- return selection.getRanges();
- }
-
- /**
- *
- * @param col
- * index to search for in column selection
- *
- * @return true if col is selected
- */
- public boolean contains(int col)
- {
- return (col > -1) ? selection.isSelected(col) : false;
- }
-
- /**
- * Answers true if no columns are selected, else false
- */
- public boolean isEmpty()
- {
- return selection == null || selection.isEmpty();
- }
-
- /**
- * rightmost selected column
- *
- * @return rightmost column in alignment that is selected
- */
- public int getMax()
- {
- if (selection.isEmpty())
- {
- return -1;
- }
- return selection.getMaxColumn();
- }
-
- /**
- * Leftmost column in selection
- *
- * @return column index of leftmost column in selection
- */
- public int getMin()
- {
- if (selection.isEmpty())
- {
- return 1000000000;
- }
- return selection.getMinColumn();
- }
-
- /**
- * propagate shift in alignment columns to column selection
- *
- * @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
- */
- public List<int[]> compensateForEdit(int start, int change)
- {
- List<int[]> deletedHiddenColumns = null;
- selection.compensateForEdits(start, change);
-
- if (hiddenColumns != null)
- {
- deletedHiddenColumns = new ArrayList<int[]>();
- int hSize = hiddenColumns.size();
- for (int i = 0; i < hSize; i++)
- {
- int[] region = hiddenColumns.elementAt(i);
- if (region[0] > start && start + change > region[1])
- {
- deletedHiddenColumns.add(region);
-
- hiddenColumns.removeElementAt(i);
- i--;
- hSize--;
- continue;
- }
-
- if (region[0] > start)
- {
- region[0] -= change;
- region[1] -= change;
- }
-
- if (region[0] < 0)
- {
- region[0] = 0;
- }
-
- }
-
- this.revealHiddenColumns(0);
- }
-
- return deletedHiddenColumns;
- }
-
- /**
- * propagate shift in alignment columns to column selection special version of
- * compensateForEdit - allowing for edits within hidden regions
- *
- * @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
- */
- private void compensateForDelEdits(int start, int change)
- {
-
- selection.compensateForEdits(start, change);
-
- if (hiddenColumns != null)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.elementAt(i);
- if (region[0] >= start)
- {
- region[0] -= change;
- }
- if (region[1] >= start)
- {
- region[1] -= change;
- }
- if (region[1] < region[0])
- {
- hiddenColumns.removeElementAt(i--);
- }
-
- if (region[0] < 0)
- {
- region[0] = 0;
- }
- if (region[1] < 0)
- {
- region[1] = 0;
- }
- }
- }
- }
-
- /**
- * Adjust hidden column boundaries based on a series of column additions or
- * deletions in visible regions.
- *
- * @param shiftrecord
- * @return
- */
- public ShiftList compensateForEdits(ShiftList shiftrecord)
- {
- if (shiftrecord != null)
- {
- final List<int[]> shifts = shiftrecord.getShifts();
- if (shifts != null && shifts.size() > 0)
- {
- int shifted = 0;
- for (int i = 0, j = shifts.size(); i < j; i++)
- {
- int[] sh = shifts.get(i);
- // compensateForEdit(shifted+sh[0], sh[1]);
- compensateForDelEdits(shifted + sh[0], sh[1]);
- shifted -= sh[1];
- }
- }
- return shiftrecord.getInverse();
- }
- return null;
- }
-
- /**
- * removes intersection of position,length ranges in deletions from the
- * start,end regions marked in intervals.
- *
- * @param shifts
- * @param intervals
- * @return
- */
- private boolean pruneIntervalVector(final List<int[]> shifts,
- Vector<int[]> intervals)
- {
- boolean pruned = false;
- int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
- int hr[] = intervals.elementAt(i);
- int sr[] = shifts.get(s);
- while (i <= j && s <= t)
- {
- boolean trailinghn = hr[1] >= sr[0];
- if (!trailinghn)
- {
- if (i < j)
- {
- hr = intervals.elementAt(++i);
- }
- else
- {
- i++;
- }
- continue;
- }
- int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
- if (endshift < hr[0] || endshift < sr[0])
- { // leadinghc disjoint or not a deletion
- if (s < t)
- {
- sr = shifts.get(++s);
- }
- else
- {
- s++;
- }
- continue;
- }
- boolean leadinghn = hr[0] >= sr[0];
- boolean leadinghc = hr[0] < endshift;
- boolean trailinghc = hr[1] < endshift;
- if (leadinghn)
- {
- if (trailinghc)
- { // deleted hidden region.
- intervals.removeElementAt(i);
- pruned = true;
- j--;
- if (i <= j)
- {
- hr = intervals.elementAt(i);
- }
- continue;
- }
- if (leadinghc)
- {
- hr[0] = endshift; // clip c terminal region
- leadinghn = !leadinghn;
- pruned = true;
- }
- }
- if (!leadinghn)
- {
- if (trailinghc)
- {
- if (trailinghn)
- {
- hr[1] = sr[0] - 1;
- pruned = true;
- }
- }
- else
- {
- // sr contained in hr
- if (s < t)
- {
- sr = shifts.get(++s);
- }
- else
- {
- s++;
- }
- continue;
- }
- }
- }
- return pruned; // true if any interval was removed or modified by
- // operations.
- }
-
- /**
- * remove any hiddenColumns or selected columns and shift remaining based on a
- * series of position, range deletions.
- *
- * @param deletions
- */
- public void pruneDeletions(ShiftList deletions)
- {
- if (deletions != null)
- {
- final List<int[]> shifts = deletions.getShifts();
- if (shifts != null && shifts.size() > 0)
- {
- // delete any intervals intersecting.
- if (hiddenColumns != null)
- {
- pruneIntervalVector(shifts, hiddenColumns);
- if (hiddenColumns != null && hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
- }
- if (selection != null && selection.size() > 0)
- {
- selection.pruneColumnList(shifts);
- if (selection != null && selection.size() == 0)
- {
- selection = null;
- }
- }
- // and shift the rest.
- this.compensateForEdits(deletions);
- }
- }
- }
-
- /**
- * This Method is used to return all the HiddenColumn regions
- *
- * @return empty list or List of hidden column intervals
- */
- public List<int[]> getHiddenColumns()
- {
- return hiddenColumns == null ? Collections.<int[]> emptyList()
- : hiddenColumns;
- }
-
- /**
- * Return absolute column index for a visible column index
- *
- * @param column
- * int column index in alignment view (count from zero)
- * @return alignment column index for column
- */
- public int adjustForHiddenColumns(int column)
- {
- int result = column;
- if (hiddenColumns != null)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.elementAt(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
- }
- }
- return result;
- }
-
- /**
- * Use this method to find out where a column will appear in the visible
- * alignment when hidden columns exist. If the column is not visible, then the
- * left-most visible column will always be returned.
- *
- * @param hiddenColumn
- * 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)
- {
- int result = hiddenColumn;
- if (hiddenColumns != null)
- {
- int index = 0;
- int[] region;
- do
- {
- region = hiddenColumns.elementAt(index++);
- if (hiddenColumn > region[1])
- {
- result -= region[1] + 1 - region[0];
- }
- } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
-
- if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
- {
- // Here the hidden column is within a region, so
- // we want to return the position of region[0]-1, adjusted for any
- // earlier hidden columns.
- // Calculate the difference between the actual hidden col position
- // and region[0]-1, and then subtract from result to convert result from
- // the adjusted hiddenColumn value to the adjusted region[0]-1 value
-
- // However, if the region begins at 0 we cannot return region[0]-1
- // just return 0
- if (region[0] == 0)
- {
- return 0;
- }
- else
- {
- return result - (hiddenColumn - region[0] + 1);
- }
- }
- }
- return result; // return the shifted position after removing hidden columns.
- }
-
- /**
- * Find the visible column which is a given visible number of columns to the
- * left of another visible column. i.e. for a startColumn x, the column which
- * is distance 1 away will be column x-1.
- *
- * @param visibleDistance
- * the number of visible columns to offset by
- * @param startColumn
- * the column to start from
- * @return the position of the column in the visible alignment
- */
- public int subtractVisibleColumns(int visibleDistance, int startColumn)
- {
- int distance = visibleDistance;
-
- // in case startColumn is in a hidden region, move it to the left
- int start = adjustForHiddenColumns(findColumnPosition(startColumn));
-
- // get index of hidden region to left of start
- int index = getHiddenIndexLeft(start);
- if (index == -1)
- {
- // no hidden regions to left of startColumn
- return start - distance;
- }
-
- // walk backwards through the alignment subtracting the counts of visible
- // columns from distance
- int[] region;
- int gap = 0;
- int nextstart = start;
-
- while ((index > -1) && (distance - gap > 0))
- {
- // subtract the gap to right of region from distance
- distance -= gap;
- start = nextstart;
-
- // calculate the next gap
- region = hiddenColumns.get(index);
- gap = start - region[1];
-
- // set start to just to left of current region
- nextstart = region[0] - 1;
- index--;
- }
-
- if (distance - gap > 0)
- {
- // fell out of loop because there are no more hidden regions
- distance -= gap;
- return nextstart - distance;
- }
- return start - distance;
-
- }
-
- /**
- * Use this method to determine where the next hiddenRegion starts
- *
- * @param hiddenRegion
- * index of hidden region (counts from 0)
- * @return column number in visible view
- */
- public int findHiddenRegionPosition(int hiddenRegion)
- {
- int result = 0;
- if (hiddenColumns != null)
- {
- int index = 0;
- int gaps = 0;
- do
- {
- int[] region = hiddenColumns.elementAt(index);
- if (hiddenRegion == 0)
- {
- return region[0];
- }
-
- gaps += region[1] + 1 - region[0];
- result = region[1] + 1;
- index++;
- } while (index <= hiddenRegion);
-
- result -= gaps;
- }
-
- return result;
- }
-
- /**
- * THis method returns the rightmost limit of a region of an alignment with
- * hidden columns. In otherwords, the next hidden column.
- *
- * @param index
- * int
- */
- public int getHiddenBoundaryRight(int alPos)
- {
- if (hiddenColumns != null)
- {
- int index = 0;
- do
- {
- int[] region = hiddenColumns.elementAt(index);
- if (alPos < region[0])
- {
- return region[0];
- }
-
- index++;
- } while (index < hiddenColumns.size());
- }
-
- return alPos;
-
- }
-
- /**
- * This method returns the leftmost limit of a region of an alignment with
- * hidden columns. In otherwords, the previous hidden column.
- *
- * @param index
- * int
- */
- public int getHiddenBoundaryLeft(int alPos)
- {
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = hiddenColumns.elementAt(index);
- if (alPos > region[1])
- {
- return region[1];
- }
-
- index--;
- } while (index > -1);
- }
-
- return alPos;
-
- }
-
- /**
- * This method returns the index of the hidden region to the left of a column
- * position. If the column is in a hidden region it returns the index of the
- * region to the left. If there is no hidden region to the left it returns -1.
- *
- * @param pos
- * int
- */
- private int getHiddenIndexLeft(int pos)
- {
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = hiddenColumns.elementAt(index);
- if (pos > region[1])
- {
- return index;
- }
-
- index--;
- } while (index > -1);
- }
-
- return -1;
-
- }
-
- public void hideSelectedColumns()
- {
- synchronized (selection)
- {
- for (int[] selregions : selection.getRanges())
- {
- hideColumns(selregions[0], selregions[1]);
- }
- selection.clear();
- }
-
- }
-
- /**
- * Adds the specified column range to the hidden columns
- *
- * @param start
- * @param end
- */
- public void hideColumns(int start, int end)
- {
- if (hiddenColumns == null)
- {
- hiddenColumns = new Vector<int[]>();
- }
-
- /*
- * traverse existing hidden ranges and insert / amend / append as
- * appropriate
- */
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.elementAt(i);
-
- if (end < region[0] - 1)
- {
- /*
- * insert discontiguous preceding range
- */
- hiddenColumns.insertElementAt(new int[] { start, end }, i);
- return;
- }
-
- if (end <= region[1])
- {
- /*
- * new range overlaps existing, or is contiguous preceding it - adjust
- * start column
- */
- region[0] = Math.min(region[0], start);
- return;
- }
-
- if (start <= region[1] + 1)
- {
- /*
- * new range overlaps existing, or is contiguous following it - adjust
- * start and end columns
- */
- region[0] = Math.min(region[0], start);
- region[1] = Math.max(region[1], end);
-
- /*
- * also update or remove any subsequent ranges
- * that are overlapped
- */
- while (i < hiddenColumns.size() - 1)
- {
- int[] nextRegion = hiddenColumns.get(i + 1);
- if (nextRegion[0] > end + 1)
- {
- /*
- * gap to next hidden range - no more to update
- */
- break;
- }
- region[1] = Math.max(nextRegion[1], end);
- hiddenColumns.remove(i + 1);
- }
- return;
- }
- }
-
- /*
- * remaining case is that the new range follows everything else
- */
- hiddenColumns.addElement(new int[] { start, end });
- }
-
- /**
- * Hides the specified column and any adjacent selected columns
- *
- * @param res
- * int
- */
- public void hideColumns(int col)
- {
- /*
- * deselect column (whether selected or not!)
- */
- removeElement(col);
-
- /*
- * find adjacent selected columns
- */
- int min = col - 1, max = col + 1;
- while (contains(min))
- {
- removeElement(min);
- min--;
- }
-
- while (contains(max))
- {
- removeElement(max);
- max++;
- }
-
- /*
- * min, max are now the closest unselected columns
- */
- min++;
- max--;
- if (min > max)
- {
- min = max;
- }
-
- hideColumns(min, max);
- }
-
- /**
- * Unhides, and adds to the selection list, all hidden columns
- */
- public void revealAllHiddenColumns()
- {
- if (hiddenColumns != null)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.elementAt(i);
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- addElement(j);
- }
- }
- }
-
- hiddenColumns = null;
- }
-
- /**
- * Reveals, and marks as selected, the hidden column range with the given
- * start column
- *
- * @param start
- */
- public void revealHiddenColumns(int start)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.elementAt(i);
- if (start == region[0])
- {
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- addElement(j);
- }
-
- hiddenColumns.removeElement(region);
- break;
- }
- }
- if (hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
- }
-
- public boolean isVisible(int column)
- {
- if (hiddenColumns != null)
- {
- for (int[] region : hiddenColumns)
- {
- if (column >= region[0] && column <= region[1])
- {
- return false;
- }
- }
- }
-
- return true;
- }
-
- /**
- * Copy constructor
- *
- * @param copy
- */
- public ColumnSelection(ColumnSelection copy)
- {
- if (copy != null)
- {
- selection = new IntList(copy.selection);
- if (copy.hiddenColumns != null)
- {
- hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
- for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
- {
- int[] rh, cp;
- rh = copy.hiddenColumns.elementAt(i);
- if (rh != null)
- {
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- hiddenColumns.addElement(cp);
- }
- }
- }
- }