int blockEnd = endRes;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- Iterator<int[]> regions = hidden.getBoundedVisRegionIterator(startRes,
- endRes);
+ Iterator<int[]> regions = hidden.iterator();
while (regions.hasNext())
{
int[] region = regions.next();
+ int hideStart = region[0];
+ int hideEnd = region[1];
- blockStart = region[0];
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
/*
* draw up to just before the next hidden region, or the end of
* the visible region, whichever comes first
*/
- blockEnd = Math.min(region[1], blockStart + screenYMax - screenY);
-
+ blockEnd = Math.min(hideStart - 1,
+ blockStart + screenYMax - screenY);
g1.translate(screenY * avcharWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
* draw the downline of the hidden column marker (ScalePanel draws the
* triangle on top) if we reached it
*/
- if (av.getShowHiddenMarkers() && blockEnd == region[1])
+ if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
{
g1.setColor(Color.blue);
g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
g1.translate(-screenY * avcharWidth, 0);
screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
if (screenY > screenYMax)
{
return;
}
}
+
if (screenY <= screenYMax)
{
// remaining visible region to render
- blockEnd = blockStart + (endRes - startRes) - screenY;
+ blockEnd = blockStart + screenYMax - screenY;
g1.translate(screenY * avcharWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
g1.translate(-screenY * avcharWidth, 0);
}
}
-
}
// int startRes, int endRes, int startSeq, int endSeq, int x, int y,
return new BoundedStartRegionIterator(start, end, useCopy);
}
- public Iterator<int[]> getBoundedVisRegionIterator(int start, int end)
- {
- return new BoundedVisRegionIterator(start, end, true);
- }
-
/**
* An iterator which iterates over hidden column regions in a range.
*
return result;
}
}
-
- class BoundedVisRegionIterator implements Iterator<int[]>
- {
- private int start; // start position to iterate from
-
- private int end; // end position to iterate to
-
- // current region in visColumns
- private int[] currentRegion;
-
- // current index in visColumns
- private int currentPosition = 0;
-
- private List<int[]> vcontigs = null;
-
- /**
- * Construct an iterator over visibleColumn regions bounded at
- * [lowerBound,upperBound]
- *
- * @param lowerBound
- * lower bound to iterate from
- * @param upperBound
- * upper bound to iterate to
- * @param useCopyCols
- * whether to make a local copy for iteration (set to true if
- * calling from outwith the HiddenColumns class)
- */
- BoundedVisRegionIterator(int lowerBound, int upperBound,
- boolean useCopy)
- {
- try
- {
- start = lowerBound;
- end = upperBound;
-
- if (useCopy)
- {
- // assume that if useCopy is false the calling code has locked
- // hiddenColumns
- LOCK.readLock().lock();
- }
-
- int visStart = start;
-
- if (hiddenColumns != null)
- {
- vcontigs = new ArrayList<>(hiddenColumns.size() + 1);
-
- // navigate to start, keeping count of hidden columns
- int i = 0;
- int[] region = null;
- while ((i < hiddenColumns.size())
- && (hiddenColumns.get(i)[0] <= start))
- {
- i++;
- }
- // if there was a hidden region before (i>=1), and it ended after
- // start
- // and before end, adjust visStart to be just after that region
- if (i > 0)
- {
- region = hiddenColumns.get(i - 1);
- if ((region[1] > start) && (region[1] < end))
- {
- visStart = region[1] + 1;
- }
- else if (region[1] >= end)
- {
- // previous hidden region covers whole range [start,end]
- // early exit - vcontigs is empty
- return;
- }
- }
-
- // iterate from start to end, adding start positions of each
- // hidden region. Positions are visible columns count, not absolute
- while (i < hiddenColumns.size()
- && (hiddenColumns.get(i)[0] < end))
- {
- region = hiddenColumns.get(i);
- int[] prevVisibleRegion = new int[] { visStart, region[0] - 1 };
- vcontigs.add(prevVisibleRegion);
- visStart = region[1] + 1;
- i++;
- }
- // add on a final visible region if needed
- if (visStart <= end)
- {
- int[] lastRegion = new int[] { visStart, end };
- vcontigs.add(lastRegion);
- }
- }
- else
- {
- vcontigs = new ArrayList<>();
- int[] lastRegion = new int[] { start, end };
- vcontigs.add(lastRegion);
- }
- } finally
- {
- if (useCopy)
- {
- LOCK.readLock().unlock();
- }
- }
- }
-
- @Override
- public boolean hasNext()
- {
- return (currentPosition < vcontigs.size());
- }
-
- @Override
- public int[] next()
- {
- currentRegion = vcontigs.get(currentPosition);
- currentPosition++;
- return currentRegion;
- }
- }
}
int blockEnd = endRes;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- Iterator<int[]> regions = hidden.getBoundedVisRegionIterator(startRes,
- endRes);
+ Iterator<int[]> regions = hidden.iterator();
while (regions.hasNext())
{
int[] region = regions.next();
+ int hideStart = region[0];
+ int hideEnd = region[1];
- blockStart = region[0];
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
/*
* draw up to just before the next hidden region, or the end of
* the visible region, whichever comes first
*/
- blockEnd = Math.min(region[1], blockStart + screenYMax - screenY);
-
+ blockEnd = Math.min(hideStart - 1,
+ blockStart + screenYMax - screenY);
g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
* draw the downline of the hidden column marker (ScalePanel draws the
* triangle on top) if we reached it
*/
- if (av.getShowHiddenMarkers() && blockEnd == region[1])
+ if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
{
g1.setColor(Color.blue);
g1.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
if (screenY > screenYMax)
{
blockEnd = blockStart + screenYMax - screenY;
g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
-
+
g1.translate(-screenY * charWidth, 0);
}
}
int blockEnd = endRes;
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- Iterator<int[]> regions = hidden.getBoundedVisRegionIterator(startRes,
- endRes);
+ Iterator<int[]> regions = hidden.iterator();
while (regions.hasNext())
{
int[] region = regions.next();
+ int hideStart = region[0];
+ int hideEnd = region[1];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
- blockStart = region[0];
- blockEnd = region[1];
+ blockEnd = hideStart - 1;
g.translate(screenY * charWidth, 0);
drawPartialGroupOutline(g, group,
g.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
if (screenY > (endRes - startRes))
{
assertEquals(6, next);
assertFalse(it.hasNext());
}
-
- @Test(groups = "Functional")
- public void testVisRegionsIterator()
- {
- HiddenColumns h = new HiddenColumns();
- Iterator<int[]> it = h.getBoundedVisRegionIterator(0, 15);
-
- // no hidden columns = single visible contig
- assertTrue(it.hasNext());
- assertEquals("[0, 15]", Arrays.toString(it.next()));
-
- // hidden column region at start
- h.hideColumns(0, 5);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertTrue(it.hasNext());
- assertEquals("[6, 15]", Arrays.toString(it.next()));
-
- // hidden column region at end
- h = new HiddenColumns();
- h.hideColumns(8, 15);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertTrue(it.hasNext());
- assertEquals("[0, 7]", Arrays.toString(it.next()));
-
- // hidden column region across whole region
- h = new HiddenColumns();
- h.hideColumns(0, 20);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertFalse(it.hasNext());
-
- // hidden column region in middle
- h = new HiddenColumns();
- h.hideColumns(1, 14);
- it = h.getBoundedVisRegionIterator(0, 15);
- assertTrue(it.hasNext());
- assertEquals("[0, 0]", Arrays.toString(it.next()));
- assertTrue(it.hasNext());
- assertEquals("[15, 15]", Arrays.toString(it.next()));
-
- // hidden column region just off either end
- h = new HiddenColumns();
- h.hideColumns(3, 14);
- it = h.getBoundedVisRegionIterator(4, 13);
- assertFalse(it.hasNext());
-
- // multiple regions
- h = new HiddenColumns();
- h.hideColumns(3, 5);
- h.hideColumns(7, 11);
- h.hideColumns(14, 19);
- h.hideColumns(24, 25);
- h.hideColumns(35, 39);
- it = h.getBoundedVisRegionIterator(8, 26);
- assertTrue(it.hasNext());
- assertEquals("[12, 13]", Arrays.toString(it.next()));
- assertTrue(it.hasNext());
- assertEquals("[20, 23]", Arrays.toString(it.next()));
- assertTrue(it.hasNext());
- assertEquals("[26, 26]", Arrays.toString(it.next()));
- assertFalse(it.hasNext());
- }
}
git://source.jalview.org / jalview.git / commitdiff