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 --cc src/jalview/datamodel/Alignment.java
Simple merge

diff --cc src/jalview/datamodel/AlignmentI.java
Simple merge

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/AlignmentPanel.java
index 82e2113,d8f1629..51e703d
--- 1/src/jalview/gui/AlignmentPanel.java
--- 2/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@@ -954,20 -991,29 +947,20 @@@ public class AlignmentPanel extends GAl
      /*
       * How many sequences and residues can we fit on a printable page?
       */
 -    int totalRes = (pageWidth - idWidth) / av.getCharWidth();
 +    final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
  
 -    int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
 +    final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
  
-     final int alignmentWidth = av.getAlignment().getWidth();
-     final int pagesWide = (alignmentWidth / totalRes) + 1;
 -    int alignmentWidth = av.getAlignment().getVisibleWidth();
++    final int alignmentWidth = av.getAlignment().getVisibleWidth();
+     int pagesWide = (alignmentWidth / totalRes) + 1;
  
 -    final int startRes = (pi % pagesWide) * totalRes;
 -    int endRes = (startRes + totalRes) - 1;
 +    final int startRes = (pageIndex % pagesWide) * totalRes;
 +    final int endRes = Math.min(startRes + totalRes - 1,
 +            alignmentWidth - 1);
  
 -    if (endRes > (alignmentWidth - 1))
 -    {
 -      endRes = alignmentWidth - 1;
 -    }
 -
 -    final int startSeq = (pi / pagesWide) * totalSeq;
 -    int endSeq = startSeq + totalSeq;
 -
 -    int alignmentHeight = av.getAlignment().getHeight();
 -    if (endSeq > alignmentHeight)
 -    {
 -      endSeq = alignmentHeight;
 -    }
 +    final int startSeq = (pageIndex / pagesWide) * totalSeq;
 +    final int alignmentHeight = av.getAlignment().getHeight();
 +    final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
  
      int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
  
@@@ -1076,15 -1161,10 +1069,10 @@@
  
      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(pwidth - idWidth);
 +            .getWrappedCanvasWidth(pageWidth - idWidth);
  
      int totalHeight = cHeight * (maxwidth / resWidth + 1);
  

diff --cc src/jalview/gui/IdCanvas.java
index cf88c90,9ff0652..951db78
--- 1/src/jalview/gui/IdCanvas.java
--- 2/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@@ -367,29 -367,19 +367,23 @@@ public class IdCanvas extends JPanel im
    }
  
    /**
 -   * Draws sequence ids in wrapped mode
 +   * Draws sequence ids, and annotation labels if annotations are shown, in
 +   * wrapped mode
     * 
 -   * @param starty
 -   * @param hasHiddenRows
 +   * @param g
 +   * @param alignViewport
 +   * @param startSeq
     */
 -  protected void drawIdsWrapped(int starty, boolean hasHiddenRows)
 +  void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
 +          int startSeq, int pageHeight)
    {
 -    int maxwidth = av.getAlignment().getVisibleWidth();
 -    int alheight = av.getAlignment().getHeight();
 +    int alignmentWidth = alignViewport.getAlignment().getWidth();
 +    final int alheight = alignViewport.getAlignment().getHeight();
  
-     if (alignViewport.hasHiddenColumns())
-     {
-       alignmentWidth = alignViewport.getAlignment().getHiddenColumns()
-               .absoluteToVisibleColumn(alignmentWidth) - 1;
-     }
- 
      int annotationHeight = 0;
  
 -    if (av.isShowAnnotation())
 +    AnnotationLabels labels = null;
 +    if (alignViewport.isShowAnnotation())
      {
        if (ap == null)
        {

diff --cc src/jalview/gui/ScalePanel.java
Simple merge

diff --cc src/jalview/gui/SeqCanvas.java
Simple merge

diff --cc test/jalview/datamodel/AlignmentTest.java
index 8aed114,5e400c0..dd19eb6
--- 1/test/jalview/datamodel/AlignmentTest.java
--- 2/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@@ -1485,51 -1485,33 +1485,81 @@@ public class AlignmentTes
      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'
 +  }
++
+   @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());
+   }
  }