JAL-2570 don't zap group colour scheme when mapping over split frame

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 8c29ca5..463b909 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -110,13 +110,23 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   private boolean normaliseSequenceLogo;
 
-  /**
-   * @return the includeAllConsSymbols
+  /*
+   * visibility of rows or represented rows covered by group
    */
-  public boolean isShowSequenceLogo()
-  {
-    return showSequenceLogo;
-  }
+  private boolean hidereps = false;
+
+  /*
+   * visibility of columns intersecting this group
+   */
+  private boolean hidecols = false;
+
+  AlignmentAnnotation consensus = null;
+
+  AlignmentAnnotation conservation = null;
+
+  private boolean showConsensusHistogram;
+
+  private AnnotatedCollectionI context;
 
   /**
    * Creates a new SequenceGroup object.
@@ -178,13 +188,17 @@ public class SequenceGroup implements AnnotatedCollectionI
       colourText = seqsel.colourText;
       startRes = seqsel.startRes;
       endRes = seqsel.endRes;
-      cs = seqsel.cs;
+      cs = new ResidueShader(seqsel.getColourScheme());
       if (seqsel.description != null)
       {
         description = new String(seqsel.description);
       }
       hidecols = seqsel.hidecols;
       hidereps = seqsel.hidereps;
+      showNonconserved = seqsel.showNonconserved;
+      showSequenceLogo = seqsel.showSequenceLogo;
+      normaliseSequenceLogo = seqsel.normaliseSequenceLogo;
+      showConsensusHistogram = seqsel.showConsensusHistogram;
       idColour = seqsel.idColour;
       outlineColour = seqsel.outlineColour;
       seqrep = seqsel.seqrep;
@@ -201,6 +215,11 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
+  public boolean isShowSequenceLogo()
+  {
+    return showSequenceLogo;
+  }
+
   public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
   {
     int iSize = sequences.size();
@@ -957,11 +976,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * visibility of rows or represented rows covered by group
-   */
-  private boolean hidereps = false;
-
-  /**
    * set visibility of sequences covered by (if no sequence representative is
    * defined) or represented by this group.
    * 
@@ -983,11 +997,6 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * visibility of columns intersecting this group
-   */
-  private boolean hidecols = false;
-
-  /**
    * set intended visibility of columns covered by this group
    * 
    * @param visibility
@@ -1049,13 +1058,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     this.showNonconserved = displayNonconserved;
   }
 
-  AlignmentAnnotation consensus = null, conservation = null;
-
-  /**
-   * flag indicating if consensus histogram should be rendered
-   */
-  private boolean showConsensusHistogram;
-
   /**
    * set this alignmentAnnotation object as the one used to render consensus
    * annotation
@@ -1346,8 +1348,6 @@ public class SequenceGroup implements AnnotatedCollectionI
     }
   }
 
-  private AnnotatedCollectionI context;
-
   /**
    * Sets the alignment or group context for this group, and whether it is
    * defined as a group

diff --git a/test/jalview/datamodel/SequenceGroupTest.java b/test/jalview/datamodel/SequenceGroupTest.java
index 7837b49..f6d4028 100644 (file)
--- a/test/jalview/datamodel/SequenceGroupTest.java
+++ b/test/jalview/datamodel/SequenceGroupTest.java
@@ -3,17 +3,21 @@ 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.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
 
-import org.testng.annotations.Test;
+import java.awt.Color;
 
 import junit.extensions.PA;
 
+import org.testng.annotations.Test;
+
 public class SequenceGroupTest
 {
   @Test(groups={"Functional"})
@@ -217,6 +221,73 @@ 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());
+    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());
+    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());
   }
 }