*/
package jalview.datamodel;
-import jalview.util.Comparison;
-
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;
public class HiddenColumns
{
+ private static final int HASH_MULTIPLIER = 31;
+
private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
+ private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
+
+ private int numColumns = 0;
+
/*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
{
if (copy.hiddenColumns != null)
{
- hiddenColumns = copy.copyHiddenRegionsToArrayList();
+ hiddenColumns = new ArrayList<>();
+ Iterator<int[]> it = copy.iterator();
+ while (it.hasNext())
+ {
+ hiddenColumns.add(it.next());
+ }
+ 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.
+ *
+ * @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
*
- * @return empty list or List of hidden column intervals
*/
- private List<int[]> getHiddenRegions()
+ public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
{
- return hiddenColumns == null ? Collections.<int[]> emptyList()
- : hiddenColumns;
+ try
+ {
+ LOCK.writeLock().lock();
+ if (copy != null)
+ {
+ hiddenColumns = new ArrayList<>();
+ numColumns = 0;
+ Iterator<int[]> it = copy.getBoundedIterator(start, end);
+ while (it.hasNext())
+ {
+ 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;
+ }
+ }
+ cursor.resetCursor(hiddenColumns);
+ }
+ } finally
+ {
+ LOCK.writeLock().unlock();
+ }
}
/**
StringBuilder regionBuilder = new StringBuilder();
if (hiddenColumns != null)
{
- for (int[] range : hiddenColumns)
+ 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);
+ }
}
-
- regionBuilder.deleteCharAt(0);
}
return regionBuilder.toString();
} finally
try
{
LOCK.readLock().lock();
- int size = 0;
- if (hasHiddenColumns())
+
+ if (numColumns == 0 && hiddenColumns != null)
{
- for (int[] range : hiddenColumns)
+ // numColumns is out of date, so recalculate
+ int size = 0;
+ if (hiddenColumns != null)
{
- size += range[1] - range[0] + 1;
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
+ {
+ int[] range = it.next();
+ size += range[1] - range[0] + 1;
+ }
}
+ numColumns = size;
}
- return size;
+
+ return numColumns;
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
+
+ /**
+ * Get the number of distinct hidden regions
+ *
+ * @return number of regions
+ */
+ public int getNumberOfRegions()
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ int num = 0;
+ if (hasHiddenColumns())
+ {
+ num = hiddenColumns.size();
+ }
+ return num;
} finally
{
LOCK.readLock().unlock();
{
return false;
}
- int i = 0;
- for (int[] thisRange : hiddenColumns)
+
+ Iterator<int[]> it = hiddenColumns.iterator();
+ Iterator<int[]> thatit = that.iterator();
+ while (it.hasNext())
{
- int[] thatRange = that.hiddenColumns.get(i++);
+ int[] thisRange = it.next();
+ int[] thatRange = thatit.next();
if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
{
return false;
{
LOCK.readLock().lock();
int result = column;
+
if (hiddenColumns != null)
{
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.get(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
- }
+ result += cursor.getHiddenOffset(column).getHiddenSoFar();
}
+
return result;
} finally
{
{
LOCK.readLock().lock();
int result = hiddenColumn;
+
if (hiddenColumns != null)
{
- 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])
+ 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())
{
- // 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
+ int[] region = hiddenColumns.get(index);
+ if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
{
- return result - (hiddenColumn - region[0] + 1);
+ // actually col is hidden, return region[0]-1
+ // unless region[0]==0 in which case return 0
+ if (region[0] == 0)
+ {
+ result = 0;
+ }
+ else
+ {
+ result = region[0] - 1 - hiddenBeforeCol;
+ }
}
}
}
+
return result; // return the shifted position after removing hidden
// columns.
} finally
{
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;
+ Iterator<int[]> it = new ReverseRegionsIterator(0, start,
+ hiddenColumns);
- while ((index > -1) && (distance - gap > 0))
+ while (it.hasNext() && (distance > 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--;
- }
+ int[] region = it.next();
- if (distance - gap > 0)
- {
- // fell out of loop because there are no more hidden regions
- distance -= gap;
- return nextstart - distance;
- }
- return start - distance;
- } finally
- {
- LOCK.readLock().unlock();
- }
-
- }
-
- /**
- * Use this method to determine the set of hiddenRegion start positions
- *
- * @return list of column number in visible view where hidden regions start
- */
- public List<Integer> findHiddenRegionPositions()
- {
- try
- {
- LOCK.readLock().lock();
- List<Integer> positions = null;
-
- if (hiddenColumns != null)
- {
- positions = new ArrayList<>(hiddenColumns.size());
-
- positions.add(hiddenColumns.get(0)[0]);
- for (int i = 1; i < hiddenColumns.size(); ++i)
+ if (start > region[1])
{
-
- int result = 0;
- if (hiddenColumns != null)
+ // subtract the gap to right of region from distance
+ if (start - region[1] <= distance)
{
- int index = 0;
- int gaps = 0;
- do
- {
- int[] region = hiddenColumns.get(index);
- gaps += region[1] + 1 - region[0];
- result = region[1] + 1;
- index++;
- } while (index <= i);
-
- result -= gaps;
+ distance -= start - region[1];
+ start = region[0] - 1;
+ }
+ else
+ {
+ start = start - distance;
+ distance = 0;
}
- positions.add(result);
}
}
- else
- {
- positions = new ArrayList<>();
- }
- return positions;
+ return start - distance;
+
} 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.
*
- * @param index
- * int
+ * @param alPos
+ * the absolute (visible) alignmentPosition to find the next hidden
+ * column for
*/
public int getHiddenBoundaryRight(int alPos)
{
LOCK.readLock().lock();
if (hiddenColumns != null)
{
- int index = 0;
- do
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+ if (index < hiddenColumns.size())
{
int[] region = hiddenColumns.get(index);
if (alPos < region[0])
{
return region[0];
}
-
- index++;
- } while (index < hiddenColumns.size());
+ else if ((alPos <= region[1])
+ && (index + 1 < hiddenColumns.size()))
+ {
+ // alPos is within a hidden region, return the next one
+ // if there is one
+ region = hiddenColumns.get(index + 1);
+ return region[0];
+ }
+ }
}
-
return alPos;
} finally
{
LOCK.readLock().unlock();
}
-
}
/**
* This method returns the leftmost limit of a region of an alignment with
* hidden columns. In otherwords, the previous hidden column.
*
- * @param index
- * int
+ * @param alPos
+ * the absolute (visible) alignmentPosition to find the previous
+ * hidden column for
*/
public int getHiddenBoundaryLeft(int alPos)
{
if (hiddenColumns != null)
{
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = hiddenColumns.get(index);
- if (alPos > region[1])
- {
- return region[1];
- }
-
- index--;
- } while (index > -1);
- }
-
- return alPos;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
- /**
- * 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
- {
+ int index = cursor.findRegionForColumn(alPos).getRegionIndex();
- LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
+ if (index > 0)
{
- int[] region = hiddenColumns.get(index);
- if (pos > region[1])
- {
- return index;
- }
-
- index--;
- } while (index > -1);
+ int[] region = hiddenColumns.get(index - 1);
+ return region[1];
+ }
}
-
- return -1;
+ return alPos;
} finally
{
LOCK.readLock().unlock();
}
-
}
/**
- * Adds the specified column range to the hidden columns
+ * 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)
{
}
/*
- * traverse existing hidden ranges and insert / amend / append as
- * appropriate
+ * new range follows everything else; check first to avoid looping over whole hiddenColumns collection
*/
- for (int i = 0; i < hiddenColumns.size(); i++)
+ if (hiddenColumns.isEmpty()
+ || start > hiddenColumns.get(hiddenColumns.size() - 1)[1])
{
- int[] region = hiddenColumns.get(i);
-
- if (end < region[0] - 1)
- {
- /*
- * 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)
+ 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++)
{
- /*
- * new range overlaps existing, or is contiguous following it - adjust
- * start and end columns
- */
- region[0] = Math.min(region[0], start);
- region[1] = Math.max(region[1], end);
-
- /*
- * also update or remove any subsequent ranges
- * that are overlapped
- */
- while (i < hiddenColumns.size() - 1)
- {
- int[] nextRegion = hiddenColumns.get(i + 1);
- if (nextRegion[0] > end + 1)
- {
- /*
- * gap to next hidden range - no more to update
- */
- break;
- }
- region[1] = Math.max(nextRegion[1], end);
- hiddenColumns.remove(i + 1);
- }
- return;
- }
+ added = insertRangeAtRegion(i, start, end);
+ } // for
}
-
- /*
- * 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();
+ cursor.resetCursor(hiddenColumns);
- if (hiddenColumns != null)
- {
- for (int[] region : hiddenColumns)
- {
- if (column >= region[0] && column <= region[1])
- {
- return false;
- }
- }
+ // reset the number of columns so they will be recounted
+ numColumns = 0;
}
-
- 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)
+ if (!wasAlreadyLocked)
{
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- copy.add(cp);
+ LOCK.writeLock().unlock();
}
}
-
- 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.
+ * Insert [start, range] at the region at index i in hiddenColumns, if
+ * feasible
*
- * @return hidden regions as an ArrayList of [start,end] pairs
+ * @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 ArrayList<int[]> getHiddenColumnsCopy()
+ 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();
- return copyHiddenRegionsToArrayList();
- } 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;
}
- }
-
- /**
- * propagate shift in alignment columns to column selection
- *
- * @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
- */
- public List<int[]> compensateForEdit(int start, int change,
- ColumnSelection sel)
- {
- try
+ else if (start <= region[1] + 1)
{
- LOCK.writeLock().lock();
- List<int[]> deletedHiddenColumns = null;
+ /*
+ * new range overlaps existing, or is contiguous following it - adjust
+ * start and end columns
+ */
+ region[0] = Math.min(region[0], start);
+ region[1] = Math.max(region[1], end);
- if (hiddenColumns != null)
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ while (i < hiddenColumns.size() - 1)
{
- deletedHiddenColumns = new ArrayList<>();
- int hSize = hiddenColumns.size();
- for (int i = 0; i < hSize; i++)
+ int[] nextRegion = hiddenColumns.get(i + 1);
+ if (nextRegion[0] > end + 1)
{
- 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;
- }
-
+ /*
+ * gap to next hidden range - no more to update
+ */
+ break;
}
-
- this.revealHiddenColumns(0, sel);
+ region[1] = Math.max(nextRegion[1], end);
+ hiddenColumns.subList(i + 1, i + 2).clear();
}
-
- return deletedHiddenColumns;
- } finally
- {
- LOCK.writeLock().unlock();
+ added = true;
}
+ return added;
}
/**
- * propagate shift in alignment columns to column selection special version of
- * compensateForEdit - allowing for edits within hidden regions
+ * Answers if a column in the alignment is visible
*
- * @param start
- * beginning of edit
- * @param left
- * shift in edit (+ve for removal, or -ve for inserts)
+ * @param column
+ * absolute position of column in the alignment
+ * @return true if column is visible
*/
- public void compensateForDelEdits(int start, int change)
+ 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);
+ if (column >= region[0] && column <= region[1])
{
- 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;
- }
+ return false;
}
}
+ return true;
+
} finally
{
- LOCK.writeLock().unlock();
+ LOCK.readLock().unlock();
}
}
/**
- * return all visible segments between the given start and end boundaries
+ * Get the visible sections of a set of sequences
*
* @param start
- * (first column inclusive from 0)
+ * sequence position to start from
* @param end
- * (last column - not inclusive)
- * @return int[] {i_start, i_end, ..} where intervals lie in
- * start<=i_start<=i_end<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 int[] getVisibleContigs(int start, int end)
- {
- 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 (hideEnd < vstart)
- {
- continue;
- }
- if (hideStart > vstart)
- {
- visiblecontigs.add(new int[] { vstart, hideStart - 1 });
- }
- vstart = hideEnd + 1;
- }
-
- if (vstart < end)
- {
- visiblecontigs.add(new int[] { vstart, end - 1 });
- }
- int[] vcontigs = new int[visiblecontigs.size() * 2];
- for (int i = 0, j = visiblecontigs.size(); i < j; i++)
- {
- int[] vc = visiblecontigs.get(i);
- visiblecontigs.set(i, null);
- vcontigs[i * 2] = vc[0];
- vcontigs[i * 2 + 1] = vc[1];
- }
- visiblecontigs.clear();
- return vcontigs;
- }
- else
- {
- return new int[] { start, end - 1 };
- }
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
-
public String[] getVisibleSequenceStrings(int start, int end,
SequenceI[] seqs)
{
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;
+ Iterator<int[]> blocks = new VisibleContigsIterator(start,
+ end + 1, hiddenColumns);
- for (int j = 0; j < regions.size(); j++)
+ while (blocks.hasNext())
{
- 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)
+ int[] block = blocks.next();
+ if (blocks.hasNext())
{
- break;
+ visibleSeq
+ .append(seqs[i].getSequence(block[0], block[1] + 1));
+ }
+ else
+ {
+ visibleSeq
+ .append(seqs[i].getSequence(block[0], block[1]));
}
-
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
-
- if (end > blockStart)
- {
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
}
selections[i] = visibleSeq.toString();
}
/**
- * 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
+ * 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
- * @return int[] { visible start, visible end, first seqpos, last seqpos,
- * alignment index for seq start, alignment index for seq end }
+ * sequence to find position for
+ * @return visible start position
*/
- public int[] locateVisibleBoundsOfSequence(SequenceI seq)
+ public int locateVisibleStartOfSequence(SequenceI seq)
{
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, ifpos, ilpos };
+ return seq.findIndex(seq.getStart()) - 1;
}
// Simply walk along the sequence whilst watching for hidden column
// boundaries
- List<int[]> regions = getHiddenRegions();
- int spos = fpos;
- int lastvispos = -1;
- int rcount = 0;
+ Iterator<int[]> regions = hiddenColumns.iterator();
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++)
+
+ // step through the non-gapped positions of the sequence
+ for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++)
{
- if (!Comparison.isGap(seq.getCharAt(p)))
+ // 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())
{
- // keep track of first/last column
- // containing sequence data regardless of visibility
- if (firstP == -1)
- {
- firstP = p;
- }
- lastP = p;
- // update hidden region start/end
- while (hideEnd < p && rcount < regions.size())
- {
- int[] region = regions.get(rcount++);
- visPrev = visNext;
- visNext += region[0] - visPrev;
- hideStart = region[0];
- hideEnd = region[1];
- }
- if (hideEnd < p)
- {
- hideStart = seq.getLength();
- }
- // update visible boundary for sequence
- if (p < hideStart)
- {
- if (!foundStart)
- {
- fpos = spos;
- start = p;
- foundStart = true;
- }
- lastvispos = p;
- lpos = spos;
- }
- // look for next sequence position
- spos++;
+ 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 new int[] { findColumnPosition(start), firstP, lastP };
+ return findColumnPosition(start);
}
// otherwise, sequence was completely hidden
- return new int[] { visPrev, firstP, lastP };
+ return visPrev;
} finally
{
LOCK.readLock().unlock();
*/
public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
{
- makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+ makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
+ alignmentAnnotation);
}
/**
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];
-
- if (hideStart < start)
- {
- continue;
- }
-
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
- {
- break;
- }
- annels.addElement(els = new Annotation[blockEnd - blockStart]);
- System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
- 0, els.length);
- w += els.length;
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
+ int startFrom = start;
+ int endAt = end;
- if (end > blockStart)
+ if (alignmentAnnotation.annotations != null)
+ {
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- annels.addElement(els = new Annotation[end - blockStart + 1]);
- if ((els.length
- + blockStart) <= alignmentAnnotation.annotations.length)
- {
- // copy just the visible segment of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0, els.length);
- }
- else
- {
- // copy to the end of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0,
- (alignmentAnnotation.annotations.length - blockStart));
- }
- w += els.length;
+ removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
}
- if (w == 0)
+ else
{
- return;
+ alignmentAnnotation.restrict(startFrom, endAt);
}
+ }
+ } finally
+ {
+ LOCK.readLock().unlock();
+ }
+ }
- alignmentAnnotation.annotations = new Annotation[w];
- w = 0;
-
- for (Annotation[] chnk : annels)
- {
- System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
- chnk.length);
- w += chnk.length;
- }
+ 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())
+ {
+ // copy just the visible segment of the annotation row
+ copylength = annotationLength;
}
else
{
- alignmentAnnotation.restrict(start, end);
+ 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];
+ }
}
- } finally
+
+ els = new Annotation[annotationLength];
+ annels.add(els);
+ System.arraycopy(alignmentAnnotation.annotations, block[0], els, 0,
+ copylength);
+ w += annotationLength;
+ }
+
+ if (w != 0)
{
- LOCK.readLock().unlock();
+ alignmentAnnotation.annotations = new Annotation[w];
+
+ w = 0;
+ for (Annotation[] chnk : annels)
+ {
+ System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+ chnk.length);
+ w += chnk.length;
+ }
}
}
{
hideColumns(r[0], r[1]);
}
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
LOCK.writeLock().lock();
if (hiddenColumns != null)
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ Iterator<int[]> it = hiddenColumns.iterator();
+ while (it.hasNext())
{
- int[] region = hiddenColumns.get(i);
+ int[] region = it.next();
for (int j = region[0]; j < region[1] + 1; j++)
{
sel.addElement(j);
}
}
+ hiddenColumns = null;
+ cursor.resetCursor(hiddenColumns);
+ numColumns = 0;
}
-
- hiddenColumns = null;
} finally
{
LOCK.writeLock().unlock();
try
{
LOCK.writeLock().lock();
- for (int i = 0; i < hiddenColumns.size(); i++)
+
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.get(i);
- if (start == region[0])
+ int regionIndex = cursor.findRegionForColumn(start)
+ .getRegionIndex();
+
+ if (regionIndex != -1 && regionIndex != hiddenColumns.size())
{
- for (int j = region[0]; j < region[1] + 1; j++)
+ // regionIndex is the region which either contains start
+ // or lies to the right of start
+ int[] region = hiddenColumns.get(regionIndex);
+ if (start == region[0])
{
- sel.addElement(j);
- }
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
+ int colsToRemove = region[1] - region[0] + 1;
+ hiddenColumns.remove(regionIndex);
- hiddenColumns.remove(region);
- break;
+ if (hiddenColumns.isEmpty())
+ {
+ hiddenColumns = null;
+ numColumns = 0;
+ }
+ else
+ {
+ numColumns -= colsToRemove;
+ }
+ cursor.updateForDeletedRegion(hiddenColumns);
+
+ }
}
}
- if (hiddenColumns.size() == 0)
- {
- hiddenColumns = null;
- }
} finally
{
LOCK.writeLock().unlock();
private void propagateInsertions(SequenceI profileseq, AlignmentI al,
SequenceI origseq)
{
- char gc = al.getGapCharacter();
+ try
+ {
+ LOCK.writeLock().lock();
+
+ char gc = al.getGapCharacter();
+
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
- // take the set of hidden columns, and the set of gaps in origseq,
- // and remove all the hidden gaps from hiddenColumns
-
- // first get the gaps as a Bitset
- BitSet gaps = origseq.gapBitset();
-
- // now calculate hidden ^ not(gap)
- BitSet hidden = new BitSet();
- markHiddenRegions(hidden);
- hidden.andNot(gaps);
- hiddenColumns = null;
- this.hideMarkedBits(hidden);
-
- // for each sequence in the alignment, except the profile sequence,
- // insert gaps corresponding to each hidden region
- // but where each hidden column region is shifted backwards by the number of
- // preceding visible gaps
- // update hidden columns at the same time
- ArrayList<int[]> regions = getHiddenColumnsCopy();
- ArrayList<int[]> newhidden = new ArrayList<>();
-
- int numGapsBefore = 0;
- int gapPosition = 0;
- for (int[] region : regions)
- {
- // get region coordinates accounting for gaps
- // we can rely on gaps not being *in* hidden regions because we already
- // removed those
- while (gapPosition < region[0])
+ // first get the gaps as a Bitset
+ BitSet gaps = origseq.gapBitset();
+
+ // now calculate hidden ^ not(gap)
+ BitSet hidden = new BitSet();
+ markHiddenRegions(hidden);
+ hidden.andNot(gaps);
+ hiddenColumns = null;
+ this.hideMarkedBits(hidden);
+
+ // for each sequence in the alignment, except the profile sequence,
+ // insert gaps corresponding to each hidden region
+ // but where each hidden column region is shifted backwards by the number
+ // of
+ // preceding visible gaps
+ // update hidden columns at the same time
+ Iterator<int[]> regions = hiddenColumns.iterator();
+ ArrayList<int[]> newhidden = new ArrayList<>();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ while (regions.hasNext())
{
- gapPosition++;
- if (gaps.get(gapPosition))
+ // 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])
{
- numGapsBefore++;
+ gapPosition++;
+ if (gaps.get(gapPosition))
+ {
+ numGapsBefore++;
+ }
}
- }
- int left = region[0] - numGapsBefore;
- int right = region[1] - numGapsBefore;
- newhidden.add(new int[] { left, right });
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+ newhidden.add(new int[] { left, right });
- // make a string with number of gaps = length of hidden region
- StringBuffer sb = new StringBuffer();
- for (int s = 0; s < right - left + 1; s++)
- {
- sb.append(gc);
- }
- padGaps(sb, left, profileseq, al);
+ // 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.writeLock().unlock();
}
- hiddenColumns = newhidden;
}
/**
{
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
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
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)
{
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)
+ {
+ reveal = hiddenColumns.get(regionindex);
+ }
+ // check if the region ends just after adjres
+ else if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[0] == adjres + 1)
{
- if (adjres + 1 == region[0] || adjres - 1 == region[1])
+ reveal = hiddenColumns.get(regionindex);
+ }
+ // or try the next region
+ else
+ {
+ regionindex++;
+ if (regionindex < hiddenColumns.size()
+ && hiddenColumns.get(regionindex)[0] == adjres + 1)
{
- reveal = region;
- break;
+ 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();
+ return new BoundedStartRegionIterator(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)
+ */
+ public Iterator<int[]> getVisContigsIterator(int start, int end)
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ return new VisibleContigsIterator(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 - inclusive)
+ * @param useVisibleCoords
+ * if true, start and end are visible column positions, not absolute
+ * positions
+ */
+ public Iterator<int[]> getVisibleBlocksIterator(int start, int end,
+ boolean useVisibleCoords)
+ {
+ if (useVisibleCoords)
+ {
+ // 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
+ {
+ try
+ {
+ LOCK.readLock().lock();
+ return new VisibleContigsIterator(start, end + 1, 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.
+ */
+ public class VisibleBlocksVisBoundsIterator implements Iterator<int[]>
+ {
+ 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;
+
+ // next visible region starts after this hidden region
+ blockStart = region[1] + 1;
+
+ hiddenSoFar += region[1] - region[0] + 1;
+
+ // reset blockEnd to absolute position of 'end', assuming we've now
+ // passed all hidden regions before end
+ blockEnd = end + hiddenSoFar;
+
+ i++;
+ }
+ if (visSoFar < end - start + 1)
+ {
+ // 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();
+ }
+ }
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return (currentPosition < vcontigs.size());
+ }
+
+ @Override
+ public int[] next()
+ {
+ int[] result = vcontigs.get(currentPosition);
+ currentPosition++;
+ return result;
+ }
+
+ public boolean endsAtHidden()
+ {
+ return endsAtHidden;
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff