*/
package jalview.datamodel;
-import jalview.util.Comparison;
-import jalview.util.ShiftList;
-
import java.util.ArrayList;
import java.util.BitSet;
-import java.util.Collections;
+import java.util.Iterator;
import java.util.List;
-import java.util.Vector;
import java.util.concurrent.locks.ReentrantReadWriteLock;
+/**
+ * This class manages the collection of hidden columns associated with an
+ * alignment. To iterate over the collection, or over visible columns/regions,
+ * use an iterator obtained from one of:
+ *
+ * - getBoundedIterator: iterates over the hidden regions, within some bounds,
+ * returning absolute positions
+ *
+ * - getBoundedStartIterator: iterates over the start positions of hidden
+ * regions, within some bounds, returning visible positions
+ *
+ * - getVisContigsIterator: iterates over visible regions in a range, returning
+ * absolute positions
+ *
+ * - getVisibleColsIterator: iterates over the visible *columns*
+ *
+ * For performance reasons, provide bounds where possible.
+ *
+ * @author kmourao
+ *
+ */
public class HiddenColumns
{
+ private static final int HASH_MULTIPLIER = 31;
+
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;
+
/*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
{
}
+ /*
+ * 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
+ * (so that it will later be updated when needed).
+ */
+
/**
* 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)
{
- hiddenColumns = copy.copyHiddenRegionsToArrayList();
+ hiddenColumns = new ArrayList<>();
+ Iterator<int[]> it = copy.iterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+ hiddenColumns.add(region);
+ numColumns += region[1] - region[0] + 1;
+ }
+ cursor.resetCursor(hiddenColumns);
}
}
} finally
}
/**
- * This method is used to return all the HiddenColumn regions and is intended
- * to remain private. External callers which need a copy of the regions can
- * call getHiddenColumnsCopyAsList.
+ * Copy constructor within bounds and with offset. Copies hidden column
+ * regions fully contained between start and end, and offsets positions by
+ * subtracting offset.
*
- * @return empty list or List of hidden column intervals
- */
- private List<int[]> getHiddenRegions()
- {
- return hiddenColumns == null ? Collections.<int[]> emptyList()
- : 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]
+ * @param copy
+ * HiddenColumns instance to copy from
+ * @param start
+ * lower bound to copy from
+ * @param end
+ * upper bound to copy to
+ * @param offset
+ * offset to subtract from each region boundary position
*
- * @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 String regionsToString(String delimiter, String between)
+ public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
{
try
{
- LOCK.readLock().lock();
- StringBuilder regionBuilder = new StringBuilder();
- if (hiddenColumns != null)
+ LOCK.writeLock().lock();
+ if (copy != null)
{
- for (int[] range : hiddenColumns)
+ hiddenColumns = new ArrayList<>();
+ numColumns = 0;
+ Iterator<int[]> it = copy.getBoundedIterator(start, end);
+ while (it.hasNext())
{
- regionBuilder.append(delimiter).append(range[0]).append(between)
- .append(range[1]);
+ int[] region = it.next();
+ // still need to check boundaries because iterator returns
+ // all overlapping regions and we need contained regions
+ if (region[0] >= start && region[1] <= end)
+ {
+ hiddenColumns.add(
+ new int[]
+ { region[0] - offset, region[1] - offset });
+ numColumns += region[1] - region[0] + 1;
+ }
}
-
- regionBuilder.deleteCharAt(0);
+ cursor.resetCursor(hiddenColumns);
}
- return regionBuilder.toString();
} finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
}
/**
- * Find the number of hidden columns
+ * Adds the specified column range to the hidden columns collection
*
- * @return number of hidden columns
+ * @param start
+ * start of range to add (absolute position in alignment)
+ * @param end
+ * end of range to add (absolute position in alignment)
*/
- public int getSize()
+ public void hideColumns(int start, int end)
{
+ boolean wasAlreadyLocked = false;
try
{
- LOCK.readLock().lock();
- int size = 0;
- if (hasHiddenColumns())
+ // 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())
{
- for (int[] range : hiddenColumns)
- {
- size += range[1] - range[0] + 1;
- }
+ LOCK.writeLock().lock();
+ }
+ else
+ {
+ wasAlreadyLocked = true;
}
- return size;
- }
- finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- @Override
- public boolean equals(Object obj)
- {
- try
- {
- LOCK.readLock().lock();
- if (!(obj instanceof HiddenColumns))
+ int previndex = 0;
+ int prevHiddenCount = 0;
+ int regionindex = 0;
+ if (hiddenColumns == null)
{
- return false;
+ hiddenColumns = new ArrayList<>();
+ }
+ else
+ {
+ // set up cursor reset values
+ HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
+ regionindex = cursorPos.getRegionIndex();
+
+ if (regionindex > 0)
+ {
+ // get previous index and hidden count for updating the cursor later
+ previndex = regionindex - 1;
+ int[] prevRegion = hiddenColumns.get(previndex);
+ prevHiddenCount = cursorPos.getHiddenSoFar()
+ - (prevRegion[1] - prevRegion[0] + 1);
+ }
}
- HiddenColumns that = (HiddenColumns) obj;
/*
- * check hidden columns are either both null, or match
+ * new range follows everything else; check first to avoid looping over whole hiddenColumns collection
*/
- if (this.hiddenColumns == null)
- {
- return (that.hiddenColumns == null);
- }
- if (that.hiddenColumns == null
- || that.hiddenColumns.size() != this.hiddenColumns.size())
+ if (hiddenColumns.isEmpty()
+ || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
{
- return false;
+ hiddenColumns.add(new int[] { start, end });
}
- int i = 0;
- for (int[] thisRange : hiddenColumns)
+ else
{
- int[] thatRange = that.hiddenColumns.get(i++);
- if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ /*
+ * traverse existing hidden ranges and insert / amend / append as
+ * appropriate
+ */
+ boolean added = false;
+ if (regionindex > 0)
{
- return false;
+ added = insertRangeAtRegion(regionindex - 1, start, end);
+ }
+ if (!added && regionindex < hiddenColumns.size())
+ {
+ insertRangeAtRegion(regionindex, start, end);
}
}
- return true;
+
+ // reset the cursor to just before our insertion point: this saves
+ // a lot of reprocessing in large alignments
+ cursor.resetCursor(hiddenColumns, previndex, prevHiddenCount);
+
+ // reset the number of columns so they will be recounted
+ numColumns = 0;
+
} finally
{
- LOCK.readLock().unlock();
+ if (!wasAlreadyLocked)
+ {
+ LOCK.writeLock().unlock();
+ }
}
}
/**
- * Return absolute column index for a visible column index
+ * Insert [start, range] at the region at index i in hiddenColumns, if
+ * feasible
*
- * @param column
- * int column index in alignment view (count from zero)
- * @return alignment column index for column
+ * @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 adjustForHiddenColumns(int column)
+ 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();
- int result = column;
- if (hiddenColumns != null)
+ /*
+ * 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);
+
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ while (i < hiddenColumns.size() - 1)
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ int[] nextRegion = hiddenColumns.get(i + 1);
+ if (nextRegion[0] > end + 1)
{
- int[] region = hiddenColumns.get(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
+ /*
+ * gap to next hidden range - no more to update
+ */
+ break;
}
+ region[1] = Math.max(nextRegion[1], end);
+
+ // in theory this is faster than hiddenColumns.remove(i+1)
+ // benchmarking results a bit ambivalent
+ hiddenColumns.subList(i + 1, i + 2).clear();
}
- return result;
- } finally
- {
- LOCK.readLock().unlock();
+ added = true;
}
+ return added;
}
/**
- * 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.
+ * mark the columns corresponding to gap characters as hidden in the column
+ * selection
*
- * @param hiddenColumn
- * the column index in the full alignment including hidden columns
- * @return the position of the column in the visible alignment
+ * @param sr
*/
- public int findColumnPosition(int hiddenColumn)
+ public void hideInsertionsFor(SequenceI sr)
{
try
{
- LOCK.readLock().lock();
- int result = hiddenColumn;
- if (hiddenColumns != null)
+ LOCK.writeLock().lock();
+ List<int[]> inserts = sr.getInsertions();
+ for (int[] r : inserts)
{
- int index = 0;
- int[] region;
- do
- {
- region = hiddenColumns.get(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);
- }
- }
+ hideColumns(r[0], r[1]);
}
- return result; // return the shifted position after removing hidden
- // columns.
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} 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.
- *
- * @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
+ * Unhides, and adds to the selection list, all hidden columns
*/
- public int subtractVisibleColumns(int visibleDistance, int startColumn)
+ public void revealAllHiddenColumns(ColumnSelection sel)
{
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));
-
- // 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;
+ LOCK.writeLock().lock();
+ if (hiddenColumns != null)
+ {
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
+ }
+ hiddenColumns = null;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
+ }
} finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
-
}
/**
- * Use this method to determine the set of hiddenRegion start positions
+ * Reveals, and marks as selected, the hidden column range with the given
+ * start column
*
- * @return list of column number in visible view where hidden regions start
+ * @param start
+ * the start column to look for
+ * @param sel
+ * the column selection to add the hidden column range to
*/
- public List<Integer> findHiddenRegionPositions()
+ public void revealHiddenColumns(int start, ColumnSelection sel)
{
try
{
- LOCK.readLock().lock();
- List<Integer> positions = null;
+ LOCK.writeLock().lock();
if (hiddenColumns != null)
{
- positions = new ArrayList<>(hiddenColumns.size());
+ int regionIndex = cursor.findRegionForColumn(start)
+ .getRegionIndex();
- positions.add(hiddenColumns.get(0)[0]);
- for (int i = 1; i < hiddenColumns.size(); ++i)
+ if (regionIndex != -1 && regionIndex != hiddenColumns.size())
{
-
- int result = 0;
- if (hiddenColumns != null)
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(regionIndex);
+ if (start == region[0])
{
- int index = 0;
- int gaps = 0;
- do
+ for (int j = region[0]; j < region[1] + 1; j++)
{
- int[] region = hiddenColumns.get(index);
- gaps += region[1] + 1 - region[0];
- result = region[1] + 1;
- index++;
- } while (index <= i);
+ sel.addElement(j);
+ }
+ int colsToRemove = region[1] - region[0] + 1;
+ hiddenColumns.remove(regionIndex);
- result -= gaps;
+ if (hiddenColumns.isEmpty())
+ {
+ hiddenColumns = null;
+ numColumns = 0;
+ }
+ else
+ {
+ numColumns -= colsToRemove;
+ }
+ cursor.updateForDeletedRegion(hiddenColumns);
}
- positions.add(result);
}
}
- else
- {
- positions = new ArrayList<>();
- }
-
- return positions;
- }
- finally
+ } finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
}
/**
- * This method returns the rightmost limit of a region of an alignment with
- * hidden columns. In otherwords, the next hidden column.
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
*
- * @param index
- * int
+ * @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 getHiddenBoundaryRight(int alPos)
+ public static HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentI al, AlignmentView input)
{
- try
- {
- LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = 0;
- do
- {
- int[] region = hiddenColumns.get(index);
- if (alPos < region[0])
- {
- return region[0];
- }
-
- index++;
- } while (index < hiddenColumns.size());
- }
-
- return alPos;
- } finally
- {
- LOCK.readLock().unlock();
- }
+ 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;
}
/**
- * This method returns the leftmost limit of a region of an alignment with
- * hidden columns. In otherwords, the previous hidden column.
*
- * @param index
- * int
+ * @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 getHiddenBoundaryLeft(int alPos)
+ private void propagateInsertions(SequenceI profileseq, AlignmentI al,
+ SequenceI origseq)
{
try
{
- LOCK.readLock().lock();
+ LOCK.writeLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = hiddenColumns.get(index);
- if (alPos > region[1])
- {
- return region[1];
- }
+ char gc = al.getGapCharacter();
- index--;
- } while (index > -1);
- }
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
- return alPos;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
+ // first get the gaps as a Bitset
+ BitSet gaps = origseq.gapBitset();
- /**
- * 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)
- {
- try
- {
-
- LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
+ // 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[] region = hiddenColumns.get(index);
- if (pos > region[1])
+ // 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])
{
- return index;
+ gapPosition++;
+ if (gaps.get(gapPosition))
+ {
+ numGapsBefore++;
+ }
}
- index--;
- } while (index > -1);
- }
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+ newhidden.add(new int[] { left, right });
- return -1;
+ // make a string with number of gaps = length of hidden region
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0; s < right - left + 1; s++)
+ {
+ sb.append(gc);
+ }
+ padGaps(sb, left, profileseq, al);
+
+ }
+ hiddenColumns = newhidden;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
-
}
/**
- * Adds the specified column range to the hidden columns
+ * Pad gaps in all sequences in alignment except profileseq
*
- * @param start
- * @param end
+ * @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
*/
- public void hideColumns(int start, int end)
+ private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
+ AlignmentI al)
{
- boolean wasAlreadyLocked = false;
- try
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
{
- // 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<>();
- }
-
- /*
- * traverse existing hidden ranges and insert / amend / append as
- * appropriate
- */
- for (int i = 0; i < hiddenColumns.size(); i++)
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj != profileseq)
{
- int[] region = hiddenColumns.get(i);
-
- if (end < region[0] - 1)
+ String sq = al.getSequenceAt(s).getSequenceAsString();
+ if (sq.length() <= pos)
{
- /*
- * insert discontiguous preceding range
- */
- hiddenColumns.add(i, new int[] { start, end });
- 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)
+ // pad sequence
+ int diff = pos - sq.length() - 1;
+ if (diff > 0)
{
- int[] nextRegion = hiddenColumns.get(i + 1);
- if (nextRegion[0] > end + 1)
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = pos - sq.length() - 1) > 0)
{
- /*
- * gap to next hidden range - no more to update
- */
- break;
+ if (diff >= sb.length())
+ {
+ sq += sb.toString();
+ }
+ else
+ {
+ char[] buf = new char[diff];
+ sb.getChars(0, diff, buf, 0);
+ sq += buf.toString();
+ }
}
- region[1] = Math.max(nextRegion[1], end);
- hiddenColumns.remove(i + 1);
}
- return;
+ sq += sb.toString();
}
- }
-
- /*
- * remaining case is that the new range follows everything else
- */
- hiddenColumns.add(new int[] { start, end });
- } finally
- {
- if (!wasAlreadyLocked)
- {
- LOCK.writeLock().unlock();
- }
- }
- }
-
- public boolean isVisible(int column)
- {
- try
- {
- LOCK.readLock().lock();
-
- if (hiddenColumns != null)
- {
- for (int[] region : hiddenColumns)
- {
- if (column >= region[0] && column <= region[1])
+ else
{
- return false;
+ al.getSequenceAt(s).setSequence(
+ sq.substring(0, pos) + sb.toString() + sq.substring(pos));
}
}
}
-
- return true;
- } finally
- {
- LOCK.readLock().unlock();
- }
}
- private ArrayList<int[]> copyHiddenRegionsToArrayList()
- {
- int size = 0;
- if (hiddenColumns != null)
- {
- size = hiddenColumns.size();
- }
- ArrayList<int[]> copy = new ArrayList<>(size);
-
- for (int i = 0, j = size; i < j; i++)
- {
- int[] rh;
- int[] cp;
- rh = hiddenColumns.get(i);
- if (rh != null)
- {
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- copy.add(cp);
- }
- }
+ /*
+ * 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.
+ */
- return copy;
- }
-
/**
- * Returns a copy of the vector of hidden regions, as an ArrayList. Before
- * using this method please consider if you really need access to the hidden
- * regions - a new (or existing!) method on HiddenColumns might be more
- * appropriate.
+ * Output regions data as a string. String is in the format:
+ * reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
*
- * @return hidden regions as an ArrayList of [start,end] pairs
+ * @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 ArrayList<int[]> getHiddenColumnsCopy()
+ public String regionsToString(String delimiter, String between)
{
try
{
LOCK.readLock().lock();
- return copyHiddenRegionsToArrayList();
+ StringBuilder regionBuilder = new StringBuilder();
+ if (hiddenColumns != null)
+ {
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
+ {
+ int[] range = it.next();
+ regionBuilder.append(delimiter).append(range[0]).append(between)
+ .append(range[1]);
+ if (!it.hasNext())
+ {
+ regionBuilder.deleteCharAt(0);
+ }
+ }
+ }
+ return regionBuilder.toString();
} finally
{
LOCK.readLock().unlock();
}
/**
- * propagate shift in alignment columns to column selection
+ * Find the number of hidden columns
*
- * @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
+ * @return number of hidden columns
*/
- public List<int[]> compensateForEdit(int start, int change,
- ColumnSelection sel)
+ public int getSize()
{
try
{
- LOCK.writeLock().lock();
- List<int[]> deletedHiddenColumns = null;
+ LOCK.readLock().lock();
- if (hiddenColumns != null)
+ if (numColumns == 0 && hiddenColumns != null)
{
- deletedHiddenColumns = new ArrayList<>();
- int hSize = hiddenColumns.size();
- for (int i = 0; i < hSize; i++)
- {
- int[] region = hiddenColumns.get(i);
- if (region[0] > start && start + change > region[1])
- {
- deletedHiddenColumns.add(region);
-
- hiddenColumns.remove(i);
- i--;
- hSize--;
- continue;
- }
-
- if (region[0] > start)
- {
- region[0] -= change;
- region[1] -= change;
- }
-
- if (region[0] < 0)
- {
- region[0] = 0;
- }
+ // numColumns is out of date, so recalculate
+ int size = 0;
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
+ {
+ int[] range = it.next();
+ size += range[1] - range[0] + 1;
}
- this.revealHiddenColumns(0, sel);
+ numColumns = size;
}
- return deletedHiddenColumns;
+ return numColumns;
} finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
/**
- * propagate shift in alignment columns to column selection special version of
- * compensateForEdit - allowing for edits within hidden regions
+ * Get the number of distinct hidden regions
*
- * @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
+ * @return number of regions
*/
- public void compensateForDelEdits(int start, int change)
+ public int getNumberOfRegions()
{
try
{
- LOCK.writeLock().lock();
- if (hiddenColumns != null)
+ LOCK.readLock().lock();
+ int num = 0;
+ if (hasHiddenColumns())
{
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.get(i);
- if (region[0] >= start)
- {
- region[0] -= change;
- }
- if (region[1] >= start)
- {
- region[1] -= change;
- }
- if (region[1] < region[0])
- {
- hiddenColumns.remove(i--);
- }
-
- if (region[0] < 0)
- {
- region[0] = 0;
- }
- if (region[1] < 0)
- {
- region[1] = 0;
- }
- }
+ num = hiddenColumns.size();
}
- }
- finally
+ return num;
+ } finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
- /**
- * 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<end
- */
- public int[] getVisibleContigs(int start, int end)
+ @Override
+ public boolean equals(Object obj)
{
try
{
LOCK.readLock().lock();
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- List<int[]> visiblecontigs = new ArrayList<>();
- List<int[]> regions = getHiddenRegions();
-
- int vstart = start;
- int[] region;
- int hideStart;
- int hideEnd;
- for (int j = 0; vstart < end && j < regions.size(); j++)
- {
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
+ if (!(obj instanceof HiddenColumns))
+ {
+ return false;
+ }
+ HiddenColumns that = (HiddenColumns) obj;
- if (hideEnd < vstart)
- {
- continue;
- }
- if (hideStart > vstart)
- {
- visiblecontigs.add(new int[] { vstart, hideStart - 1 });
- }
- vstart = hideEnd + 1;
- }
+ /*
+ * 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 (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++)
+ Iterator<int[]> it = hiddenColumns.iterator();
+ Iterator<int[]> thatit = that.iterator();
+ while (it.hasNext())
+ {
+ int[] thisRange = it.next();
+ int[] thatRange = thatit.next();
+ if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
{
- int[] vc = visiblecontigs.get(i);
- visiblecontigs.set(i, null);
- vcontigs[i * 2] = vc[0];
- vcontigs[i * 2 + 1] = vc[1];
+ return false;
}
- visiblecontigs.clear();
- return vcontigs;
- }
- else
- {
- return new int[] { start, end - 1 };
}
- }
- finally
+ return true;
+ } finally
{
LOCK.readLock().unlock();
}
}
- public String[] getVisibleSequenceStrings(int start, int end,
- SequenceI[] seqs)
+ /**
+ * 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)
{
try
{
LOCK.readLock().lock();
- int iSize = seqs.length;
- String[] selections = new String[iSize];
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- for (int i = 0; i < iSize; i++)
- {
- StringBuffer visibleSeq = new StringBuffer();
- List<int[]> regions = getHiddenRegions();
-
- int blockStart = start;
- int blockEnd = end;
- int[] region;
- int hideStart;
- int 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));
- }
+ int result = column;
- selections[i] = visibleSeq.toString();
- }
- }
- else
+ if (hiddenColumns != null)
{
- for (int i = 0; i < iSize; i++)
- {
- selections[i] = seqs[i].getSequenceAsString(start, end);
- }
+ result += cursor.getHiddenOffset(column).getHiddenSoFar();
}
- return selections;
- }
- finally
+ return result;
+ } finally
{
LOCK.readLock().unlock();
}
}
/**
- * 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
+ * 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 seq
- * @return int[] { visible start, visible end, first seqpos, last seqpos,
- * alignment index for seq start, alignment index for seq end }
+ * @param hiddenColumn
+ * the column index in the full alignment including hidden columns
+ * @return the position of the column in the visible alignment
*/
- public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+ public int findColumnPosition(int hiddenColumn)
{
try
{
LOCK.readLock().lock();
- int fpos = seq.getStart();
- int lpos = seq.getEnd();
- int start = 0;
-
- if (hiddenColumns == null || hiddenColumns.size() == 0)
- {
- int ifpos = seq.findIndex(fpos) - 1;
- int ilpos = seq.findIndex(lpos) - 1;
- return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
- }
+ int result = hiddenColumn;
- // Simply walk along the sequence whilst watching for hidden column
- // boundaries
- List<int[]> regions = getHiddenRegions();
- int spos = fpos;
- int lastvispos = -1;
- int rcount = 0;
- int hideStart = seq.getLength();
- int hideEnd = -1;
- int visPrev = 0;
- int visNext = 0;
- int firstP = -1;
- int lastP = -1;
- boolean foundStart = false;
- for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
- && p < pLen; p++)
+ if (hiddenColumns != null)
{
- if (!Comparison.isGap(seq.getCharAt(p)))
+ 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())
{
- // 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)
+ int[] region = hiddenColumns.get(index);
+ if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
{
- if (!foundStart)
+ // actually col is hidden, return region[0]-1
+ // unless region[0]==0 in which case return 0
+ if (region[0] == 0)
+ {
+ result = 0;
+ }
+ else
{
- fpos = spos;
- start = p;
- foundStart = true;
+ result = region[0] - 1 - hiddenBeforeCol;
}
- 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 };
- }
- finally
+
+ return result; // return the shifted position after removing hidden
+ // columns.
+ } finally
{
LOCK.readLock().unlock();
}
}
/**
- * 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).
+ * 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 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 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 void makeVisibleAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
+ public int subtractVisibleColumns(int visibleDistance, int startColumn)
{
try
{
LOCK.readLock().lock();
- 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<Annotation[]> annels = new Vector<>();
- Annotation[] els = null;
- List<int[]> regions = getHiddenRegions();
- int blockStart = start;
- int blockEnd = end;
- int[] region;
- int hideStart;
- int hideEnd;
- int w = 0;
-
- for (int j = 0; j < regions.size(); j++)
- {
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
+ int distance = visibleDistance;
- if (hideStart < start)
- {
- continue;
- }
+ // in case startColumn is in a hidden region, move it to the left
+ int start = adjustForHiddenColumns(findColumnPosition(startColumn));
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
- {
- break;
- }
+ Iterator<int[]> it = new ReverseRegionsIterator(0, start,
+ hiddenColumns);
- annels.addElement(els = new Annotation[blockEnd - blockStart]);
- System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
- 0, els.length);
- w += els.length;
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
+ while (it.hasNext() && (distance > 0))
+ {
+ int[] region = it.next();
- if (end > blockStart)
+ if (start > region[1])
{
- annels.addElement(els = new Annotation[end - blockStart + 1]);
- if ((els.length
- + blockStart) <= alignmentAnnotation.annotations.length)
+ // subtract the gap to right of region from distance
+ if (start - region[1] <= distance)
{
- // copy just the visible segment of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0, els.length);
+ distance -= start - region[1];
+ start = region[0] - 1;
}
else
{
- // copy to the end of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0,
- (alignmentAnnotation.annotations.length - blockStart));
+ start = start - distance;
+ distance = 0;
}
- 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);
- }
- }
- finally
- {
- LOCK.readLock().unlock();
- }
- }
+ return start - distance;
- /**
- *
- * @return true if there are columns hidden
- */
- public boolean hasHiddenColumns()
- {
- try
- {
- LOCK.readLock().lock();
- return hiddenColumns != null && hiddenColumns.size() > 0;
} 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 more than one set of columns hidden
+ * @param alPos
+ * the absolute (visible) alignmentPosition to find the next hidden
+ * column for
+ * @return the index of the next hidden column, or alPos if there is no next
+ * hidden column
*/
- public boolean hasManyHiddenColumns()
+ public int getHiddenBoundaryRight(int alPos)
{
try
{
LOCK.readLock().lock();
- return hiddenColumns != null && hiddenColumns.size() > 1;
+ 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();
}
/**
- * mark the columns corresponding to gap characters as hidden in the column
- * selection
+ * This method returns the leftmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the previous hidden column.
*
- * @param sr
+ * @param alPos
+ * the absolute (visible) alignmentPosition to find the previous
+ * hidden column for
*/
- public void hideInsertionsFor(SequenceI sr)
+ public int getHiddenBoundaryLeft(int alPos)
{
try
{
- LOCK.writeLock().lock();
- List<int[]> inserts = sr.getInsertions();
- for (int[] r : inserts)
+ LOCK.readLock().lock();
+
+ if (hiddenColumns != null)
{
- hideColumns(r[0], r[1]);
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+
+ if (index > 0)
+ {
+ int[] region = hiddenColumns.get(index - 1);
+ return region[1];
+ }
}
+ return alPos;
} finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
+
/**
- * Unhides, and adds to the selection list, all hidden columns
+ * Answers if a column in the alignment is visible
+ *
+ * @param column
+ * absolute position of column in the alignment
+ * @return true if column is visible
*/
- public void revealAllHiddenColumns(ColumnSelection sel)
+ public boolean isVisible(int column)
{
try
{
- LOCK.writeLock().lock();
- if (hiddenColumns != null)
+ LOCK.readLock().lock();
+
+ int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
+ if (regionindex > -1 && regionindex < hiddenColumns.size())
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ int[] region = hiddenColumns.get(regionindex);
+ // already know that column <= region[1] as cursor returns containing
+ // region or region to right
+ if (column >= region[0])
{
- int[] region = hiddenColumns.get(i);
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
+ return false;
}
}
+ return true;
- hiddenColumns = null;
- }
- finally
+ } finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
/**
- * Reveals, and marks as selected, the hidden column range with the given
- * start column
+ * 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 revealHiddenColumns(int start, ColumnSelection sel)
+ public String[] getVisibleSequenceStrings(int start, int end,
+ SequenceI[] seqs)
{
try
{
- LOCK.writeLock().lock();
- for (int i = 0; i < hiddenColumns.size(); i++)
+ LOCK.readLock().lock();
+ int iSize = seqs.length;
+ String[] selections = new String[iSize];
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- int[] region = hiddenColumns.get(i);
- if (start == region[0])
+ for (int i = 0; i < iSize; i++)
{
- 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]));
+ }
}
- hiddenColumns.remove(region);
- break;
+ selections[i] = visibleSeq.toString();
}
}
- if (hiddenColumns.size() == 0)
+ else
{
- hiddenColumns = null;
+ for (int i = 0; i < iSize; i++)
+ {
+ selections[i] = seqs[i].getSequenceAsString(start, end);
+ }
}
- }
- finally
+
+ return selections;
+ } finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
/**
- * removes intersection of position,length ranges in deletions from the
- * start,end regions marked in intervals.
+ * 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 shifts
- * @param intervals
- * @return
+ * @param seq
+ * sequence to find position for
+ * @return visible start position
*/
- private boolean pruneIntervalList(final List<int[]> shifts,
- ArrayList<int[]> intervals)
+ public int locateVisibleStartOfSequence(SequenceI seq)
{
- boolean pruned = false;
- int i = 0;
- int j = intervals.size() - 1;
- int s = 0;
- int t = shifts.size() - 1;
- int[] hr = intervals.get(i);
- int[] sr = shifts.get(s);
- while (i <= j && s <= t)
- {
- boolean trailinghn = hr[1] >= sr[0];
- if (!trailinghn)
+ try
+ {
+ LOCK.readLock().lock();
+ int start = 0;
+
+ if (hiddenColumns == null || hiddenColumns.size() == 0)
{
- if (i < j)
- {
- hr = intervals.get(++i);
- }
- else
- {
- i++;
- }
- continue;
+ return seq.findIndex(seq.getStart()) - 1;
}
- 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)
+
+ // 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;
+
+ // 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())
{
- sr = shifts.get(++s);
+ int[] region = regions.next();
+ visPrev = visNext;
+ visNext += region[0] - visPrev;
+ hideStart = region[0];
+ hideEnd = region[1];
}
- else
+ if (hideEnd < p)
{
- 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.remove(i);
- pruned = true;
- j--;
- if (i <= j)
- {
- hr = intervals.get(i);
- }
- continue;
+ hideStart = seq.getLength();
}
- if (leadinghc)
+ // update visible boundary for sequence
+ if (p < hideStart)
{
- hr[0] = endshift; // clip c terminal region
- leadinghn = !leadinghn;
- pruned = true;
+ start = p;
+ foundStart = true;
}
}
- if (!leadinghn)
+
+ if (foundStart)
{
- 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 findColumnPosition(start);
}
+ // otherwise, sequence was completely hidden
+ return visPrev;
+ } finally
+ {
+ LOCK.readLock().unlock();
}
- 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.
+ * delete any columns in alignmentAnnotation that are hidden (including
+ * sequence associated annotation).
*
- * @param deletions
+ * @param alignmentAnnotation
*/
- public void pruneDeletions(List<int[]> shifts)
+ public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
{
- try
- {
- LOCK.writeLock().lock();
- // delete any intervals intersecting.
- if (hiddenColumns != null)
- {
- pruneIntervalList(shifts, hiddenColumns);
- if (hiddenColumns != null && hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
- }
- }
- finally
+ if (alignmentAnnotation != null
+ && alignmentAnnotation.annotations != null)
{
- LOCK.writeLock().unlock();
+ makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
+ alignmentAnnotation);
}
}
/**
- * 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 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 static HiddenColumns propagateInsertions(SequenceI profileseq,
- AlignmentI al, AlignmentView input)
+ public void makeVisibleAnnotation(int start, int end,
+ AlignmentAnnotation alignmentAnnotation)
{
- int profsqpos = 0;
+ try
+ {
+ LOCK.readLock().lock();
- 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;
- }
+ int startFrom = start;
+ int endAt = end;
- /**
- *
- * @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
- */
- private 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 = al.getHiddenColumns().getVisibleContigs(0,
- profileseq.getLength());
- int spos = 0;
- int offset = 0;
-
- // add profile to visible contigs
- for (int v = 0; v < viscontigs.length; v += 2)
- {
- if (viscontigs[v] > spos)
+ if (alignmentAnnotation != null
+ && alignmentAnnotation.annotations != null)
{
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- sb.append(gc);
+ removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
}
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ else
{
- 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));
- }
- }
+ alignmentAnnotation.restrict(startFrom, endAt);
}
- // offset+=sb.length();
}
- spos = viscontigs[v + 1] + 1;
- }
- if ((offset + spos) < profileseq.getLength())
+ } finally
{
- // pad the final region with gaps.
- StringBuffer sb = new StringBuffer();
- for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+ LOCK.readLock().unlock();
+ }
+ }
+
+ private void removeHiddenAnnotation(int start, int end,
+ AlignmentAnnotation alignmentAnnotation)
+ {
+ // 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())
+ {
+ int[] block = blocks.next();
+ annotationLength = block[1] - block[0] + 1;
+
+ if (blocks.hasNext())
{
- sb.append(gc);
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
}
- for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ else
{
- SequenceI sqobj = al.getSequenceAt(s);
- if (sqobj == profileseq)
+ if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
{
- continue;
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
}
- String sq = sqobj.getSequenceAsString();
- // pad sequence
- int diff = origseq.getLength() - sq.length();
- while (diff > 0)
+ else
{
- // 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();
+ // 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;
+ }
}
}
/**
- * remove any hiddenColumns or selected columns and shift remaining based on a
- * series of position, range deletions.
*
- * @param deletions
+ * @return true if there are columns hidden
*/
- private void pruneDeletions(ShiftList deletions)
+ public boolean hasHiddenColumns()
{
- if (deletions != null)
+ try
{
- final List<int[]> shifts = deletions.getShifts();
- if (shifts != null && shifts.size() > 0)
- {
- pruneDeletions(shifts);
-
- // and shift the rest.
- this.compensateForEdits(deletions);
- }
+ LOCK.readLock().lock();
+ return hiddenColumns != null && hiddenColumns.size() > 0;
+ } finally
+ {
+ LOCK.readLock().unlock();
}
}
/**
- * Adjust hidden column boundaries based on a series of column additions or
- * deletions in visible regions.
*
- * @param shiftrecord
- * @return
+ * @return true if there are more than one set of columns hidden
*/
- private ShiftList compensateForEdits(ShiftList shiftrecord)
+ public boolean hasManyHiddenColumns()
{
- if (shiftrecord != null)
+ try
{
- final List<int[]> shifts = shiftrecord.getShifts();
- if (shifts != null && shifts.size() > 0)
- {
- int shifted = 0;
- for (int i = 0, j = shifts.size(); i < j; i++)
- {
- int[] sh = shifts.get(i);
- compensateForDelEdits(shifted + sh[0], sh[1]);
- shifted -= sh[1];
- }
- }
- return shiftrecord.getInverse();
+ LOCK.readLock().lock();
+ return hiddenColumns != null && hiddenColumns.size() > 1;
+ } finally
+ {
+ LOCK.readLock().unlock();
}
- return null;
}
+
/**
* Returns a hashCode built from hidden column ranges
*/
{
LOCK.readLock().lock();
int hashCode = 1;
- if (hiddenColumns != null)
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
- for (int[] hidden : hiddenColumns)
- {
- hashCode = 31 * hashCode + hidden[0];
- hashCode = 31 * hashCode + hidden[1];
- }
+ int[] hidden = it.next();
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
}
return hashCode;
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
lastSet = inserts.nextClearBit(firstSet);
hideColumns(firstSet, lastSet - 1);
}
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
{
return;
}
- for (int[] range : hiddenColumns)
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
+ int[] range = it.next();
inserts.set(range[0], range[1] + 1);
}
- }
- finally
+ } finally
{
LOCK.readLock().unlock();
}
return new int[] { startPos, endPos };
}
- for (int[] hiddenCol : hiddenColumns)
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
- lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
- higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+ int[] range = it.next();
+ lowestRange = (range[0] <= startPos) ? range : lowestRange;
+ higestRange = (range[1] >= endPos) ? range : higestRange;
}
- if (lowestRange[0] == -1 && lowestRange[1] == -1)
+ if (lowestRange[0] == -1) // includes (lowestRange[1] == -1)
{
startPos = alignmentStartEnd[0];
}
startPos = lowestRange[1] + 1;
}
- if (higestRange[0] == -1 && higestRange[1] == -1)
+ if (higestRange[0] == -1) // includes (higestRange[1] == -1)
{
endPos = alignmentStartEnd[1];
}
{
LOCK.readLock().unlock();
}
-
}
/**
int adjres = adjustForHiddenColumns(res);
int[] reveal = null;
+
if (hiddenColumns != null)
{
- for (int[] region : hiddenColumns)
+ // look for a region ending just before adjres
+ int regionindex = cursor.findRegionForColumn(adjres - 1)
+ .getRegionIndex();
+ if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[1] == adjres - 1)
{
- if (adjres + 1 == region[0] || adjres - 1 == region[1])
- {
- reveal = region;
- break;
- }
+ reveal = hiddenColumns.get(regionindex);
+ }
+ // check if the region ends just after adjres
+ else if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[0] == adjres + 1)
+ {
+ reveal = hiddenColumns.get(regionindex);
}
}
return reveal;
+
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
+
+ /**
+ * Return an iterator over the hidden regions
+ */
+ public Iterator<int[]> iterator()
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ return new BoundedHiddenColsIterator(hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
+
+ /**
+ * Return a bounded iterator over the hidden regions
+ *
+ * @param start
+ * position to start from (inclusive, absolute column position)
+ * @param end
+ * position to end at (inclusive, absolute column position)
+ * @return
+ */
+ public Iterator<int[]> getBoundedIterator(int start, int end)
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ return new BoundedHiddenColsIterator(start, end, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
+
+ /**
+ * Return a bounded iterator over the *visible* start positions of hidden
+ * regions
+ *
+ * @param start
+ * position to start from (inclusive, visible column position)
+ * @param end
+ * position to end at (inclusive, visible column position)
+ */
+ public Iterator<Integer> getBoundedStartIterator(int start, int end)
+ {
+ try
+ {
+ LOCK.readLock().lock();
+
+ // get absolute position of column in alignment
+ int absoluteStart = adjustForHiddenColumns(start);
+
+ // Get cursor position and supply it to the iterator:
+ // Since we want visible region start, we look for a cursor for the
+ // (absoluteStart-1), then if absoluteStart is the start of a visible
+ // region we'll get the cursor pointing to the region before, which is
+ // what we want
+ HiddenCursorPosition pos = cursor
+ .findRegionForColumn(absoluteStart - 1);
+
+ return new BoundedStartRegionIterator(pos, start, end,
+ hiddenColumns);
} finally
{
LOCK.readLock().unlock();
}
}
+ /**
+ * Return an iterator over visible *columns* (not regions) between the given
+ * start and end boundaries
+ *
+ * @param start
+ * first column (inclusive)
+ * @param end
+ * last column (inclusive)
+ */
+ public Iterator<Integer> getVisibleColsIterator(int start, int end)
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ return new VisibleColsIterator(start, end, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
+
+ /**
+ * return an iterator over visible segments between the given start and end
+ * boundaries
+ *
+ * @param start
+ * first column, inclusive from 0
+ * @param end
+ * last column - not inclusive
+ * @param useVisibleCoords
+ * if true, start and end are visible column positions, not absolute
+ * positions*
+ */
+ public Iterator<int[]> getVisContigsIterator(int start, int end,
+ boolean useVisibleCoords)
+ {
+ int adjstart = start;
+ int adjend = end;
+ if (useVisibleCoords)
+ {
+ adjstart = adjustForHiddenColumns(start);
+ adjend = adjustForHiddenColumns(end);
+ }
+
+ try
+ {
+ LOCK.readLock().lock();
+ return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff