hiddenColumns;
- index--;
- }
- while(index >-1);
- }
+ /**
+ * Add a column to the selection
+ *
+ * @param col
+ * index of column
+ */
+ public void addElement(int col)
+ {
+ selection.add(col);
+ }
- return alPos;
+ /**
+ * 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);
+ }
- public void hideSelectedColumns()
+ /**
+ * 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++)
{
- while (size() > 0)
+ colInt = new Integer(i);
+ if (selection.contains(colInt))
{
- int column = ( (Integer) getSelected().firstElement()).intValue();
- hideColumns(column);
+ 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();
+ }
- public void hideColumns(int start, int end)
+ /**
+ * Leftmost column in selection
+ *
+ * @return column index of leftmost column in selection
+ */
+ public int getMin()
+ {
+ if (selection.isEmpty())
{
- if(hiddenColumns==null)
- hiddenColumns = new Vector();
+ return 1000000000;
+ }
+ return selection.getMinColumn();
+ }
- boolean added = false;
- boolean overlap = false;
+ /**
+ * 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);
- for (int i = 0; i < hiddenColumns.size(); i++)
+ if (hiddenColumns != null)
+ {
+ deletedHiddenColumns = new ArrayList();
+ int hSize = hiddenColumns.size();
+ for (int i = 0; i < hSize; i++)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- if ( start<=region[1] && end>=region[0])
+ int[] region = hiddenColumns.elementAt(i);
+ if (region[0] > start && start + change > region[1])
{
+ deletedHiddenColumns.add(region);
+
hiddenColumns.removeElementAt(i);
- overlap = true;
- break;
+ i--;
+ hSize--;
+ continue;
}
- else if (end < region[0] && start < region[0])
+
+ if (region[0] > start)
{
- hiddenColumns.insertElementAt(new int[]
- {start, end}, i);
- added = true;
- break;
+ region[0] -= change;
+ region[1] -= change;
+ }
+
+ if (region[0] < 0)
+ {
+ region[0] = 0;
}
- }
- if(overlap)
- {
- hideColumns(start, end);
}
- else if (!added)
- hiddenColumns.addElement(new int[] {start, end});
+ this.revealHiddenColumns(0);
}
- /**
- * 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 ++; }
+ return deletedHiddenColumns;
+ }
- min++; max--;
+ /**
+ * 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)
+ {
- hideColumns(min, max);
- }
+ selection.compensateForEdits(start, change);
- public void revealAllHiddenColumns()
+ if (hiddenColumns != null)
{
- if(hiddenColumns!=null)
+ for (int i = 0; i < hiddenColumns.size(); i++)
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ int[] region = hiddenColumns.elementAt(i);
+ if (region[0] >= start)
{
- int[] region = (int[]) hiddenColumns.elementAt(i);
- for (int j = region[0]; j < region[1]+1; j++)
- {
- addElement(j);
- }
+ region[0] -= change;
+ }
+ if (region[1] >= start)
+ {
+ region[1] -= change;
+ }
+ if (region[1] < region[0])
+ {
+ hiddenColumns.removeElementAt(i--);
}
- }
- hiddenColumns = null;
+ if (region[0] < 0)
+ {
+ region[0] = 0;
+ }
+ if (region[1] < 0)
+ {
+ region[1] = 0;
+ }
+ }
}
+ }
- public void revealHiddenColumns(int res)
+ /**
+ * 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)
{
- for(int i=0; i shifts = shiftrecord.getShifts();
+ if (shifts != null && shifts.size() > 0)
{
- int [] region = (int[])hiddenColumns.elementAt(i);
- if( res == region[0])
+ int shifted = 0;
+ for (int i = 0, j = shifts.size(); i < j; i++)
{
- for (int j = region[0]; j < region[1]+1; j++)
- {
- addElement(j);
- }
-
- hiddenColumns.removeElement(region);
- break;
+ int[] sh = shifts.get(i);
+ // compensateForEdit(shifted+sh[0], sh[1]);
+ compensateForDelEdits(shifted + sh[0], sh[1]);
+ shifted -= sh[1];
}
}
- if(hiddenColumns.size()==0)
- hiddenColumns = null;
+ return shiftrecord.getInverse();
}
+ return null;
+ }
- public boolean isVisible(int column)
+ /**
+ * 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)
{
- for(int i=0; i= sr[0];
+ if (!trailinghn)
{
- int [] region = (int[])hiddenColumns.elementAt(i);
- if( column >= region[0] && column <= region[1])
+ if (i < j)
{
- return false;
+ 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 true;
}
- /**
- * Copy constructor
- * @param copy
- */
- public ColumnSelection(ColumnSelection copy) {
- if (copy!=null) {
- if (copy.selected!=null) {
- selected = new Vector();
- for (int i=0,j=copy.selected.size(); i 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 (copy.hiddenColumns!=null) {
- hiddenColumns=new Vector();
- for (int i=0,j=copy.hiddenColumns.size(); i 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
+ * 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])
+ {
+ result -= region[1] + 1 - region[0];
+ }
+ } 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
+ *
+ * @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;
+
+ }
+
+ 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);
+ 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
@@ -668,4 +1016,801 @@ public class 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;
+ }
+
}