/*
- * 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.
*
import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
import java.util.ArrayList;
-import java.util.Enumeration;
+import java.util.BitSet;
+import java.util.Collections;
import java.util.List;
import java.util.Vector;
*/
public class ColumnSelection
{
- Vector selected = new Vector();
+ private class IntList
+ {
+ /*
+ * list of selected columns (ordered by selection order, not column order)
+ */
+ private List<Integer> order = new ArrayList<Integer>();
+
+ /**
+ * bitfield for column selection - allows quick lookup
+ */
+ private BitSet selected = new BitSet();
+
+ /**
+ * adds a new column i to the selection - only if i is not already selected
+ *
+ * @param i
+ */
+ public void add(int i)
+ {
+ if (!selected.get(i))
+ {
+ order.add(Integer.valueOf(i));
+ selected.set(i);
+ }
+ }
+
+ public void clear()
+ {
+ order.clear();
+ selected.clear();
+ }
+
+ public void remove(int col)
+ {
+
+ Integer colInt = new Integer(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);
+ }
+ }
+
+ public boolean contains(Integer colInt)
+ {
+ return selected.get(colInt);
+ }
+
+ public boolean isEmpty()
+ {
+ return order.isEmpty();
+ }
+
+ public List<Integer> getList()
+ {
+ return order;
+ }
+
+ public int size()
+ {
+ return order.size();
+ }
+
+ /**
+ * gets the column that was selected first, second or i'th
+ *
+ * @param i
+ * @return
+ */
+ public int elementAt(int i)
+ {
+ return order.get(i);
+ }
- // Vector of int [] {startCol, endCol}
- Vector hiddenColumns;
+ 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
+ */
+ public 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, new Integer(temp - change));
+ }
+ }
+ // lastly update the bitfield all at once
+ selected.or(mask);
+ }
+
+ public boolean isSelected(int column)
+ {
+ return selected.get(column);
+ }
+
+ public int getMaxColumn()
+ {
+ return selected.length() - 1;
+ }
+
+ public 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[]> rlist = new ArrayList<int[]>();
+ 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;
+ }
+ }
+
+ IntList selected = new IntList();
+ /*
+ * list of hidden column [start, end] ranges; the list is maintained in
+ * ascending start column order
+ */
+ Vector<int[]> hiddenColumns;
/**
* Add a column to the selection
*/
public void addElement(int col)
{
- Integer column = new Integer(col);
- if (!selected.contains(column))
- {
- selected.addElement(column);
- }
+ selected.add(col);
}
/**
*/
public void clear()
{
- selected.removeAllElements();
+ selected.clear();
}
/**
- * removes col from selection
+ * Removes value 'col' from the selection (not the col'th item)
*
* @param col
* index of column to be removed
*/
public void removeElement(int col)
{
- Integer colInt = new Integer(col);
-
- if (selected.contains(colInt))
- {
- selected.removeElement(colInt);
- }
+ selected.remove(col);
}
/**
colInt = new Integer(i);
if (selected.contains(colInt))
{
- selected.removeElement(colInt);
+ selected.remove(colInt);
}
}
}
/**
- *
- * @return Vector containing selected columns as Integers
+ * 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
*/
- public Vector getSelected()
+ public List<Integer> getSelected()
{
- return selected;
+ return selected.getList();
}
/**
- *
- * @param col
- * index to search for in column selection
- *
- * @return true if Integer(col) is in selection.
+ * @return list of int arrays containing start and end column position for
+ * runs of selected columns ordered from right to left.
*/
- public boolean contains(int col)
+ public List<int[]> getSelectedRanges()
{
- return selected.contains(new Integer(col));
+ return selected.getRanges();
}
/**
- * Column number at position i in selection
*
- * @param i
- * index into selected columns
+ * @param col
+ * index to search for in column selection
*
- * @return column number in alignment
+ * @return true if col is selected
*/
- public int columnAt(int i)
+ public boolean contains(int col)
{
- return ((Integer) selected.elementAt(i)).intValue();
+ return (col > -1) ? selected.isSelected(col) : 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 selected == null || selected.isEmpty();
}
/**
*/
public int getMax()
{
- int max = -1;
-
- for (int i = 0; i < selected.size(); i++)
+ if (selected.isEmpty())
{
- if (columnAt(i) > max)
- {
- max = columnAt(i);
- }
+ return -1;
}
-
- return max;
+ return selected.getMaxColumn();
}
/**
*/
public int getMin()
{
- int min = 1000000000;
-
- for (int i = 0; i < selected.size(); i++)
+ if (selected.isEmpty())
{
- if (columnAt(i) < min)
- {
- min = columnAt(i);
- }
+ return 1000000000;
}
-
- return min;
+ return selected.getMinColumn();
}
/**
public List<int[]> compensateForEdit(int start, int change)
{
List<int[]> deletedHiddenColumns = null;
- for (int i = 0; i < size(); i++)
- {
- int temp = columnAt(i);
-
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
- }
+ selected.compensateForEdits(start, change);
if (hiddenColumns != null)
{
int hSize = hiddenColumns.size();
for (int i = 0; i < hSize; i++)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
+ int[] region = hiddenColumns.elementAt(i);
if (region[0] > start && start + change > region[1])
{
deletedHiddenColumns.add(region);
*/
private void compensateForDelEdits(int start, int change)
{
- for (int i = 0; i < size(); i++)
- {
- int temp = columnAt(i);
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
- }
+ selected.compensateForEdits(start, change);
if (hiddenColumns != null)
{
for (int i = 0; i < hiddenColumns.size(); i++)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
+ int[] region = hiddenColumns.elementAt(i);
if (region[0] >= start)
{
region[0] -= change;
{
if (shiftrecord != null)
{
- Vector shifts = shiftrecord.shifts;
+ final List<int[]> shifts = shiftrecord.getShifts();
if (shifts != null && shifts.size() > 0)
{
int shifted = 0;
for (int i = 0, j = shifts.size(); i < j; i++)
{
- int[] sh = (int[]) shifts.elementAt(i);
+ int[] sh = shifts.get(i);
// compensateForEdit(shifted+sh[0], sh[1]);
compensateForDelEdits(shifted + sh[0], sh[1]);
shifted -= sh[1];
* removes intersection of position,length ranges in deletions from the
* start,end regions marked in intervals.
*
- * @param deletions
+ * @param shifts
* @param intervals
* @return
*/
- private boolean pruneIntervalVector(Vector deletions, Vector intervals)
+ private boolean pruneIntervalVector(final List<int[]> shifts,
+ Vector<int[]> 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);
+ 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 (i < j)
{
- hr = (int[]) intervals.elementAt(++i);
+ hr = intervals.elementAt(++i);
}
else
{
{ // leadinghc disjoint or not a deletion
if (s < t)
{
- sr = (int[]) deletions.elementAt(++s);
+ sr = shifts.get(++s);
}
else
{
j--;
if (i <= j)
{
- hr = (int[]) intervals.elementAt(i);
+ hr = intervals.elementAt(i);
}
continue;
}
// sr contained in hr
if (s < t)
{
- sr = (int[]) deletions.elementAt(++s);
+ sr = shifts.get(++s);
}
else
{
// 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)
- {
- int c = ((Integer) 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 = (int[]) deletion.elementAt(s);
- }
- s++;
- }
- }
- }
- return pruned;
- }
-
/**
* remove any hiddenColumns or selected columns and shift remaining based on a
* series of position, range deletions.
{
if (deletions != null)
{
- Vector shifts = deletions.shifts;
+ final List<int[]> shifts = deletions.getShifts();
if (shifts != null && shifts.size() > 0)
{
// delete any intervals intersecting.
}
if (selected != null && selected.size() > 0)
{
- pruneColumnList(shifts, selected);
+ selected.pruneColumnList(shifts);
if (selected != null && selected.size() == 0)
{
selected = null;
}
/**
- * This Method is used to return all the HiddenColumn regions less than the
- * given index.
+ * This Method is used to return all the HiddenColumn regions
*
- * @param end
- * int
- * @return Vector
+ * @return empty list or List of hidden column intervals
*/
- public Vector getHiddenColumns()
+ public List<int[]> getHiddenColumns()
{
- return hiddenColumns;
+ return hiddenColumns == null ? Collections.<int[]> emptyList()
+ : hiddenColumns;
}
/**
{
for (int i = 0; i < hiddenColumns.size(); i++)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
+ int[] region = hiddenColumns.elementAt(i);
if (result >= region[0])
{
result += region[1] - region[0] + 1;
int[] region;
do
{
- region = (int[]) hiddenColumns.elementAt(index++);
+ region = hiddenColumns.elementAt(index++);
if (hiddenColumn > region[1])
{
result -= region[1] + 1 - region[0];
/**
* 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 gaps = 0;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
+ 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 + 1);
+ } while (index <= hiddenRegion);
result -= gaps;
}
int index = 0;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
+ int[] region = hiddenColumns.elementAt(index);
if (alPos < region[0])
{
return region[0];
int index = hiddenColumns.size() - 1;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
+ int[] region = hiddenColumns.elementAt(index);
if (alPos > region[1])
{
return region[1];
public void hideSelectedColumns()
{
- while (size() > 0)
- {
- int column = ((Integer) getSelected().firstElement()).intValue();
- hideColumns(column);
+ synchronized (selected) {
+ for (int[] selregions:selected.getRanges())
+ {
+ hideColumns(selregions[0], selregions[1]);
+ }
+ selected.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();
+ hiddenColumns = new Vector<int[]>();
}
- boolean added = false;
- boolean overlap = false;
-
+ /*
+ * traverse existing hidden ranges and insert / amend / append as
+ * appropriate
+ */
for (int i = 0; i < hiddenColumns.size(); i++)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if (start <= region[1] && end >= region[0])
+ int[] region = hiddenColumns.elementAt(i);
+
+ if (end < region[0] - 1)
{
- hiddenColumns.removeElementAt(i);
- overlap = true;
- break;
+ /*
+ * insert discontiguous preceding range
+ */
+ hiddenColumns.insertElementAt(new int[] { start, end }, i);
+ return;
}
- else if (end < region[0] && start < region[0])
+
+ if (end <= region[1])
{
- hiddenColumns.insertElementAt(new int[]
- { start, end }, i);
- added = true;
- break;
+ /*
+ * new range overlaps existing, or is contiguous preceding it - adjust
+ * start column
+ */
+ region[0] = Math.min(region[0], start);
+ return;
}
- }
- if (overlap)
- {
- hideColumns(start, end);
- }
- else if (!added)
- {
- hiddenColumns.addElement(new int[]
- { start, end });
+ 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 });
}
/**
- * This method will find a range of selected columns around the column
- * specified
+ * Hides the specified column and any adjacent selected columns
*
* @param res
* int
*/
public void hideColumns(int col)
{
- // First find out range of columns to hide
- int min = col, max = col + 1;
+ /*
+ * deselect column (whether selected or not!)
+ */
+ removeElement(col);
+
+ /*
+ * find adjacent selected columns
+ */
+ int min = col - 1, max = col + 1;
while (contains(min))
{
removeElement(min);
max++;
}
+ /*
+ * min, max are now the closest unselected columns
+ */
min++;
max--;
if (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 = (int[]) hiddenColumns.elementAt(i);
+ int[] region = hiddenColumns.elementAt(i);
for (int j = region[0]; j < region[1] + 1; j++)
{
addElement(j);
hiddenColumns = null;
}
- public void revealHiddenColumns(int res)
+ /**
+ * 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 = (int[]) hiddenColumns.elementAt(i);
- if (res == region[0])
+ int[] region = hiddenColumns.elementAt(i);
+ if (start == region[0])
{
for (int j = region[0]; j < region[1] + 1; j++)
{
{
if (hiddenColumns != null)
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ for (int[] region : hiddenColumns)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
if (column >= region[0] && column <= region[1])
{
return false;
{
if (copy.selected != null)
{
- selected = new Vector();
+ selected = new IntList();
for (int i = 0, j = copy.selected.size(); i < j; i++)
{
- selected.addElement(copy.selected.elementAt(i));
+ selected.add(copy.selected.elementAt(i));
}
}
if (copy.hiddenColumns != null)
{
- hiddenColumns = new Vector(copy.hiddenColumns.size());
+ hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
{
int[] rh, cp;
- rh = (int[]) copy.hiddenColumns.elementAt(i);
+ rh = copy.hiddenColumns.elementAt(i);
if (rh != null)
{
cp = new int[rh.length];
for (i = 0; i < iSize; i++)
{
StringBuffer visibleSeq = new StringBuffer();
- Vector regions = getHiddenColumns();
+ List<int[]> regions = getHiddenColumns();
int blockStart = start, blockEnd = end;
int[] region;
for (int j = 0; j < regions.size(); j++)
{
- region = (int[]) regions.elementAt(j);
+ region = regions.get(j);
hideStart = region[0];
hideEnd = region[1];
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- Vector visiblecontigs = new Vector();
- Vector regions = getHiddenColumns();
+ List<int[]> visiblecontigs = new ArrayList<int[]>();
+ List<int[]> regions = getHiddenColumns();
int vstart = start;
int[] region;
for (int j = 0; vstart < end && j < regions.size(); j++)
{
- region = (int[]) regions.elementAt(j);
+ region = regions.get(j);
hideStart = region[0];
hideEnd = region[1];
}
if (hideStart > vstart)
{
- visiblecontigs.addElement(new int[]
- { vstart, hideStart - 1 });
+ visiblecontigs.add(new int[] { vstart, hideStart - 1 });
}
vstart = hideEnd + 1;
}
if (vstart < end)
{
- visiblecontigs.addElement(new int[]
- { vstart, end - 1 });
+ 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 = (int[]) visiblecontigs.elementAt(i);
- visiblecontigs.setElementAt(null, i);
+ int[] vc = visiblecontigs.get(i);
+ visiblecontigs.set(i, null);
vcontigs[i * 2] = vc[0];
vcontigs[i * 2 + 1] = vc[1];
}
- visiblecontigs.removeAllElements();
+ visiblecontigs.clear();
return vcontigs;
}
else
{
- return new int[]
- { start, end - 1 };
+ return new int[] { start, end - 1 };
}
}
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
- Vector annels = new Vector();
+ Vector<Annotation[]> annels = new Vector<Annotation[]>();
Annotation[] els = null;
- Vector regions = getHiddenColumns();
+ 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 = (int[]) regions.elementAt(j);
+ region = regions.get(j);
hideStart = region[0];
hideEnd = region[1];
{
return;
}
- Enumeration e = annels.elements();
+
alignmentAnnotation.annotations = new Annotation[w];
w = 0;
- while (e.hasMoreElements())
+
+ for (Annotation[] chnk : annels)
{
- Annotation[] chnk = (Annotation[]) e.nextElement();
System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
chnk.length);
w += chnk.length;
*/
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 && isVisible(col.intValue()))
{
- if (!selected.contains(eo))
- {
- selected.addElement(eo);
- }
+ selected.add(col);
}
}
}
*/
public void setElementsFrom(ColumnSelection colsel)
{
- selected = new Vector();
+ selected = new IntList();
if (colsel.selected != null && colsel.selected.size() > 0)
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// 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 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)
{
git://source.jalview.org / jalview.git / blobdiff