Merge branch 'bug/JAL-3099alignmentVisibleWidth' into merge/JAL-3099

Conflicts:
	src/jalview/gui/AlignmentPanel.java
	src/jalview/gui/IdCanvas.java
	test/jalview/datamodel/AlignmentTest.java

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 83d8ade..e9081b0 100644 (file)
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -669,14 +669,9 @@ public class AlignmentPanel extends Panel
     }
     else
     {
-      int width = av.getAlignment().getWidth();
+      int width = av.getAlignment().getVisibleWidth();
       int height = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns())
-      {
-        width = av.getAlignment().getHiddenColumns()
-                .absoluteToVisibleColumn(width);
-      }
       if (x < 0)
       {
         x = 0;

diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 296f898..ef80616 100755 (executable)
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -280,15 +280,9 @@ public class IdCanvas extends Panel implements ViewportListenerI
   protected void drawIdsWrapped(int starty, final boolean doHiddenCheck,
           boolean hiddenRows)
   {
-    int maxwidth = av.getAlignment().getWidth();
+    int maxwidth = av.getAlignment().getVisibleWidth();
     int alheight = av.getAlignment().getHeight();
 
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
-
     int annotationHeight = 0;
     AnnotationLabels labels = null;
 

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 35d73de..96eb6b9 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -136,13 +136,6 @@ public class SeqCanvas extends Panel implements ViewportListenerI
               .visibleToAbsoluteColumn(endx);
     }
 
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
-
     // WEST SCALE
     for (int i = 0; i < av.getAlignment().getHeight(); i++)
     {
@@ -450,13 +443,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     int endx;
     int ypos = hgap;
   
-    int maxwidth = av.getAlignment().getWidth();
-  
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
   
     while ((ypos <= canvasHeight) && (startRes < maxwidth))
     {
@@ -565,7 +552,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
       int blockEnd;
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      VisibleContigsIterator regions = (VisibleContigsIterator) hidden
+      VisibleContigsIterator regions = hidden
               .getVisContigsIterator(startRes, endRes + 1, true);
 
       while (regions.hasNext())

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3e0856a..0f51b7e 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -720,31 +720,17 @@ public class Alignment implements AlignmentI
   
     return maxLength;
   }
-  /*
+
   @Override
-  public int getWidth()
+  public int getVisibleWidth()
   {
-    final Wrapper temp = new Wrapper();
-  
-    forEachSequence(new Consumer<SequenceI>()
+    int w = getWidth();
+    if (hiddenCols != null)
     {
-      @Override
-      public void accept(SequenceI s)
-      {
-        if (s.getLength() > temp.inner)
-        {
-          temp.inner = s.getLength();
-        }
-      }
-    }, 0, sequences.size() - 1);
-  
-    return temp.inner;
+      w -= hiddenCols.getSize();
+    }
+    return w;
   }
-  
-  public static class Wrapper
-  {
-    public int inner;
-  }*/
 
   /**
    * DOCUMENT ME!

diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index 9c73873..93a2456 100755 (executable)
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -48,15 +48,29 @@ public interface AlignmentI extends AnnotatedCollectionI
 
   /**
    * 
-   * Calculates the maximum width of the alignment, including gaps.
+   * Answers the width of the alignment, including gaps, that is, the length of
+   * the longest sequence, or -1 if there are no sequences. Avoid calling this
+   * method repeatedly where possible, as it has to perform a calculation. Note
+   * that this width includes any hidden columns.
    * 
-   * @return Greatest sequence length within alignment, or -1 if no sequences
-   *         present
+   * @return
+   * @see AlignmentI#getVisibleWidth()
    */
   @Override
   int getWidth();
 
   /**
+   * 
+   * Answers the visible width of the alignment, including gaps, that is, the
+   * length of the longest sequence, excluding any hidden columns. Answers -1 if
+   * there are no sequences. Avoid calling this method repeatedly where
+   * possible, as it has to perform a calculation.
+   * 
+   * @return
+   */
+  int getVisibleWidth();
+
+  /**
    * Calculates if this set of sequences (visible and invisible) are all the
    * same length
    * 

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 606e2e7..b080a25 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3049,6 +3049,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     viewport.expandColSelection(sg, false);
     viewport.hideAllSelectedSeqs();
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }
@@ -3073,6 +3074,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void hideSelColumns_actionPerformed(ActionEvent e)
   {
     viewport.hideSelectedColumns();
+    alignPanel.updateLayout();
     alignPanel.paintAlignment(true, true);
     viewport.sendSelection();
   }

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 82e2113..51e703d 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -637,16 +637,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
     }
     else
     {
-      int width = av.getAlignment().getWidth();
+      int width = av.getAlignment().getVisibleWidth();
       int height = av.getAlignment().getHeight();
 
-      if (av.hasHiddenColumns())
-      {
-        // reset the width to exclude hidden columns
-        width = av.getAlignment().getHiddenColumns()
-                .absoluteToVisibleColumn(width);
-      }
-
       hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
       vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
 
@@ -958,8 +951,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
 
-    final int alignmentWidth = av.getAlignment().getWidth();
-    final int pagesWide = (alignmentWidth / totalRes) + 1;
+    final int alignmentWidth = av.getAlignment().getVisibleWidth();
+    int pagesWide = (alignmentWidth / totalRes) + 1;
 
     final int startRes = (pageIndex % pagesWide) * totalRes;
     final int endRes = Math.min(startRes + totalRes - 1,
@@ -1076,12 +1069,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     int idWidth = getVisibleIdWidth(false);
 
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth) - 1;
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     int resWidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(pageWidth - idWidth);
@@ -1243,12 +1231,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public AlignmentDimension getAlignmentDimension()
   {
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
             + getScalePanel().getHeight();

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index cf88c90..951db78 100755 (executable)
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -380,12 +380,6 @@ public class IdCanvas extends JPanel implements ViewportListenerI
     int alignmentWidth = alignViewport.getAlignment().getWidth();
     final int alheight = alignViewport.getAlignment().getHeight();
 
-    if (alignViewport.hasHiddenColumns())
-    {
-      alignmentWidth = alignViewport.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(alignmentWidth) - 1;
-    }
-
     int annotationHeight = 0;
 
     AnnotationLabels labels = null;

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index d181804..9788ec6 100755 (executable)
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -157,7 +157,12 @@ public class ScalePanel extends JPanel
   protected void rightMouseButtonPressed(MouseEvent evt, final int res)
   {
     JPopupMenu pop = new JPopupMenu();
-    if (reveal != null)
+
+    /*
+     * grab the hidden range in case mouseMoved nulls it
+     */
+    final int[] hiddenRange = reveal;
+    if (hiddenRange != null)
     {
       JMenuItem item = new JMenuItem(
               MessageManager.getString("label.reveal"));
@@ -166,8 +171,9 @@ public class ScalePanel extends JPanel
         @Override
         public void actionPerformed(ActionEvent e)
         {
-          av.showColumn(reveal[0]);
+          av.showColumn(hiddenRange[0]);
           reveal = null;
+          ap.updateLayout();
           ap.paintAlignment(true, true);
           av.sendSelection();
         }
@@ -184,6 +190,7 @@ public class ScalePanel extends JPanel
           {
             av.showAllHiddenColumns();
             reveal = null;
+            ap.updateLayout();
             ap.paintAlignment(true, true);
             av.sendSelection();
           }
@@ -208,6 +215,7 @@ public class ScalePanel extends JPanel
             av.setSelectionGroup(null);
           }
 
+          ap.updateLayout();
           ap.paintAlignment(true, true);
           av.sendSelection();
         }

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index dc87eba..2a370c4 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -870,13 +870,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     int startx = startRes;
     int endx;
     int ypos = hgap; // vertical offset
-    int maxwidth = av.getAlignment().getWidth();
-
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .absoluteToVisibleColumn(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
 
     // chop the wrapped alignment extent up into panel-sized blocks and treat
     // each block as if it were a block from an unwrapped alignment

diff --git a/src/jalview/viewmodel/ViewportRanges.java b/src/jalview/viewmodel/ViewportRanges.java
index 691e492..6f817bb 100644 (file)
--- a/src/jalview/viewmodel/ViewportRanges.java
+++ b/src/jalview/viewmodel/ViewportRanges.java
@@ -97,7 +97,7 @@ public class ViewportRanges extends ViewportProperties
    */
   public int getVisibleAlignmentWidth()
   {
-    return al.getWidth() - al.getHiddenColumns().getSize();
+    return al.getVisibleWidth();
   }
 
   /**

diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 8aed114..dd19eb6 100644 (file)
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1532,4 +1532,34 @@ public class AlignmentTest
     assertFalse(hc.equals(hc2));
     assertTrue(al.setHiddenColumns(hc)); // 'changed'
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getWidth());
+
+    // width includes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(9, a.getWidth());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetVisibleWidth()
+  {
+    SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
+    SequenceI seq2 = new Sequence("seq2", "-JKLMNO--");
+    SequenceI seq3 = new Sequence("seq2", "-PQR");
+    AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
+
+    assertEquals(9, a.getVisibleWidth());
+
+    // width excludes hidden columns
+    a.getHiddenColumns().hideColumns(2, 5);
+    assertEquals(5, a.getVisibleWidth());
+  }
 }