*/
package jalview.datamodel;
-import jalview.util.ShiftList;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
-
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Collections;
import java.util.List;
-import java.util.Vector;
+import java.util.regex.PatternSyntaxException;
+
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
/**
- * 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<Integer> selected = new Vector<Integer>();
+ /**
+ * 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;
+
+ /*
+ * an unmodifiable view of the selected columns list
+ */
+ private List<Integer> _uorder;
+
+ /**
+ * bitfield for column selection - allows quick lookup
+ */
+ private BitSet selected;
+
+ /**
+ * Constructor
+ */
+ IntList()
+ {
+ order = new ArrayList<>();
+ _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
+ */
+ void add(int i)
+ {
+ if (!selected.get(i))
+ {
+ order.add(Integer.valueOf(i));
+ selected.set(i);
+ }
+ }
+
+ void clear()
+ {
+ order.clear();
+ selected.clear();
+ }
+
+ void remove(int col)
+ {
+
+ Integer colInt = Integer.valueOf(col);
+
+ if (selected.get(col))
+ {
+ // 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);
+ }
+ }
+
+ boolean contains(Integer colInt)
+ {
+ return selected.get(colInt);
+ }
+
+ boolean isEmpty()
+ {
+ return order.isEmpty();
+ }
+
+ /**
+ * Returns a read-only view of the selected columns list
+ *
+ * @return
+ */
+ List<Integer> getList()
+ {
+ return _uorder;
+ }
+
+ int size()
+ {
+ return order.size();
+ }
+
+ /**
+ * gets the column that was selected first, second or i'th
+ *
+ * @param i
+ * @return
+ */
+ int elementAt(int i)
+ {
+ return order.get(i);
+ }
+
+ protected boolean pruneColumnList(final List<int[]> shifts)
+ {
+ 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 c = order.get(i++).intValue();
+ if (sr[0] <= c)
+ {
+ 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;
+ }
+
+ /**
+ * 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 (temp >= start)
+ {
+ // clear shifted bits and update List of selected columns
+ selected.clear(temp);
+ mask.set(temp - change);
+ order.set(i, Integer.valueOf(temp - change));
+ }
+ }
+ // lastly update the bitfield all at once
+ selected.or(mask);
+ }
+
+ boolean isSelected(int column)
+ {
+ return selected.get(column);
+ }
+
+ int getMaxColumn()
+ {
+ return selected.length() - 1;
+ }
+
+ int getMinColumn()
+ {
+ return selected.get(0) ? 0 : selected.nextSetBit(0);
+ }
+
+ /**
+ * @return a series of selection intervals along the range
+ */
+ List<int[]> getRanges()
+ {
+ List<int[]> rlist = new ArrayList<>();
+ if (selected.isEmpty())
+ {
+ return rlist;
+ }
+ int next = selected.nextSetBit(0), clear = -1;
+ while (next != -1)
+ {
+ clear = selected.nextClearBit(next);
+ rlist.add(new int[] { next, clear - 1 });
+ next = selected.nextSetBit(clear);
+ }
+ 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;
+ }
+ }
- // Vector of int [] {startCol, endCol}
- Vector<int[]> hiddenColumns;
+ private IntList selection = new IntList();
/**
* Add a column to the selection
*/
public void addElement(int col)
{
- Integer column = new Integer(col);
- if (!selected.contains(column))
+ selection.add(col);
+ }
+
+ /**
+ * add a series of start,end (inclusive) ranges to the column selection
+ *
+ * @param rng
+ * [start_0, end_0, start_1, end_1, ... ]
+ * @param baseOne
+ * - when true, ranges are base 1 and will be mapped to base 0
+ */
+ public void addRangeOfElements(int[] rng, boolean baseOne)
+ {
+ int base = baseOne ? -1 : 0;
+ for (int c = 0; c < rng.length; c += 2)
{
- selected.addElement(column);
+ for (int p = rng[c]; p <= rng[c + 1]; p++)
+ {
+ selection.add(base + p);
+ }
}
+
}
/**
*/
public void clear()
{
- selected.removeAllElements();
+ selection.clear();
}
/**
*/
public void removeElement(int col)
{
- Integer colInt = new Integer(col);
-
- if (selected.contains(colInt))
- {
- // 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
- selected.removeElement(colInt);
- }
+ selection.remove(col);
}
/**
Integer colInt;
for (int i = start; i < end; i++)
{
- colInt = new Integer(i);
- if (selected.contains(colInt))
+ colInt = Integer.valueOf(i);
+ if (selection.contains(colInt))
{
- selected.removeElement(colInt);
+ selection.remove(colInt);
}
}
}
/**
- *
- * @return Vector containing selected columns as Integers
+ * Returns a read-only view of the (possibly empty) list of selected columns
+ * (base 1)
+ * <p>
+ * The list contains no duplicates but is not necessarily ordered. Columns are
+ * reported in alignment coordinates (base 1), so may also 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 selection.getList();
+ }
+
+ /**
+ * @return list of int arrays containing start and end column position for
+ * runs of selected columns ordered from right to left.
*/
- public Vector<Integer> getSelected()
+ public List<int[]> getSelectedRanges()
{
- return selected;
+ return selection.getRanges();
}
/**
* @param col
* index to search for in column selection
*
- * @return true if Integer(col) is in selection.
+ * @return true if col is selected
*/
public boolean contains(int col)
{
- return selected.contains(new Integer(col));
+ return (col > -1) ? selection.isSelected(col) : false;
}
/**
- * Column number at position i in selection
*
- * @param i
- * index into selected columns
- *
- * @return column number in alignment
*/
- public int columnAt(int i)
+ public boolean intersects(int from, int to)
{
- return selected.elementAt(i).intValue();
+ // TODO: do this in a more efficient bitwise way
+ for (int f = from; f <= to; f++)
+ {
+ if (selection.isSelected(f))
+ {
+ return true;
+ }
+ }
+ return false;
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Answers true if no columns are selected, else false
*/
- public int size()
+ public boolean isEmpty()
{
- return selected.size();
+ return selection == null || selection.isEmpty();
}
/**
*/
public int getMax()
{
- int max = -1;
-
- for (int i = 0; i < selected.size(); i++)
+ if (selection.isEmpty())
{
- if (columnAt(i) > max)
- {
- max = columnAt(i);
- }
+ return -1;
}
-
- return max;
+ return selection.getMaxColumn();
}
/**
*/
public int getMin()
{
- int min = 1000000000;
+ if (selection.isEmpty())
+ {
+ return 1000000000;
+ }
+ return selection.getMinColumn();
+ }
- for (int i = 0; i < selected.size(); i++)
+ public void hideSelectedColumns(AlignmentI al)
+ {
+ synchronized (selection)
{
- if (columnAt(i) < min)
+ for (int[] selregions : selection.getRanges())
{
- min = columnAt(i);
+ al.getHiddenColumns().hideColumns(selregions[0], selregions[1]);
}
+ selection.clear();
}
- return min;
}
/**
- * propagate shift in alignment columns to column selection
+ * Hides the specified column and any adjacent selected columns
*
- * @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
+ * @param res
+ * int
*/
- public List<int[]> compensateForEdit(int start, int change)
+ public void hideSelectedColumns(int col, HiddenColumns hidden)
{
- List<int[]> deletedHiddenColumns = null;
- for (int i = 0; i < size(); i++)
- {
- int temp = columnAt(i);
+ /*
+ * deselect column (whether selected or not!)
+ */
+ removeElement(col);
- if (temp >= start)
- {
- // if this ever changes to List.set(), swap parameter order!!
- selected.setElementAt(new Integer(temp - change), i);
- }
+ /*
+ * find adjacent selected columns
+ */
+ int min = col - 1, max = col + 1;
+ while (contains(min))
+ {
+ removeElement(min);
+ min--;
}
- if (hiddenColumns != null)
+ while (contains(max))
{
- 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;
- }
-
- }
+ removeElement(max);
+ max++;
+ }
- this.revealHiddenColumns(0);
+ /*
+ * min, max are now the closest unselected columns
+ */
+ min++;
+ max--;
+ if (min > max)
+ {
+ min = max;
}
- return deletedHiddenColumns;
+ hidden.hideColumns(min, max);
}
/**
- * propagate shift in alignment columns to column selection special version of
- * compensateForEdit - allowing for edits within hidden regions
+ * Copy constructor
*
- * @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
+ * @param copy
*/
- private void compensateForDelEdits(int start, int change)
+ public ColumnSelection(ColumnSelection copy)
{
- for (int i = 0; i < size(); i++)
+ if (copy != null)
{
- int temp = columnAt(i);
-
- if (temp >= start)
- {
- // if this ever changes to List.set(), swap parameter order!!
- selected.setElementAt(new Integer(temp - change), i);
- }
+ selection = new IntList(copy.selection);
}
+ }
- 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;
- }
- }
- }
+ /**
+ * ColumnSelection
+ */
+ public ColumnSelection()
+ {
}
/**
- * Adjust hidden column boundaries based on a series of column additions or
- * deletions in visible regions.
+ * Invert the column selection from first to end-1. leaves hiddenColumns
+ * untouched (and unselected)
*
- * @param shiftrecord
- * @return
+ * @param first
+ * @param end
*/
- public ShiftList compensateForEdits(ShiftList shiftrecord)
+ public void invertColumnSelection(int first, int width, AlignmentI al)
{
- if (shiftrecord != null)
+ boolean hasHidden = al.getHiddenColumns().hasHiddenColumns();
+ for (int i = first; i < width; i++)
{
- final List<int[]> shifts = shiftrecord.getShifts();
- if (shifts != null && shifts.size() > 0)
+ if (contains(i))
+ {
+ removeElement(i);
+ }
+ else
{
- int shifted = 0;
- for (int i = 0, j = shifts.size(); i < j; i++)
+ if (!hasHidden || al.getHiddenColumns().isVisible(i))
{
- int[] sh = shifts.get(i);
- // compensateForEdit(shifted+sh[0], sh[1]);
- compensateForDelEdits(shifted + sh[0], sh[1]);
- shifted -= sh[1];
+ addElement(i);
}
}
- return shiftrecord.getInverse();
}
- return null;
}
/**
- * removes intersection of position,length ranges in deletions from the
- * start,end regions marked in intervals.
+ * set the selected columns to the given column selection, excluding any
+ * columns that are hidden.
*
- * @param shifts
- * @param intervals
- * @return
+ * @param colsel
*/
- private boolean pruneIntervalVector(final List<int[]> shifts,
- Vector<int[]> intervals)
+ public void setElementsFrom(ColumnSelection colsel,
+ HiddenColumns hiddenColumns)
{
- 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)
+ selection = new IntList();
+ if (colsel.selection != null && colsel.selection.size() > 0)
{
- boolean trailinghn = hr[1] >= sr[0];
- if (!trailinghn)
+ if (hiddenColumns.hasHiddenColumns())
{
- 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
+ // only select visible columns in this columns selection
+ for (Integer col : colsel.getSelected())
{
- 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)
+ if (hiddenColumns != null
+ && hiddenColumns.isVisible(col.intValue()))
{
- hr = intervals.elementAt(i);
+ selection.add(col);
}
- continue;
- }
- if (leadinghc)
- {
- hr[0] = endshift; // clip c terminal region
- leadinghn = !leadinghn;
- pruned = true;
}
}
- if (!leadinghn)
+ else
{
- if (trailinghc)
- {
- if (trailinghn)
- {
- hr[1] = sr[0] - 1;
- pruned = true;
- }
- }
- else
+ // add everything regardless
+ for (Integer col : colsel.getSelected())
{
- // sr contained in hr
- if (s < t)
- {
- sr = shifts.get(++s);
- }
- else
- {
- s++;
- }
- continue;
+ addElement(col);
}
}
}
- return pruned; // true if any interval was removed or modified by
- // operations.
}
- private boolean pruneColumnList(final List<int[]> shifts,
- Vector<Integer> list)
+ /**
+ *
+ * @return true if there are columns marked
+ */
+ public boolean hasSelectedColumns()
{
- int s = 0, t = shifts.size();
- int[] sr = shifts.get(s++);
- boolean pruned = false;
- int i = 0, j = list.size();
- while (i < j && s <= t)
- {
- int c = list.elementAt(i++).intValue();
- if (sr[0] <= c)
- {
- if (sr[1] + sr[0] >= c)
- { // sr[1] -ve means inseriton.
- list.removeElementAt(--i);
- j--;
- }
- else
- {
- if (s < t)
- {
- sr = shifts.get(s);
- }
- s++;
- }
- }
- }
- return pruned;
+ return (selection != null && selection.size() > 0);
}
/**
- * remove any hiddenColumns or selected columns and shift remaining based on a
- * series of position, range deletions.
+ * Selects columns where the given annotation matches the provided filter
+ * condition(s). Any existing column selections are first cleared. Answers the
+ * number of columns added.
*
- * @param deletions
+ * @param annotations
+ * @param filterParams
+ * @return
*/
- public void pruneDeletions(ShiftList deletions)
+ public int filterAnnotations(AlignmentAnnotation ann_row,
+ AnnotationFilterParameter filterParams)
{
- if (deletions != null)
+ Annotation[] annotations = ann_row.annotations;
+ // JBPNote - this method needs to be refactored to become independent of
+ // viewmodel package
+ this.clear();
+
+ if (ann_row.graph == AlignmentAnnotation.CONTACT_MAP && (filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+ || filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD))
{
- final List<int[]> shifts = deletions.getShifts();
- if (shifts != null && shifts.size() > 0)
+ float tVal = filterParams.getThresholdValue();
+ if (ann_row.sequenceRef != null)
{
- // delete any intervals intersecting.
- if (hiddenColumns != null)
+ // TODO - get ContactList from AlignmentView for non-seq-ref associatd
+ for (int column = 0; column < annotations.length; column++)
{
- pruneIntervalVector(shifts, hiddenColumns);
- if (hiddenColumns != null && hiddenColumns.size() == 0)
+ if (ann_row.annotations[column] == null)
{
- hiddenColumns = null;
+ continue;
}
- }
- if (selected != null && selected.size() > 0)
- {
- pruneColumnList(shifts, selected);
- if (selected != null && selected.size() == 0)
+
+ int cpos = ann_row.sequenceRef.findPosition(column) - 1;
+ ContactListI clist = ann_row.sequenceRef
+ .getContactListFor(ann_row, cpos);
+ for (int row = column + 8, rowEnd = clist
+ .getContactHeight(); row < rowEnd; row++)
{
- selected = null;
+ if (filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+ ? (clist.getContactAt(row) > tVal)
+ : (clist.getContactAt(row) < tVal))
+ {
+ addElement(column);
+ break;
+ // int column_forrowpos = ann_row.sequenceRef.findIndex(row + 1);
+ // addElement(column_forrowpos);
+ }
}
}
- // and shift the rest.
- this.compensateForEdits(deletions);
}
+ return selection.size();
}
- }
- /**
- * 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)
+ int addedCount = 0;
+ int column = 0;
+ do
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ Annotation ann = annotations[column];
+ if (ann != null)
{
- int[] region = hiddenColumns.elementAt(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
- }
- }
- return result;
- }
+ float value = ann.value;
+ boolean matched = false;
- /**
- * 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])
+ /*
+ * filter may have multiple conditions -
+ * these are or'd until a match is found
+ */
+ if (filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+ && value > filterParams.getThresholdValue())
{
- result -= region[1] + 1 - region[0];
+ matched = true;
}
- } 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
- */
- 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)
+ if (!matched && filterParams
+ .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+ && value < filterParams.getThresholdValue())
{
- return region[0];
+ matched = true;
}
- gaps += region[1] + 1 - region[0];
- result = region[1] + 1;
- index++;
- } while (index < hiddenRegion + 1);
-
- 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])
+ if (!matched && filterParams.isFilterAlphaHelix()
+ && ann.secondaryStructure == 'H')
{
- return region[0];
+ matched = true;
}
- 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])
+ if (!matched && filterParams.isFilterBetaSheet()
+ && ann.secondaryStructure == 'E')
{
- return region[1];
+ matched = true;
}
- index--;
- } while (index > -1);
- }
-
- return alPos;
-
- }
-
- public void hideSelectedColumns()
- {
- while (size() > 0)
- {
- int column = getSelected().firstElement().intValue();
- hideColumns(column);
- }
-
- }
-
- public void hideColumns(int start, int end)
- {
- if (hiddenColumns == null)
- {
- hiddenColumns = new Vector<int[]>();
- }
-
- boolean added = false;
- boolean overlap = false;
-
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = 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 });
- }
-
- }
-
- /**
- * This method will find a range of selected columns around the column
- * specified
- *
- * @param res
- * int
- */
- public void hideColumns(int col)
- {
- // First find out range of columns to hide
- int min = col, max = col + 1;
- while (contains(min))
- {
- removeElement(min);
- min--;
- }
-
- while (contains(max))
- {
- removeElement(max);
- max++;
- }
-
- min++;
- max--;
- if (min > max)
- {
- min = max;
- }
-
- hideColumns(min, max);
- }
-
- 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++)
+ if (!matched && filterParams.isFilterTurn()
+ && ann.secondaryStructure == 'S')
{
- addElement(j);
+ matched = true;
}
- }
- }
- hiddenColumns = null;
- }
-
- public void revealHiddenColumns(int res)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.elementAt(i);
- if (res == region[0])
- {
- for (int j = region[0]; j < region[1] + 1; j++)
+ String regexSearchString = filterParams.getRegexString();
+ if (!matched && regexSearchString != null)
{
- addElement(j);
+ List<SearchableAnnotationField> fields = filterParams
+ .getRegexSearchFields();
+ for (SearchableAnnotationField field : fields)
+ {
+ String compareTo = field == SearchableAnnotationField.DISPLAY_STRING
+ ? ann.displayCharacter // match 'Label'
+ : ann.description; // and/or 'Description'
+ if (compareTo != null)
+ {
+ try
+ {
+ if (compareTo.matches(regexSearchString))
+ {
+ matched = true;
+ }
+ } catch (PatternSyntaxException pse)
+ {
+ if (compareTo.equals(regexSearchString))
+ {
+ matched = true;
+ }
+ }
+ if (matched)
+ {
+ break;
+ }
+ }
+ }
}
- hiddenColumns.removeElement(region);
- break;
- }
- }
- if (hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
- }
-
- public boolean isVisible(int column)
- {
- if (hiddenColumns != null)
- {
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.elementAt(i);
- if (column >= region[0] && column <= region[1])
+ if (matched)
{
- return false;
+ this.addElement(column);
+ addedCount++;
}
}
- }
+ column++;
+ } while (column < annotations.length);
- return true;
+ return addedCount;
}
/**
- * Copy constructor
- *
- * @param copy
+ * Returns a hashCode built from selected columns ranges
*/
- public ColumnSelection(ColumnSelection copy)
+ @Override
+ public int hashCode()
{
- if (copy != null)
- {
- if (copy.selected != null)
- {
- selected = new Vector<Integer>();
- for (int i = 0, j = copy.selected.size(); i < j; i++)
- {
- selected.addElement(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);
- }
- }
- }
- }
+ return selection.hashCode();
}
/**
- * ColumnSelection
+ * Answers true if comparing to a ColumnSelection with the same selected
+ * columns and hidden columns, else false
*/
- public ColumnSelection()
+ @Override
+ public boolean equals(Object obj)
{
- }
-
- 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 (!(obj instanceof ColumnSelection))
{
- 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 false;
}
+ ColumnSelection that = (ColumnSelection) obj;
- 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)
+ /*
+ * check columns selected are either both null, or match
+ */
+ if (this.selection == null)
{
- 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++)
+ if (that.selection != null)
{
- int[] vc = visiblecontigs.get(i);
- visiblecontigs.set(i, null);
- vcontigs[i * 2] = vc[0];
- vcontigs[i * 2 + 1] = vc[1];
+ return false;
}
- visiblecontigs.clear();
- return vcontigs;
}
- else
+ if (!this.selection.equals(that.selection))
{
- return new int[] { start, end - 1 };
+ return false;
}
- }
- /**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
- *
- * @param alignmentAnnotation
- */
- public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
- {
- makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+ return true;
}
/**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
+ * Updates the column selection depending on the parameters, and returns true
+ * if any change was made to the selection
*
- * @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
+ * @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 void makeVisibleAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
+ public boolean markColumns(BitSet markedColumns, int startCol, int endCol,
+ boolean invert, boolean extendCurrent, boolean toggle)
{
- if (alignmentAnnotation.annotations == null)
- {
- return;
- }
- if (start == end && end == -1)
+ boolean changed = false;
+ if (!extendCurrent && !toggle)
{
- start = 0;
- end = alignmentAnnotation.annotations.length;
+ changed = !this.isEmpty();
+ clear();
}
- if (hiddenColumns != null && hiddenColumns.size() > 0)
+ if (invert)
{
- // 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)
+ // invert only in the currently selected sequence region
+ int i = markedColumns.nextClearBit(startCol);
+ int ibs = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
{
- annels.addElement(els = new Annotation[end - blockStart + 1]);
- if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
+ if (ibs < 0 || i < ibs)
{
- // copy just the visible segment of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0, els.length);
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i++);
+ }
+ else
+ {
+ addElement(i++);
+ }
}
else
{
- // copy to the end of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0,
- (alignmentAnnotation.annotations.length - blockStart));
+ i = markedColumns.nextClearBit(ibs);
+ ibs = markedColumns.nextSetBit(i);
}
- 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
- * untouched (and unselected)
- *
- * @param first
- * @param end
- */
- public void invertColumnSelection(int first, int width)
- {
- boolean hasHidden = hiddenColumns != null && hiddenColumns.size() > 0;
- for (int i = first; i < width; i++)
- {
- if (contains(i))
+ int i = markedColumns.nextSetBit(startCol);
+ while (i >= startCol && i <= endCol)
{
- removeElement(i);
- }
- else
- {
- if (!hasHidden || isVisible(i))
+ changed = true;
+ if (toggle && contains(i))
+ {
+ removeElement(i);
+ }
+ else
{
addElement(i);
}
+ i = markedColumns.nextSetBit(i + 1);
}
}
+ return changed;
}
/**
- * add in any unselected columns from the given column selection, excluding
- * any that are hidden.
+ * 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 colsel
+ * @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 addElementsFrom(ColumnSelection colsel)
+ public void stretchGroup(int res, SequenceGroup sg, int min, int max)
{
- if (colsel != null && colsel.size() > 0)
+ if (!contains(res))
{
- for (Integer col : colsel.getSelected())
- {
- if (hiddenColumns != null && isVisible(col.intValue()))
- {
- if (!selected.contains(col))
- {
- selected.addElement(col);
- }
- }
- }
+ addElement(res);
}
- }
- /**
- * set the selected columns the given column selection, excluding any columns
- * that are hidden.
- *
- * @param colsel
- */
- public void setElementsFrom(ColumnSelection colsel)
- {
- selected = new Vector<Integer>();
- if (colsel.selected != null && colsel.selected.size() > 0)
+ if (res > sg.getStartRes())
{
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- // only select visible columns in this columns selection
- addElementsFrom(colsel);
- }
- else
- {
- // add everything regardless
- for (Integer col : colsel.getSelected())
- {
- addElement(col);
- }
- }
+ // expand selection group to the right
+ sg.setEndRes(res);
}
- }
-
- /**
- * Add gaps into the sequences aligned to profileseq under the given
- * AlignmentView
- *
- * @param profileseq
- * @param al
- * - alignment to have gaps inserted into it
- * @param input
- * - alignment view where sequence corresponding to profileseq is
- * first entry
- * @return new Column selection for new alignment view, with insertions into
- * profileseq marked as hidden.
- */
- public static ColumnSelection propagateInsertions(SequenceI profileseq,
- AlignmentI al, AlignmentView input)
- {
- int profsqpos = 0;
-
- // return propagateInsertions(profileseq, al, )
- char gc = al.getGapCharacter();
- Object[] alandcolsel = input.getAlignmentAndColumnSelection(gc);
- ColumnSelection nview = (ColumnSelection) alandcolsel[1];
- SequenceI origseq = ((SequenceI[]) alandcolsel[0])[profsqpos];
- nview.propagateInsertions(profileseq, al, origseq);
- return nview;
- }
-
- /**
- *
- * @param profileseq
- * - sequence in al which corresponds to origseq
- * @param al
- * - alignment which is to have gaps inserted into it
- * @param origseq
- * - sequence corresponding to profileseq which defines gap map for
- * modifying al
- */
- public 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 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)
+ if (res < sg.getStartRes())
{
- if (viscontigs[v] > spos)
- {
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
- {
- sb.append(gc);
- }
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
- {
- SequenceI sqobj = al.getSequenceAt(s);
- if (sqobj != profileseq)
- {
- String sq = al.getSequenceAt(s).getSequenceAsString();
- if (sq.length() <= spos + offset)
- {
- // pad sequence
- int diff = spos + offset - sq.length() - 1;
- if (diff > 0)
- {
- // pad gaps
- sq = sq + sb;
- while ((diff = spos + offset - sq.length() - 1) > 0)
- {
- // sq = sq
- // + ((diff >= sb.length()) ? sb.toString() : sb
- // .substring(0, diff));
- if (diff >= sb.length())
- {
- sq += sb.toString();
- }
- else
- {
- char[] buf = new char[diff];
- sb.getChars(0, diff, buf, 0);
- sq += buf.toString();
- }
- }
- }
- sq += sb.toString();
- }
- else
- {
- al.getSequenceAt(s).setSequence(
- sq.substring(0, spos + offset) + sb.toString()
- + sq.substring(spos + offset));
- }
- }
- }
- // offset+=sb.length();
- }
- spos = viscontigs[v + 1] + 1;
+ // expand selection group to the left
+ sg.setStartRes(res);
}
- if ((offset + spos) < profileseq.getLength())
+
+ /*
+ * expand or shrink column selection to match the
+ * range of the drag operation
+ */
+ for (int col = min; col <= max; col++)
{
- // pad the final region with gaps.
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+ if (col < sg.getStartRes() || col > sg.getEndRes())
{
- sb.append(gc);
+ // shrinking drag - remove from selection
+ removeElement(col);
}
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ else
{
- SequenceI sqobj = al.getSequenceAt(s);
- if (sqobj == profileseq)
- {
- continue;
- }
- String sq = sqobj.getSequenceAsString();
- // pad sequence
- int diff = origseq.getLength() - sq.length();
- while (diff > 0)
- {
- // sq = sq
- // + ((diff >= sb.length()) ? sb.toString() : sb
- // .substring(0, diff));
- if (diff >= sb.length())
- {
- sq += sb.toString();
- }
- else
- {
- char[] buf = new char[diff];
- sb.getChars(0, diff, buf, 0);
- sq += buf.toString();
- }
- diff = origseq.getLength() - sq.length();
- }
+ // expanding drag - add to selection
+ addElement(col);
}
}
}
-
- /**
- *
- * @return true if there are columns marked
- */
- 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 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();
- 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;
- }
}
git://source.jalview.org / jalview.git / blobdiff