hiddenColumns;
/**
* Add a column to the selection
*
* @param col
* index of column
*/
public void addElement(int col)
{
selection.add(col);
}
/**
* clears column selection
*/
public void clear()
{
selection.clear();
}
/**
* Removes value 'col' from the selection (not the col'th item)
*
* @param col
* index of column to be removed
*/
public void removeElement(int col)
{
selection.remove(col);
}
/**
* 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++)
{
colInt = new Integer(i);
if (selection.contains(colInt))
{
selection.remove(colInt);
}
}
}
/**
* 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 List 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 List getSelectedRanges()
{
return selection.getRanges();
}
/**
*
* @param col
* index to search for in column selection
*
* @return true if col is selected
*/
public boolean contains(int col)
{
return (col > -1) ? selection.isSelected(col) : false;
}
/**
* Answers true if no columns are selected, else false
*/
public boolean isEmpty()
{
return selection == null || selection.isEmpty();
}
/**
* rightmost selected column
*
* @return rightmost column in alignment that is selected
*/
public int getMax()
{
if (selection.isEmpty())
{
return -1;
}
return selection.getMaxColumn();
}
/**
* Leftmost column in selection
*
* @return column index of leftmost column in selection
*/
public int getMin()
{
if (selection.isEmpty())
{
return 1000000000;
}
return selection.getMinColumn();
}
/**
* 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 compensateForEdit(int start, int change)
{
List deletedHiddenColumns = null;
selection.compensateForEdits(start, change);
if (hiddenColumns != null)
{
deletedHiddenColumns = new ArrayList();
int hSize = hiddenColumns.size();
for (int i = 0; i < hSize; i++)
{
int[] region = hiddenColumns.elementAt(i);
if (region[0] > start && start + change > region[1])
{
deletedHiddenColumns.add(region);
hiddenColumns.removeElementAt(i);
i--;
hSize--;
continue;
}
if (region[0] > start)
{
region[0] -= change;
region[1] -= change;
}
if (region[0] < 0)
{
region[0] = 0;
}
}
this.revealHiddenColumns(0);
}
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)
{
selection.compensateForEdits(start, change);
if (hiddenColumns != null)
{
for (int i = 0; i < hiddenColumns.size(); i++)
{
int[] region = hiddenColumns.elementAt(i);
if (region[0] >= start)
{
region[0] -= change;
}
if (region[1] >= start)
{
region[1] -= change;
}
if (region[1] < region[0])
{
hiddenColumns.removeElementAt(i--);
}
if (region[0] < 0)
{
region[0] = 0;
}
if (region[1] < 0)
{
region[1] = 0;
}
}
}
}
/**
* 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)
{
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 = shifts.get(i);
// compensateForEdit(shifted+sh[0], sh[1]);
compensateForDelEdits(shifted + sh[0], sh[1]);
shifted -= sh[1];
}
}
return shiftrecord.getInverse();
}
return null;
}
/**
* removes intersection of position,length ranges in deletions from the
* start,end regions marked in intervals.
*
* @param shifts
* @param intervals
* @return
*/
private boolean pruneIntervalVector(final List shifts,
Vector intervals)
{
boolean pruned = false;
int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
int hr[] = intervals.elementAt(i);
int sr[] = shifts.get(s);
while (i <= j && s <= t)
{
boolean trailinghn = hr[1] >= sr[0];
if (!trailinghn)
{
if (i < j)
{
hr = intervals.elementAt(++i);
}
else
{
i++;
}
continue;
}
int endshift = sr[0] + sr[1]; // deletion ranges - -ve means an insert
if (endshift < hr[0] || endshift < sr[0])
{ // leadinghc disjoint or not a deletion
if (s < t)
{
sr = shifts.get(++s);
}
else
{
s++;
}
continue;
}
boolean leadinghn = hr[0] >= sr[0];
boolean leadinghc = hr[0] < endshift;
boolean trailinghc = hr[1] < endshift;
if (leadinghn)
{
if (trailinghc)
{ // deleted hidden region.
intervals.removeElementAt(i);
pruned = true;
j--;
if (i <= j)
{
hr = intervals.elementAt(i);
}
continue;
}
if (leadinghc)
{
hr[0] = endshift; // clip c terminal region
leadinghn = !leadinghn;
pruned = true;
}
}
if (!leadinghn)
{
if (trailinghc)
{
if (trailinghn)
{
hr[1] = sr[0] - 1;
pruned = true;
}
}
else
{
// sr contained in hr
if (s < t)
{
sr = shifts.get(++s);
}
else
{
s++;
}
continue;
}
}
}
return pruned; // true if any interval was removed or modified by
// operations.
}
/**
* remove any hiddenColumns or selected columns and shift remaining based on a
* series of position, range deletions.
*
* @param deletions
*/
public void pruneDeletions(ShiftList deletions)
{
if (deletions != null)
{
final List shifts = deletions.getShifts();
if (shifts != null && shifts.size() > 0)
{
// delete any intervals intersecting.
if (hiddenColumns != null)
{
pruneIntervalVector(shifts, hiddenColumns);
if (hiddenColumns != null && hiddenColumns.size() == 0)
{
hiddenColumns = null;
}
}
if (selection != null && selection.size() > 0)
{
selection.pruneColumnList(shifts);
if (selection != null && selection.size() == 0)
{
selection = null;
}
}
// and shift the rest.
this.compensateForEdits(deletions);
}
}
}
/**
* This Method is used to return all the HiddenColumn regions
*
* @return empty list or List of hidden column intervals
*/
public List getHiddenColumns()
{
return hiddenColumns == null ? Collections. emptyList()
: hiddenColumns;
}
/**
* Return absolute column index for a visible column index
*
* @param column
* int column index in alignment view (count from zero)
* @return alignment column index for column
*/
public int adjustForHiddenColumns(int column)
{
int result = column;
if (hiddenColumns != null)
{
for (int i = 0; i < hiddenColumns.size(); i++)
{
int[] region = hiddenColumns.elementAt(i);
if (result >= region[0])
{
result += region[1] - region[0] + 1;
}
}
}
return result;
}
/**
* Use this method to find out where a column will appear in the visible
* alignment when hidden columns exist. If the column is not visible, then the
* left-most visible column will always be returned.
*
* @param hiddenColumn
* the column index in the full alignment including hidden columns
* @return the position of the column in the visible alignment
*/
public int findColumnPosition(int hiddenColumn)
{
int result = hiddenColumn;
if (hiddenColumns != null)
{
int index = 0;
int[] region;
do
{
region = hiddenColumns.elementAt(index++);
if (hiddenColumn > region[1])
{
result -= region[1] + 1 - region[0];
}
} while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
{
// Here the hidden column is within a region, so
// we want to return the position of region[0]-1, adjusted for any
// earlier hidden columns.
// Calculate the difference between the actual hidden col position
// and region[0]-1, and then subtract from result to convert result from
// the adjusted hiddenColumn value to the adjusted region[0]-1 value
// However, if the region begins at 0 we cannot return region[0]-1
// just return 0
if (region[0] == 0)
{
return 0;
}
else
{
return result - (hiddenColumn - region[0] + 1);
}
}
}
return result; // return the shifted position after removing hidden columns.
}
/**
* Find the visible column which is a given visible number of columns to the
* left of another visible column. i.e. for a startColumn x, the column which
* is distance 1 away will be column x-1.
*
* @param visibleDistance
* the number of visible columns to offset by
* @param startColumn
* the column to start from
* @return the position of the column in the visible alignment
*/
public int findColumnNToLeft(int visibleDistance, int startColumn)
{
int distance = visibleDistance;
// in case startColumn is in a hidden region, move it to the left
int start = adjustForHiddenColumns(findColumnPosition(startColumn));
// get index of hidden region to left of start
int index = getHiddenIndexLeft(start);
if (index == -1)
{
// no hidden regions to left of startColumn
return start - distance;
}
// walk backwards through the alignment subtracting the counts of visible
// columns from distance
int[] region;
int gap = 0;
int nextstart = start;
while ((index > -1) && (distance - gap > 0))
{
// subtract the gap to right of region from distance
distance -= gap;
start = nextstart;
// calculate the next gap
region = hiddenColumns.get(index);
gap = start - region[1];
// set start to just to left of current region
nextstart = region[0] - 1;
index--;
}
if (distance - gap > 0)
{
// fell out of loop because there are no more hidden regions
distance -= gap;
return nextstart - distance;
}
return start - distance;
}
/**
* Use this method to determine where the next hiddenRegion starts
*
* @param hiddenRegion
* index of hidden region (counts from 0)
* @return column number in visible view
*/
public int findHiddenRegionPosition(int hiddenRegion)
{
int result = 0;
if (hiddenColumns != null)
{
int index = 0;
int gaps = 0;
do
{
int[] region = hiddenColumns.elementAt(index);
if (hiddenRegion == 0)
{
return region[0];
}
gaps += region[1] + 1 - region[0];
result = region[1] + 1;
index++;
} while (index <= hiddenRegion);
result -= gaps;
}
return result;
}
/**
* THis method returns the rightmost limit of a region of an alignment with
* hidden columns. In otherwords, the next hidden column.
*
* @param index
* int
*/
public int getHiddenBoundaryRight(int alPos)
{
if (hiddenColumns != null)
{
int index = 0;
do
{
int[] region = hiddenColumns.elementAt(index);
if (alPos < region[0])
{
return region[0];
}
index++;
} while (index < hiddenColumns.size());
}
return alPos;
}
/**
* This method returns the leftmost limit of a region of an alignment with
* hidden columns. In otherwords, the previous hidden column.
*
* @param index
* int
*/
public int getHiddenBoundaryLeft(int alPos)
{
if (hiddenColumns != null)
{
int index = hiddenColumns.size() - 1;
do
{
int[] region = hiddenColumns.elementAt(index);
if (alPos > region[1])
{
return region[1];
}
index--;
} while (index > -1);
}
return alPos;
}
/**
* This method returns the index of the hidden region to the left of a column
* position. If the column is in a hidden region it returns the index of the
* region to the left. If there is no hidden region to the left it returns -1.
*
* @param pos
* int
*/
private int getHiddenIndexLeft(int pos)
{
if (hiddenColumns != null)
{
int index = hiddenColumns.size() - 1;
do
{
int[] region = hiddenColumns.elementAt(index);
if (pos > region[1])
{
return index;
}
index--;
} while (index > -1);
}
return -1;
}
public void hideSelectedColumns()
{
synchronized (selection)
{
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();
}
/*
* traverse existing hidden ranges and insert / amend / append as
* appropriate
*/
for (int i = 0; i < hiddenColumns.size(); i++)
{
int[] region = hiddenColumns.elementAt(i);
if (end < region[0] - 1)
{
/*
* insert discontiguous preceding range
*/
hiddenColumns.insertElementAt(new int[] { start, end }, i);
return;
}
if (end <= region[1])
{
/*
* new range overlaps existing, or is contiguous preceding it - adjust
* start column
*/
region[0] = Math.min(region[0], start);
return;
}
if (start <= region[1] + 1)
{
/*
* new range overlaps existing, or is contiguous following it - adjust
* start and end columns
*/
region[0] = Math.min(region[0], start);
region[1] = Math.max(region[1], end);
/*
* 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 });
}
/**
* Hides the specified column and any adjacent selected columns
*
* @param res
* int
*/
public void hideColumns(int col)
{
/*
* deselect column (whether selected or not!)
*/
removeElement(col);
/*
* find adjacent selected columns
*/
int min = col - 1, max = col + 1;
while (contains(min))
{
removeElement(min);
min--;
}
while (contains(max))
{
removeElement(max);
max++;
}
/*
* min, max are now the closest unselected columns
*/
min++;
max--;
if (min > max)
{
min = max;
}
hideColumns(min, max);
}
/**
* Unhides, and adds to the selection list, all hidden columns
*/
public void revealAllHiddenColumns()
{
if (hiddenColumns != null)
{
for (int i = 0; i < hiddenColumns.size(); i++)
{
int[] region = hiddenColumns.elementAt(i);
for (int j = region[0]; j < region[1] + 1; j++)
{
addElement(j);
}
}
}
hiddenColumns = null;
}
/**
* Reveals, and marks as selected, the hidden column range with the given
* start column
*
* @param start
*/
public void revealHiddenColumns(int start)
{
for (int i = 0; i < hiddenColumns.size(); i++)
{
int[] region = hiddenColumns.elementAt(i);
if (start == region[0])
{
for (int j = region[0]; j < region[1] + 1; j++)
{
addElement(j);
}
hiddenColumns.removeElement(region);
break;
}
}
if (hiddenColumns.size() == 0)
{
hiddenColumns = null;
}
}
public boolean isVisible(int column)
{
if (hiddenColumns != null)
{
for (int[] region : hiddenColumns)
{
if (column >= region[0] && column <= region[1])
{
return false;
}
}
}
return true;
}
/**
* Copy constructor
*
* @param copy
*/
public ColumnSelection(ColumnSelection copy)
{
if (copy != null)
{
selection = new IntList(copy.selection);
if (copy.hiddenColumns != null)
{
hiddenColumns = new Vector(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);
}
}
}
}
}
/**
* ColumnSelection
*/
public ColumnSelection()
{
}
public String[] getVisibleSequenceStrings(int start, int end,
SequenceI[] seqs)
{
int i, iSize = seqs.length;
String selections[] = new String[iSize];
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
for (i = 0; i < iSize; i++)
{
StringBuffer visibleSeq = new StringBuffer();
List 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));
}
selections[i] = visibleSeq.toString();
}
}
else
{
for (i = 0; i < iSize; i++)
{
selections[i] = seqs[i].getSequenceAsString(start, end);
}
}
return selections;
}
/**
* 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 0)
{
List visiblecontigs = new ArrayList();
List regions = getHiddenColumns();
int vstart = start;
int[] region;
int hideStart, hideEnd;
for (int j = 0; vstart < end && j < regions.size(); j++)
{
region = regions.get(j);
hideStart = region[0];
hideEnd = region[1];
if (hideEnd < vstart)
{
continue;
}
if (hideStart > vstart)
{
visiblecontigs.add(new int[] { vstart, hideStart - 1 });
}
vstart = hideEnd + 1;
}
if (vstart < end)
{
visiblecontigs.add(new int[] { vstart, end - 1 });
}
int[] vcontigs = new int[visiblecontigs.size() * 2];
for (int i = 0, j = visiblecontigs.size(); i < j; i++)
{
int[] vc = visiblecontigs.get(i);
visiblecontigs.set(i, null);
vcontigs[i * 2] = vc[0];
vcontigs[i * 2 + 1] = vc[1];
}
visiblecontigs.clear();
return vcontigs;
}
else
{
return new int[] { start, end - 1 };
}
}
/**
* 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 };
}
/**
* delete any columns in alignmentAnnotation that are hidden (including
* sequence associated annotation).
*
* @param alignmentAnnotation
*/
public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
{
makeVisibleAnnotation(-1, -1, alignmentAnnotation);
}
/**
* delete any columns in alignmentAnnotation that are hidden (including
* sequence associated annotation).
*
* @param start
* remove any annotation to the right of this column
* @param end
* remove any annotation to the left of this column
* @param alignmentAnnotation
* the annotation to operate on
*/
public void makeVisibleAnnotation(int start, int end,
AlignmentAnnotation alignmentAnnotation)
{
if (alignmentAnnotation.annotations == null)
{
return;
}
if (start == end && end == -1)
{
start = 0;
end = alignmentAnnotation.annotations.length;
}
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
// then mangle the alignmentAnnotation annotation array
Vector annels = new Vector();
Annotation[] els = null;
List regions = getHiddenColumns();
int blockStart = start, blockEnd = end;
int[] region;
int hideStart, hideEnd, w = 0;
for (int j = 0; j < regions.size(); j++)
{
region = regions.get(j);
hideStart = region[0];
hideEnd = region[1];
if (hideStart < start)
{
continue;
}
blockStart = Math.min(blockStart, hideEnd + 1);
blockEnd = Math.min(blockEnd, hideStart);
if (blockStart > blockEnd)
{
break;
}
annels.addElement(els = new Annotation[blockEnd - blockStart]);
System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
0, els.length);
w += els.length;
blockStart = hideEnd + 1;
blockEnd = end;
}
if (end > blockStart)
{
annels.addElement(els = new Annotation[end - blockStart + 1]);
if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
{
// copy just the visible segment of the annotation row
System.arraycopy(alignmentAnnotation.annotations, blockStart,
els, 0, els.length);
}
else
{
// copy to the end of the annotation row
System.arraycopy(alignmentAnnotation.annotations, blockStart,
els, 0,
(alignmentAnnotation.annotations.length - blockStart));
}
w += els.length;
}
if (w == 0)
{
return;
}
alignmentAnnotation.annotations = new Annotation[w];
w = 0;
for (Annotation[] chnk : annels)
{
System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
chnk.length);
w += chnk.length;
}
}
else
{
alignmentAnnotation.restrict(start, end);
}
}
/**
* Invert the column selection from first to end-1. leaves hiddenColumns
* 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))
{
removeElement(i);
}
else
{
if (!hasHidden || isVisible(i))
{
addElement(i);
}
}
}
}
/**
* add in any unselected columns from the given column selection, excluding
* any that are hidden.
*
* @param colsel
*/
public void addElementsFrom(ColumnSelection colsel)
{
if (colsel != null && !colsel.isEmpty())
{
for (Integer col : colsel.getSelected())
{
if (hiddenColumns != null && isVisible(col.intValue()))
{
selection.add(col);
}
}
}
}
/**
* set the selected columns the given column selection, excluding any columns
* that are hidden.
*
* @param colsel
*/
public void setElementsFrom(ColumnSelection colsel)
{
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
addElementsFrom(colsel);
}
else
{
// add everything regardless
for (Integer col : colsel.getSelected())
{
addElement(col);
}
}
}
}
/**
* 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 (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;
}
if ((offset + spos) < profileseq.getLength())
{
// pad the final region with gaps.
StringBuffer sb = new StringBuffer();
for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
{
sb.append(gc);
}
for (int s = 0, ns = al.getHeight(); s < ns; s++)
{
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();
}
}
}
}
/**
*
* @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;
}
/**
* Adjusts column selections, and the given selection group, to match the
* range of a stretch (e.g. mouse drag) operation
*
* 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);
}
}
}
}