Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index a882bce..5ca2cb1 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();
+    ssm = StructureSelectionManager.getStructureSelectionManager(null);
+    ssm.resetAll();
   }
 
   @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);
 
@@ -137,10 +140,11 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
     ssm.registerMappings(set2);
     ssm.registerMappings(set2);
 
-    assertEquals(3, ssm.getSequenceMappings().size());
-    assertTrue(ssm.getSequenceMappings().contains(acf1));
-    assertTrue(ssm.getSequenceMappings().contains(acf2));
-    assertTrue(ssm.getSequenceMappings().contains(acf3));
+    List<AlignedCodonFrame> mappings = ssm.getSequenceMappings();
+    assertEquals(3, mappings.size());
+    assertTrue(mappings.contains(acf1));
+    assertTrue(mappings.contains(acf2));
+    assertTrue(mappings.contains(acf3));
   }
 
   /**
@@ -153,7 +157,7 @@ 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 +201,14 @@ 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) {}; 
     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 },
@@ -216,7 +220,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
     assertEquals(1, pmap.getSeqs().size());
     assertEquals("4IM2|A", pmap.getSeqs().get(0).getName());
 
-    List<int[]> structuremap1 = new ArrayList(
+    List<int[]> structuremap1 = new ArrayList<>(
             sm.getMapping(P4IM2_MISSING)[0]
                     .getPDBResNumRanges(seq.getStart(), seq.getEnd()));
 
@@ -311,8 +315,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
     // positional mapping to atoms for color by structure is still wrong, even
     // though panel looks correct.
 
-    StructureMappingcommandSet smcr[] = JmolCommands
-            .getColourBySequenceCommand(apssm,
+    String[] smcr = new JmolCommands().colourBySequence(apssm,
             new String[]
             { pdbe.getFile() },
             new SequenceI[][]
@@ -320,12 +323,10 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
                     new SequenceRenderer(alf.alignPanel.getAlignViewport()),
                     alf.alignPanel);
     // Expected - all residues are white
-    for (StructureMappingcommandSet smm : smcr)
+    for (String c : smcr)
     {
-      for (String c : smm.commands)
-      {
-        System.out.println(c);
-      }
+      assertTrue(c.contains("color[255,255,255]"));
+      System.out.println(c);
     }
   }
 
@@ -349,6 +350,9 @@ 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" + 
@@ -413,7 +417,7 @@ 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())
     {