/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import jalview.util.ShiftList;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
-import jalview.util.*;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.List;
/**
- * 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
{
- Vector selected = new Vector();
-
- // Vector of int [] {startCol, endCol}
- Vector hiddenColumns;
-
/**
- * Add a column to the selection
- *
- * @param col
- * index of column
+ * A class to hold an efficient representation of selected columns
*/
- public void addElement(int col)
+ private class IntList
{
- Integer column = new Integer(col);
- if (!selected.contains(column))
+ /*
+ * list of selected columns (ordered by selection order, not column order)
+ */
+ 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;
+
+ /**
+ * Constructor
+ */
+ IntList()
{
- selected.addElement(column);
+ order = new ArrayList<Integer>();
+ _uorder = Collections.unmodifiableList(order);
+ selected = new BitSet();
}
- }
- /**
- * clears column selection
- */
- public void clear()
- {
- selected.removeAllElements();
- }
-
- /**
- * removes col from selection
- *
- * @param col
- * index of column to be removed
- */
- public void removeElement(int col)
- {
- Integer colInt = new Integer(col);
-
- if (selected.contains(colInt))
+ /**
+ * Copy constructor
+ *
+ * @param other
+ */
+ IntList(IntList other)
{
- selected.removeElement(colInt);
+ this();
+ if (other != null)
+ {
+ int j = other.size();
+ for (int i = 0; i < j; i++)
+ {
+ add(other.elementAt(i));
+ }
+ }
}
- }
- /**
- * removes a range of columns from the selection
- *
- * @param start
- * int - first column in range to be removed
- * @param end
- * int - last col
- */
- public void removeElements(int start, int end)
- {
- Integer colInt;
- for (int i = start; i < end; i++)
+ /**
+ * adds a new column i to the selection - only if i is not already selected
+ *
+ * @param i
+ */
+ void add(int i)
{
- colInt = new Integer(i);
- if (selected.contains(colInt))
+ if (!selected.get(i))
{
- selected.removeElement(colInt);
+ order.add(Integer.valueOf(i));
+ selected.set(i);
}
}
- }
-
- /**
- *
- * @return Vector containing selected columns as Integers
- */
- public Vector getSelected()
- {
- return selected;
- }
-
- /**
- *
- * @param col
- * index to search for in column selection
- *
- * @return true if Integer(col) is in selection.
- */
- public boolean contains(int col)
- {
- return selected.contains(new Integer(col));
- }
- /**
- * Column number at position i in selection
- *
- * @param i
- * index into selected columns
- *
- * @return column number in alignment
- */
- public int columnAt(int i)
- {
- return ((Integer) selected.elementAt(i)).intValue();
- }
+ void clear()
+ {
+ order.clear();
+ selected.clear();
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int size()
- {
- return selected.size();
- }
+ void remove(int col)
+ {
- /**
- * rightmost selected column
- *
- * @return rightmost column in alignment that is selected
- */
- public int getMax()
- {
- int max = -1;
+ Integer colInt = new Integer(col);
- for (int i = 0; i < selected.size(); i++)
- {
- if (columnAt(i) > max)
+ if (selected.get(col))
{
- max = columnAt(i);
+ // if this ever changes to List.remove(), ensure Integer not int
+ // argument
+ // as List.remove(int i) removes the i'th item which is wrong
+ order.remove(colInt);
+ selected.clear(col);
}
}
- return max;
- }
-
- /**
- * Leftmost column in selection
- *
- * @return column index of leftmost column in selection
- */
- public int getMin()
- {
- int min = 1000000000;
+ boolean contains(Integer colInt)
+ {
+ return selected.get(colInt);
+ }
- for (int i = 0; i < selected.size(); i++)
+ boolean isEmpty()
{
- if (columnAt(i) < min)
- {
- min = columnAt(i);
- }
+ return order.isEmpty();
}
- return min;
- }
+ /**
+ * Returns a read-only view of the selected columns list
+ *
+ * @return
+ */
+ List<Integer> getList()
+ {
+ return _uorder;
+ }
- /**
- * 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 Vector compensateForEdit(int start, int change)
- {
- Vector deletedHiddenColumns = null;
- for (int i = 0; i < size(); i++)
+ int size()
{
- int temp = columnAt(i);
+ return order.size();
+ }
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
+ /**
+ * gets the column that was selected first, second or i'th
+ *
+ * @param i
+ * @return
+ */
+ int elementAt(int i)
+ {
+ return order.get(i);
}
- if (hiddenColumns != null)
+ protected boolean pruneColumnList(final List<int[]> shifts)
{
- deletedHiddenColumns = new Vector();
- int hSize = hiddenColumns.size();
- for (int i = 0; i < hSize; i++)
+ int s = 0, t = shifts.size();
+ int[] sr = shifts.get(s++);
+ boolean pruned = false;
+ int i = 0, j = order.size();
+ while (i < j && s <= t)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (region[0] > start && start + change > region[1])
+ int c = order.get(i++).intValue();
+ if (sr[0] <= c)
{
- deletedHiddenColumns.addElement(hiddenColumns.elementAt(i));
-
- hiddenColumns.removeElementAt(i);
- i--;
- hSize--;
- continue;
+ if (sr[1] + sr[0] >= c)
+ { // sr[1] -ve means inseriton.
+ order.remove(--i);
+ selected.clear(c);
+ j--;
+ }
+ else
+ {
+ if (s < t)
+ {
+ sr = shifts.get(s);
+ }
+ s++;
+ }
}
+ }
+ return pruned;
+ }
- if (region[0] > start)
- {
- region[0] -= change;
- region[1] -= change;
- }
+ /**
+ * shift every selected column at or above start by change
+ *
+ * @param start
+ * - leftmost column to be shifted
+ * @param change
+ * - delta for shift
+ */
+ void compensateForEdits(int start, int change)
+ {
+ BitSet mask = new BitSet();
+ for (int i = 0; i < order.size(); i++)
+ {
+ int temp = order.get(i);
- if (region[0] < 0)
+ if (temp >= start)
{
- region[0] = 0;
+ // clear shifted bits and update List of selected columns
+ selected.clear(temp);
+ mask.set(temp - change);
+ order.set(i, new Integer(temp - change));
}
-
}
-
- this.revealHiddenColumns(0);
+ // lastly update the bitfield all at once
+ selected.or(mask);
}
- 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)
- {
- for (int i = 0; i < size(); i++)
+ boolean isSelected(int column)
{
- int temp = columnAt(i);
-
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
+ return selected.get(column);
}
- if (hiddenColumns != null)
+ int getMaxColumn()
{
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = (int[]) 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;
- }
- }
+ return selected.length() - 1;
}
- }
- /**
- * 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)
+ int getMinColumn()
{
- Vector shifts = shiftrecord.shifts;
- if (shifts != null && shifts.size() > 0)
- {
- int shifted = 0;
- for (int i = 0, j = shifts.size(); i < j; i++)
- {
- int[] sh = (int[]) shifts.elementAt(i);
- // compensateForEdit(shifted+sh[0], sh[1]);
- compensateForDelEdits(shifted + sh[0], sh[1]);
- shifted -= sh[1];
- }
- }
- return shiftrecord.getInverse();
+ return selected.get(0) ? 0 : selected.nextSetBit(0);
}
- return null;
- }
- /**
- * removes intersection of position,length ranges in deletions from the
- * start,end regions marked in intervals.
- *
- * @param deletions
- * @param intervals
- * @return
- */
- private boolean pruneIntervalVector(Vector deletions, Vector intervals)
- {
- boolean pruned = false;
- int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1;
- int hr[] = (int[]) intervals.elementAt(i);
- int sr[] = (int[]) deletions.elementAt(s);
- while (i <= j && s <= t)
+ /**
+ * @return a series of selection intervals along the range
+ */
+ List<int[]> getRanges()
{
- boolean trailinghn = hr[1] >= sr[0];
- if (!trailinghn)
+ List<int[]> rlist = new ArrayList<int[]>();
+ if (selected.isEmpty())
{
- if (i < j)
- {
- hr = (int[]) intervals.elementAt(++i);
- }
- else
- {
- i++;
- }
- continue;
+ return rlist;
}
- 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 = (int[]) deletions.elementAt(++s);
- }
- else
- {
- s++;
- }
- continue;
- }
- boolean leadinghn = hr[0] >= sr[0];
- boolean leadinghc = hr[0] < endshift;
- boolean trailinghc = hr[1] < endshift;
- if (leadinghn)
+ int next = selected.nextSetBit(0), clear = -1;
+ while (next != -1)
{
- if (trailinghc)
- { // deleted hidden region.
- intervals.removeElementAt(i);
- pruned = true;
- j--;
- if (i <= j)
- {
- hr = (int[]) 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 = (int[]) deletions.elementAt(++s);
- }
- else
- {
- s++;
- }
- continue;
- }
+ clear = selected.nextClearBit(next);
+ rlist.add(new int[] { next, clear - 1 });
+ next = selected.nextSetBit(clear);
}
+ return rlist;
}
- return pruned; // true if any interval was removed or modified by
- // operations.
- }
- private boolean pruneColumnList(Vector deletion, Vector list)
- {
- int s = 0, t = deletion.size();
- int[] sr = (int[]) list.elementAt(s++);
- boolean pruned = false;
- int i = 0, j = list.size();
- while (i < j && s <= t)
+ @Override
+ public int hashCode()
+ {
+ // TODO Auto-generated method stub
+ return selected.hashCode();
+ }
+
+ @Override
+ public boolean equals(Object obj)
{
- int c = ((Integer) list.elementAt(i++)).intValue();
- if (sr[0] <= c)
+ if (obj instanceof IntList)
{
- if (sr[1] + sr[0] >= c)
- { // sr[1] -ve means inseriton.
- list.removeElementAt(--i);
- j--;
- }
- else
- {
- if (s < t)
- {
- sr = (int[]) deletion.elementAt(s);
- }
- s++;
- }
+ return ((IntList) obj).selected.equals(selected);
}
+ return false;
}
- return pruned;
}
+ IntList selection = new IntList();
+
+ HiddenColumns hiddenColumns = new HiddenColumns();
+
/**
- * remove any hiddenColumns or selected columns and shift remaining based on a
- * series of position, range deletions.
+ * Add a column to the selection
*
- * @param deletions
+ * @param col
+ * index of column
*/
- public void pruneDeletions(ShiftList deletions)
+ public void addElement(int col)
{
- if (deletions != null)
- {
- Vector shifts = deletions.shifts;
- 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)
- {
- pruneColumnList(shifts, selected);
- if (selected != null && selected.size() == 0)
- {
- selected = null;
- }
- }
- // and shift the rest.
- this.compensateForEdits(deletions);
- }
- }
+ selection.add(col);
}
/**
- * This Method is used to return all the HiddenColumn regions less than the
- * given index.
- *
- * @param end
- * int
- * @return Vector
+ * clears column selection
*/
- public Vector getHiddenColumns()
+ public void clear()
{
- return hiddenColumns;
+ selection.clear();
}
/**
- * Return absolute column index for a visible column index
+ * Removes value 'col' from the selection (not the col'th item)
*
- * @param column
- * int column index in alignment view
- * @return alignment column index for column
+ * @param col
+ * index of column to be removed
*/
- public int adjustForHiddenColumns(int column)
+ public void removeElement(int col)
{
- int result = column;
- if (hiddenColumns != null)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
- }
- }
- return result;
+ selection.remove(col);
}
/**
- * 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.
+ * removes a range of columns from the selection
*
- * @param hiddenColumn
- * int
- * @return int
+ * @param start
+ * int - first column in range to be removed
+ * @param end
+ * int - last col
*/
- public int findColumnPosition(int hiddenColumn)
+ public void removeElements(int start, int end)
{
- int result = hiddenColumn;
- if (hiddenColumns != null)
+ Integer colInt;
+ for (int i = start; i < end; i++)
{
- int index = 0;
- int[] region;
- do
- {
- region = (int[]) 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])
+ colInt = new Integer(i);
+ if (selection.contains(colInt))
{
- return region[0] + hiddenColumn - result;
+ selection.remove(colInt);
}
}
- return result; // return the shifted position after removing hidden columns.
}
/**
- * Use this method to determine where the next hiddenRegion starts
+ * 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 int findHiddenRegionPosition(int hiddenRegion)
+ public List<Integer> getSelected()
{
- int result = 0;
- if (hiddenColumns != null)
- {
- int index = 0;
- int gaps = 0;
- do
- {
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if (hiddenRegion == 0)
- {
- return region[0];
- }
-
- gaps += region[1] + 1 - region[0];
- result = region[1] + 1;
- index++;
- } while (index < hiddenRegion + 1);
-
- result -= gaps;
- }
-
- return result;
+ return selection.getList();
}
/**
- * THis method returns the rightmost limit of a region of an alignment with
- * hidden columns. In otherwords, the next hidden column.
- *
- * @param index
- * int
+ * @return list of int arrays containing start and end column position for
+ * runs of selected columns ordered from right to left.
*/
- public int getHiddenBoundaryRight(int alPos)
+ public List<int[]> getSelectedRanges()
{
- if (hiddenColumns != null)
- {
- int index = 0;
- do
- {
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if (alPos < region[0])
- {
- return region[0];
- }
-
- index++;
- } while (index < hiddenColumns.size());
- }
-
- return alPos;
-
+ return selection.getRanges();
}
/**
- * This method returns the leftmost limit of a region of an alignment with
- * hidden columns. In otherwords, the previous hidden column.
*
- * @param index
- * int
+ * @param col
+ * index to search for in column selection
+ *
+ * @return true if col is selected
*/
- public int getHiddenBoundaryLeft(int alPos)
+ public boolean contains(int col)
{
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = (int[]) hiddenColumns.elementAt(index);
- if (alPos > region[1])
- {
- return region[1];
- }
-
- index--;
- } while (index > -1);
- }
-
- return alPos;
-
+ return (col > -1) ? selection.isSelected(col) : false;
}
- public void hideSelectedColumns()
- {
- while (size() > 0)
- {
- int column = ((Integer) getSelected().firstElement()).intValue();
- hideColumns(column);
- }
-
- }
-
- public void hideColumns(int start, int end)
+ /**
+ * Answers true if no columns are selected, else false
+ */
+ public boolean isEmpty()
{
- if (hiddenColumns == null)
- {
- hiddenColumns = new Vector();
- }
-
- boolean added = false;
- boolean overlap = false;
-
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (start <= region[1] && end >= region[0])
- {
- hiddenColumns.removeElementAt(i);
- overlap = true;
- break;
- }
- else if (end < region[0] && start < region[0])
- {
- hiddenColumns.insertElementAt(new int[]
- { start, end }, i);
- added = true;
- break;
- }
- }
-
- if (overlap)
- {
- hideColumns(start, end);
- }
- else if (!added)
- {
- hiddenColumns.addElement(new int[]
- { start, end });
- }
-
+ return selection == null || selection.isEmpty();
}
/**
- * This method will find a range of selected columns around the column
- * specified
+ * rightmost selected column
*
- * @param res
- * int
+ * @return rightmost column in alignment that is selected
*/
- public void hideColumns(int col)
+ public int getMax()
{
- // First find out range of columns to hide
- int min = col, max = col + 1;
- while (contains(min))
- {
- removeElement(min);
- min--;
- }
-
- while (contains(max))
+ if (selection.isEmpty())
{
- removeElement(max);
- max++;
+ return -1;
}
-
- min++;
- max--;
- if (min > max)
- {
- min = max;
- }
-
- hideColumns(min, max);
+ return selection.getMaxColumn();
}
- public void revealAllHiddenColumns()
+ /**
+ * Leftmost column in selection
+ *
+ * @return column index of leftmost column in selection
+ */
+ public int getMin()
{
- if (hiddenColumns != null)
+ if (selection.isEmpty())
{
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = (int[]) hiddenColumns.elementAt(i);
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- addElement(j);
- }
- }
+ return 1000000000;
}
-
- hiddenColumns = null;
+ return selection.getMinColumn();
}
- public void revealHiddenColumns(int res)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (res == region[0])
- {
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- addElement(j);
- }
-
- hiddenColumns.removeElement(region);
- break;
- }
- }
- if (hiddenColumns.size() == 0)
+ /**
+ * 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)
{
- hiddenColumns = null;
+ selection.compensateForEdits(start, change);
+ return hiddenColumns.compensateForEdit(start, change, this);
}
- }
-
- public boolean isVisible(int column)
- {
- if (hiddenColumns != null)
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (column >= region[0] && column <= region[1])
- {
- return false;
- }
- }
-
- return true;
+ */
+ /**
+ * 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);
+ hiddenColumns.compensateForDelEdits(start, change);
}
/**
- * Copy constructor
+ * Adjust hidden column boundaries based on a series of column additions or
+ * deletions in visible regions.
*
- * @param copy
+ * @param shiftrecord
+ * @return
*/
- public ColumnSelection(ColumnSelection copy)
+ private ShiftList compensateForEdits(ShiftList shiftrecord)
{
- if (copy != null)
+ if (shiftrecord != null)
{
- if (copy.selected != null)
- {
- selected = new Vector();
- for (int i = 0, j = copy.selected.size(); i < j; i++)
- {
- selected.addElement(copy.selected.elementAt(i));
- }
- }
- if (copy.hiddenColumns != null)
+ final List<int[]> shifts = shiftrecord.getShifts();
+ if (shifts != null && shifts.size() > 0)
{
- hiddenColumns = new Vector(copy.hiddenColumns.size());
- for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
+ int shifted = 0;
+ for (int i = 0, j = shifts.size(); i < j; i++)
{
- int[] rh, cp;
- rh = (int[]) copy.hiddenColumns.elementAt(i);
- if (rh != null)
- {
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- hiddenColumns.addElement(cp);
- }
+ int[] sh = shifts.get(i);
+ compensateForDelEdits(shifted + sh[0], sh[1]);
+ shifted -= sh[1];
}
}
+ return shiftrecord.getInverse();
}
+ return null;
}
+
/**
- * ColumnSelection
+ * remove any hiddenColumns or selected columns and shift remaining based on a
+ * series of position, range deletions.
+ *
+ * @param deletions
*/
- public ColumnSelection()
+ private void pruneDeletions(ShiftList deletions)
{
- }
-
- 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)
+ if (deletions != null)
{
- for (i = 0; i < iSize; i++)
+ final List<int[]> shifts = deletions.getShifts();
+ if (shifts != null && shifts.size() > 0)
{
- StringBuffer visibleSeq = new StringBuffer();
- Vector regions = getHiddenColumns();
-
- int blockStart = start, blockEnd = end;
- int[] region;
- int hideStart, hideEnd;
+ hiddenColumns.pruneDeletions(shifts);
- for (int j = 0; j < regions.size(); j++)
+ if (selection != null && selection.size() > 0)
{
- region = (int[]) regions.elementAt(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)
+ selection.pruneColumnList(shifts);
+ if (selection != null && selection.size() == 0)
{
- break;
+ selection = null;
}
-
- 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();
+ // and shift the rest.
+ this.compensateForEdits(deletions);
}
}
- else
+ }
+
+
+ public void hideSelectedColumns(AlignmentI al)
+ {
+ synchronized (selection)
{
- for (i = 0; i < iSize; i++)
+ for (int[] selregions : selection.getRanges())
{
- selection[i] = seqs[i].getSequenceAsString(start, end);
+ al.getHiddenColumns().hideColumns(selregions[0], selregions[1]);
}
+ selection.clear();
}
- return selection;
}
+
/**
- * return all visible segments between the given start and end boundaries
+ * Hides the specified column and any adjacent selected columns
*
- * @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
+ * @param res
+ * int
*/
- public int[] getVisibleContigs(int start, int end)
+ public void hideSelectedColumns(int col, AlignmentI al)
{
- if (hiddenColumns != null && hiddenColumns.size() > 0)
+ /*
+ * deselect column (whether selected or not!)
+ */
+ removeElement(col);
+
+ /*
+ * find adjacent selected columns
+ */
+ int min = col - 1, max = col + 1;
+ while (contains(min))
{
- Vector visiblecontigs = new Vector();
- Vector regions = getHiddenColumns();
-
- int vstart = start;
- int[] region;
- int hideStart, hideEnd;
-
- for (int j = 0; vstart < end && j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideEnd < vstart)
- {
- continue;
- }
- if (hideStart > vstart)
- {
- visiblecontigs.addElement(new int[]
- { vstart, hideStart - 1 });
- }
- vstart = hideEnd + 1;
- }
+ removeElement(min);
+ min--;
+ }
- if (vstart < end)
- {
- visiblecontigs.addElement(new int[]
- { vstart, end - 1 });
- }
- int[] vcontigs = new int[visiblecontigs.size() * 2];
- for (int i = 0, j = visiblecontigs.size(); i < j; i++)
- {
- int[] vc = (int[]) visiblecontigs.elementAt(i);
- visiblecontigs.setElementAt(null, i);
- vcontigs[i * 2] = vc[0];
- vcontigs[i * 2 + 1] = vc[1];
- }
- visiblecontigs.removeAllElements();
- return vcontigs;
+ while (contains(max))
+ {
+ removeElement(max);
+ max++;
}
- else
+
+ /*
+ * min, max are now the closest unselected columns
+ */
+ min++;
+ max--;
+ if (min > max)
{
- return new int[]
- { start, end - 1 };
+ min = max;
}
+
+ al.getHiddenColumns().hideColumns(min, max);
}
+
+
+
+
/**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
+ * Copy constructor
*
- * @param alignmentAnnotation
+ * @param copy
*/
- public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+ public ColumnSelection(ColumnSelection copy)
{
- makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+ if (copy != null)
+ {
+ selection = new IntList(copy.selection);
+ }
}
/**
- * 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
+ * ColumnSelection
*/
- public void makeVisibleAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
+ public ColumnSelection()
{
- 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 annels = new Vector();
- Annotation[] els = null;
- Vector regions = getHiddenColumns();
- int blockStart = start, blockEnd = end;
- int[] region;
- int hideStart, hideEnd, w = 0;
-
- for (int j = 0; j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(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;
- Enumeration e = annels.elements();
- alignmentAnnotation.annotations = new Annotation[w];
- w = 0;
- while (e.hasMoreElements())
- {
- Annotation[] chnk = (Annotation[]) e.nextElement();
- 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);
}
*/
public void addElementsFrom(ColumnSelection colsel)
{
- if (colsel != null && colsel.size() > 0)
+ if (colsel != null && !colsel.isEmpty())
{
- Enumeration e = colsel.getSelected().elements();
- while (e.hasMoreElements())
+ for (Integer col : colsel.getSelected())
{
- Object eo = e.nextElement();
- if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+ if (hiddenColumns != null
+ && hiddenColumns.isVisible(col.intValue()))
{
- if (!selected.contains(eo))
- {
- selected.addElement(eo);
- }
+ selection.add(col);
}
}
}
*/
public void setElementsFrom(ColumnSelection colsel)
{
- selected = new Vector();
- 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
- selected = new Vector();
addElementsFrom(colsel);
}
else
{
// add everything regardless
- Enumeration en = colsel.selected.elements();
- while (en.hasMoreElements())
+ for (Integer col : colsel.getSelected())
{
- selected.addElement(en.nextElement());
+ addElement(col);
}
}
}
* profileseq marked as hidden.
*/
public static ColumnSelection propagateInsertions(SequenceI profileseq,
- Alignment al, AlignmentView input)
+ AlignmentI al, AlignmentView input)
{
int profsqpos = 0;
// 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)
{
}
}
}
+
+ /**
+ *
+ * @return true if there are columns marked
+ */
+ public boolean hasSelectedColumns()
+ {
+ return (selection != null && selection.size() > 0);
+ }
+
+
+
+ public boolean filterAnnotations(Annotation[] annotations,
+ AnnotationFilterParameter filterParams)
+ {
+ // JBPNote - this method needs to be refactored to become independent of
+ // viewmodel package
+ hiddenColumns.revealAllHiddenColumns(this);
+ this.clear();
+ int count = 0;
+ do
+ {
+ if (annotations[count] != null)
+ {
+
+ boolean itemMatched = false;
+
+ if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+ && annotations[count].value >= filterParams
+ .getThresholdValue())
+ {
+ itemMatched = true;
+ }
+ if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+ && annotations[count].value <= filterParams
+ .getThresholdValue())
+ {
+ itemMatched = true;
+ }
+
+ if (filterParams.isFilterAlphaHelix()
+ && annotations[count].secondaryStructure == 'H')
+ {
+ itemMatched = true;
+ }
+
+ if (filterParams.isFilterBetaSheet()
+ && annotations[count].secondaryStructure == 'E')
+ {
+ itemMatched = true;
+ }
+
+ if (filterParams.isFilterTurn()
+ && annotations[count].secondaryStructure == 'S')
+ {
+ itemMatched = true;
+ }
+
+ String regexSearchString = filterParams.getRegexString();
+ if (regexSearchString != null
+ && !filterParams.getRegexSearchFields().isEmpty())
+ {
+ List<SearchableAnnotationField> fields = filterParams
+ .getRegexSearchFields();
+ try
+ {
+ if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
+ && annotations[count].displayCharacter
+ .matches(regexSearchString))
+ {
+ itemMatched = true;
+ }
+ } catch (java.util.regex.PatternSyntaxException pse)
+ {
+ if (annotations[count].displayCharacter
+ .equals(regexSearchString))
+ {
+ itemMatched = true;
+ }
+ }
+ if (fields.contains(SearchableAnnotationField.DESCRIPTION)
+ && annotations[count].description != null
+ && annotations[count].description
+ .matches(regexSearchString))
+ {
+ itemMatched = true;
+ }
+ }
+
+ if (itemMatched)
+ {
+ this.addElement(count);
+ }
+ }
+ count++;
+ } 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