package jalview.datamodel;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
-import java.util.NoSuchElementException;
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. Note that column
+ * numbering begins at 0 throughout this class.
+ *
+ * @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
*/
- private ArrayList<int[]> hiddenColumns;
+ private List<int[]> hiddenColumns = new ArrayList<>();
/**
* Constructor
{
}
+ /*
+ * 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();
- if (copy != null)
- {
- if (copy.hiddenColumns != null)
- {
- hiddenColumns = new ArrayList<>();
- Iterator<int[]> it = copy.iterator();
- while (it.hasNext())
- {
- hiddenColumns.add(it.next());
- }
- }
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
+ this(copy, Integer.MIN_VALUE, Integer.MAX_VALUE, 0);
}
/**
LOCK.writeLock().lock();
if (copy != null)
{
- hiddenColumns = new ArrayList<>();
+ numColumns = 0;
Iterator<int[]> it = copy.getBoundedIterator(start, end);
while (it.hasNext())
{
hiddenColumns.add(
new int[]
{ region[0] - offset, region[1] - offset });
+ numColumns += region[1] - region[0] + 1;
}
}
+ cursor.resetCursor(hiddenColumns);
}
} finally
{
}
/**
- * 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();
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
+ // 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;
+ }
+
+ int previndex = 0;
+ int prevHiddenCount = 0;
+ int regionindex = 0;
+ if (!hiddenColumns.isEmpty())
{
- int[] range = it.next();
- regionBuilder.append(delimiter).append(range[0]).append(between)
- .append(range[1]);
- if (!it.hasNext())
+ // set up cursor reset values
+ HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
+ regionindex = cursorPos.getRegionIndex();
+
+ if (regionindex > 0)
{
- regionBuilder.deleteCharAt(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);
}
}
- return regionBuilder.toString();
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
- /**
- * Find the number of hidden columns
- *
- * @return number of hidden columns
- */
- public int getSize()
- {
- try
- {
- LOCK.readLock().lock();
- int size = 0;
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
+ /*
+ * 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
{
- int[] range = it.next();
- size += range[1] - range[0] + 1;
+ /*
+ * traverse existing hidden ranges and insert / amend / append as
+ * appropriate
+ */
+ boolean added = false;
+ if (regionindex > 0)
+ {
+ added = insertRangeAtRegion(regionindex - 1, start, end);
+ }
+ if (!added && regionindex < hiddenColumns.size())
+ {
+ insertRangeAtRegion(regionindex, start, end);
+ }
}
- return size;
+ // 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();
+ }
}
}
/**
- * Get the number of distinct hidden regions
+ * Insert [start, range] at the region at index i in hiddenColumns, if
+ * feasible
*
- * @return number of regions
+ * @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 getNumberOfRegions()
+ 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 num = 0;
- if (hasHiddenColumns())
- {
- num = hiddenColumns.size();
- }
- return num;
- } finally
+ /*
+ * insert discontiguous preceding range
+ */
+ hiddenColumns.add(i, new int[] { start, end });
+ added = true;
+ }
+ else if (end <= region[1])
{
- LOCK.readLock().unlock();
+ /*
+ * new range overlaps existing, or is contiguous preceding it - adjust
+ * start column
+ */
+ region[0] = Math.min(region[0], start);
+ added = true;
}
- }
-
- @Override
- public boolean equals(Object obj)
- {
- try
+ else if (start <= region[1] + 1)
{
- LOCK.readLock().lock();
-
- if (!(obj instanceof HiddenColumns))
- {
- return false;
- }
- HiddenColumns that = (HiddenColumns) obj;
-
/*
- * check hidden columns are either both null, or match
+ * new range overlaps existing, or is contiguous following it - adjust
+ * start and end columns
*/
- if (this.hiddenColumns == null)
- {
- return (that.hiddenColumns == null);
- }
- if (that.hiddenColumns == null
- || that.hiddenColumns.size() != this.hiddenColumns.size())
- {
- return false;
- }
+ region[0] = Math.min(region[0], start);
+ region[1] = Math.max(region[1], end);
- Iterator<int[]> it = new RegionsIterator();
- Iterator<int[]> thatit = that.iterator();
- while (it.hasNext())
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ while (i < hiddenColumns.size() - 1)
{
- int[] thisRange = it.next();
- int[] thatRange = thatit.next();
- if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ int[] nextRegion = hiddenColumns.get(i + 1);
+ if (nextRegion[0] > end + 1)
{
- return false;
+ /*
+ * 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 true;
- } finally
- {
- LOCK.readLock().unlock();
+ added = true;
}
+ return added;
}
/**
- * Return absolute column index for a visible column index
+ * hide a list of ranges
*
- * @param column
- * int column index in alignment view (count from zero)
- * @return alignment column index for column
+ * @param ranges
*/
- public int adjustForHiddenColumns(int column)
+ public void hideList(List<int[]> ranges)
{
try
{
- LOCK.readLock().lock();
- int result = column;
-
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
+ LOCK.writeLock().lock();
+ for (int[] r : ranges)
{
- int[] region = it.next();
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
+ hideColumns(r[0], r[1]);
}
-
- return result;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
}
/**
- * 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
+ * Unhides, and adds to the selection list, all hidden columns
*/
- public int findColumnPosition(int hiddenColumn)
+ public void revealAllHiddenColumns(ColumnSelection sel)
{
try
{
- LOCK.readLock().lock();
- int result = hiddenColumn;
- int[] region = null;
- if (hiddenColumns != null)
- {
- Iterator<int[]> it = new RegionsIterator(0,
- hiddenColumn);
- while (it.hasNext())
- {
- region = it.next();
- if (hiddenColumn > region[1])
- {
- result -= region[1] + 1 - region[0];
- }
- }
+ LOCK.writeLock().lock();
- if (region != null && hiddenColumn >= region[0]
- && hiddenColumn <= region[1])
+ for (int[] region : hiddenColumns)
+ {
+ for (int j = region[0]; j < region[1] + 1; j++)
{
- // 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);
- }
+ sel.addElement(j);
}
}
- return result; // return the shifted position after removing hidden
- // columns.
+ hiddenColumns.clear();
+ 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.
+ * Reveals, and marks as selected, the hidden column range with the given
+ * start column
*
- * @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 start
+ * the start column to look for
+ * @param sel
+ * the column selection to add the hidden column range to
*/
- public int subtractVisibleColumns(int visibleDistance, int startColumn)
+ public void revealHiddenColumns(int start, 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));
-
- Iterator<int[]> it = new ReverseRegionsIterator(0, start);
+ LOCK.writeLock().lock();
- while (it.hasNext() && (distance > 0))
+ if (!hiddenColumns.isEmpty())
{
- int[] region = it.next();
+ int regionIndex = cursor.findRegionForColumn(start)
+ .getRegionIndex();
- if (start > region[1])
+ if (regionIndex != -1 && regionIndex != hiddenColumns.size())
{
- // subtract the gap to right of region from distance
- if (start - region[1] <= distance)
- {
- distance -= start - region[1];
- start = region[0] - 1;
- }
- else
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(regionIndex);
+ if (start == region[0])
{
- start = start - distance;
- distance = 0;
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
+ int colsToRemove = region[1] - region[0] + 1;
+ hiddenColumns.remove(regionIndex);
+
+ if (hiddenColumns.isEmpty())
+ {
+ hiddenColumns.clear();
+ numColumns = 0;
+ }
+ else
+ {
+ numColumns -= colsToRemove;
+ }
+ cursor.updateForDeletedRegion(hiddenColumns);
}
}
}
-
- return start - distance;
-
} 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.
- *
- * @param alPos
- * the (visible) alignmentPosition to find the next hidden column for
- */
- public int getHiddenBoundaryRight(int alPos)
- {
- try
- {
- LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
- {
- int[] region = it.next();
- if (alPos < region[0])
- {
- 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.
- *
- * @param alPos
- * the (visible) alignmentPosition to find the previous hidden column
- * for
- */
- public int getHiddenBoundaryLeft(int alPos)
- {
- try
- {
- LOCK.readLock().lock();
-
- Iterator<int[]> it = new ReverseRegionsIterator(0, alPos);
- while (it.hasNext())
- {
- int[] region = it.next();
- if (alPos > region[1])
- {
- return region[1];
- }
- }
-
- 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
- }
- } finally
- {
- if (!wasAlreadyLocked)
- {
- LOCK.writeLock().unlock();
- }
- }
- }
-
- private boolean insertRangeAtRegion(int i, int start, int end)
- {
- 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)
- {
- /*
- * new range overlaps existing, or is contiguous following it - adjust
- * start and end columns
- */
- region[0] = Math.min(region[0], start);
- region[1] = Math.max(region[1], end);
-
- /*
- * also update or remove any subsequent ranges
- * that are overlapped
- */
- while (i < hiddenColumns.size() - 1)
- {
- int[] nextRegion = hiddenColumns.get(i + 1);
- if (nextRegion[0] > end + 1)
- {
- /*
- * gap to next hidden range - no more to update
- */
- break;
- }
- region[1] = Math.max(nextRegion[1], end);
- hiddenColumns.remove(i + 1);
- }
- added = true;
- }
- return added;
- }
-
- /**
- * 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 boolean isVisible(int column)
- {
- try
- {
- LOCK.readLock().lock();
-
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
- {
- int[] region = it.next();
- if (column >= region[0] && column <= region[1])
- {
- return false;
- }
- }
-
- return true;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * 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 String[] getVisibleSequenceStrings(int start, int end,
- SequenceI[] seqs)
- {
- 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();
-
- Iterator<int[]> blocks = new VisibleContigsIterator(start,
- end + 1, false);
-
- while (blocks.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]));
- }
- }
-
- selections[i] = visibleSeq.toString();
- }
- }
- else
- {
- for (int i = 0; i < iSize; i++)
- {
- selections[i] = seqs[i].getSequenceAsString(start, end);
- }
- }
-
- return selections;
- } 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.
- *
- * @param seq
- * sequence to find position for
- * @return visible start position
- */
- public int locateVisibleStartOfSequence(SequenceI seq)
- {
- try
- {
- LOCK.readLock().lock();
- int start = 0;
-
- if (hiddenColumns == null || hiddenColumns.size() == 0)
- {
- return seq.findIndex(seq.getStart()) - 1;
- }
-
- // Simply walk along the sequence whilst watching for hidden column
- // boundaries
- Iterator<int[]> regions = new RegionsIterator();
- 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())
- {
- 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.readLock().unlock();
- }
- }
-
- /**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
- *
- * @param alignmentAnnotation
- */
- public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
- {
- makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
- alignmentAnnotation);
- }
-
- /**
- * delete any columns in alignmentAnnotation that are hidden (including
- * sequence associated annotation).
- *
- * @param start
- * remove any annotation to the right of this column
- * @param end
- * remove any annotation to the left of this column
- * @param alignmentAnnotation
- * the annotation to operate on
- */
- public void makeVisibleAnnotation(int start, int end,
- AlignmentAnnotation alignmentAnnotation)
- {
- try
- {
- LOCK.readLock().lock();
-
- int startFrom = start;
- int endAt = end;
-
- if (alignmentAnnotation.annotations != null)
- {
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
- }
- else
- {
- alignmentAnnotation.restrict(startFrom, endAt);
- }
- }
- } finally
- {
- 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,
- false);
-
- 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
- {
- if (annotationLength + block[0] <= alignmentAnnotation.annotations.length)
- {
- // copy just the visible segment of the annotation row
- copylength = annotationLength;
- }
- else
- {
- // 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();
- }
- }
-
- /**
- * mark the columns corresponding to gap characters as hidden in the column
- * selection
- *
- * @param sr
- */
- public void hideInsertionsFor(SequenceI sr)
- {
- try
- {
- LOCK.writeLock().lock();
- List<int[]> inserts = sr.getInsertions();
- for (int[] r : inserts)
- {
- hideColumns(r[0], r[1]);
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- * Unhides, and adds to the selection list, all hidden columns
- */
- public void revealAllHiddenColumns(ColumnSelection sel)
- {
- try
- {
- LOCK.writeLock().lock();
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
- {
- int[] region = it.next();
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
- }
-
- hiddenColumns = null;
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- * Reveals, and marks as selected, the hidden column range with the given
- * start column
- *
- * @param start
- */
- public void revealHiddenColumns(int start, ColumnSelection sel)
- {
- try
- {
- LOCK.writeLock().lock();
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
- {
- int[] region = it.next();
- if (start == region[0])
- {
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
-
- hiddenColumns.remove(region);
- break;
- }
- else if (start < region[0])
- {
- break; // passed all possible matching regions
- }
- }
-
- if (hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
- } finally
- {
- LOCK.writeLock().unlock();
- }
- }
-
- /**
- * Add gaps into the sequences aligned to profileseq under the given
- * AlignmentView
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
*
* @param profileseq
+ * sequence in al which sequences are aligned to
* @param al
- * - alignment to have gaps inserted into it
+ * alignment to have gaps inserted into it
* @param input
- * - alignment view where sequence corresponding to profileseq is
- * first entry
+ * 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 profileseq
- * - sequence in al which corresponds to origseq
+ * sequence in al which corresponds to origseq
* @param al
- * - alignment which is to have gaps inserted into it
+ * alignment which is to have gaps inserted into it
* @param origseq
- * - sequence corresponding to profileseq which defines gap map for
+ * sequence corresponding to profileseq which defines gap map for
* modifying al
*/
private void propagateInsertions(SequenceI profileseq, AlignmentI al,
// 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
+ // first get the non-gaps as a Bitset
+ // then calculate hidden ^ not(gap)
BitSet gaps = origseq.gapBitset();
-
- // now calculate hidden ^ not(gap)
- BitSet hidden = new BitSet();
- markHiddenRegions(hidden);
- hidden.andNot(gaps);
- hiddenColumns = null;
- this.hideMarkedBits(hidden);
+ this.andNot(gaps);
// 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 = new RegionsIterator();
- ArrayList<int[]> newhidden = new ArrayList<>();
+ // 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
+ List<int[]> newhidden = new ArrayList<>();
int numGapsBefore = 0;
int gapPosition = 0;
- while (regions.hasNext())
+ for (int[] region : hiddenColumns)
{
// 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])
{
gapPosition++;
newhidden.add(new int[] { left, right });
// make a string with number of gaps = length of hidden region
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
for (int s = 0; s < right - left + 1; s++)
{
sb.append(gc);
}
hiddenColumns = newhidden;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
* @param al
* alignment to pad sequences in
*/
- private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
+ private void padGaps(StringBuilder sb, int pos, SequenceI profileseq,
AlignmentI al)
{
// loop over the sequences and pad with gaps where required
}
}
+ /*
+ * 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.
+ */
+
/**
- * Returns a hashCode built from hidden column ranges
+ * 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 delimiter
+ * string to delimit regions
+ * @param betweenstring
+ * to put between start and end region values
+ * @return regions formatted according to delimiter and between strings
*/
- @Override
- public int hashCode()
+ public String regionsToString(String delimiter, String between)
{
try
{
LOCK.readLock().lock();
- int hashCode = 1;
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
+ StringBuilder regionBuilder = new StringBuilder();
+
+ boolean first = true;
+ for (int[] range : hiddenColumns)
{
- int[] hidden = it.next();
- hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
- hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
+ if (!first)
+ {
+ regionBuilder.append(delimiter);
+ }
+ else
+ {
+ first = false;
+ }
+ regionBuilder.append(range[0]).append(between).append(range[1]);
+
}
- return hashCode;
+
+ return regionBuilder.toString();
} finally
{
LOCK.readLock().unlock();
}
/**
- * Hide columns corresponding to the marked bits
+ * Find the number of hidden columns
*
- * @param inserts
- * - columns map to bits starting from zero
+ * @return number of hidden columns
*/
- public void hideMarkedBits(BitSet inserts)
+ public int getSize()
{
try
{
- LOCK.writeLock().lock();
- for (int firstSet = inserts
- .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
- .nextSetBit(lastSet))
+ LOCK.readLock().lock();
+
+ if (numColumns == 0)
{
- lastSet = inserts.nextClearBit(firstSet);
- hideColumns(firstSet, lastSet - 1);
+ // numColumns is out of date, so recalculate
+ int size = 0;
+
+ for (int[] range : hiddenColumns)
+ {
+ size += range[1] - range[0] + 1;
+ }
+
+ numColumns = size;
}
+
+ return numColumns;
} finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
/**
+ * Get the number of distinct hidden regions
*
- * @param inserts
- * BitSet where hidden columns will be marked
+ * @return number of regions
*/
- public void markHiddenRegions(BitSet inserts)
+ public int getNumberOfRegions()
{
try
{
LOCK.readLock().lock();
- if (hiddenColumns == null)
- {
- return;
- }
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
- {
- int[] range = it.next();
- inserts.set(range[0], range[1] + 1);
- }
+ return hiddenColumns.size();
} finally
{
LOCK.readLock().unlock();
}
}
- /**
- * Calculate the visible start and end index of an alignment.
- *
- * @param width
- * full alignment width
- * @return integer array where: int[0] = startIndex, and int[1] = endIndex
- */
- public int[] getVisibleStartAndEndIndex(int width)
+ @Override
+ public boolean equals(Object obj)
{
try
{
LOCK.readLock().lock();
- int[] alignmentStartEnd = new int[] { 0, width - 1 };
- int startPos = alignmentStartEnd[0];
- int endPos = alignmentStartEnd[1];
-
- int[] lowestRange = new int[] { -1, -1 };
- int[] higestRange = new int[] { -1, -1 };
- if (hiddenColumns == null)
+ if (!(obj instanceof HiddenColumns))
{
- return new int[] { startPos, endPos };
+ return false;
}
+ HiddenColumns that = (HiddenColumns) obj;
- Iterator<int[]> it = new RegionsIterator();
- while (it.hasNext())
- {
- int[] range = it.next();
- lowestRange = (range[0] <= startPos) ? range : lowestRange;
- higestRange = (range[1] >= endPos) ? range : higestRange;
- }
+ /*
+ * check hidden columns are either both null, or match
+ */
- if (lowestRange[0] == -1 && lowestRange[1] == -1)
- {
- startPos = alignmentStartEnd[0];
- }
- else
+ if (that.hiddenColumns.size() != this.hiddenColumns.size())
{
- startPos = lowestRange[1] + 1;
+ return false;
}
- if (higestRange[0] == -1 && higestRange[1] == -1)
- {
- endPos = alignmentStartEnd[1];
- }
- else
+ Iterator<int[]> it = this.iterator();
+ Iterator<int[]> thatit = that.iterator();
+ while (it.hasNext())
{
- endPos = higestRange[0] - 1;
+ if (!(Arrays.equals(it.next(), thatit.next())))
+ {
+ return false;
+ }
}
- return new int[] { startPos, endPos };
+ return true;
+
} finally
{
LOCK.readLock().unlock();
}
-
}
/**
- * Finds the hidden region (if any) which starts or ends at res
+ * Return absolute column index for a visible column index
*
- * @param res
- * visible residue position, unadjusted for hidden columns
- * @return region as [start,end] or null if no matching region is found
+ * @param column
+ * int column index in alignment view (count from zero)
+ * @return alignment column index for column
*/
- public int[] getRegionWithEdgeAtRes(int res)
+ public int visibleToAbsoluteColumn(int column)
{
try
{
LOCK.readLock().lock();
- int adjres = adjustForHiddenColumns(res);
+ int result = column;
- int[] reveal = null;
- Iterator<int[]> it = new RegionsIterator(adjres - 2,
- adjres + 2);
- while (it.hasNext())
+ if (!hiddenColumns.isEmpty())
{
- int[] region = it.next();
- if (adjres + 1 == region[0] || adjres - 1 == region[1])
- {
- reveal = region;
- break;
- }
+ result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
}
- return reveal;
+
+ return result;
} finally
{
LOCK.readLock().unlock();
}
/**
- * Return an iterator over the hidden regions
- */
- public Iterator<int[]> iterator()
- {
- return new BoundedHiddenColsIterator();
- }
-
- /**
- * Return a bounded iterator over the hidden regions
+ * 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
+ * index of the next visible column on the left will be returned (or 0 if
+ * there is no visible column on the left)
*
- * @param start
- * position to start from (inclusive, absolute column position)
- * @param end
- * position to end at (inclusive, absolute column position)
- * @return
+ * @param hiddenColumn
+ * the column index in the full alignment including hidden columns
+ * @return the position of the column in the visible alignment
*/
- public Iterator<int[]> getBoundedIterator(int start, int end)
+ public int absoluteToVisibleColumn(int hiddenColumn)
{
- return new BoundedHiddenColsIterator(start, end);
- }
+ try
+ {
+ LOCK.readLock().lock();
+ int result = hiddenColumn;
- /**
- * 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)
- {
- return new BoundedStartRegionIterator(start, end, true);
- }
+ if (!hiddenColumns.isEmpty())
+ {
+ 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())
+ {
+ 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 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)
- {
- return new VisibleColsIterator(start, end);
+ return result; // return the shifted position after removing hidden
+ // columns.
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
- * return an iterator over visible segments between the given start and end
- * boundaries
+ * Find the visible column which is a given visible number of columns to the
+ * left (negative visibleDistance) or right (positive visibleDistance) of
+ * startColumn. If startColumn is not visible, we use the visible column at
+ * the left boundary of the hidden region containing startColumn.
*
- * @param start
- * (first column inclusive from 0)
- * @param end
- * (last column - not inclusive)
+ * @param visibleDistance
+ * the number of visible columns to offset by (left offset = negative
+ * value; right offset = positive value)
+ * @param startColumn
+ * the position of the column to start from (absolute position)
+ * @return the position of the column which is <visibleDistance> away
+ * (absolute position)
*/
- public Iterator<int[]> getVisContigsIterator(int start, int end)
+ public int offsetByVisibleColumns(int visibleDistance, int startColumn)
{
- // return new VisibleBlocksIterator(start, end, true)
- return new VisibleContigsIterator(start, end, true);
+ try
+ {
+ LOCK.readLock().lock();
+ int start = absoluteToVisibleColumn(startColumn);
+ return visibleToAbsoluteColumn(start + visibleDistance);
+
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
- * return an iterator over visible segments between the given start and end
- * boundaries
+ * This method returns the rightmost limit of a region of an alignment with
+ * hidden columns. In otherwords, the next hidden column.
*
- * @param start
- * (first column - inclusive from 0)
- * @param end
- * (last column - inclusive)
- * @param useVisibleCoords
- * if true, start and end are visible column positions, not absolute
- * positions
+ * @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 Iterator<int[]> getVisibleBlocksIterator(int start, int end,
- boolean useVisibleCoords)
+ public int getHiddenBoundaryRight(int alPos)
{
- if (useVisibleCoords)
+ try
{
- // TODO
- // we should really just convert start and end here with
- // adjustForHiddenColumns
- // 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);
- }
- else
+ LOCK.readLock().lock();
+ if (!hiddenColumns.isEmpty())
+ {
+ 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
{
- return new VisibleContigsIterator(start, end - 1, true);
+ LOCK.readLock().unlock();
}
}
/**
- * A local iterator which iterates over hidden column regions in a range.
- * Intended for use ONLY within the HiddenColumns class, because it works
- * directly with the hiddenColumns collection without locking (callers should
- * lock hiddenColumns).
+ * 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
*/
- private class RegionsIterator implements Iterator<int[]>
+ public int getHiddenBoundaryLeft(int alPos)
{
- // start position to iterate from
- private int start;
-
- // end position to iterate to
- private int end;
-
- // current index in hiddenColumns
- private int currentPosition = 0;
+ try
+ {
+ LOCK.readLock().lock();
- // current column in hiddenColumns
- private int[] nextRegion = null;
+ if (!hiddenColumns.isEmpty())
+ {
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
- // Constructor with bounds
- RegionsIterator(int lowerBound, int upperBound)
+ if (index > 0)
+ {
+ int[] region = hiddenColumns.get(index - 1);
+ return region[1];
+ }
+ }
+ return alPos;
+ } finally
{
- init(lowerBound, upperBound);
+ LOCK.readLock().unlock();
}
+ }
- // Unbounded constructor
- RegionsIterator()
+
+ /**
+ * 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 boolean isVisible(int column)
+ {
+ try
{
- if (hiddenColumns != null)
- {
- // iterator over full hiddenColumns collection
- int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
- init(0, last);
- }
- else
- {
- // empty iterator
- init(0, 0);
- }
- }
+ LOCK.readLock().lock();
- /**
- * Construct an iterator over hiddenColums bounded at
- * [lowerBound,upperBound]
- *
- * @param lowerBound
- * lower bound to iterate from
- * @param upperBound
- * upper bound to iterate to
- */
- private void init(int lowerBound, int upperBound)
- {
- start = lowerBound;
- end = upperBound;
-
- if (hiddenColumns != null)
+ int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
+ if (regionindex > -1 && regionindex < hiddenColumns.size())
{
- // iterate until a region overlaps with [start,end]
- currentPosition = 0;
- while ((currentPosition < hiddenColumns.size())
- && (hiddenColumns.get(currentPosition)[1] < start))
- {
- currentPosition++;
- }
- if (currentPosition < hiddenColumns.size())
+ int[] region = hiddenColumns.get(regionindex);
+ // already know that column <= region[1] as cursor returns containing
+ // region or region to right
+ if (column >= region[0])
{
- nextRegion = hiddenColumns.get(currentPosition);
+ return false;
}
}
- }
+ return true;
- @Override
- public boolean hasNext()
+ } finally
{
- return (hiddenColumns != null) && (nextRegion != null)
- && (nextRegion[0] <= end);
+ LOCK.readLock().unlock();
}
+ }
- @Override
- public int[] next()
+ /**
+ * 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 String[] getVisibleSequenceStrings(int start, int end,
+ SequenceI[] seqs)
+ {
+ try
{
- int[] region = nextRegion;
- currentPosition++;
- if (currentPosition < hiddenColumns.size())
+ LOCK.readLock().lock();
+ int iSize = seqs.length;
+ String[] selections = new String[iSize];
+ if (!hiddenColumns.isEmpty())
{
- nextRegion = hiddenColumns.get(currentPosition);
+ for (int i = 0; i < iSize; i++)
+ {
+ StringBuilder visibleSeq = new StringBuilder();
+
+ Iterator<int[]> blocks = new VisibleContigsIterator(start,
+ end + 1, hiddenColumns);
+
+ while (blocks.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]));
+ }
+ }
+
+ selections[i] = visibleSeq.toString();
+ }
}
else
{
- nextRegion = null;
+ for (int i = 0; i < iSize; i++)
+ {
+ selections[i] = seqs[i].getSequenceAsString(start, end);
+ }
}
- return region;
- }
+ return selections;
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
}
/**
- * A local iterator which reverse iterates over hidden column regions in a
- * range. Intended for use ONLY within the HiddenColumns class, because it
- * works directly with the hiddenColumns collection without locking (callers
- * should lock hiddenColumns).
+ * 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 seq
+ * sequence to find position for
+ * @return visible start position
*/
- private class ReverseRegionsIterator implements Iterator<int[]>
+ public int locateVisibleStartOfSequence(SequenceI seq)
{
- // start position to iterate to
- private int start;
-
- // end position to iterate from
- private int end;
-
- // current index in hiddenColumns
- private int currentPosition = 0;
+ try
+ {
+ LOCK.readLock().lock();
+ int start = 0;
- // current column in hiddenColumns
- private int[] nextRegion = null;
+ if (hiddenColumns.isEmpty())
+ {
+ return seq.findIndex(seq.getStart()) - 1;
+ }
- // Constructor with bounds
- ReverseRegionsIterator(int lowerBound, int upperBound)
- {
- init(lowerBound, upperBound);
- }
+ // 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;
- /**
- * Construct an iterator over hiddenColums bounded at
- * [lowerBound,upperBound]
- *
- * @param lowerBound
- * lower bound to iterate to
- * @param upperBound
- * upper bound to iterate from
- */
- private void init(int lowerBound, int upperBound)
- {
- start = lowerBound;
- end = upperBound;
-
- if (hiddenColumns != null)
+ // step through the non-gapped positions of the sequence
+ for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++)
{
- // iterate until a region overlaps with [start,end]
- currentPosition = hiddenColumns.size() - 1;
- while (currentPosition >= 0
- && hiddenColumns.get(currentPosition)[1] > end)
+ // 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)
{
- currentPosition--;
+ hideStart = seq.getLength();
}
- if (currentPosition >= 0)
+ // update visible boundary for sequence
+ if (p < hideStart)
{
- nextRegion = hiddenColumns.get(currentPosition);
+ start = p;
+ foundStart = true;
}
}
- }
-
- @Override
- public boolean hasNext()
- {
- return (hiddenColumns != null) && (nextRegion != null)
- && (nextRegion[1] >= start);
- }
- @Override
- public int[] next()
- {
- int[] region = nextRegion;
- currentPosition--;
- if (currentPosition >= 0)
- {
- nextRegion = hiddenColumns.get(currentPosition);
- }
- else
+ if (foundStart)
{
- nextRegion = null;
+ return absoluteToVisibleColumn(start);
}
- return region;
+ // otherwise, sequence was completely hidden
+ return visPrev;
+ } finally
+ {
+ LOCK.readLock().unlock();
}
-
}
+
/**
- * An iterator which iterates over hidden column regions in a range. Works
- * with a copy of the hidden columns collection. Intended to be used by
- * callers OUTSIDE of HiddenColumns.
+ *
+ * @return true if there are columns hidden
*/
- private class BoundedHiddenColsIterator implements Iterator<int[]>
+ public boolean hasHiddenColumns()
{
- // start position to iterate from
- private int start;
-
- // end position to iterate to
- private int end;
+ try
+ {
+ LOCK.readLock().lock();
- // current index in hiddenColumns
- private int currentPosition = 0;
+ // we don't use getSize()>0 here because it has to iterate over
+ // the full hiddenColumns collection and so will be much slower
+ return (!hiddenColumns.isEmpty());
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
- // current column in hiddenColumns
- private int[] currentRegion;
+ /**
+ *
+ * @return true if there is more than one hidden column region
+ */
+ public boolean hasMultiHiddenColumnRegions()
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ return !hiddenColumns.isEmpty() && hiddenColumns.size() > 1;
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
- // local copy or reference to hiddenColumns
- private List<int[]> localHidden;
- /**
- * Unbounded constructor
- */
- BoundedHiddenColsIterator()
+ /**
+ * Returns a hashCode built from hidden column ranges
+ */
+ @Override
+ public int hashCode()
+ {
+ try
{
- if (hiddenColumns != null)
- {
- int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
- init(0, last);
- }
- else
+ LOCK.readLock().lock();
+ int hashCode = 1;
+ for (int[] hidden : hiddenColumns)
{
- init(0, 0);
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
}
+ return hashCode;
+ } finally
+ {
+ LOCK.readLock().unlock();
}
+ }
- /**
- * Construct an iterator over hiddenColums bounded at
- * [lowerBound,upperBound]
- *
- * @param lowerBound
- * lower bound to iterate from
- * @param upperBound
- * upper bound to iterate to
- */
- BoundedHiddenColsIterator(int lowerBound, int upperBound)
- {
- init(lowerBound, upperBound);
- }
-
- /**
- * Construct an iterator over hiddenColums bounded at
- * [lowerBound,upperBound]
- *
- * @param lowerBound
- * lower bound to iterate from
- * @param upperBound
- * upper bound to iterate to
- */
- private void init(int lowerBound, int upperBound)
- {
- start = lowerBound;
- end = upperBound;
-
- try
- {
- LOCK.readLock().lock();
-
- if (hiddenColumns != null)
- {
- localHidden = new ArrayList<>();
-
- // iterate until a region overlaps with [start,end]
- int i = 0;
- while ((i < hiddenColumns.size())
- && (hiddenColumns.get(i)[1] < start))
- {
- i++;
- }
-
- // iterate from start to end, adding each hidden region. Positions are
- // absolute, and all regions which *overlap* [start,end] are added.
- while (i < hiddenColumns.size()
- && (hiddenColumns.get(i)[0] <= end))
- {
- int[] rh = hiddenColumns.get(i);
- int[] cp = new int[2];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- localHidden.add(cp);
- i++;
- }
- }
- }
- finally
+ /**
+ * Hide columns corresponding to the marked bits
+ *
+ * @param inserts
+ * - columns mapped to bits starting from zero
+ */
+ public void hideColumns(BitSet inserts)
+ {
+ try
+ {
+ LOCK.writeLock().lock();
+ for (int firstSet = inserts
+ .nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
+ .nextSetBit(lastSet))
{
- LOCK.readLock().unlock();
+ lastSet = inserts.nextClearBit(firstSet);
+ hideColumns(firstSet, lastSet - 1);
}
- }
-
- @Override
- public boolean hasNext()
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
+ } finally
{
- return (localHidden != null)
- && (currentPosition < localHidden.size());
+ LOCK.writeLock().unlock();
}
+ }
+
+ /**
+ * Hide columns corresponding to the marked bits, within the range
+ * [start,end]. Entries in tohide which are outside [start,end] are ignored.
+ *
+ * @param tohide
+ * columns mapped to bits starting from zero
+ * @param start
+ * start of range to hide columns within
+ * @param end
+ * end of range to hide columns within
+ */
+ public void hideColumns(BitSet tohide, int start, int end)
+ {
+ clearHiddenColumnsInRange(start, end);
- @Override
- public int[] next()
+ // make sure only bits between start and end are set
+ if (!tohide.isEmpty())
{
- currentRegion = localHidden.get(currentPosition);
- currentPosition++;
- return currentRegion;
+ tohide.clear(0, start);
+ tohide.clear(Math.min(end + 1, tohide.length() + 1),
+ tohide.length() + 1);
}
+
+ hideColumns(tohide);
}
/**
- * An iterator which iterates over visible start positions of hidden column
- * regions in a range.
+ * Make all columns in the range [start,end] visible
+ *
+ * @param start
+ * start of range to show columns
+ * @param end
+ * end of range to show columns
*/
- private class BoundedStartRegionIterator implements Iterator<Integer>
+ private void clearHiddenColumnsInRange(int start, int end)
{
- // start position to iterate from
- private int start;
-
- // end position to iterate to
- private int end;
-
- // current index in hiddenColumns
- private int currentPosition = 0;
-
- // local copy or reference to hiddenColumns
- private List<Integer> positions = null;
-
- /**
- * Construct an iterator over hiddenColums bounded at
- * [lowerBound,upperBound]
- *
- * @param lowerBound
- * lower bound to iterate from
- * @param upperBound
- * upper bound to iterate to
- * @param useCopyCols
- * whether to make a local copy of hiddenColumns for iteration (set
- * to true if calling from outwith the HiddenColumns class)
- */
- BoundedStartRegionIterator(int lowerBound, int upperBound,
- boolean useCopy)
- {
- start = lowerBound;
- end = upperBound;
+ try
+ {
+ LOCK.writeLock().lock();
- try
+ if (!hiddenColumns.isEmpty())
{
- if (useCopy)
- {
- // assume that if useCopy is false the calling code has locked
- // hiddenColumns
- LOCK.readLock().lock();
- }
+ HiddenCursorPosition pos = cursor.findRegionForColumn(start);
+ int index = pos.getRegionIndex();
+ int startindex = index; // first index in hiddenColumns to remove
- if (hiddenColumns != null)
+ if (index != -1 && index != hiddenColumns.size())
{
- positions = new ArrayList<>(hiddenColumns.size());
-
- // navigate to start, keeping count of hidden columns
- int i = 0;
- int hiddenSoFar = 0;
- while ((i < hiddenColumns.size())
- && (hiddenColumns.get(i)[0] < start + hiddenSoFar))
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(index);
+ if (region[0] < start && region[1] >= start)
{
- int[] region = hiddenColumns.get(i);
- hiddenSoFar += region[1] - region[0] + 1;
- i++;
+ // region contains start, truncate so that it ends just before start
+ region[1] = start - 1;
+ startindex++;
}
+ }
+
+ pos = cursor.findRegionForColumn(end);
+ index = pos.getRegionIndex();
+ int endindex = index - 1; // last index in hiddenColumns to remove
- // iterate from start to end, adding start positions of each
- // hidden region. Positions are visible columns count, not absolute
- while (i < hiddenColumns.size()
- && (hiddenColumns.get(i)[0] <= end + hiddenSoFar))
+ if (index != -1 && index != hiddenColumns.size())
+ {
+ // regionIndex is the region which either contains end
+ // or lies to the right of end
+ int[] region = hiddenColumns.get(index);
+ if (region[0] <= end && region[1] > end)
{
- int[] region = hiddenColumns.get(i);
- positions.add(region[0] - hiddenSoFar);
- hiddenSoFar += region[1] - region[0] + 1;
- i++;
+ // region contains end, truncate so that it starts just after end
+ region[0] = end + 1;
}
}
- else
- {
- positions = new ArrayList<>();
- }
- } finally
- {
- if (useCopy)
- {
- LOCK.readLock().unlock();
- }
- }
- }
-
- @Override
- public boolean hasNext()
- {
- return (currentPosition < positions.size());
- }
- /**
- * Get next hidden region start position
- *
- * @return the start position in *visible* coordinates
- */
- @Override
- public Integer next()
+ hiddenColumns.subList(startindex, endindex + 1).clear();
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
+ }
+ } finally
{
- int result = positions.get(currentPosition);
- currentPosition++;
- return result;
+ LOCK.writeLock().unlock();
}
}
/**
- * Iterator over the visible *columns* (not regions) as determined by the set
- * of hidden columns. Uses a local copy of hidden columns.
*
- * @author kmourao
- *
+ * @param inserts
+ * BitSet where hidden columns will be marked
*/
- private class VisibleColsIterator implements Iterator<Integer>
+ private void andNot(BitSet updates)
{
- private int last;
-
- private int current;
-
- private int next;
-
- private List<int[]> localHidden = new ArrayList<>();
-
- private int nexthiddenregion;
-
- VisibleColsIterator(int firstcol, int lastcol)
+ try
{
- last = lastcol;
- current = firstcol;
- next = firstcol;
- nexthiddenregion = 0;
-
LOCK.readLock().lock();
- if (hiddenColumns != null)
+ BitSet hiddenBitSet = new BitSet();
+ for (int[] range : hiddenColumns)
{
- int i = 0;
- for (i = 0; i < hiddenColumns.size()
- && (current <= hiddenColumns.get(i)[0]); ++i)
- {
- if (current >= hiddenColumns.get(i)[0]
- && current <= hiddenColumns.get(i)[1])
- {
- // current is hidden, move to right
- current = hiddenColumns.get(i)[1] + 1;
- next = current;
- nexthiddenregion = i + 1;
- }
- }
-
- for (i = hiddenColumns.size() - 1; i >= 0
- && (last >= hiddenColumns.get(i)[1]); --i)
- {
- if (last >= hiddenColumns.get(i)[0]
- && last <= hiddenColumns.get(i)[1])
- {
- // last is hidden, move to left
- last = hiddenColumns.get(i)[0] - 1;
- }
- }
-
- // make a local copy of the bit we need
- i = nexthiddenregion;
- while (i < hiddenColumns.size() && hiddenColumns.get(i)[0] <= last)
- {
- int[] region = new int[] { hiddenColumns.get(i)[0],
- hiddenColumns.get(i)[1] };
- localHidden.add(region);
- i++;
- }
+ hiddenBitSet.set(range[0], range[1] + 1);
}
-
+ hiddenBitSet.andNot(updates);
+ hiddenColumns.clear();
+ hideColumns(hiddenBitSet);
+ } finally
+ {
LOCK.readLock().unlock();
}
+ }
- @Override
- public boolean hasNext()
+ /**
+ * Calculate the visible start and end index of an alignment.
+ *
+ * @param width
+ * full alignment width
+ * @return integer array where: int[0] = startIndex, and int[1] = endIndex
+ */
+ public int[] getVisibleStartAndEndIndex(int width)
+ {
+ try
{
- return next <= last;
- }
+ LOCK.readLock().lock();
+ int[] alignmentStartEnd = new int[] { 0, width - 1 };
+ int startPos = alignmentStartEnd[0];
+ int endPos = alignmentStartEnd[1];
- @Override
- public Integer next()
- {
- if (next > last)
+ int[] lowestRange = new int[] { -1, -1 };
+ int[] higestRange = new int[] { -1, -1 };
+
+ if (hiddenColumns.isEmpty())
{
- throw new NoSuchElementException();
+ return new int[] { startPos, endPos };
}
- current = next;
- if ((localHidden != null)
- && (nexthiddenregion < localHidden.size()))
+
+ for (int[] range : hiddenColumns)
{
- // still some more hidden regions
- if (next + 1 < localHidden.get(nexthiddenregion)[0])
- {
- // next+1 is still before the next hidden region
- next++;
- }
- else if ((next + 1 >= localHidden.get(nexthiddenregion)[0])
- && (next + 1 <= localHidden.get(nexthiddenregion)[1]))
- {
- // next + 1 is in the next hidden region
- next = localHidden.get(nexthiddenregion)[1] + 1;
- nexthiddenregion++;
- }
+ lowestRange = (range[0] <= startPos) ? range : lowestRange;
+ higestRange = (range[1] >= endPos) ? range : higestRange;
+ }
+
+ if (lowestRange[0] == -1) // includes (lowestRange[1] == -1)
+ {
+ startPos = alignmentStartEnd[0];
}
else
{
- // finished with hidden regions, just increment normally
- next++;
+ startPos = lowestRange[1] + 1;
}
- return current;
- }
- @Override
- public void remove()
+ if (higestRange[0] == -1) // includes (higestRange[1] == -1)
+ {
+ endPos = alignmentStartEnd[1];
+ }
+ else
+ {
+ endPos = higestRange[0] - 1;
+ }
+ return new int[] { startPos, endPos };
+ } finally
{
- throw new UnsupportedOperationException();
+ LOCK.readLock().unlock();
}
}
/**
- * An iterator which iterates over visible regions in a range.
+ * Finds the hidden region (if any) which starts or ends at res
+ *
+ * @param res
+ * visible residue position, unadjusted for hidden columns
+ * @return region as [start,end] or null if no matching region is found. If
+ * res is adjacent to two regions, returns the left region.
*/
- private class VisibleContigsIterator implements Iterator<int[]>
+ public int[] getRegionWithEdgeAtRes(int res)
{
- private List<int[]> vcontigs = new ArrayList<>();
-
- private int currentPosition = 0;
-
- VisibleContigsIterator(int start, int end, boolean usecopy)
+ try
{
- try
- {
- if (usecopy)
- {
- LOCK.readLock().lock();
- }
-
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- int vstart = start;
- int hideStart;
- int hideEnd;
-
- for (int[] region : hiddenColumns)
- {
- hideStart = region[0];
- hideEnd = region[1];
-
- // navigate to start
- if (hideEnd < vstart)
- {
- continue;
- }
- if (hideStart > vstart)
- {
- int[] contig = new int[] { vstart, hideStart - 1 };
- vcontigs.add(contig);
- }
- vstart = hideEnd + 1;
+ LOCK.readLock().lock();
+ int adjres = visibleToAbsoluteColumn(res);
- // exit if we're past the end
- if (vstart >= end)
- {
- break;
- }
- }
+ int[] reveal = null;
- if (vstart < end)
- {
- int[] contig = new int[] { vstart, end - 1 };
- vcontigs.add(contig);
- }
- }
- else
+ if (!hiddenColumns.isEmpty())
+ {
+ // 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)
{
- int[] contig = new int[] { start, end - 1 };
- vcontigs.add(contig);
+ reveal = hiddenColumns.get(regionindex);
}
- } finally
- {
- if (usecopy)
+ // check if the region ends just after adjres
+ else if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[0] == adjres + 1)
{
- LOCK.readLock().unlock();
+ reveal = hiddenColumns.get(regionindex);
}
}
- }
+ return reveal;
- @Override
- public boolean hasNext()
+ } finally
{
- return (currentPosition < vcontigs.size());
+ LOCK.readLock().unlock();
}
+ }
- @Override
- public int[] next()
+ /**
+ * Return an iterator over the hidden regions
+ */
+ public Iterator<int[]> iterator()
+ {
+ try
{
- int[] result = vcontigs.get(currentPosition);
- currentPosition++;
- return result;
+ LOCK.readLock().lock();
+ return new HiddenColsIterator(hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
}
}
/**
- * An iterator which iterates over visible regions in a range. The range is
- * specified in terms of visible column positions. Provides a special
- * "endsAtHidden" indicator to allow callers to determine if the final visible
- * column is adjacent to a hidden region.
+ * 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 class VisibleBlocksVisBoundsIterator implements Iterator<int[]>
+ public Iterator<int[]> getBoundedIterator(int start, int end)
{
- private List<int[]> vcontigs = new ArrayList<>();
-
- private int currentPosition = 0;
-
- private boolean endsAtHidden = false;
-
- /**
- * Constructor for iterator over visible regions in a range.
- *
- * @param start
- * start position in terms of visible column position
- * @param end
- * end position in terms of visible column position
- * @param usecopy
- * whether to use a local copy of hidden columns
- */
- VisibleBlocksVisBoundsIterator(int start, int end, boolean usecopy)
- {
- /* actually this implementation always uses a local copy but this may change in future */
- try
- {
- if (usecopy)
- {
- LOCK.readLock().lock();
- }
-
- if (hiddenColumns != null && hiddenColumns.size() > 0)
- {
- int blockStart = start;
- int blockEnd = end;
- int hiddenSoFar = 0;
- int visSoFar = 0;
-
- // iterate until a region begins within (start,end]
- int i = 0;
- while ((i < hiddenColumns.size())
- && (hiddenColumns.get(i)[0] <= blockStart + hiddenSoFar))
- {
- hiddenSoFar += hiddenColumns.get(i)[1] - hiddenColumns.get(i)[0]
- + 1;
- i++;
- }
-
- blockStart += hiddenSoFar; // convert start to absolute position
- blockEnd += hiddenSoFar; // convert end to absolute position
-
- // iterate from start to end, adding each visible region. Positions
- // are
- // absolute, and all hidden regions which overlap [start,end] are
- // used.
- while (i < hiddenColumns.size()
- && (hiddenColumns.get(i)[0] <= blockEnd))
- {
- int[] region = hiddenColumns.get(i);
-
- // end position of this visible region is either just before the
- // start of the next hidden region, or the absolute position of
- // 'end', whichever is lowest
- blockEnd = Math.min(blockEnd, region[0] - 1);
-
- vcontigs.add(new int[] { blockStart, blockEnd });
-
- visSoFar += blockEnd - blockStart + 1;
+ try
+ {
+ LOCK.readLock().lock();
+ return new HiddenColsIterator(start, end, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
- // next visible region starts after this hidden region
- blockStart = region[1] + 1;
+ /**
+ * 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();
- hiddenSoFar += region[1] - region[0] + 1;
+ // get absolute position of column in alignment
+ int absoluteStart = visibleToAbsoluteColumn(start);
- // reset blockEnd to absolute position of 'end', assuming we've now
- // passed all hidden regions before end
- blockEnd = end + hiddenSoFar;
+ // 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);
- i++;
- }
- if (visSoFar < end - start)
- {
- // the number of visible columns we've accounted for is less than
- // the number specified by end-start; work out the end position of
- // the last visible region
- blockEnd = blockStart + end - start - visSoFar;
- vcontigs.add(new int[] { blockStart, blockEnd });
-
- // if the last visible region ends at the next hidden region, set
- // endsAtHidden=true
- if (i < hiddenColumns.size()
- && hiddenColumns.get(i)[0] - 1 == blockEnd)
- {
- endsAtHidden = true;
- }
- }
- }
- else
- {
- // there are no hidden columns, return a single visible contig
- vcontigs.add(new int[] { start, end });
- endsAtHidden = false;
- }
- } finally
- {
- if (usecopy)
- {
- LOCK.readLock().unlock();
- }
- }
+ return new BoundedStartRegionIterator(pos, start, end,
+ hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
}
+ }
- @Override
- public boolean hasNext()
+ /**
+ * 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
{
- return (currentPosition < vcontigs.size());
+ LOCK.readLock().unlock();
}
+ }
- @Override
- public int[] next()
+ /**
+ * 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 VisibleContigsIterator getVisContigsIterator(int start,
+ int end,
+ boolean useVisibleCoords)
+ {
+ int adjstart = start;
+ int adjend = end;
+ if (useVisibleCoords)
{
- int[] result = vcontigs.get(currentPosition);
- currentPosition++;
- return result;
+ adjstart = visibleToAbsoluteColumn(start);
+ adjend = visibleToAbsoluteColumn(end);
}
- public boolean endsAtHidden()
+ try
{
- return endsAtHidden;
+ LOCK.readLock().lock();
+ return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
+ } finally
+ {
+ LOCK.readLock().unlock();
}
}
}
git://source.jalview.org / jalview.git / blobdiff