JAL-1270 use test properties file

[jalview.git] / test / jalview / gui / AlignViewportTest.java

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 0a53f10..eff3fdc 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -36,9 +36,10 @@ import jalview.datamodel.SequenceI;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.MapList;
 
-import java.util.LinkedHashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
@@ -73,15 +74,16 @@ public class AlignViewportTest
   @Test(groups = { "Functional" })
   public void testCollateForPdb()
   {
+    // JBP: What behaviour is this supposed to test ?
     /*
      * Set up sequence pdb ids
      */
-    PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb");
-    PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb");
-    PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb");
+    PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb");
+    PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb");
+    PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb");
 
     /*
-     * seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC
+     * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD
      */
     al.getSequenceAt(0).getDatasetSequence()
             .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
@@ -133,10 +135,15 @@ public class AlignViewportTest
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq1\nCAGT\n", FormatAdapter.PASTE);
 
+    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
+            1, 1));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
+            1, 1));
 
-    Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
     mappings.add(acf1);
     mappings.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings);
@@ -148,18 +155,18 @@ public class AlignViewportTest
      */
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
-    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));
 
     /*
      * Close the second view. Verify that mappings are not removed as the first
      * view still holds a reference to them.
      */
     af1.closeMenuItem_actionPerformed(false);
-    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));
   }
 
   /**
@@ -178,16 +185,26 @@ public class AlignViewportTest
             ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq2\nDGEL\n", FormatAdapter.PASTE);
-
+    SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
+    SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
+    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
+    SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
+    // need to be distinct
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 12 }, 1, 3));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 12 }, 1, 3));
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
+    acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+        12 }, 1, 1));
 
-    Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
     mappings1.add(acf1);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
 
-    Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@ -196,7 +213,7 @@ public class AlignViewportTest
      * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
      */
 
-    Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
     assertEquals(0, ssmMappings.size());
     ssm.registerMapping(acf1);
     assertEquals(1, ssmMappings.size());
@@ -231,17 +248,27 @@ public class AlignViewportTest
             ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq2\nDGEL\n", FormatAdapter.PASTE);
-
+    SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
+    SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
+    SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
+    SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
+    // need to be distinct
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
+    acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 12 }, 1, 3));
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
+    acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
+            new int[] { 1, 12 }, 1, 3));
     AlignedCodonFrame acf3 = new AlignedCodonFrame();
+    acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+        12 }, 1, 1));
 
-    Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
     mappings1.add(acf1);
     mappings1.add(acf2);
     af1.getViewport().getAlignment().setCodonFrames(mappings1);
 
-    Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+    List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
     mappings2.add(acf2);
     mappings2.add(acf3);
     af2.getViewport().getAlignment().setCodonFrames(mappings2);
@@ -250,7 +277,7 @@ public class AlignViewportTest
      * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
      */
 
-    Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+    List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
     assertEquals(0, ssmMappings.size());
     ssm.registerMapping(acf1);
     assertEquals(1, ssmMappings.size());