Merge branch 'develop' into feature/JAL-2759

Conflicts:
	src/jalview/gui/SeqCanvas.java
	src/jalview/renderer/ScaleRenderer.java
	test/jalview/datamodel/SequenceTest.java

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

diff --cc src/jalview/appletgui/AnnotationColumnChooser.java
Simple merge

diff --cc src/jalview/appletgui/AnnotationLabels.java
Simple merge

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

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

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

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

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

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

diff --cc src/jalview/gui/Jalview2XML.java
Simple merge

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

diff --cc src/jalview/gui/SeqCanvas.java
index f72acae,2a9c704..6c4391c
--- 1/src/jalview/gui/SeqCanvas.java
--- 2/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@@ -42,7 -42,7 +43,8 @@@ import java.awt.RenderingHints
  import java.awt.Shape;
  import java.awt.image.BufferedImage;
  import java.beans.PropertyChangeEvent;
 +import java.util.Iterator;
+ import java.util.List;
  
  import javax.swing.JComponent;
  
@@@ -694,59 -854,54 +856,57 @@@ public class SeqCanvas extends JCompone
  
        if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
        {
-         g.setColor(Color.blue);
-         int res;
-         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- 
-         Iterator<Integer> it = hidden.getBoundedStartIterator(startRes,
-                 endx + 1);
-         while (it.hasNext())
-         {
-           res = it.next() - startRes;
-           gg.fillPolygon(
-                   new int[]
-           { res * charWidth - charHeight / 4,
-               res * charWidth + charHeight / 4, res * charWidth },
-                   new int[]
-           { ypos - (charHeight / 2), ypos - (charHeight / 2),
-               ypos - (charHeight / 2) + 8 }, 3);
-         }
+         drawHiddenColumnMarkers(g, ypos, startCol, endColumn);
        }
  
-       // When printing we have an extra clipped region,
-       // the Printable page which we need to account for here
-       Shape clip = g.getClip();
+       g.translate(-labelWidthWest, 0);
  
-       if (clip == null)
-       {
-         g.setClip(0, 0, cWidth * charWidth, canvasHeight);
-       }
-       else
-       {
-         g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
-                 (int) clip.getBounds().getHeight());
-       }
+       ypos += wrappedRepeatHeightPx;
+       startCol += viewportWidth;
+       widthsDrawn++;
+     }
+   }
  
-       drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
+   /**
+    * Draws markers (triangles) above hidden column positions between startColumn
+    * and endColumn.
+    * 
+    * @param g
+    * @param ypos
+    * @param startColumn
+    * @param endColumn
+    */
+   protected void drawHiddenColumnMarkers(Graphics g, int ypos,
+           int startColumn, int endColumn)
+   {
+     int charHeight = av.getCharHeight();
+     int charWidth = av.getCharWidth();
  
-       if (av.isShowAnnotation())
-       {
-         g.translate(0, cHeight + ypos + 3);
-         if (annotations == null)
-         {
-           annotations = new AnnotationPanel(av);
-         }
+     g.setColor(Color.blue);
++    int res;
+     HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 -    List<Integer> positions = hidden.findHiddenRegionPositions();
 -    for (int pos : positions)
 +
-         annotations.renderer.drawComponent(annotations, av, g, -1, startRes,
-                 endx + 1);
-         g.translate(0, -cHeight - ypos - 3);
-       }
-       g.setClip(clip);
-       g.translate(-labelWidthWest, 0);
++    Iterator<Integer> it = hidden.getBoundedStartIterator(startColumn,
++            endColumn);
++    while (it.hasNext())
+     {
 -      int res = pos - startColumn;
++      res = it.next() - startColumn;
  
-       ypos += cHeight + annotationHeight + hgap;
+       if (res < 0 || res > endColumn - startColumn + 1)
+       {
+         continue;
+       }
  
-       startRes += cWidth;
+       /*
+        * draw a downward-pointing triangle at the hidden columns location
+        * (before the following visible column)
+        */
+       int xMiddle = res * charWidth;
+       int[] xPoints = new int[] { xMiddle - charHeight / 4,
+           xMiddle + charHeight / 4, xMiddle };
+       int yTop = ypos - (charHeight / 2);
+       int[] yPoints = new int[] { yTop, yTop, yTop + 8 };
+       g.fillPolygon(xPoints, yPoints, 3);
      }
    }
  

diff --cc src/jalview/renderer/ScaleRenderer.java
Simple merge

diff --cc src/jalview/util/MappingUtils.java
Simple merge

diff --cc test/jalview/datamodel/SequenceTest.java
index b9f93c3,c0cb09c..549f13a
--- 1/test/jalview/datamodel/SequenceTest.java
--- 2/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@@ -1674,17 -1674,133 +1674,147 @@@ public class SequenceTes
    }
  
    @Test(groups = { "Functional" })
 +  public void testGapBitset()
 +  {
 +    SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
 +    BitSet bs = sq.gapBitset();
 +    BitSet expected = new BitSet();
 +    expected.set(0);
 +    expected.set(4, 7);
 +    expected.set(9);
 +    expected.set(11, 13);
 +
 +    assertTrue(bs.equals(expected));
 +
 +  }
++
+   public void testFindFeatures_largeEndPos()
+   {
+     /*
+      * imitate a PDB sequence where end is larger than end position
+      */
+     SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
+     sq.createDatasetSequence();
+   
+     assertTrue(sq.findFeatures(1, 9).isEmpty());
+     // should be no array bounds exception - JAL-2772
+     assertTrue(sq.findFeatures(1, 15).isEmpty());
+   
+     // add feature on BCD
+     SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+             null);
+     sq.addSequenceFeature(sfBCD);
+   
+     // no features in columns 1-2 (-A)
+     List<SequenceFeature> found = sq.findFeatures(1, 2);
+     assertTrue(found.isEmpty());
+   
+     // columns 1-6 (-ABC--) includes BCD
+     found = sq.findFeatures(1, 6);
+     assertEquals(1, found.size());
+     assertTrue(found.contains(sfBCD));
+ 
+     // columns 10-11 (--) should find nothing
+     found = sq.findFeatures(10, 11);
+     assertEquals(0, found.size());
+   }
+ 
+   @Test(groups = { "Functional" })
+   public void testSetName()
+   {
+     SequenceI sq = new Sequence("test", "-ABC---DE-F--");
+     assertEquals("test", sq.getName());
+     assertEquals(1, sq.getStart());
+     assertEquals(6, sq.getEnd());
+ 
+     sq.setName("testing");
+     assertEquals("testing", sq.getName());
+ 
+     sq.setName("test/8-10");
+     assertEquals("test", sq.getName());
+     assertEquals(8, sq.getStart());
+     assertEquals(13, sq.getEnd()); // note end is recomputed
+ 
+     sq.setName("testing/7-99");
+     assertEquals("testing", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd()); // end may be beyond physical end
+ 
+     sq.setName("/2-3");
+     assertEquals("", sq.getName());
+     assertEquals(2, sq.getStart());
+     assertEquals(7, sq.getEnd());
+ 
+     sq.setName("test/"); // invalid
+     assertEquals("test/", sq.getName());
+     assertEquals(2, sq.getStart());
+     assertEquals(7, sq.getEnd());
+ 
+     sq.setName("test/6-13/7-99");
+     assertEquals("test/6-13", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd());
+ 
+     sq.setName("test/0-5"); // 0 is invalid - ignored
+     assertEquals("test/0-5", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd());
+ 
+     sq.setName("test/a-5"); // a is invalid - ignored
+     assertEquals("test/a-5", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd());
+ 
+     sq.setName("test/6-5"); // start > end is invalid - ignored
+     assertEquals("test/6-5", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd());
+ 
+     sq.setName("test/5"); // invalid - ignored
+     assertEquals("test/5", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd());
+ 
+     sq.setName("test/-5"); // invalid - ignored
+     assertEquals("test/-5", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd());
+ 
+     sq.setName("test/5-"); // invalid - ignored
+     assertEquals("test/5-", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd());
+ 
+     sq.setName("test/5-6-7"); // invalid - ignored
+     assertEquals("test/5-6-7", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd());
+ 
+     sq.setName(null); // invalid, gets converted to space
+     assertEquals("", sq.getName());
+     assertEquals(7, sq.getStart());
+     assertEquals(99, sq.getEnd());
+   }
+ 
+   @Test(groups = { "Functional" })
+   public void testCheckValidRange()
+   {
+     Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
+     assertEquals(7, sq.getStart());
+     assertEquals(12, sq.getEnd());
+ 
+     /*
+      * checkValidRange ensures end is at least the last residue position
+      */
+     PA.setValue(sq, "end", 2);
+     sq.checkValidRange();
+     assertEquals(12, sq.getEnd());
+ 
+     /*
+      * end may be beyond the last residue position
+      */
+     PA.setValue(sq, "end", 22);
+     sq.checkValidRange();
+     assertEquals(22, sq.getEnd());
+   }
  }

diff --cc test/jalview/util/MappingUtilsTest.java
Simple merge