JAL-2349 JAL-3855 helper method to make it easy to transfer a single ‘reference annot...

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

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index 66514f9..ac8235d 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -25,6 +25,18 @@ import static org.testng.Assert.assertNotNull;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
@@ -50,18 +62,6 @@ import jalview.util.MapList;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.sifts.SiftsSettings;
 
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
-import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 @Test(singleThreaded = true)
 public class StructureSelectionManagerTest extends Jalview2xmlBase
 {
@@ -164,7 +164,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
     sm.setAddTempFacAnnot(true);
     StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
             new String[]
-            { null }, "examples/1gaq.txt", DataSourceType.FILE);
+            { null }, "examples/1gaq.txt", DataSourceType.FILE, null, null);
     assertTrue(pmap != null);
 
     assertEquals(3, pmap.getSeqs().size());
@@ -220,7 +220,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
     sm.setAddTempFacAnnot(true);
     StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
             new String[]
-            { null }, P4IM2_MISSING, DataSourceType.FILE);
+            { null }, P4IM2_MISSING, DataSourceType.FILE, null, null);
     assertTrue(pmap != null);
 
     assertEquals(1, pmap.getSeqs().size());
@@ -433,7 +433,7 @@ public class StructureSelectionManagerTest extends Jalview2xmlBase
       AlignmentUtils.findAddableReferenceAnnotations(al.getSequences(),
               tipEntries, candidates, al);
       AlignmentUtils.addReferenceAnnotations(candidates, al, null);
-
+      // FAILS BECAUSE LABEL HAS PDB ID STRING
       if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator()
               .hasNext())
       {