import java.util.BitSet;
import java.util.Collections;
import java.util.List;
-import java.util.Vector;
/**
- * NOTE: Columns are zero based.
+ * Data class holding the selected columns and hidden column ranges for a view.
+ * Ranges are base 1.
*/
public class ColumnSelection
{
+ /**
+ * A class to hold an efficient representation of selected columns
+ */
private class IntList
{
/*
* list of selected columns (ordered by selection order, not column order)
*/
- private List<Integer> order = new ArrayList<Integer>();
+ private List<Integer> order;
+
+ /*
+ * an unmodifiable view of the selected columns list
+ */
+ private List<Integer> _uorder;
/**
* bitfield for column selection - allows quick lookup
*/
- private BitSet selected = new BitSet();
+ private BitSet selected;
+
+ /**
+ * Constructor
+ */
+ IntList()
+ {
+ order = new ArrayList<Integer>();
+ _uorder = Collections.unmodifiableList(order);
+ selected = new BitSet();
+ }
+
+ /**
+ * Copy constructor
+ *
+ * @param other
+ */
+ IntList(IntList other)
+ {
+ this();
+ if (other != null)
+ {
+ int j = other.size();
+ for (int i = 0; i < j; i++)
+ {
+ add(other.elementAt(i));
+ }
+ }
+ }
/**
* adds a new column i to the selection - only if i is not already selected
*
* @param i
*/
- public void add(int i)
+ void add(int i)
{
if (!selected.get(i))
{
}
}
- public void clear()
+ void clear()
{
order.clear();
selected.clear();
}
- public void remove(int col)
+ void remove(int col)
{
Integer colInt = new Integer(col);
}
}
- public boolean contains(Integer colInt)
+ boolean contains(Integer colInt)
{
return selected.get(colInt);
}
- public boolean isEmpty()
+ boolean isEmpty()
{
return order.isEmpty();
}
- public List<Integer> getList()
+ /**
+ * Returns a read-only view of the selected columns list
+ *
+ * @return
+ */
+ List<Integer> getList()
{
- return order;
+ return _uorder;
}
- public int size()
+ int size()
{
return order.size();
}
* @param i
* @return
*/
- public int elementAt(int i)
+ int elementAt(int i)
{
return order.get(i);
}
* @param change
* - delta for shift
*/
- public void compensateForEdits(int start, int change)
+ void compensateForEdits(int start, int change)
{
BitSet mask = new BitSet();
for (int i = 0; i < order.size(); i++)
selected.or(mask);
}
- public boolean isSelected(int column)
+ boolean isSelected(int column)
{
return selected.get(column);
}
- public int getMaxColumn()
+ int getMaxColumn()
{
return selected.length() - 1;
}
- public int getMinColumn()
+ int getMinColumn()
{
return selected.get(0) ? 0 : selected.nextSetBit(0);
}
/**
* @return a series of selection intervals along the range
*/
- public List<int[]> getRanges()
+ List<int[]> getRanges()
{
List<int[]> rlist = new ArrayList<int[]>();
if (selected.isEmpty())
}
return rlist;
}
+
+ @Override
+ public int hashCode()
+ {
+ // TODO Auto-generated method stub
+ return selected.hashCode();
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj instanceof IntList)
+ {
+ return ((IntList) obj).selected.equals(selected);
+ }
+ return false;
+ }
}
- IntList selected = new IntList();
+ IntList selection = new IntList();
- /*
- * list of hidden column [start, end] ranges; the list is maintained in
- * ascending start column order
- */
- Vector<int[]> hiddenColumns;
+ HiddenColumns hiddenColumns = new HiddenColumns();
/**
* Add a column to the selection
*/
public void addElement(int col)
{
- selected.add(col);
+ selection.add(col);
}
/**
*/
public void clear()
{
- selected.clear();
+ selection.clear();
}
/**
*/
public void removeElement(int col)
{
- selected.remove(col);
+ selection.remove(col);
}
/**
for (int i = start; i < end; i++)
{
colInt = new Integer(i);
- if (selected.contains(colInt))
+ if (selection.contains(colInt))
{
- selected.remove(colInt);
+ selection.remove(colInt);
}
}
}
/**
- * Returns a list of selected columns. The list contains no duplicates but is
- * not necessarily ordered. It also may include columns hidden from the
- * current view
+ * Returns a read-only view of the (possibly empty) list of selected columns
+ * <p>
+ * The list contains no duplicates but is not necessarily ordered. It also may
+ * include columns hidden from the current view. To modify (for example sort)
+ * the list, you should first make a copy.
+ * <p>
+ * The list is not thread-safe: iterating over it could result in
+ * ConcurrentModificationException if it is modified by another thread.
*/
public List<Integer> getSelected()
{
- return selected.getList();
+ return selection.getList();
}
/**
*/
public List<int[]> getSelectedRanges()
{
- return selected.getRanges();
+ return selection.getRanges();
}
/**
*/
public boolean contains(int col)
{
- return (col > -1) ? selected.isSelected(col) : false;
+ return (col > -1) ? selection.isSelected(col) : false;
}
/**
*/
public boolean isEmpty()
{
- return selected == null || selected.isEmpty();
+ return selection == null || selection.isEmpty();
}
/**
*/
public int getMax()
{
- if (selected.isEmpty())
+ if (selection.isEmpty())
{
return -1;
}
- return selected.getMaxColumn();
+ return selection.getMaxColumn();
}
/**
*/
public int getMin()
{
- if (selected.isEmpty())
+ if (selection.isEmpty())
{
return 1000000000;
}
- return selected.getMinColumn();
+ return selection.getMinColumn();
}
/**
* @param left
* shift in edit (+ve for removal, or -ve for inserts)
*/
- public List<int[]> compensateForEdit(int start, int change)
- {
- List<int[]> deletedHiddenColumns = null;
- selected.compensateForEdits(start, change);
-
- if (hiddenColumns != null)
+ /* public List<int[]> compensateForEdit(int start, int change)
{
- 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);
+ selection.compensateForEdits(start, change);
+ return hiddenColumns.compensateForEdit(start, change, this);
}
-
- return deletedHiddenColumns;
- }
-
+ */
/**
* propagate shift in alignment columns to column selection special version of
* compensateForEdit - allowing for edits within hidden regions
*/
private void compensateForDelEdits(int start, int change)
{
-
- selected.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;
- }
- }
- }
+ selection.compensateForEdits(start, change);
+ hiddenColumns.compensateForDelEdits(start, change);
}
/**
* @param shiftrecord
* @return
*/
- public ShiftList compensateForEdits(ShiftList shiftrecord)
+ private ShiftList compensateForEdits(ShiftList shiftrecord)
{
if (shiftrecord != null)
{
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 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
*
* @param deletions
*/
- public void pruneDeletions(ShiftList deletions)
+ private 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 (selected != null && selected.size() > 0)
+ hiddenColumns.pruneDeletions(shifts);
+
+ if (selection != null && selection.size() > 0)
{
- selected.pruneColumnList(shifts);
- if (selected != null && selected.size() == 0)
+ selection.pruneColumnList(shifts);
+ if (selection != null && selection.size() == 0)
{
- selected = null;
+ selection = null;
}
}
// and shift the rest.
}
}
- /**
- * 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
- * @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
- * int
- * @return int
- */
- 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])
- {
- return region[0] + hiddenColumn - result;
- }
- }
- return result; // return the shifted position after removing hidden columns.
- }
-
- /**
- * 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;
-
- }
-
- public void hideSelectedColumns()
+ public void hideSelectedColumns(AlignmentI al)
{
- synchronized (selected)
+ synchronized (selection)
{
- for (int[] selregions : selected.getRanges())
+ for (int[] selregions : selection.getRanges())
{
- hideColumns(selregions[0], selregions[1]);
+ al.getHiddenColumns().hideColumns(selregions[0], selregions[1]);
}
- selected.clear();
+ 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);
- 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)
+ public void hideSelectedColumns(int col, AlignmentI al)
{
/*
* deselect column (whether selected or not!)
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;
+ al.getHiddenColumns().hideColumns(min, max);
}
- /**
- * 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
{
if (copy != null)
{
- if (copy.selected != null)
- {
- selected = new IntList();
- for (int i = 0, j = copy.selected.size(); i < j; i++)
- {
- selected.add(copy.selected.elementAt(i));
- }
- }
- 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);
- }
- }
- }
+ selection = new IntList(copy.selection);
}
}
{
}
- public String[] getVisibleSequenceStrings(int start, int end,
- SequenceI[] seqs)
- {
- int i, iSize = seqs.length;
- String selection[] = new String[iSize];
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- for (i = 0; i < iSize; i++)
- {
- StringBuffer visibleSeq = new StringBuffer();
- List<int[]> regions = getHiddenColumns();
- int blockStart = start, blockEnd = end;
- int[] region;
- int hideStart, hideEnd;
- for (int j = 0; j < regions.size(); j++)
- {
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
- if (hideStart < start)
- {
- continue;
- }
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
- {
- break;
- }
-
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
-
- if (end > blockStart)
- {
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
- }
-
- selection[i] = visibleSeq.toString();
- }
- }
- else
- {
- for (i = 0; i < iSize; i++)
- {
- selection[i] = seqs[i].getSequenceAsString(start, end);
- }
- }
-
- return selection;
- }
-
- /**
- * return all visible segments between the given start and end boundaries
- *
- * @param start
- * (first column inclusive from 0)
- * @param end
- * (last column - not inclusive)
- * @return int[] {i_start, i_end, ..} where intervals lie in
- * start<=i_start<=i_end<end
- */
- public int[] getVisibleContigs(int start, int end)
- {
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- List<int[]> visiblecontigs = new ArrayList<int[]>();
- List<int[]> regions = getHiddenColumns();
-
- int vstart = start;
- int[] region;
- int hideStart, hideEnd;
-
- for (int j = 0; vstart < end && j < regions.size(); j++)
- {
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideEnd < vstart)
- {
- continue;
- }
- if (hideStart > vstart)
- {
- visiblecontigs.add(new int[] { vstart, hideStart - 1 });
- }
- vstart = hideEnd + 1;
- }
-
- if (vstart < end)
- {
- visiblecontigs.add(new int[] { vstart, end - 1 });
- }
- int[] vcontigs = new int[visiblecontigs.size() * 2];
- for (int i = 0, j = visiblecontigs.size(); i < j; i++)
- {
- int[] vc = visiblecontigs.get(i);
- visiblecontigs.set(i, null);
- vcontigs[i * 2] = vc[0];
- vcontigs[i * 2 + 1] = vc[1];
- }
- visiblecontigs.clear();
- return vcontigs;
- }
- else
- {
- return new int[] { start, end - 1 };
- }
- }
-
- /**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
- *
- * @param alignmentAnnotation
- */
- public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
- {
- makeVisibleAnnotation(-1, -1, alignmentAnnotation);
- }
-
- /**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
- *
- * @param start
- * remove any annotation to the right of this column
- * @param end
- * remove any annotation to the left of this column
- * @param alignmentAnnotation
- * the annotation to operate on
- */
- public void makeVisibleAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
- {
- if (alignmentAnnotation.annotations == null)
- {
- return;
- }
- if (start == end && end == -1)
- {
- start = 0;
- end = alignmentAnnotation.annotations.length;
- }
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- // then mangle the alignmentAnnotation annotation array
- Vector<Annotation[]> annels = new Vector<Annotation[]>();
- Annotation[] els = null;
- List<int[]> regions = getHiddenColumns();
- int blockStart = start, blockEnd = end;
- int[] region;
- int hideStart, hideEnd, w = 0;
-
- for (int j = 0; j < regions.size(); j++)
- {
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideStart < start)
- {
- continue;
- }
-
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
- {
- break;
- }
-
- annels.addElement(els = new Annotation[blockEnd - blockStart]);
- System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
- 0, els.length);
- w += els.length;
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
-
- if (end > blockStart)
- {
- annels.addElement(els = new Annotation[end - blockStart + 1]);
- if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
- {
- // copy just the visible segment of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0, els.length);
- }
- else
- {
- // copy to the end of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0,
- (alignmentAnnotation.annotations.length - blockStart));
- }
- w += els.length;
- }
- if (w == 0)
- {
- return;
- }
-
- alignmentAnnotation.annotations = new Annotation[w];
- w = 0;
-
- for (Annotation[] chnk : annels)
- {
- System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
- chnk.length);
- w += chnk.length;
- }
- }
- else
- {
- alignmentAnnotation.restrict(start, end);
- }
- }
/**
* Invert the column selection from first to end-1. leaves hiddenColumns
* @param first
* @param end
*/
- public void invertColumnSelection(int first, int width)
+ public void invertColumnSelection(int first, int width, AlignmentI al)
{
- boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;
+ boolean hasHidden = al.getHiddenColumns().hasHidden();
for (int i = first; i < width; i++)
{
if (contains(i))
}
else
{
- if (!hasHidden || isVisible(i))
+ if (!hasHidden || al.getHiddenColumns().isVisible(i))
{
addElement(i);
}
{
for (Integer col : colsel.getSelected())
{
- if (hiddenColumns != null && isVisible(col.intValue()))
+ if (hiddenColumns != null
+ && hiddenColumns.isVisible(col.intValue()))
{
- selected.add(col);
+ selection.add(col);
}
}
}
*/
public void setElementsFrom(ColumnSelection colsel)
{
- selected = new IntList();
- if (colsel.selected != null && colsel.selected.size() > 0)
+ selection = new IntList();
+ if (colsel.selection != null && colsel.selection.size() > 0)
{
- if (hiddenColumns != null && hiddenColumns.size() > 0)
+ if (hiddenColumns.hasHidden())
{
// only select visible columns in this columns selection
addElementsFrom(colsel);
// return propagateInsertions(profileseq, al, )
char gc = al.getGapCharacter();
- Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
+ Object[] alandcolsel = input.getAlignmentAndHiddenColumns(gc);
ColumnSelection nview = (ColumnSelection) alandcolsel[1];
SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos];
nview.propagateInsertions(profileseq, al, origseq);
* - sequence corresponding to profileseq which defines gap map for
* modifying al
*/
- public void propagateInsertions(SequenceI profileseq, AlignmentI al,
+ private void propagateInsertions(SequenceI profileseq, AlignmentI al,
SequenceI origseq)
{
char gc = al.getGapCharacter();
// recover mapping between sequence's non-gap positions and positions
// mapping to view.
pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
- int[] viscontigs = getVisibleContigs(0, profileseq.getLength());
+ int[] viscontigs = hiddenColumns.getVisibleContigs(0,
+ profileseq.getLength());
int spos = 0;
int offset = 0;
- // input.pruneDeletions(ShiftList.parseMap(((SequenceI[])
- // alandcolsel[0])[0].gapMap()))
+
// add profile to visible contigs
for (int v = 0; v < viscontigs.length; v += 2)
{
*/
public boolean hasSelectedColumns()
{
- return (selected != null && selected.size() > 0);
- }
-
- /**
- *
- * @return true if there are columns hidden
- */
- public boolean hasHiddenColumns()
- {
- return hiddenColumns != null && hiddenColumns.size() > 0;
+ return (selection != null && selection.size() > 0);
}
- /**
- *
- * @return true if there are more than one set of columns hidden
- */
- public boolean hasManyHiddenColumns()
- {
- return hiddenColumns != null && hiddenColumns.size() > 1;
- }
- /**
- * mark the columns corresponding to gap characters as hidden in the column
- * selection
- *
- * @param sr
- */
- public void hideInsertionsFor(SequenceI sr)
- {
- List<int[]> inserts = sr.getInsertions();
- for (int[] r : inserts)
- {
- hideColumns(r[0], r[1]);
- }
- }
public boolean filterAnnotations(Annotation[] annotations,
AnnotationFilterParameter filterParams)
{
- this.revealAllHiddenColumns();
+ // JBPNote - this method needs to be refactored to become independent of
+ // viewmodel package
+ hiddenColumns.revealAllHiddenColumns(this);
this.clear();
int count = 0;
do
} while (count < annotations.length);
return false;
}
+
+ /**
+ * Returns a hashCode built from selected columns and hidden column ranges
+ */
+ @Override
+ public int hashCode()
+ {
+ int hashCode = selection.hashCode();
+ return hiddenColumns.hashCode(hashCode);
+ }
+
+ /**
+ * Answers true if comparing to a ColumnSelection with the same selected
+ * columns and hidden columns, else false
+ */
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (!(obj instanceof ColumnSelection))
+ {
+ return false;
+ }
+ ColumnSelection that = (ColumnSelection) obj;
+
+ /*
+ * check columns selected are either both null, or match
+ */
+ if (this.selection == null)
+ {
+ if (that.selection != null)
+ {
+ return false;
+ }
+ }
+ if (!this.selection.equals(that.selection))
+ {
+ return false;
+ }
+
+ return this.hiddenColumns.equals(that.hiddenColumns);
+ }
+
+ /**
+ * Updates the column selection depending on the parameters, and returns true
+ * if any change was made to the selection
+ *
+ * @param markedColumns
+ * a set identifying marked columns (base 0)
+ * @param startCol
+ * the first column of the range to operate over (base 0)
+ * @param endCol
+ * the last column of the range to operate over (base 0)
+ * @param invert
+ * if true, deselect marked columns and select unmarked
+ * @param extendCurrent
+ * if true, extend rather than replacing the current column selection
+ * @param toggle
+ * if true, toggle the selection state of marked columns
+ *
+ * @return
+ */
+ public boolean markColumns(BitSet markedColumns, int startCol,
+ int endCol, boolean invert, boolean extendCurrent, boolean toggle)
+ {
+ boolean changed = false;
+ if (!extendCurrent && !toggle)
+ {
+ changed = !this.isEmpty();
+ clear();
+ }
+ if (invert)
+ {
+ // invert only in the currently selected sequence region
+ int i = markedColumns.nextClearBit(startCol);
+ int ibs = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
+ {
+ if (ibs < 0 || i < ibs)
+ {
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i++);
+ }
+ else
+ {
+ addElement(i++);
+ }
+ }
+ else
+ {
+ i = markedColumns.nextClearBit(ibs);
+ ibs = markedColumns.nextSetBit(i);
+ }
+ }
+ }
+ else
+ {
+ int i = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
+ {
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i);
+ }
+ else
+ {
+ addElement(i);
+ }
+ i = markedColumns.nextSetBit(i + 1);
+ }
+ }
+ return changed;
+ }
+
+ /**
+ * Adjusts column selections, and the given selection group, to match the
+ * range of a stretch (e.g. mouse drag) operation
+ * <p>
+ * Method refactored from ScalePanel.mouseDragged
+ *
+ * @param res
+ * current column position, adjusted for hidden columns
+ * @param sg
+ * current selection group
+ * @param min
+ * start position of the stretch group
+ * @param max
+ * end position of the stretch group
+ */
+ public void stretchGroup(int res, SequenceGroup sg, int min, int max)
+ {
+ if (!contains(res))
+ {
+ addElement(res);
+ }
+
+ if (res > sg.getStartRes())
+ {
+ // expand selection group to the right
+ sg.setEndRes(res);
+ }
+ if (res < sg.getStartRes())
+ {
+ // expand selection group to the left
+ sg.setStartRes(res);
+ }
+
+ /*
+ * expand or shrink column selection to match the
+ * range of the drag operation
+ */
+ for (int col = min; col <= max; col++)
+ {
+ if (col < sg.getStartRes() || col > sg.getEndRes())
+ {
+ // shrinking drag - remove from selection
+ removeElement(col);
+ }
+ else
+ {
+ // expanding drag - add to selection
+ addElement(col);
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff