Merge branch 'develop' of https://source.jalview.org/git/jalview into develop

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

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index ddee3ac..baaa96b 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -28,6 +28,8 @@ 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.ArrayList;
 import java.util.List;
@@ -35,8 +37,6 @@ 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();
   }
 
@@ -51,7 +52,11 @@ 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.getSequenceMappings().size());
@@ -75,8 +80,14 @@ public class StructureSelectionManagerTest
   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));
 
     List<AlignedCodonFrame> set1 = new ArrayList<AlignedCodonFrame>();
     set1.add(acf1);
@@ -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);
 
@@ -127,7 +138,7 @@ public class StructureSelectionManagerTest
     SequenceFeature sf = pmap.getSeqs().get(0).getSequenceFeatures()[0];
     assertEquals("RESNUM", sf.getType());
     assertEquals("1gaq", sf.getFeatureGroup());
-    assertEquals("GLU:  19  1gaqA", sf.getDescription());
+    assertEquals("GLU:19 1gaqA", sf.getDescription());
 
     /*
      * Verify a RESNUM sequence feature in the StructureSelectionManager mapped
@@ -137,6 +148,6 @@ public class StructureSelectionManagerTest
     sf = map.sequence.getSequenceFeatures()[0];
     assertEquals("RESNUM", sf.getType());
     assertEquals("1gaq", sf.getFeatureGroup());
-    assertEquals("ALA:   1  1gaqB", sf.getDescription());
+    assertEquals("ALA:1 1gaqB", sf.getDescription());
   }
 }