JAL-2835 spike updated with latest

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

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 346d74d..5ed0cac 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -46,6 +46,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
+import jalview.viewmodel.ViewportRanges;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -74,6 +75,13 @@ public class AlignViewportTest
   {
     Jalview.main(new String[] { "-nonews", "-props",
         "test/jalview/testProps.jvprops" });
+
+    /*
+     * remove any sequence mappings left lying around by other tests
+     */
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+    ssm.resetAll();
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -88,57 +96,6 @@ public class AlignViewportTest
     testee = new AlignViewport(al);
   }
 
-  @Test(groups = { "Functional" })
-  public void testCollateForPdb()
-  {
-    // JBP: What behaviour is this supposed to test ?
-    /*
-     * Set up sequence pdb ids
-     */
-    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 1abcB, seq2 to 2abcC, none to 3abcD
-     */
-    al.getSequenceAt(0).getDatasetSequence()
-            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
-    al.getSequenceAt(2).getDatasetSequence()
-            .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
-    al.getSequenceAt(1).getDatasetSequence()
-            .addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
-    /*
-     * Add a second chain PDB xref to Seq2 - should not result in a duplicate in
-     * the results
-     */
-    al.getSequenceAt(1).getDatasetSequence()
-            .addPDBId(new PDBEntry("2ABC", "D", Type.PDB, "2ABC.pdb"));
-    /*
-     * Seq3 refers to 3abc - this does not match 3ABC (as the code stands)
-     */
-    al.getSequenceAt(2).getDatasetSequence()
-            .addPDBId(new PDBEntry("3abc", "D", Type.PDB, "3ABC.pdb"));
-
-    /*
-     * run method under test
-     */
-    SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
-        pdb3 });
-
-    // seq1 and seq3 refer to PDBEntry[0]
-    assertEquals(2, seqs[0].length);
-    assertSame(al.getSequenceAt(0), seqs[0][0]);
-    assertSame(al.getSequenceAt(2), seqs[0][1]);
-
-    // seq2 refers to PDBEntry[1]
-    assertEquals(1, seqs[1].length);
-    assertSame(al.getSequenceAt(1), seqs[1][0]);
-
-    // no sequence refers to PDBEntry[2]
-    assertEquals(0, seqs[2].length);
-  }
-
   /**
    * Test that a mapping is not deregistered when a second view is closed but
    * the first still holds a reference to the mapping
@@ -172,18 +129,19 @@ public class AlignViewportTest
      */
     StructureSelectionManager ssm = StructureSelectionManager
             .getStructureSelectionManager(Desktop.instance);
-    assertEquals(2, ssm.getSequenceMappings().size());
-    assertTrue(ssm.getSequenceMappings().contains(acf1));
-    assertTrue(ssm.getSequenceMappings().contains(acf2));
+    List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
+    assertEquals(2, sequenceMappings.size());
+    assertTrue(sequenceMappings.contains(acf1));
+    assertTrue(sequenceMappings.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.getSequenceMappings().size());
-    assertTrue(ssm.getSequenceMappings().contains(acf1));
-    assertTrue(ssm.getSequenceMappings().contains(acf2));
+    assertEquals(2, sequenceMappings.size());
+    assertTrue(sequenceMappings.contains(acf1));
+    assertTrue(sequenceMappings.contains(acf2));
   }
 
   /**
@@ -469,4 +427,46 @@ public class AlignViewportTest
     SequenceI cons = testme.getConsensusSeq();
     assertEquals("A-C", cons.getSequenceAsString());
   }
+
+  @Test(groups = { "Functional" })
+  public void testHideRevealSequences()
+  {
+    ViewportRanges ranges = testee.getRanges();
+    assertEquals(3, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(2, ranges.getEndSeq());
+
+    /*
+     * hide first sequence
+     */
+    testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) });
+    assertEquals(2, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(1, ranges.getEndSeq());
+
+    /*
+     * reveal hidden sequences above the first
+     */
+    testee.showSequence(0);
+    assertEquals(3, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(2, ranges.getEndSeq());
+
+    /*
+     * hide first and third sequences
+     */
+    testee.hideSequence(new SequenceI[] { al.getSequenceAt(0),
+        al.getSequenceAt(2) });
+    assertEquals(1, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(0, ranges.getEndSeq());
+
+    /*
+     * reveal all hidden sequences
+     */
+    testee.showAllHiddenSeqs();
+    assertEquals(3, al.getHeight());
+    assertEquals(0, ranges.getStartSeq());
+    assertEquals(2, ranges.getEndSeq());
+  }
 }