* int column index in alignment view (count from zero)
* @return alignment column index for column
*/
- public int adjustForHiddenColumns(int column)
+ public int visibleToAbsoluteColumn(int column)
{
try
{
* the column index in the full alignment including hidden columns
* @return the position of the column in the visible alignment
*/
- public int findColumnPosition(int hiddenColumn)
+ public int absoluteToVisibleColumn(int hiddenColumn)
{
try
{
int distance = visibleDistance;
// in case startColumn is in a hidden region, move it to the left
- int start = adjustForHiddenColumns(findColumnPosition(startColumn));
+ int start = visibleToAbsoluteColumn(absoluteToVisibleColumn(startColumn));
Iterator<int[]> it = new ReverseRegionsIterator(0, start,
hiddenColumns);
if (foundStart)
{
- return findColumnPosition(start);
+ return absoluteToVisibleColumn(start);
}
// otherwise, sequence was completely hidden
return visPrev;
try
{
LOCK.readLock().lock();
- int adjres = adjustForHiddenColumns(res);
+ int adjres = visibleToAbsoluteColumn(res);
int[] reveal = null;
LOCK.readLock().lock();
// get absolute position of column in alignment
- int absoluteStart = adjustForHiddenColumns(start);
+ int absoluteStart = visibleToAbsoluteColumn(start);
// Get cursor position and supply it to the iterator:
// Since we want visible region start, we look for a cursor for the
int adjend = end;
if (useVisibleCoords)
{
- adjstart = adjustForHiddenColumns(start);
- adjend = adjustForHiddenColumns(end);
+ adjstart = visibleToAbsoluteColumn(start);
+ adjend = visibleToAbsoluteColumn(end);
}
try