spike branch updated from latest features/JAL-2446

[jalview.git] / test / jalview / datamodel / SequenceGroupTest.java

diff --git a/test/jalview/datamodel/SequenceGroupTest.java b/test/jalview/datamodel/SequenceGroupTest.java
index 6e1c2db..b0af5c8 100644 (file)
--- a/test/jalview/datamodel/SequenceGroupTest.java
+++ b/test/jalview/datamodel/SequenceGroupTest.java
@@ -3,12 +3,18 @@ package jalview.datamodel;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 import static org.testng.Assert.fail;
 
+import jalview.analysis.Conservation;
 import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+
+import java.awt.Color;
+import java.util.Collections;
 
 import junit.extensions.PA;
 
@@ -121,13 +127,32 @@ public class SequenceGroupTest
     PA.setValue(sg2, "context", sg2);
     try
     {
-      sg3.setContext(sg2); // circular reference in sg2
+      sg3.setContext(sg2, false); // circular reference in sg2
       fail("Expected exception");
     } catch (IllegalArgumentException e)
     {
       // expected
       assertNull(sg3.getContext());
     }
+
+    // test isDefined setting behaviour
+    sg2 = new SequenceGroup();
+    sg1.setContext(null, false);
+    assertFalse(sg1.isDefined());
+
+    sg1.setContext(sg2, false);
+    assertFalse(sg1.isDefined());
+
+    sg1.setContext(sg2, true);
+    assertTrue(sg1.isDefined());
+
+    // setContext without defined parameter does not change isDefined
+    sg1.setContext(null);
+    assertTrue(sg1.isDefined());
+
+    sg1.setContext(null, false);
+    sg1.setContext(sg2);
+    assertFalse(sg1.isDefined());
   }
 
   @Test(groups = { "Functional" })
@@ -198,6 +223,82 @@ public class SequenceGroupTest
     assertTrue(sg2.contains(seq2, 8));
     sg2.deleteSequence(seq2, false);
     assertFalse(sg2.contains(seq2));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCopyConstructor()
+  {
+    SequenceI seq = new Sequence("seq", "ABC");
+    SequenceGroup sg = new SequenceGroup();
+    sg.addSequence(seq, false);
+    sg.setName("g1");
+    sg.setDescription("desc");
+    sg.setColourScheme(new PIDColourScheme());
+    Conservation cons = new Conservation("Cons", 2,
+            Collections.<SequenceI> emptyList(), 3, 12);
+    PA.setValue(cons, "consSequence", new Sequence("s", "abc"));
+    sg.getGroupColourScheme().setConservation(cons);
+    sg.getGroupColourScheme().setConsensus(new Profiles(null));
+    sg.setDisplayBoxes(false);
+    sg.setDisplayText(false);
+    sg.setColourText(true);
+    sg.isDefined = true;
+    sg.setShowNonconserved(true);
+    sg.setOutlineColour(Color.red);
+    sg.setIdColour(Color.blue);
+    sg.thresholdTextColour = 1;
+    sg.textColour = Color.orange;
+    sg.textColour2 = Color.yellow;
+    sg.setIgnoreGapsConsensus(false);
+    sg.setshowSequenceLogo(true);
+    sg.setNormaliseSequenceLogo(true);
+    sg.setHidereps(true);
+    sg.setHideCols(true);
+    sg.setShowConsensusHistogram(true);
+    sg.setContext(new SequenceGroup());
+
+    SequenceGroup sg2 = new SequenceGroup(sg);
+    assertEquals(sg2.getName(), sg.getName());
+    assertEquals(sg2.getDescription(), sg.getDescription());
+    assertNotSame(sg2.getGroupColourScheme(), sg.getGroupColourScheme());
+    assertSame(sg2.getColourScheme(), sg.getColourScheme());
+    assertSame(PA.getValue(sg2.getGroupColourScheme(), "consensus"),
+            PA.getValue(sg.getGroupColourScheme(), "consensus"));
+    assertSame(PA.getValue(sg2.getGroupColourScheme(), "conservation"),
+            PA.getValue(sg.getGroupColourScheme(), "conservation"));
+    assertEquals(sg2.getDisplayBoxes(), sg.getDisplayBoxes());
+    assertEquals(sg2.getDisplayText(), sg.getDisplayText());
+    assertEquals(sg2.getColourText(), sg.getColourText());
+    assertEquals(sg2.getShowNonconserved(), sg.getShowNonconserved());
+    assertEquals(sg2.getOutlineColour(), sg.getOutlineColour());
+    assertEquals(sg2.getIdColour(), sg.getIdColour());
+    assertEquals(sg2.thresholdTextColour, sg.thresholdTextColour);
+    assertEquals(sg2.textColour, sg.textColour);
+    assertEquals(sg2.textColour2, sg.textColour2);
+    assertEquals(sg2.getIgnoreGapsConsensus(), sg.getIgnoreGapsConsensus());
+    assertEquals(sg2.isShowSequenceLogo(), sg.isShowSequenceLogo());
+    assertEquals(sg2.isNormaliseSequenceLogo(),
+            sg.isNormaliseSequenceLogo());
+    assertEquals(sg2.isHidereps(), sg.isHidereps());
+    assertEquals(sg2.isHideCols(), sg.isHideCols());
+    assertEquals(sg2.isShowConsensusHistogram(),
+            sg.isShowConsensusHistogram());
+
+    /*
+     * copy of sequences
+     */
+    assertNotSame(sg2.getSequences(), sg.getSequences());
+    assertEquals(sg2.getSequences(), sg.getSequences());
 
+    /*
+     * isDefined should only be set true when a new group is added to
+     * an alignment, not in the copy constructor
+     */
+    assertFalse(sg2.isDefined());
+
+    /*
+     * context should be set explicitly, not by copy
+     */
+    assertNull(sg2.getContext());
   }
 }