*/
package jalview.datamodel;
+import java.util.ArrayList;
import java.util.List;
+import java.util.concurrent.atomic.AtomicReference;
public class HiddenColumnsCursor
{
// absolute position of first hidden column
private int firstColumn;
- // index of last visited region
- private int regionIndex;
+ private List<int[]> hiddenColumns = new ArrayList<>();
- // number of hidden columns before last visited region
- private int hiddenSoFar;
-
- private List<int[]> hiddenColumns;
+ // AtomicReference to hold the current region index and hidden column count
+ // Could be done with synchronisation but benchmarking shows this way is 2x
+ // faster
+ private final AtomicReference<HiddenCursorPosition> cursorPos = new AtomicReference<>(
+ new HiddenCursorPosition(0, 0));
protected HiddenColumnsCursor()
{
}
/**
- * Set the cursor to a position
+ * Reset the cursor with a new hidden columns collection. Calls to resetCursor
+ * should be made from within a writeLock in the HiddenColumns class - since
+ * changes to the hiddenColumns collection require a writeLock the lock should
+ * already exist.
*
* @param hiddenCols
+ * new hidden columns collection
*/
protected void resetCursor(List<int[]> hiddenCols)
{
- synchronized (this)
+ resetCursor(hiddenCols, 0, 0);
+ }
+
+ /**
+ * Reset the cursor with a new hidden columns collection, where we know in
+ * advance the index and hidden columns count of a particular location.
+ *
+ * @param hiddenCols
+ * new hidden columns collection
+ * @param index
+ * cursor index to reset to
+ * @param hiddencount
+ * hidden columns count to reset to
+ */
+ protected void resetCursor(List<int[]> hiddenCols, int index,
+ int hiddencount)
+ {
+ hiddenColumns = hiddenCols;
+ if (!hiddenCols.isEmpty())
{
- hiddenColumns = hiddenCols;
- if ((hiddenCols != null) && (!hiddenCols.isEmpty()))
- {
- firstColumn = hiddenColumns.get(0)[0];
- regionIndex = 0;
- hiddenSoFar = 0;
- }
+ firstColumn = hiddenColumns.get(0)[0];
+ HiddenCursorPosition oldpos = cursorPos.get();
+ HiddenCursorPosition newpos = new HiddenCursorPosition(index,
+ hiddencount);
+ cursorPos.compareAndSet(oldpos, newpos);
}
}
/**
* Delete the region the cursor is currently at. Avoids having to reset the
* cursor just because we deleted a region.
+ *
+ * Calls to updateForDeletedRegion should be made from within a writeLock in
+ * the HiddenColumns class - since changes to the hiddenColumns collection
+ * require a writeLock the lock should already exist.
*
* @param hiddenCols
*/
protected void updateForDeletedRegion(List<int[]> hiddenCols)
{
- if ((hiddenCols != null) && (!hiddenCols.isEmpty()))
+ if (!hiddenCols.isEmpty())
{
// if there is a region to the right of the current region,
// nothing changes; otherwise
// we deleted the last region (index=hiddenCols.size()-1)
// or the index was at the end of the alignment (index=hiddenCols.size())
- if (regionIndex >= hiddenColumns.size() - 1)
+ HiddenCursorPosition oldpos = cursorPos.get();
+
+ int index = oldpos.getRegionIndex();
+ if (index >= hiddenColumns.size() - 1)
{
// deleted last region, index is now end of alignment
- regionIndex = hiddenCols.size();
+ index = hiddenCols.size();
+
+ HiddenCursorPosition newpos = new HiddenCursorPosition(index,
+ oldpos.getHiddenSoFar());
+ cursorPos.compareAndSet(oldpos, newpos);
}
}
-
hiddenColumns = hiddenCols;
}
- protected void updateCursor(int index, int hiddenCount)
- {
- synchronized (this)
- {
- regionIndex = index;
- hiddenSoFar = hiddenCount;
- }
- }
-
- protected synchronized int getIndex()
- {
- return regionIndex;
- }
-
- protected synchronized int getHiddenSoFar()
- {
- return hiddenSoFar;
- }
-
-
/**
- * Get the index of the region that column is within (if column is hidden) or
- * which is to the right of column (if column is visible). If no hidden
- * columns are to the right, will return size of hiddenColumns. If hidden
- * columns is empty returns -1.
+ * Get the cursor pointing to the hidden region that column is within (if
+ * column is hidden) or which is to the right of column (if column is
+ * visible). If no hidden columns are to the right, returns a cursor pointing
+ * to an imaginary hidden region beyond the end of the hidden columns
+ * collection (this ensures the count of previous hidden columns is correct).
+ * If hidden columns is empty returns null.
*
* @param column
* absolute position of a column in the alignment
- * @return region index
+ * @return cursor pointing to hidden region containing the column (if hidden)
+ * or to the right of the column (if visible)
*/
- protected int findRegionForColumn(int column)
+ protected HiddenCursorPosition findRegionForColumn(int column)
{
- if (hiddenColumns == null)
+ if (hiddenColumns.isEmpty())
{
- return -1;
+ return null;
}
- int index = regionIndex;
- int hiddenCount = hiddenSoFar;
+ HiddenCursorPosition oldpos = cursorPos.get();
+ int index = oldpos.getRegionIndex();
+ int hiddenCount = oldpos.getHiddenSoFar();
if (index == hiddenColumns.size())
{
hiddenCount -= region[1] - region[0] + 1;
}
- if ((hiddenColumns.get(index)[0] <= column)
- && hiddenColumns.get(index)[1] >= column)
- {
- // column is in the current region
- // we hit the jackpot
- // don't need to move index
- }
- else if (column < firstColumn)
+ // this if statement excludes case where column is in current region
+ // - no changes needed
+ if (column < firstColumn)
{
index = 0;
hiddenCount = 0;
}
// column is after current region
- else if (column > hiddenColumns.get(index)[1]) // includes if column >
- // lastColumn
+ else if (column > hiddenColumns.get(index)[1])
{
// iterate from where we are now, if we're lucky we'll be close by
// (but still better than iterating from 0)
index++;
}
}
-
// column is before current region
else if (column < hiddenColumns.get(index)[0])
{
// column is before or in the previous region
- if ((index > 0) && (hiddenColumns.get(index - 1)[1] >= column))
+ while ((index > 0) && (hiddenColumns.get(index - 1)[1] >= column))
{
- while ((index > 0) && (hiddenColumns.get(index)[1] > column))
- {
- index--;
- int[] region = hiddenColumns.get(index);
- hiddenCount -= region[1] - region[0] + 1;
- }
+ index--;
+ int[] region = hiddenColumns.get(index);
+ hiddenCount -= region[1] - region[0] + 1;
}
}
- updateCursor(index, hiddenCount);
- return index;
+
+ if (index != oldpos.getRegionIndex()
+ || hiddenCount != oldpos.getHiddenSoFar())
+ {
+ HiddenCursorPosition newpos = new HiddenCursorPosition(index,
+ hiddenCount);
+ cursorPos.compareAndSet(oldpos, newpos);
+ return newpos;
+ }
+ return oldpos;
}
/**
- * Get the number of hidden columns in regions before column i.e. excludes
- * hidden columns in the region column is in, if any
+ * Get the cursor pointing to the hidden region just after a visible column
*
* @param column
- * index of column in visible alignment
- * @return
+ * index of column in *visible* alignment (therefore by definition
+ * column is visible)
+ * @return cursor pointing to hidden region to the right of the column
*/
- protected int getHiddenOffset(int column)
+ protected HiddenCursorPosition findRegionForVisColumn(int column)
{
- if (hiddenColumns == null)
+ if (hiddenColumns.isEmpty())
{
- return -1;
+ return null;
}
- int index = getIndex();
- int hiddenCount = getHiddenSoFar();
+ HiddenCursorPosition oldpos = cursorPos.get();
+ int index = oldpos.getRegionIndex();
+ int hiddenCount = oldpos.getHiddenSoFar();
if (column < firstColumn)
{
}
}
- updateCursor(index, hiddenCount);
- return hiddenCount;
+
+ if (index != oldpos.getRegionIndex()
+ || hiddenCount != oldpos.getHiddenSoFar())
+ {
+ HiddenCursorPosition newpos = new HiddenCursorPosition(index,
+ hiddenCount);
+ cursorPos.compareAndSet(oldpos, newpos);
+ return newpos;
+ }
+ return oldpos;
}
}
git://source.jalview.org / jalview.git / blobdiff