureSelectionManager sm = StructureSelectionManager
+            .getStructureSelectionManager(null);
     sm.setProcessSecondaryStructure(true);
     sm.setAddTempFacAnnot(true);
     StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
@@ -349,6 +354,9 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
   public void testAssociatedMappingToSubSeq() throws Exception
   {
 
+    // currently this test fails if trimming is enabled
+    Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
+            Boolean.FALSE.toString());
     String TEMP_FACTOR_AA="Temperature Factor";
     String PDBID = "4IM2";
     String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" + 
@@ -401,7 +409,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
             ">TBK1_HUMAN/470-502 Serine/threonine-protein kinase TBK1\nFCIRNIEKTVKVYEKLMKINLEAAELGEISDIH",
             DataSourceType.PASTE);
     Desktop.addInternalFrame(alf, "Foo", 800, 600);
-    ;
+    
     AlignmentI al = alf.getViewport().getAlignment();
     SequenceI seq = al.getSequenceAt(0);
     assertEquals(470, seq.getStart());
@@ -413,7 +421,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
             PDBID);
 
     AlignmentAnnotation subseq_tf=null;
-    assertTrue(seq.getDBRefs() != null && seq.getDBRefs().length > 0);
+    assertTrue(seq.getDBRefs() != null && seq.getDBRefs().size() > 0);
     
     if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
     {
@@ -454,14 +462,12 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
         Assert.assertNull(subseq,
                 "Expected no annotation transferred at position " + p);
       }
-      ;
       if (orig != null)
       {
         Assert.assertNotNull(subseq,
                 "Expected annotation transfer at position " + p);
         assertEquals(orig.value, subseq.value);
       }
-      ;
 
     }
   }
@@ -482,7 +488,6 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
     } catch (InterruptedException q)
     {
     }
-    ;
     Assert.assertTrue(schoose.selectStructure(pDBID),
             "Couldn't select structure via structure chooser: " + pDBID);
     schoose.showStructures(true);