From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 28 Nov 2018 15:22:28 +0000 (+0000)
Subject: JAL-3164 redraw complement overview on hide columns
X-Git-Tag: Release_2_11_0~17^2~90^2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=06476b6d02ef690bf684905cba39eb7b5db7525b;p=jalview.git

JAL-3164 redraw complement overview on hide columns
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3ba35b6..3e0856a 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1922,9 +1922,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setHiddenColumns(HiddenColumns cols)
+  public boolean setHiddenColumns(HiddenColumns cols)
   {
+    boolean changed = cols == null ? hiddenCols != null
+            : !cols.equals(hiddenCols);
     hiddenCols = cols;
+    return changed;
   }
 
   @Override
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 5fb16d6..9c73873 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -581,11 +581,13 @@ public interface AlignmentI extends AnnotatedCollectionI
   AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
 
   /**
-   * Set the hidden columns collection on the alignment
+   * Set the hidden columns collection on the alignment. Answers true if the
+   * hidden column selection changed, else false.
    * 
    * @param cols
+   * @return
    */
-  public void setHiddenColumns(HiddenColumns cols);
+  public boolean setHiddenColumns(HiddenColumns cols);
 
   /**
    * Set the first sequence as representative and hide its insertions. Typically
diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index a7e93da..2d43f02 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -469,6 +469,10 @@ public class HiddenColumns
     }
   }
 
+  /**
+   * Answers true if obj is an instance of HiddenColumns, and holds the same
+   * array of start-end column ranges as this, else answers false
+   */
   @Override
   public boolean equals(Object obj)
   {
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 8b2e7bc..2d3eb10 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -2280,7 +2280,7 @@ public class SeqPanel extends JPanel
     HiddenColumns hs = new HiddenColumns();
     MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
     av.setColumnSelection(cs);
-    av.getAlignment().setHiddenColumns(hs);
+    boolean hiddenChanged = av.getAlignment().setHiddenColumns(hs);
 
     // lastly, update any dependent dialogs
     if (ap.getCalculationDialog() != null)
@@ -2288,7 +2288,11 @@ public class SeqPanel extends JPanel
       ap.getCalculationDialog().validateCalcTypes();
     }
 
-    PaintRefresher.Refresh(this, av.getSequenceSetId());
+    /*
+     * repaint alignment, and also Overview or Structure
+     * if hidden column selection has changed
+     */
+    ap.paintAlignment(hiddenChanged, hiddenChanged);
 
     return true;
   }
diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 1d1ebd6..8aed114 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1484,4 +1484,52 @@ public class AlignmentTest
     assertEquals(".JKLMNO", seq2.getSequenceAsString());
     assertEquals(".PQR...", seq3.getSequenceAsString());
   }
+
+  /**
+   * Test for setHiddenColumns, to check it returns true if the hidden columns
+   * have changed, else false
+   */
+  @Test(groups = { "Functional" })
+  public void testSetHiddenColumns()
+  {
+    AlignmentI al = new Alignment(new SequenceI[] {});
+    assertFalse(al.getHiddenColumns().hasHiddenColumns());
+
+    HiddenColumns hc = new HiddenColumns();
+    assertFalse(al.setHiddenColumns(hc)); // no change
+    assertSame(hc, al.getHiddenColumns());
+
+    hc.hideColumns(2, 4);
+    assertTrue(al.getHiddenColumns().hasHiddenColumns());
+
+    /*
+     * set a different object but with the same columns hidden
+     */
+    HiddenColumns hc2 = new HiddenColumns();
+    hc2.hideColumns(2, 4);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+    assertSame(hc2, al.getHiddenColumns());
+
+    assertTrue(al.setHiddenColumns(null));
+    assertNull(al.getHiddenColumns());
+    assertTrue(al.setHiddenColumns(hc));
+    assertSame(hc, al.getHiddenColumns());
+
+    al.getHiddenColumns().hideColumns(10, 12);
+    hc2.hideColumns(10, 12);
+    assertFalse(al.setHiddenColumns(hc2)); // no change
+
+    /*
+     * hide columns 15-16 then 17-18 in hc
+     * hide columns 15-18 in hc2
+     * these are not now 'equal' objects even though they
+     * represent the same set of columns
+     */
+    assertSame(hc2, al.getHiddenColumns());
+    hc.hideColumns(15, 16);
+    hc.hideColumns(17, 18);
+    hc2.hideColumns(15, 18);
+    assertFalse(hc.equals(hc2));
+    assertTrue(al.setHiddenColumns(hc)); // 'changed'
+  }
 }