private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
+ /*
+ * Cursor which tracks the last used hidden columns region, and the number
+ * of hidden columns up to (but not including) that region.
+ */
private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+ /*
+ * cache of the number of hidden columns
+ */
private int numColumns = 0;
/*
{
}
+ /*
+ * Methods which change the hiddenColumns collection. These methods should
+ * use a writeLock to prevent other threads accessing the hiddenColumns
+ * collection while changes are being made. They should also reset the hidden
+ * columns cursor, and either update the hidden columns count, or set it to 0.
+ */
+
/**
* Copy constructor
*
* @param copy
+ * the HiddenColumns object to copy from
*/
public HiddenColumns(HiddenColumns copy)
{
try
{
LOCK.writeLock().lock();
+ numColumns = 0;
if (copy != null)
{
if (copy.hiddenColumns != null)
Iterator<int[]> it = copy.iterator();
while (it.hasNext())
{
- hiddenColumns.add(it.next());
+ int[] region = it.next();
+ hiddenColumns.add(region);
+ numColumns += region[1] - region[0] + 1;
}
cursor.resetCursor(hiddenColumns);
}
}
/**
- * Output regions data as a string. String is in the format:
- * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
+ * Adds the specified column range to the hidden columns collection
*
- * @param delimiter
- * string to delimit regions
- * @param betweenstring
- * to put between start and end region values
- * @return regions formatted according to delimiter and between strings
+ * @param start
+ * start of range to add (absolute position in alignment)
+ * @param end
+ * end of range to add (absolute position in alignment)
*/
- public String regionsToString(String delimiter, String between)
+ public void hideColumns(int start, int end)
{
+ boolean wasAlreadyLocked = false;
try
{
- LOCK.readLock().lock();
- StringBuilder regionBuilder = new StringBuilder();
- if (hiddenColumns != null)
+ // check if the write lock was already locked by this thread,
+ // as this method can be called internally in loops within HiddenColumns
+ if (!LOCK.isWriteLockedByCurrentThread())
{
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ LOCK.writeLock().lock();
+ }
+ else
+ {
+ wasAlreadyLocked = true;
+ }
+
+ if (hiddenColumns == null)
+ {
+ hiddenColumns = new ArrayList<>();
+ }
+
+ /*
+ * new range follows everything else; check first to avoid looping over whole hiddenColumns collection
+ */
+ if (hiddenColumns.isEmpty()
+ || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
+ {
+ hiddenColumns.add(new int[] { start, end });
+ }
+ else
+ {
+ /*
+ * traverse existing hidden ranges and insert / amend / append as
+ * appropriate
+ */
+ boolean added = false;
+ for (int i = 0; !added && i < hiddenColumns.size(); i++)
{
- int[] range = it.next();
- regionBuilder.append(delimiter).append(range[0]).append(between)
- .append(range[1]);
- if (!it.hasNext())
- {
- regionBuilder.deleteCharAt(0);
- }
- }
+ added = insertRangeAtRegion(i, start, end);
+ } // for
+ }
+ if (!wasAlreadyLocked)
+ {
+ cursor.resetCursor(hiddenColumns);
+
+ // reset the number of columns so they will be recounted
+ numColumns = 0;
}
- return regionBuilder.toString();
} finally
{
- LOCK.readLock().unlock();
+ if (!wasAlreadyLocked)
+ {
+ LOCK.writeLock().unlock();
+ }
}
}
/**
- * Find the number of hidden columns
+ * Insert [start, range] at the region at index i in hiddenColumns, if
+ * feasible
*
- * @return number of hidden columns
+ * @param i
+ * index to insert at
+ * @param start
+ * start of range to insert
+ * @param end
+ * end of range to insert
+ * @return true if range was successfully inserted
*/
- public int getSize()
+ private boolean insertRangeAtRegion(int i, int start, int end)
{
- try
+ boolean added = false;
+
+ int[] region = hiddenColumns.get(i);
+ if (end < region[0] - 1)
{
- LOCK.readLock().lock();
+ /*
+ * insert discontiguous preceding range
+ */
+ hiddenColumns.add(i, new int[] { start, end });
+ added = true;
+ }
+ else if (end <= region[1])
+ {
+ /*
+ * new range overlaps existing, or is contiguous preceding it - adjust
+ * start column
+ */
+ region[0] = Math.min(region[0], start);
+ added = true;
+ }
+ else 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);
- if (numColumns == 0 && hiddenColumns != null)
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ while (i < hiddenColumns.size() - 1)
{
- // numColumns is out of date, so recalculate
- int size = 0;
- if (hiddenColumns != null)
+ int[] nextRegion = hiddenColumns.get(i + 1);
+ if (nextRegion[0] > end + 1)
{
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
- {
- int[] range = it.next();
- size += range[1] - range[0] + 1;
- }
+ /*
+ * gap to next hidden range - no more to update
+ */
+ break;
}
- numColumns = size;
+ region[1] = Math.max(nextRegion[1], end);
+ hiddenColumns.subList(i + 1, i + 2).clear();
}
-
- return numColumns;
- } finally
- {
- LOCK.readLock().unlock();
+ added = true;
}
+ return added;
}
/**
- * Get the number of distinct hidden regions
+ * mark the columns corresponding to gap characters as hidden in the column
+ * selection
*
- * @return number of regions
+ * @param sr
*/
- public int getNumberOfRegions()
+ public void hideInsertionsFor(SequenceI sr)
{
try
{
- LOCK.readLock().lock();
- int num = 0;
- if (hasHiddenColumns())
+ LOCK.writeLock().lock();
+ List<int[]> inserts = sr.getInsertions();
+ for (int[] r : inserts)
{
- num = hiddenColumns.size();
+ hideColumns(r[0], r[1]);
}
- return num;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
}
- @Override
- public boolean equals(Object obj)
+ /**
+ * Unhides, and adds to the selection list, all hidden columns
+ */
+ public void revealAllHiddenColumns(ColumnSelection sel)
{
try
{
- LOCK.readLock().lock();
-
- if (!(obj instanceof HiddenColumns))
- {
- return false;
- }
- HiddenColumns that = (HiddenColumns) obj;
-
- /*
- * 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;
- }
-
- Iterator<int[]> it = hiddenColumns.iterator();
- Iterator<int[]> thatit = that.iterator();
- while (it.hasNext())
+ LOCK.writeLock().lock();
+ if (hiddenColumns != null)
{
- int[] thisRange = it.next();
- int[] thatRange = thatit.next();
- if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
- return false;
+ int[] region = it.next();
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
}
+ hiddenColumns = null;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
}
- return true;
} finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
}
/**
- * Return absolute column index for a visible column index
+ * Reveals, and marks as selected, the hidden column range with the given
+ * start column
*
- * @param column
- * int column index in alignment view (count from zero)
- * @return alignment column index for column
+ * @param start
+ * the start column to look for
+ * @param sel
+ * the column selection to add the hidden column range to
*/
- public int adjustForHiddenColumns(int column)
+ public void revealHiddenColumns(int start, ColumnSelection sel)
{
try
{
- LOCK.readLock().lock();
- int result = column;
+ LOCK.writeLock().lock();
if (hiddenColumns != null)
{
- result += cursor.getHiddenOffset(column).getHiddenSoFar();
- }
-
- return result;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
+ int regionIndex = cursor.findRegionForColumn(start)
+ .getRegionIndex();
- /**
- * 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)
- {
- try
- {
- LOCK.readLock().lock();
- int result = hiddenColumn;
-
- if (hiddenColumns != null)
- {
- HiddenCursorPosition cursorPos = cursor
- .findRegionForColumn(hiddenColumn);
- int index = cursorPos.getRegionIndex();
- int hiddenBeforeCol = cursorPos.getHiddenSoFar();
-
- // just subtract hidden cols count - this works fine if column is
- // visible
- result = hiddenColumn - hiddenBeforeCol;
-
- // now check in case column is hidden - it will be in the returned
- // hidden region
- if (index < hiddenColumns.size())
+ if (regionIndex != -1 && regionIndex != hiddenColumns.size())
{
- int[] region = hiddenColumns.get(index);
- if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(regionIndex);
+ if (start == region[0])
{
- // actually col is hidden, return region[0]-1
- // unless region[0]==0 in which case return 0
- if (region[0] == 0)
+ for (int j = region[0]; j < region[1] + 1; j++)
{
- result = 0;
+ sel.addElement(j);
+ }
+ int colsToRemove = region[1] - region[0] + 1;
+ hiddenColumns.remove(regionIndex);
+
+ if (hiddenColumns.isEmpty())
+ {
+ hiddenColumns = null;
+ numColumns = 0;
}
else
{
- result = region[0] - 1 - hiddenBeforeCol;
+ numColumns -= colsToRemove;
}
+ cursor.updateForDeletedRegion(hiddenColumns);
}
}
}
-
- return result; // return the shifted position after removing hidden
- // columns.
} finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
}
/**
- * 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.
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
*
- * @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
+ * @param profileseq
+ * sequence in al which sequences are aligned to
+ * @param al
+ * alignment to have gaps inserted into it
+ * @param input
+ * alignment view where sequence corresponding to profileseq is first
+ * entry
+ * @return new HiddenColumns for new alignment view, with insertions into
+ * profileseq marked as hidden.
*/
- public int subtractVisibleColumns(int visibleDistance, int startColumn)
+ public static HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentI al, AlignmentView input)
{
- try
- {
- LOCK.readLock().lock();
- int distance = visibleDistance;
-
- // in case startColumn is in a hidden region, move it to the left
- int start = adjustForHiddenColumns(findColumnPosition(startColumn));
-
- Iterator<int[]> it = new ReverseRegionsIterator(0, start,
- hiddenColumns);
-
- while (it.hasNext() && (distance > 0))
- {
- int[] region = it.next();
-
- if (start > region[1])
- {
- // subtract the gap to right of region from distance
- if (start - region[1] <= distance)
- {
- distance -= start - region[1];
- start = region[0] - 1;
- }
- else
- {
- start = start - distance;
- distance = 0;
- }
- }
- }
-
- return start - distance;
+ int profsqpos = 0;
- } finally
- {
- LOCK.readLock().unlock();
- }
+ char gc = al.getGapCharacter();
+ Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+ HiddenColumns nview = (HiddenColumns) alandhidden[1];
+ SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+ nview.propagateInsertions(profileseq, al, origseq);
+ return nview;
}
/**
- * This method returns the rightmost limit of a region of an alignment with
- * hidden columns. In otherwords, the next hidden column.
*
- * @param alPos
- * the absolute (visible) alignmentPosition to find the next hidden
- * column for
+ * @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 int getHiddenBoundaryRight(int alPos)
+ private void propagateInsertions(SequenceI profileseq, AlignmentI al,
+ SequenceI origseq)
{
try
{
- LOCK.readLock().lock();
- if (hiddenColumns != null)
+ LOCK.writeLock().lock();
+
+ char gc = al.getGapCharacter();
+
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
+
+ // first get the gaps as a Bitset
+ BitSet gaps = origseq.gapBitset();
+
+ // now calculate hidden ^ not(gap)
+ BitSet hidden = new BitSet();
+ markHiddenRegions(hidden);
+ hidden.andNot(gaps);
+ hiddenColumns = null;
+ this.hideMarkedBits(hidden);
+
+ // for each sequence in the alignment, except the profile sequence,
+ // insert gaps corresponding to each hidden region but where each hidden
+ // column region is shifted backwards by the number of preceding visible
+ // gaps update hidden columns at the same time
+ Iterator<int[]> regions = hiddenColumns.iterator();
+ ArrayList<int[]> newhidden = new ArrayList<>();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ while (regions.hasNext())
{
- int index = cursor.findRegionForColumn(alPos).getRegionIndex();
- if (index < hiddenColumns.size())
+ // get region coordinates accounting for gaps
+ // we can rely on gaps not being *in* hidden regions because we already
+ // removed those
+ int[] region = regions.next();
+ while (gapPosition < region[0])
{
- int[] region = hiddenColumns.get(index);
- if (alPos < region[0])
- {
- return region[0];
- }
- else if ((alPos <= region[1])
- && (index + 1 < hiddenColumns.size()))
+ gapPosition++;
+ if (gaps.get(gapPosition))
{
- // alPos is within a hidden region, return the next one
- // if there is one
- region = hiddenColumns.get(index + 1);
- return region[0];
+ numGapsBefore++;
}
}
- }
- return alPos;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
- /**
- * This method returns the leftmost limit of a region of an alignment with
- * hidden columns. In otherwords, the previous hidden column.
- *
- * @param alPos
- * the absolute (visible) alignmentPosition to find the previous
- * hidden column for
- */
- public int getHiddenBoundaryLeft(int alPos)
- {
- try
- {
- LOCK.readLock().lock();
-
- if (hiddenColumns != null)
- {
- int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+ newhidden.add(new int[] { left, right });
- if (index > 0)
+ // make a string with number of gaps = length of hidden region
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0; s < right - left + 1; s++)
{
- int[] region = hiddenColumns.get(index - 1);
- return region[1];
+ sb.append(gc);
}
- }
- return alPos;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * Adds the specified column range to the hidden columns collection
- *
- * @param start
- * start of range to add (absolute position in alignment)
- * @param end
- * end of range to add (absolute position in alignment)
- */
- public void hideColumns(int start, int end)
- {
- boolean wasAlreadyLocked = false;
- try
- {
- // check if the write lock was already locked by this thread,
- // as this method can be called internally in loops within HiddenColumns
- if (!LOCK.isWriteLockedByCurrentThread())
- {
- LOCK.writeLock().lock();
- }
- else
- {
- wasAlreadyLocked = true;
- }
-
- if (hiddenColumns == null)
- {
- hiddenColumns = new ArrayList<>();
- }
-
- /*
- * new range follows everything else; check first to avoid looping over whole hiddenColumns collection
- */
- if (hiddenColumns.isEmpty()
- || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
- {
- hiddenColumns.add(new int[] { start, end });
- }
- else
- {
- /*
- * traverse existing hidden ranges and insert / amend / append as
- * appropriate
- */
- boolean added = false;
- for (int i = 0; !added && i < hiddenColumns.size(); i++)
- {
- added = insertRangeAtRegion(i, start, end);
- } // for
- }
- if (!wasAlreadyLocked)
- {
- cursor.resetCursor(hiddenColumns);
+ padGaps(sb, left, profileseq, al);
- // reset the number of columns so they will be recounted
- numColumns = 0;
}
+ hiddenColumns = newhidden;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
- if (!wasAlreadyLocked)
- {
- LOCK.writeLock().unlock();
- }
+ LOCK.writeLock().unlock();
}
}
/**
- * Insert [start, range] at the region at index i in hiddenColumns, if
- * feasible
+ * Pad gaps in all sequences in alignment except profileseq
*
- * @param i
- * index to insert at
- * @param start
- * start of range to insert
- * @param end
- * end of range to insert
- * @return true if range was successfully inserted
+ * @param sb
+ * gap string to insert
+ * @param left
+ * position to insert at
+ * @param profileseq
+ * sequence not to pad
+ * @param al
+ * alignment to pad sequences in
*/
- private boolean insertRangeAtRegion(int i, int start, int end)
+ private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
+ AlignmentI al)
{
- boolean added = false;
-
- int[] region = hiddenColumns.get(i);
- if (end < region[0] - 1)
- {
- /*
- * insert discontiguous preceding range
- */
- hiddenColumns.add(i, new int[] { start, end });
- added = true;
- }
- else if (end <= region[1])
- {
- /*
- * new range overlaps existing, or is contiguous preceding it - adjust
- * start column
- */
- region[0] = Math.min(region[0], start);
- added = true;
- }
- else if (start <= region[1] + 1)
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
{
- /*
- * 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)
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj != profileseq)
{
- int[] nextRegion = hiddenColumns.get(i + 1);
- if (nextRegion[0] > end + 1)
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ if (sq.length() <= pos)
{
- /*
- * gap to next hidden range - no more to update
- */
- break;
+ // pad sequence
+ int diff = pos - sq.length() - 1;
+ if (diff > 0)
+ {
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = pos - sq.length() - 1) > 0)
+ {
+ 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, pos) + sb.toString() + sq.substring(pos));
}
- region[1] = Math.max(nextRegion[1], end);
- hiddenColumns.subList(i + 1, i + 2).clear();
}
- added = true;
}
- return added;
}
+ /*
+ * Methods which only need read access to the hidden columns collection.
+ * These methods should use a readLock to prevent other threads changing
+ * the hidden columns collection while it is in use.
+ */
+
/**
- * Answers if a column in the alignment is visible
+ * Output regions data as a string. String is in the format:
+ * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
*
- * @param column
- * absolute position of column in the alignment
- * @return true if column is visible
+ * @param delimiter
+ * string to delimit regions
+ * @param betweenstring
+ * to put between start and end region values
+ * @return regions formatted according to delimiter and between strings
*/
- public boolean isVisible(int column)
+ public String regionsToString(String delimiter, String between)
{
try
{
LOCK.readLock().lock();
-
- int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
- if (regionindex > -1 && regionindex < hiddenColumns.size())
+ StringBuilder regionBuilder = new StringBuilder();
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.get(regionindex);
- if (column >= region[0] && column <= region[1])
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
- return false;
+ int[] range = it.next();
+ regionBuilder.append(delimiter).append(range[0]).append(between)
+ .append(range[1]);
+ if (!it.hasNext())
+ {
+ regionBuilder.deleteCharAt(0);
+ }
}
}
- return true;
-
+ return regionBuilder.toString();
} finally
{
LOCK.readLock().unlock();
}
/**
- * Get the visible sections of a set of sequences
+ * Find the number of hidden columns
*
- * @param start
- * sequence position to start from
- * @param end
- * sequence position to end at
- * @param seqs
- * an array of sequences
- * @return an array of strings encoding the visible parts of each sequence
+ * @return number of hidden columns
*/
- public String[] getVisibleSequenceStrings(int start, int end,
- SequenceI[] seqs)
+ public int getSize()
{
try
{
LOCK.readLock().lock();
- int iSize = seqs.length;
- String[] selections = new String[iSize];
- if (hiddenColumns != null && hiddenColumns.size() > 0)
+
+ if (numColumns == 0 && hiddenColumns != null)
{
- for (int i = 0; i < iSize; i++)
+ // numColumns is out of date, so recalculate
+ int size = 0;
+ if (hiddenColumns != null)
{
- StringBuffer visibleSeq = new StringBuffer();
-
- Iterator<int[]> blocks = new VisibleContigsIterator(start,
- end + 1, hiddenColumns);
-
- while (blocks.hasNext())
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
- int[] block = blocks.next();
- if (blocks.hasNext())
- {
- visibleSeq
- .append(seqs[i].getSequence(block[0], block[1] + 1));
- }
- else
- {
- visibleSeq
- .append(seqs[i].getSequence(block[0], block[1]));
- }
+ int[] range = it.next();
+ size += range[1] - range[0] + 1;
}
-
- selections[i] = visibleSeq.toString();
- }
- }
- else
- {
- for (int i = 0; i < iSize; i++)
- {
- selections[i] = seqs[i].getSequenceAsString(start, end);
}
+ numColumns = size;
}
- return selections;
+ return numColumns;
} finally
{
LOCK.readLock().unlock();
}
/**
- * Locate the first position visible for this sequence. If seq isn't visible
- * then return the position of the left side of the hidden boundary region.
+ * Get the number of distinct hidden regions
*
- * @param seq
- * sequence to find position for
- * @return visible start position
+ * @return number of regions
*/
- public int locateVisibleStartOfSequence(SequenceI seq)
+ public int getNumberOfRegions()
{
try
{
LOCK.readLock().lock();
- int start = 0;
-
- if (hiddenColumns == null || hiddenColumns.size() == 0)
+ int num = 0;
+ if (hasHiddenColumns())
{
- return seq.findIndex(seq.getStart()) - 1;
+ num = hiddenColumns.size();
}
+ return num;
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
- // Simply walk along the sequence whilst watching for hidden column
- // boundaries
- Iterator<int[]> regions = hiddenColumns.iterator();
- int hideStart = seq.getLength();
- int hideEnd = -1;
- int visPrev = 0;
- int visNext = 0;
- boolean foundStart = false;
+ @Override
+ public boolean equals(Object obj)
+ {
+ try
+ {
+ LOCK.readLock().lock();
- // step through the non-gapped positions of the sequence
- for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++)
+ if (!(obj instanceof HiddenColumns))
{
- // get alignment position of this residue in the sequence
- int p = seq.findIndex(i) - 1;
+ return false;
+ }
+ HiddenColumns that = (HiddenColumns) obj;
- // update hidden region start/end
- while (hideEnd < p && regions.hasNext())
- {
- int[] region = regions.next();
- 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)
- {
- start = p;
- foundStart = true;
- }
+ /*
+ * 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;
}
- if (foundStart)
+ Iterator<int[]> it = hiddenColumns.iterator();
+ Iterator<int[]> thatit = that.iterator();
+ while (it.hasNext())
{
- return findColumnPosition(start);
+ int[] thisRange = it.next();
+ int[] thatRange = thatit.next();
+ if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ {
+ return false;
+ }
}
- // otherwise, sequence was completely hidden
- return visPrev;
+ return true;
} finally
{
LOCK.readLock().unlock();
}
/**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
+ * Return absolute column index for a visible column index
*
- * @param alignmentAnnotation
+ * @param column
+ * int column index in alignment view (count from zero)
+ * @return alignment column index for column
*/
- public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
+ public int adjustForHiddenColumns(int column)
{
- makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
- alignmentAnnotation);
+ try
+ {
+ LOCK.readLock().lock();
+ int result = column;
+
+ if (hiddenColumns != null)
+ {
+ result += cursor.getHiddenOffset(column).getHiddenSoFar();
+ }
+
+ return result;
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
+ * 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 start
- * remove any annotation to the right of this column
- * @param end
- * remove any annotation to the left of this column
- * @param alignmentAnnotation
- * the annotation to operate on
+ * @param hiddenColumn
+ * the column index in the full alignment including hidden columns
+ * @return the position of the column in the visible alignment
*/
- public void makeVisibleAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
+ public int findColumnPosition(int hiddenColumn)
{
try
{
LOCK.readLock().lock();
+ int result = hiddenColumn;
- int startFrom = start;
- int endAt = end;
-
- if (alignmentAnnotation.annotations != null)
+ if (hiddenColumns != null)
{
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
- }
- else
+ HiddenCursorPosition cursorPos = cursor
+ .findRegionForColumn(hiddenColumn);
+ int index = cursorPos.getRegionIndex();
+ int hiddenBeforeCol = cursorPos.getHiddenSoFar();
+
+ // just subtract hidden cols count - this works fine if column is
+ // visible
+ result = hiddenColumn - hiddenBeforeCol;
+
+ // now check in case column is hidden - it will be in the returned
+ // hidden region
+ if (index < hiddenColumns.size())
{
- alignmentAnnotation.restrict(startFrom, endAt);
+ int[] region = hiddenColumns.get(index);
+ if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
+ {
+ // actually col is hidden, return region[0]-1
+ // unless region[0]==0 in which case return 0
+ if (region[0] == 0)
+ {
+ result = 0;
+ }
+ else
+ {
+ result = region[0] - 1 - hiddenBeforeCol;
+ }
+ }
}
}
+
+ return result; // return the shifted position after removing hidden
+ // columns.
} finally
{
LOCK.readLock().unlock();
}
}
- private void removeHiddenAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
+ /**
+ * 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 subtractVisibleColumns(int visibleDistance, int startColumn)
{
- // mangle the alignmentAnnotation annotation array
- ArrayList<Annotation[]> annels = new ArrayList<>();
- Annotation[] els = null;
+ try
+ {
+ LOCK.readLock().lock();
+ int distance = visibleDistance;
+
+ // in case startColumn is in a hidden region, move it to the left
+ int start = adjustForHiddenColumns(findColumnPosition(startColumn));
- int w = 0;
-
- Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
- hiddenColumns);
+ Iterator<int[]> it = new ReverseRegionsIterator(0, start,
+ hiddenColumns);
- int copylength;
- int annotationLength;
- while (blocks.hasNext())
- {
- int[] block = blocks.next();
- annotationLength = block[1] - block[0] + 1;
-
- if (blocks.hasNext())
- {
- // copy just the visible segment of the annotation row
- copylength = annotationLength;
- }
- else
+ while (it.hasNext() && (distance > 0))
{
- if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
- {
- // copy just the visible segment of the annotation row
- copylength = annotationLength;
- }
- else
+ int[] region = it.next();
+
+ if (start > region[1])
{
- // copy to the end of the annotation row
- copylength = alignmentAnnotation.annotations.length - block[0];
+ // subtract the gap to right of region from distance
+ if (start - region[1] <= distance)
+ {
+ distance -= start - region[1];
+ start = region[0] - 1;
+ }
+ else
+ {
+ start = start - distance;
+ distance = 0;
+ }
}
}
-
- els = new Annotation[annotationLength];
- annels.add(els);
- System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
- copylength);
- w += annotationLength;
- }
-
- if (w != 0)
- {
- alignmentAnnotation.annotations = new Annotation[w];
+ return start - distance;
- w = 0;
- for (Annotation[] chnk : annels)
- {
- System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
- chnk.length);
- w += chnk.length;
- }
+ } finally
+ {
+ LOCK.readLock().unlock();
}
}
/**
+ * This method returns the rightmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the next hidden column.
*
- * @return true if there are columns hidden
+ * @param alPos
+ * the absolute (visible) alignmentPosition to find the next hidden
+ * column for
*/
- public boolean hasHiddenColumns()
+ public int getHiddenBoundaryRight(int alPos)
{
try
{
LOCK.readLock().lock();
- return hiddenColumns != null && hiddenColumns.size() > 0;
+ if (hiddenColumns != null)
+ {
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+ if (index < hiddenColumns.size())
+ {
+ int[] region = hiddenColumns.get(index);
+ if (alPos < region[0])
+ {
+ return region[0];
+ }
+ else if ((alPos <= region[1])
+ && (index + 1 < hiddenColumns.size()))
+ {
+ // alPos is within a hidden region, return the next one
+ // if there is one
+ region = hiddenColumns.get(index + 1);
+ return region[0];
+ }
+ }
+ }
+ return alPos;
} finally
{
LOCK.readLock().unlock();
}
/**
+ * This method returns the leftmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the previous hidden column.
*
- * @return true if there are more than one set of columns hidden
+ * @param alPos
+ * the absolute (visible) alignmentPosition to find the previous
+ * hidden column for
*/
- public boolean hasManyHiddenColumns()
+ public int getHiddenBoundaryLeft(int alPos)
{
try
{
LOCK.readLock().lock();
- return hiddenColumns != null && hiddenColumns.size() > 1;
+
+ if (hiddenColumns != null)
+ {
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+
+ if (index > 0)
+ {
+ int[] region = hiddenColumns.get(index - 1);
+ return region[1];
+ }
+ }
+ return alPos;
} finally
{
LOCK.readLock().unlock();
}
}
+
/**
- * mark the columns corresponding to gap characters as hidden in the column
- * selection
+ * Answers if a column in the alignment is visible
*
- * @param sr
+ * @param column
+ * absolute position of column in the alignment
+ * @return true if column is visible
*/
- public void hideInsertionsFor(SequenceI sr)
+ public boolean isVisible(int column)
{
try
{
- LOCK.writeLock().lock();
- List<int[]> inserts = sr.getInsertions();
- for (int[] r : inserts)
+ LOCK.readLock().lock();
+
+ int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
+ if (regionindex > -1 && regionindex < hiddenColumns.size())
{
- hideColumns(r[0], r[1]);
+ int[] region = hiddenColumns.get(regionindex);
+ if (column >= region[0] && column <= region[1])
+ {
+ return false;
+ }
}
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
+ return true;
+
} finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
/**
- * Unhides, and adds to the selection list, all hidden columns
+ * Get the visible sections of a set of sequences
+ *
+ * @param start
+ * sequence position to start from
+ * @param end
+ * sequence position to end at
+ * @param seqs
+ * an array of sequences
+ * @return an array of strings encoding the visible parts of each sequence
*/
- public void revealAllHiddenColumns(ColumnSelection sel)
+ public String[] getVisibleSequenceStrings(int start, int end,
+ SequenceI[] seqs)
{
try
{
- LOCK.writeLock().lock();
- if (hiddenColumns != null)
+ LOCK.readLock().lock();
+ int iSize = seqs.length;
+ String[] selections = new String[iSize];
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- Iterator<int[]> it = hiddenColumns.iterator();
- while (it.hasNext())
+ for (int i = 0; i < iSize; i++)
{
- int[] region = it.next();
- for (int j = region[0]; j < region[1] + 1; j++)
+ StringBuffer visibleSeq = new StringBuffer();
+
+ Iterator<int[]> blocks = new VisibleContigsIterator(start,
+ end + 1, hiddenColumns);
+
+ while (blocks.hasNext())
{
- sel.addElement(j);
+ int[] block = blocks.next();
+ if (blocks.hasNext())
+ {
+ visibleSeq
+ .append(seqs[i].getSequence(block[0], block[1] + 1));
+ }
+ else
+ {
+ visibleSeq
+ .append(seqs[i].getSequence(block[0], block[1]));
+ }
}
+
+ selections[i] = visibleSeq.toString();
+ }
+ }
+ else
+ {
+ for (int i = 0; i < iSize; i++)
+ {
+ selections[i] = seqs[i].getSequenceAsString(start, end);
}
- hiddenColumns = null;
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
}
+
+ return selections;
} finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
/**
- * Reveals, and marks as selected, the hidden column range with the given
- * start column
+ * Locate the first position visible for this sequence. If seq isn't visible
+ * then return the position of the left side of the hidden boundary region.
*
- * @param start
+ * @param seq
+ * sequence to find position for
+ * @return visible start position
*/
- public void revealHiddenColumns(int start, ColumnSelection sel)
+ public int locateVisibleStartOfSequence(SequenceI seq)
{
try
{
- LOCK.writeLock().lock();
+ LOCK.readLock().lock();
+ int start = 0;
- if (hiddenColumns != null)
+ if (hiddenColumns == null || hiddenColumns.size() == 0)
{
- int regionIndex = cursor.findRegionForColumn(start)
- .getRegionIndex();
+ return seq.findIndex(seq.getStart()) - 1;
+ }
- if (regionIndex != -1 && regionIndex != hiddenColumns.size())
- {
- // regionIndex is the region which either contains start
- // or lies to the right of start
- int[] region = hiddenColumns.get(regionIndex);
- if (start == region[0])
- {
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
- int colsToRemove = region[1] - region[0] + 1;
- hiddenColumns.remove(regionIndex);
+ // Simply walk along the sequence whilst watching for hidden column
+ // boundaries
+ Iterator<int[]> regions = hiddenColumns.iterator();
+ int hideStart = seq.getLength();
+ int hideEnd = -1;
+ int visPrev = 0;
+ int visNext = 0;
+ boolean foundStart = false;
- if (hiddenColumns.isEmpty())
- {
- hiddenColumns = null;
- numColumns = 0;
- }
- else
- {
- numColumns -= colsToRemove;
- }
- cursor.updateForDeletedRegion(hiddenColumns);
+ // step through the non-gapped positions of the sequence
+ for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++)
+ {
+ // get alignment position of this residue in the sequence
+ int p = seq.findIndex(i) - 1;
- }
+ // update hidden region start/end
+ while (hideEnd < p && regions.hasNext())
+ {
+ int[] region = regions.next();
+ 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)
+ {
+ start = p;
+ foundStart = true;
}
}
+
+ if (foundStart)
+ {
+ return findColumnPosition(start);
+ }
+ // otherwise, sequence was completely hidden
+ return visPrev;
} finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
/**
- * Add gaps into the sequences aligned to profileseq under the given
- * AlignmentView
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
*
- * @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 HiddenColumns for new alignment view, with insertions into
- * profileseq marked as hidden.
+ * @param alignmentAnnotation
*/
- public static HiddenColumns propagateInsertions(SequenceI profileseq,
- AlignmentI al, AlignmentView input)
+ public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
{
- int profsqpos = 0;
-
- char gc = al.getGapCharacter();
- Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
- HiddenColumns nview = (HiddenColumns) alandhidden[1];
- SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
- nview.propagateInsertions(profileseq, al, origseq);
- return nview;
+ makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
+ alignmentAnnotation);
}
/**
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
*
- * @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
+ * @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
*/
- private void propagateInsertions(SequenceI profileseq, AlignmentI al,
- SequenceI origseq)
+ public void makeVisibleAnnotation(int start, int end,
+ AlignmentAnnotation alignmentAnnotation)
{
try
{
- LOCK.writeLock().lock();
-
- char gc = al.getGapCharacter();
-
- // take the set of hidden columns, and the set of gaps in origseq,
- // and remove all the hidden gaps from hiddenColumns
-
- // first get the gaps as a Bitset
- BitSet gaps = origseq.gapBitset();
-
- // now calculate hidden ^ not(gap)
- BitSet hidden = new BitSet();
- markHiddenRegions(hidden);
- hidden.andNot(gaps);
- hiddenColumns = null;
- this.hideMarkedBits(hidden);
+ LOCK.readLock().lock();
- // for each sequence in the alignment, except the profile sequence,
- // insert gaps corresponding to each hidden region
- // but where each hidden column region is shifted backwards by the number
- // of
- // preceding visible gaps
- // update hidden columns at the same time
- Iterator<int[]> regions = hiddenColumns.iterator();
- ArrayList<int[]> newhidden = new ArrayList<>();
+ int startFrom = start;
+ int endAt = end;
- int numGapsBefore = 0;
- int gapPosition = 0;
- while (regions.hasNext())
+ if (alignmentAnnotation.annotations != null)
{
- // get region coordinates accounting for gaps
- // we can rely on gaps not being *in* hidden regions because we already
- // removed those
- int[] region = regions.next();
- while (gapPosition < region[0])
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- gapPosition++;
- if (gaps.get(gapPosition))
- {
- numGapsBefore++;
- }
+ removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
}
-
- int left = region[0] - numGapsBefore;
- int right = region[1] - numGapsBefore;
- newhidden.add(new int[] { left, right });
-
- // make a string with number of gaps = length of hidden region
- StringBuffer sb = new StringBuffer();
- for (int s = 0; s < right - left + 1; s++)
+ else
{
- sb.append(gc);
+ alignmentAnnotation.restrict(startFrom, endAt);
}
- padGaps(sb, left, profileseq, al);
-
}
- hiddenColumns = newhidden;
- cursor.resetCursor(hiddenColumns);
- numColumns = 0;
} finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
- /**
- * Pad gaps in all sequences in alignment except profileseq
- *
- * @param sb
- * gap string to insert
- * @param left
- * position to insert at
- * @param profileseq
- * sequence not to pad
- * @param al
- * alignment to pad sequences in
- */
- private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
- AlignmentI al)
+ private void removeHiddenAnnotation(int start, int end,
+ AlignmentAnnotation alignmentAnnotation)
{
- // loop over the sequences and pad with gaps where required
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ // mangle the alignmentAnnotation annotation array
+ ArrayList<Annotation[]> annels = new ArrayList<>();
+ Annotation[] els = null;
+
+ int w = 0;
+
+ Iterator<int[]> blocks = new VisibleContigsIterator(start, end + 1,
+ hiddenColumns);
+
+ int copylength;
+ int annotationLength;
+ while (blocks.hasNext())
{
- SequenceI sqobj = al.getSequenceAt(s);
- if (sqobj != profileseq)
+ int[] block = blocks.next();
+ annotationLength = block[1] - block[0] + 1;
+
+ if (blocks.hasNext())
{
- String sq = al.getSequenceAt(s).getSequenceAsString();
- if (sq.length() <= pos)
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
+ }
+ else
+ {
+ if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
{
- // pad sequence
- int diff = pos - sq.length() - 1;
- if (diff > 0)
- {
- // pad gaps
- sq = sq + sb;
- while ((diff = pos - sq.length() - 1) > 0)
- {
- 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();
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
}
else
{
- al.getSequenceAt(s).setSequence(
- sq.substring(0, pos) + sb.toString() + sq.substring(pos));
+ // copy to the end of the annotation row
+ copylength = alignmentAnnotation.annotations.length - block[0];
}
}
+
+ els = new Annotation[annotationLength];
+ annels.add(els);
+ System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
+ copylength);
+ w += annotationLength;
+ }
+
+ if (w != 0)
+ {
+ alignmentAnnotation.annotations = new Annotation[w];
+
+ w = 0;
+ for (Annotation[] chnk : annels)
+ {
+ System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+ chnk.length);
+ w += chnk.length;
+ }
+ }
+ }
+
+ /**
+ *
+ * @return true if there are columns hidden
+ */
+ public boolean hasHiddenColumns()
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ return hiddenColumns != null && hiddenColumns.size() > 0;
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
+
+ /**
+ *
+ * @return true if there are more than one set of columns hidden
+ */
+ public boolean hasManyHiddenColumns()
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ return hiddenColumns != null && hiddenColumns.size() > 1;
+ } finally
+ {
+ LOCK.readLock().unlock();
}
}
+
/**
* Returns a hashCode built from hidden column ranges
*/
// and then create a VisibleContigsIterator
// but without a cursor this will be horribly slow in some situations
// ... so until then...
- return new VisibleBlocksVisBoundsIterator(start, end, true);
+ // return new VisibleBlocksVisBoundsIterator(start, end, true);
+ try
+ {
+ LOCK.readLock().lock();
+ int adjstart = adjustForHiddenColumns(start);
+ int adjend = adjustForHiddenColumns(end);
+ return new VisibleContigsIterator(adjstart, adjend + 1,
+ hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
else
{
LOCK.readLock().lock();
return new VisibleContigsIterator(start, end + 1, hiddenColumns);
} finally
- {
+ {
LOCK.readLock().unlock();
}
}
git://source.jalview.org / jalview.git / commitdiff