wasAlreadyLocked = true;
}
+ int previndex = 0;
+ int prevHiddenCount = 0;
+ int regionindex = 0;
if (hiddenColumns == null)
{
hiddenColumns = new ArrayList<>();
}
+ else
+ {
+ // set up cursor reset values
+ HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
+ regionindex = cursorPos.getRegionIndex();
+
+ if (regionindex > 0)
+ {
+ // get previous index and hidden count for updating the cursor later
+ previndex = regionindex - 1;
+ int[] prevRegion = hiddenColumns.get(previndex);
+ prevHiddenCount = cursorPos.getHiddenSoFar()
+ - (prevRegion[1] - prevRegion[0] + 1);
+ }
+ }
/*
* new range follows everything else; check first to avoid looping over whole hiddenColumns collection
* appropriate
*/
boolean added = false;
- for (int i = 0; !added && i < hiddenColumns.size(); i++)
+ if (regionindex > 0)
+ {
+ added = insertRangeAtRegion(regionindex - 1, start, end);
+ }
+ if (!added && regionindex < hiddenColumns.size())
{
- added = insertRangeAtRegion(i, start, end);
- } // for
+ insertRangeAtRegion(regionindex, start, end);
+ }
}
- if (!wasAlreadyLocked)
- {
- cursor.resetCursor(hiddenColumns);
- // reset the number of columns so they will be recounted
- numColumns = 0;
- }
+ // reset the cursor to just before our insertion point: this saves
+ // a lot of reprocessing in large alignments
+ cursor.resetCursor(hiddenColumns, previndex, prevHiddenCount);
+
+ // reset the number of columns so they will be recounted
+ numColumns = 0;
+
} finally
{
if (!wasAlreadyLocked)
break;
}
region[1] = Math.max(nextRegion[1], end);
+
+ // in theory this is faster than hiddenColumns.remove(i+1)
+ // benchmarking results a bit ambivalent
hiddenColumns.subList(i + 1, i + 2).clear();
}
added = true;