hiddenColumns;
/**
* Add a column to the selection
@@ -39,11 +282,7 @@ public class ColumnSelection
*/
public void addElement(int col)
{
- Integer column = new Integer(col);
- if (!selected.contains(column))
- {
- selected.addElement(column);
- }
+ selection.add(col);
}
/**
@@ -51,23 +290,18 @@ public class ColumnSelection
*/
public void clear()
{
- selected.removeAllElements();
+ selection.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);
- }
+ selection.remove(col);
}
/**
@@ -84,55 +318,55 @@ public class ColumnSelection
for (int i = start; i < end; i++)
{
colInt = new Integer(i);
- if (selected.contains(colInt))
+ 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
+ *
+ * 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.
+ *
+ * The list is not thread-safe: iterating over it could result in
+ * ConcurrentModificationException if it is modified by another thread.
*/
- public Vector getSelected()
+ public List getSelected()
{
- return selected;
+ return selection.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 getSelectedRanges()
{
- return selected.contains(new Integer(col));
+ return selection.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) ? selection.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 selection == null || selection.isEmpty();
}
/**
@@ -142,17 +376,11 @@ public class ColumnSelection
*/
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();
}
/**
@@ -162,17 +390,11 @@ public class ColumnSelection
*/
public int getMin()
{
- int min = 1000000000;
-
- for (int i = 0; i < selected.size(); i++)
+ if (selection.isEmpty())
{
- if (columnAt(i) < min)
- {
- min = columnAt(i);
- }
+ return 1000000000;
}
-
- return min;
+ return selection.getMinColumn();
}
/**
@@ -183,29 +405,21 @@ public class ColumnSelection
* @param left
* shift in edit (+ve for removal, or -ve for inserts)
*/
- public Vector compensateForEdit(int start, int change)
+ public List compensateForEdit(int start, int change)
{
- Vector deletedHiddenColumns = null;
- for (int i = 0; i < size(); i++)
- {
- int temp = columnAt(i);
-
- if (temp >= start)
- {
- selected.setElementAt(new Integer(temp - change), i);
- }
- }
+ List deletedHiddenColumns = null;
+ selection.compensateForEdits(start, change);
if (hiddenColumns != null)
{
- deletedHiddenColumns = new Vector();
+ deletedHiddenColumns = new ArrayList();
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.addElement(hiddenColumns.elementAt(i));
+ deletedHiddenColumns.add(region);
hiddenColumns.removeElementAt(i);
i--;
@@ -243,21 +457,14 @@ public class ColumnSelection
*/
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);
- }
- }
+ selection.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;
@@ -294,13 +501,13 @@ public class ColumnSelection
{
if (shiftrecord != null)
{
- Vector shifts = shiftrecord.shifts;
+ final List 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];
@@ -315,16 +522,17 @@ public class ColumnSelection
* 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 shifts,
+ 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);
+ 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];
@@ -332,7 +540,7 @@ public class ColumnSelection
{
if (i < j)
{
- hr = (int[]) intervals.elementAt(++i);
+ hr = intervals.elementAt(++i);
}
else
{
@@ -345,7 +553,7 @@ public class ColumnSelection
{ // leadinghc disjoint or not a deletion
if (s < t)
{
- sr = (int[]) deletions.elementAt(++s);
+ sr = shifts.get(++s);
}
else
{
@@ -365,7 +573,7 @@ public class ColumnSelection
j--;
if (i <= j)
{
- hr = (int[]) intervals.elementAt(i);
+ hr = intervals.elementAt(i);
}
continue;
}
@@ -391,7 +599,7 @@ public class ColumnSelection
// sr contained in hr
if (s < t)
{
- sr = (int[]) deletions.elementAt(++s);
+ sr = shifts.get(++s);
}
else
{
@@ -405,35 +613,6 @@ public class ColumnSelection
// 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.
@@ -444,7 +623,7 @@ public class ColumnSelection
{
if (deletions != null)
{
- Vector shifts = deletions.shifts;
+ final List shifts = deletions.getShifts();
if (shifts != null && shifts.size() > 0)
{
// delete any intervals intersecting.
@@ -456,12 +635,12 @@ public class ColumnSelection
hiddenColumns = null;
}
}
- if (selected != null && selected.size() > 0)
+ if (selection != null && selection.size() > 0)
{
- pruneColumnList(shifts, selected);
- if (selected != null && selected.size() == 0)
+ selection.pruneColumnList(shifts);
+ if (selection != null && selection.size() == 0)
{
- selected = null;
+ selection = null;
}
}
// and shift the rest.
@@ -471,23 +650,21 @@ public class ColumnSelection
}
/**
- * 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 getHiddenColumns()
{
- return hiddenColumns;
+ return hiddenColumns == null ? Collections. emptyList()
+ : hiddenColumns;
}
/**
* Return absolute column index for a visible column index
*
* @param column
- * int column index in alignment view
+ * int column index in alignment view (count from zero)
* @return alignment column index for column
*/
public int adjustForHiddenColumns(int column)
@@ -497,7 +674,7 @@ public class ColumnSelection
{
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;
@@ -525,7 +702,7 @@ public class ColumnSelection
int[] region;
do
{
- region = (int[]) hiddenColumns.elementAt(index++);
+ region = hiddenColumns.elementAt(index++);
if (hiddenColumn > region[1])
{
result -= region[1] + 1 - region[0];
@@ -541,6 +718,10 @@ public class ColumnSelection
/**
* 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)
{
@@ -551,7 +732,7 @@ public class ColumnSelection
int gaps = 0;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
+ int[] region = hiddenColumns.elementAt(index);
if (hiddenRegion == 0)
{
return region[0];
@@ -560,7 +741,7 @@ public class ColumnSelection
gaps += region[1] + 1 - region[0];
result = region[1] + 1;
index++;
- } while (index < hiddenRegion + 1);
+ } while (index <= hiddenRegion);
result -= gaps;
}
@@ -582,7 +763,7 @@ public class ColumnSelection
int index = 0;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
+ int[] region = hiddenColumns.elementAt(index);
if (alPos < region[0])
{
return region[0];
@@ -610,7 +791,7 @@ public class ColumnSelection
int index = hiddenColumns.size() - 1;
do
{
- int[] region = (int[]) hiddenColumns.elementAt(index);
+ int[] region = hiddenColumns.elementAt(index);
if (alPos > region[1])
{
return region[1];
@@ -626,65 +807,110 @@ public class ColumnSelection
public void hideSelectedColumns()
{
- while (size() > 0)
+ synchronized (selection)
{
- int column = ((Integer) getSelected().firstElement()).intValue();
- hideColumns(column);
+ for (int[] selregions : selection.getRanges())
+ {
+ hideColumns(selregions[0], selregions[1]);
+ }
+ selection.clear();
}
}
+ /**
+ * Adds the specified column range to the hidden columns
+ *
+ * @param start
+ * @param end
+ */
public void hideColumns(int start, int end)
{
if (hiddenColumns == null)
{
- hiddenColumns = new Vector();
+ hiddenColumns = new Vector();
}
- 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);
+
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ while (i < hiddenColumns.size() - 1)
+ {
+ int[] nextRegion = hiddenColumns.get(i + 1);
+ if (nextRegion[0] > end + 1)
+ {
+ /*
+ * gap to next hidden range - no more to update
+ */
+ break;
+ }
+ region[1] = Math.max(nextRegion[1], end);
+ hiddenColumns.remove(i + 1);
+ }
+ return;
+ }
}
+ /*
+ * remaining case is that the new range follows everything else
+ */
+ hiddenColumns.addElement(new int[] { start, end });
}
/**
- * 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);
@@ -697,6 +923,9 @@ public class ColumnSelection
max++;
}
+ /*
+ * min, max are now the closest unselected columns
+ */
min++;
max--;
if (min > max)
@@ -707,13 +936,16 @@ public class ColumnSelection
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);
@@ -724,12 +956,18 @@ public class ColumnSelection
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++)
{
@@ -749,14 +987,15 @@ public class ColumnSelection
public boolean isVisible(int column)
{
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;
}
}
+ }
return true;
}
@@ -770,21 +1009,14 @@ public class ColumnSelection
{
if (copy != 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));
- }
- }
+ selection = new IntList(copy.selection);
if (copy.hiddenColumns != null)
{
- hiddenColumns = new Vector(copy.hiddenColumns.size());
+ hiddenColumns = new Vector(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];
@@ -807,13 +1039,13 @@ public class ColumnSelection
SequenceI[] seqs)
{
int i, iSize = seqs.length;
- String selection[] = new String[iSize];
+ String selections[] = new String[iSize];
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
for (i = 0; i < iSize; i++)
{
StringBuffer visibleSeq = new StringBuffer();
- Vector regions = getHiddenColumns();
+ List regions = getHiddenColumns();
int blockStart = start, blockEnd = end;
int[] region;
@@ -821,7 +1053,7 @@ public class ColumnSelection
for (int j = 0; j < regions.size(); j++)
{
- region = (int[]) regions.elementAt(j);
+ region = regions.get(j);
hideStart = region[0];
hideEnd = region[1];
@@ -849,18 +1081,18 @@ public class ColumnSelection
visibleSeq.append(seqs[i].getSequence(blockStart, end));
}
- selection[i] = visibleSeq.toString();
+ selections[i] = visibleSeq.toString();
}
}
else
{
for (i = 0; i < iSize; i++)
{
- selection[i] = seqs[i].getSequenceAsString(start, end);
+ selections[i] = seqs[i].getSequenceAsString(start, end);
}
}
- return selection;
+ return selections;
}
/**
@@ -877,8 +1109,8 @@ public class ColumnSelection
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- Vector visiblecontigs = new Vector();
- Vector regions = getHiddenColumns();
+ List visiblecontigs = new ArrayList();
+ List regions = getHiddenColumns();
int vstart = start;
int[] region;
@@ -886,7 +1118,7 @@ public class ColumnSelection
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];
@@ -896,33 +1128,108 @@ public class ColumnSelection
}
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 };
+ }
+ }
+
+ /**
+ * Locate the first and last position visible for this sequence. if seq isn't
+ * visible then return the position of the left and right of the hidden
+ * boundary region, and the corresponding alignment column indices for the
+ * extent of the sequence
+ *
+ * @param seq
+ * @return int[] { visible start, visible end, first seqpos, last seqpos,
+ * alignment index for seq start, alignment index for seq end }
+ */
+ public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+ {
+ int fpos = seq.getStart(), lpos = seq.getEnd();
+ int start = 0;
+
+ if (hiddenColumns == null || hiddenColumns.size() == 0)
+ {
+ int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
+ return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
+ }
+
+ // Simply walk along the sequence whilst watching for hidden column
+ // boundaries
+ List regions = getHiddenColumns();
+ int spos = fpos, lastvispos = -1, rcount = 0, hideStart = seq
+ .getLength(), hideEnd = -1;
+ int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
+ boolean foundStart = false;
+ for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
+ && p < pLen; p++)
+ {
+ if (!Comparison.isGap(seq.getCharAt(p)))
+ {
+ // keep track of first/last column
+ // containing sequence data regardless of visibility
+ if (firstP == -1)
+ {
+ firstP = p;
+ }
+ lastP = p;
+ // update hidden region start/end
+ while (hideEnd < p && rcount < regions.size())
+ {
+ int[] region = regions.get(rcount++);
+ visPrev = visNext;
+ visNext += region[0] - visPrev;
+ hideStart = region[0];
+ hideEnd = region[1];
+ }
+ if (hideEnd < p)
+ {
+ hideStart = seq.getLength();
+ }
+ // update visible boundary for sequence
+ if (p < hideStart)
+ {
+ if (!foundStart)
+ {
+ fpos = spos;
+ start = p;
+ foundStart = true;
+ }
+ lastvispos = p;
+ lpos = spos;
+ }
+ // look for next sequence position
+ spos++;
+ }
+ }
+ if (foundStart)
+ {
+ return new int[] { findColumnPosition(start),
+ findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
}
+ // otherwise, sequence was completely hidden
+ return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
}
/**
@@ -962,16 +1269,16 @@ public class ColumnSelection
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
- Vector annels = new Vector();
+ Vector annels = new Vector();
Annotation[] els = null;
- Vector regions = getHiddenColumns();
+ List 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];
@@ -1015,13 +1322,15 @@ public class ColumnSelection
w += els.length;
}
if (w == 0)
+ {
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;
@@ -1067,18 +1376,13 @@ public class ColumnSelection
*/
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);
- }
+ selection.add(col);
}
}
}
@@ -1092,22 +1396,20 @@ public class ColumnSelection
*/
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)
{
// 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);
}
}
}
@@ -1127,7 +1429,7 @@ public class ColumnSelection
* profileseq marked as hidden.
*/
public static ColumnSelection propagateInsertions(SequenceI profileseq,
- Alignment al, AlignmentView input)
+ AlignmentI al, AlignmentView input)
{
int profsqpos = 0;
@@ -1255,4 +1557,278 @@ public class ColumnSelection
}
}
}
+
+ /**
+ *
+ * @return true if there are columns marked
+ */
+ public boolean hasSelectedColumns()
+ {
+ return (selection != null && selection.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 inserts = sr.getInsertions();
+ for (int[] r : inserts)
+ {
+ hideColumns(r[0], r[1]);
+ }
+ }
+
+ public boolean filterAnnotations(Annotation[] annotations,
+ AnnotationFilterParameter filterParams)
+ {
+ // JBPNote - this method needs to be refactored to become independent of
+ // viewmodel package
+ 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 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();
+ if (hiddenColumns != null)
+ {
+ for (int[] hidden : hiddenColumns)
+ {
+ hashCode = 31 * hashCode + hidden[0];
+ hashCode = 31 * hashCode + hidden[1];
+ }
+ }
+ return 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;
+ }
+
+ /*
+ * check hidden columns are either both null, or match
+ */
+ if (this.hiddenColumns == null)
+ {
+ return (that.hiddenColumns == null);
+ }
+ if (that.hiddenColumns == null
+ || that.hiddenColumns.size() != this.hiddenColumns.size())
+ {
+ return false;
+ }
+ int i = 0;
+ for (int[] thisRange : hiddenColumns)
+ {
+ int[] thatRange = that.hiddenColumns.get(i++);
+ if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * 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;
+ }
+
}