/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import java.util.ArrayList;
import java.util.List;
public class HiddenColumnsCursor
{
// absolute position of first hidden column
private int firstColumn;
private List hiddenColumns = new ArrayList<>();
private HiddenCursorPosition cursorPos = new HiddenCursorPosition(0, 0);
protected HiddenColumnsCursor()
{
}
protected HiddenColumnsCursor(List hiddenCols)
{
resetCursor(hiddenCols, 0, 0);
}
protected HiddenColumnsCursor(List hiddenCols, int index,
int hiddencount)
{
resetCursor(hiddenCols, index, hiddencount);
}
/**
* 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
*/
private void resetCursor(List hiddenCols, int index,
int hiddencount)
{
hiddenColumns = hiddenCols;
if (!hiddenCols.isEmpty())
{
firstColumn = hiddenColumns.get(0)[0];
cursorPos = new HiddenCursorPosition(index,
hiddencount);
}
}
/**
* 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 hiddenCols)
{
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())
HiddenCursorPosition oldpos = cursorPos;
int index = oldpos.getRegionIndex();
if (index >= hiddenColumns.size() - 1)
{
// deleted last region, index is now end of alignment
index = hiddenCols.size();
cursorPos = new HiddenCursorPosition(index,
oldpos.getHiddenSoFar());
}
}
hiddenColumns = hiddenCols;
}
/**
* 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 cursor pointing to hidden region containing the column (if hidden)
* or to the right of the column (if visible)
*/
protected HiddenCursorPosition findRegionForColumn(int column)
{
if (hiddenColumns.isEmpty())
{
return null;
}
HiddenCursorPosition oldpos = cursorPos;
int index = oldpos.getRegionIndex();
int hiddenCount = oldpos.getHiddenSoFar();
if (index == hiddenColumns.size())
{
// went past the end of hiddenColumns collection last time
index--;
int[] region = hiddenColumns.get(index);
hiddenCount -= region[1] - region[0] + 1;
}
// 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])
{
// iterate from where we are now, if we're lucky we'll be close by
// (but still better than iterating from 0)
// stop when we find the region *before* column
// i.e. the next region starts after column or if not, ends after column
while ((index < hiddenColumns.size())
&& (column > hiddenColumns.get(index)[1]))
{
int[] region = hiddenColumns.get(index);
hiddenCount += region[1] - region[0] + 1;
index++;
}
}
// column is before current region
else if (column < hiddenColumns.get(index)[0])
{
// column is before or in the previous region
while ((index > 0) && (hiddenColumns.get(index - 1)[1] >= column))
{
index--;
int[] region = hiddenColumns.get(index);
hiddenCount -= region[1] - region[0] + 1;
}
}
if (index != oldpos.getRegionIndex()
|| hiddenCount != oldpos.getHiddenSoFar())
{
cursorPos = new HiddenCursorPosition(index,
hiddenCount);
return cursorPos;
}
return oldpos;
}
/**
* Get the cursor pointing to the hidden region just after a visible column
*
* @param column
* 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 HiddenCursorPosition findRegionForVisColumn(int column)
{
if (hiddenColumns.isEmpty())
{
return null;
}
HiddenCursorPosition oldpos = cursorPos;
int index = oldpos.getRegionIndex();
int hiddenCount = oldpos.getHiddenSoFar();
if (column < firstColumn)
{
index = 0;
hiddenCount = 0;
}
else if ((index < hiddenColumns.size())
&& (hiddenColumns.get(index)[0] <= column + hiddenCount))
{
// iterate from where we are now, if we're lucky we'll be close by
// (but still better than iterating from 0)
while ((index < hiddenColumns.size())
&& (hiddenColumns.get(index)[0] <= column + hiddenCount))
{
int[] region = hiddenColumns.get(index);
hiddenCount += region[1] - region[0] + 1;
index++;
}
}
else
{
while ((index > 0)
&& (hiddenColumns.get(index - 1)[1] >= column + hiddenCount))
{
index--;
int[] region = hiddenColumns.get(index);
hiddenCount -= region[1] - region[0] + 1;
}
}
if (index != oldpos.getRegionIndex()
|| hiddenCount != oldpos.getHiddenSoFar())
{
cursorPos = new HiddenCursorPosition(index,
hiddenCount);
return cursorPos;
}
return oldpos;
}
}