*/
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.NoSuchElementException;
-import java.util.Vector;
import java.util.concurrent.locks.ReentrantReadWriteLock;
public class HiddenColumns
{
if (copy.hiddenColumns != null)
{
- hiddenColumns = copy.copyHiddenRegionsToArrayList(0);
+ hiddenColumns = new ArrayList<>();
+ Iterator<int[]> it = copy.iterator();
+ while (it.hasNext())
+ {
+ hiddenColumns.add(it.next());
+ }
}
}
} 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.
- *
- * @return empty list or List of hidden column intervals
- */
- private List<int[]> getHiddenRegions()
- {
- return hiddenColumns == null ? Collections.<int[]> emptyList()
- : hiddenColumns;
- }
-
- /**
* Output regions data as a string. String is in the format:
* reg0[0]<between>reg0[1]<delimiter>reg1[0]<between>reg1[1] ... regn[1]
*
{
LOCK.readLock().lock();
StringBuilder regionBuilder = new StringBuilder();
- if (hiddenColumns != null)
+ Iterator<int[]> it = new RegionsIterator();
+ while (it.hasNext())
{
- for (int[] range : hiddenColumns)
- {
- regionBuilder.append(delimiter).append(range[0]).append(between)
+ 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
{
LOCK.readLock().lock();
int size = 0;
- if (hasHiddenColumns())
+ Iterator<int[]> it = new RegionsIterator();
+ while (it.hasNext())
{
- for (int[] range : hiddenColumns)
- {
- size += range[1] - range[0] + 1;
- }
+ int[] range = it.next();
+ size += range[1] - range[0] + 1;
}
+
return size;
} finally
{
{
return false;
}
- int i = 0;
- for (int[] thisRange : hiddenColumns)
+
+ Iterator<int[]> it = new RegionsIterator();
+ 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)
+
+ Iterator<int[]> it = new RegionsIterator();
+ while (it.hasNext())
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ int[] region = it.next();
+ if (result >= region[0])
{
- int[] region = hiddenColumns.get(i);
- if (result >= region[0])
- {
- result += region[1] - region[0] + 1;
- }
+ result += region[1] - region[0] + 1;
}
}
+
return result;
} finally
{
{
LOCK.readLock().lock();
int result = hiddenColumn;
+ int[] region = null;
if (hiddenColumns != null)
{
- int index = 0;
- int[] region;
- do
+ Iterator<int[]> it = new RegionsIterator(0,
+ hiddenColumn);
+ while (it.hasNext())
{
- region = hiddenColumns.get(index++);
+ region = it.next();
if (hiddenColumn > region[1])
{
result -= region[1] + 1 - region[0];
}
- } while ((hiddenColumn > region[1])
- && (index < hiddenColumns.size()));
+ }
- if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
+ if (region != null && hiddenColumn >= region[0]
+ && hiddenColumn <= region[1])
{
// Here the hidden column is within a region, so
// we want to return the position of region[0]-1, adjusted for any
// earlier hidden columns.
// Calculate the difference between the actual hidden col position
// and region[0]-1, and then subtract from result to convert result
- // from
- // the adjusted hiddenColumn value to the adjusted region[0]-1 value
+ // 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
{
try
{
-
LOCK.readLock().lock();
int distance = visibleDistance;
// in case startColumn is in a hidden region, move it to the left
int start = adjustForHiddenColumns(findColumnPosition(startColumn));
- // get index of hidden region to left of start
- int index = getHiddenIndexLeft(start);
- if (index == -1)
- {
- // no hidden regions to left of startColumn
- return start - distance;
- }
-
- // walk backwards through the alignment subtracting the counts of visible
- // columns from distance
- int[] region;
- int gap = 0;
- int nextstart = start;
-
- while ((index > -1) && (distance - gap > 0))
- {
- // subtract the gap to right of region from distance
- distance -= gap;
- start = nextstart;
-
- // calculate the next gap
- region = hiddenColumns.get(index);
- gap = start - region[1];
+ Iterator<int[]> it = new ReverseRegionsIterator(0, start);
- // set start to just to left of current region
- nextstart = region[0] - 1;
- index--;
- }
-
- if (distance - gap > 0)
- {
- // fell out of loop because there are no more hidden regions
- distance -= gap;
- return nextstart - distance;
- }
- return start - distance;
- } finally
- {
- LOCK.readLock().unlock();
- }
-
- }
-
- /**
- * Use this method to determine the set of hiddenRegion start positions
- * between absolute position <start> and absolute position <end>
- *
- * @param start
- * absolute residue to start from
- * @param end
- * absolute residue to end at
- *
- * @return list of column numbers in *visible* view where hidden regions start
- */
- public List<Integer> findHiddenRegionPositions(int start, int end)
- {
- try
- {
- LOCK.readLock().lock();
- List<Integer> positions = null;
-
- if (hiddenColumns != null)
+ while (it.hasNext() && (distance > 0))
{
- positions = new ArrayList<>(hiddenColumns.size());
+ int[] region = it.next();
- // navigate to start, keeping count of hidden columns
- int i = 0;
- int hiddenSoFar = 0;
- while ((i < hiddenColumns.size())
- && (hiddenColumns.get(i)[0] < start))
- {
- int[] region = hiddenColumns.get(i);
- hiddenSoFar += region[1] - region[0] + 1;
- i++;
- }
-
- // 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))
+ if (start > region[1])
{
- int[] region = hiddenColumns.get(i);
- positions.add(region[0] - hiddenSoFar);
- hiddenSoFar += region[1] - region[0] + 1;
- i++;
+ // subtract the gap to right of region from distance
+ if (start - region[1] <= distance)
+ {
+ distance -= start - region[1];
+ start = region[0] - 1;
+ }
+ else
+ {
+ start = start - distance;
+ distance = 0;
+ }
}
}
- 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 (visible) alignmentPosition to find the next hidden column for
*/
public int getHiddenBoundaryRight(int alPos)
{
LOCK.readLock().lock();
if (hiddenColumns != null)
{
- int index = 0;
- do
+ Iterator<int[]> it = new RegionsIterator();
+ while (it.hasNext())
{
- int[] region = hiddenColumns.get(index);
+ int[] region = it.next();
if (alPos < region[0])
{
return region[0];
}
-
- index++;
- } while (index < hiddenColumns.size());
+ }
}
-
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 (visible) alignmentPosition to find the previous hidden column
+ * for
*/
public int getHiddenBoundaryLeft(int alPos)
{
{
LOCK.readLock().lock();
- if (hiddenColumns != null)
+ Iterator<int[]> it = new ReverseRegionsIterator(0, alPos);
+ while (it.hasNext())
{
- int index = hiddenColumns.size() - 1;
- do
+ int[] region = it.next();
+ if (alPos > region[1])
{
- int[] region = hiddenColumns.get(index);
- if (alPos > region[1])
- {
- return region[1];
- }
-
- index--;
- } while (index > -1);
+ return region[1];
+ }
}
return alPos;
}
/**
- * This method returns the index of the hidden region to the left of a column
- * position. If the column is in a hidden region it returns the index of the
- * region to the left. If there is no hidden region to the left it returns -1.
- *
- * @param pos
- * int
- */
- private int getHiddenIndexLeft(int pos)
- {
- try
- {
-
- LOCK.readLock().lock();
- if (hiddenColumns != null)
- {
- int index = hiddenColumns.size() - 1;
- do
- {
- int[] region = hiddenColumns.get(index);
- if (pos > region[1])
- {
- return index;
- }
-
- index--;
- } while (index > -1);
- }
-
- return -1;
- } 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)
}
}
- public boolean isVisible(int column)
+ private boolean insertRangeAtRegion(int i, int start, int end)
{
- try
- {
- LOCK.readLock().lock();
-
- if (hiddenColumns != null)
- {
- for (int[] region : hiddenColumns)
- {
- if (column >= region[0] && column <= region[1])
- {
- return false;
- }
- }
- }
+ boolean added = false;
- return true;
- } finally
+ int[] region = hiddenColumns.get(i);
+ if (end < region[0] - 1)
{
- LOCK.readLock().unlock();
+ /*
+ * insert discontiguous preceding range
+ */
+ hiddenColumns.add(i, new int[] { start, end });
+ added = true;
}
- }
-
- private ArrayList<int[]> copyHiddenRegionsToArrayList(int startIndex)
- {
- int size = 0;
- if (hiddenColumns != null)
+ else if (end <= region[1])
{
- size = hiddenColumns.size();
+ /*
+ * new range overlaps existing, or is contiguous preceding it - adjust
+ * start column
+ */
+ region[0] = Math.min(region[0], start);
+ added = true;
}
- ArrayList<int[]> copy = new ArrayList<>(size);
-
- for (int i = startIndex, j = size; i < j; i++)
+ else if (start <= region[1] + 1)
{
- int[] rh;
- int[] cp;
- rh = hiddenColumns.get(i);
- if (rh != 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);
+
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ while (i < hiddenColumns.size() - 1)
{
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- copy.add(cp);
+ 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 copy;
+ return added;
}
/**
- * return all visible segments between the given start and end boundaries
+ * Answers if a column in the alignment is visible
*
- * @param start
- * (first column inclusive from 0)
- * @param end
- * (last column - not inclusive)
- * @return List<int[]> {[i_start, i_end], ..} where intervals lie in
- * start<=i_start<=i_end<end
+ * @param column
+ * absolute position of column in the alignment
+ * @return true if column is visible
*/
- public List<int[]> getVisibleContigs(int start, int end)
+ public boolean isVisible(int column)
{
try
{
LOCK.readLock().lock();
- List<int[]> vcontigs = new ArrayList<>();
- 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;
-
- // exit if we're past the end
- if (vstart >= end)
- {
- break;
- }
- }
-
- if (vstart < end)
+ Iterator<int[]> it = new RegionsIterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+ if (column >= region[0] && column <= region[1])
{
- int[] contig = new int[] { vstart, end - 1 };
- vcontigs.add(contig);
+ return false;
}
}
- else
- {
- int[] contig = new int[] { start, end - 1 };
- vcontigs.add(contig);
- }
- return vcontigs;
+
+ 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)
{
{
StringBuffer visibleSeq = new StringBuffer();
- int blockStart = start;
- int blockEnd = end;
- int hideStart;
- int hideEnd;
+ Iterator<int[]> blocks = new VisibleContigsIterator(start,
+ end + 1, false);
- for (int[] region : hiddenColumns)
+ while (blocks.hasNext())
{
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideStart < start)
+ int[] block = blocks.next();
+ if (blocks.hasNext())
{
- continue;
+ visibleSeq
+ .append(seqs[i].getSequence(block[0], block[1] + 1));
}
-
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
+ else
{
- break;
+ 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 rcount = 0;
+ Iterator<int[]> regions = new RegionsIterator();
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;
- }
- 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;
- int blockStart = start;
- int blockEnd = end;
- int hideStart;
- int hideEnd;
- int w = 0;
- for (int[] region : hiddenColumns)
- {
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideStart < start)
- {
- continue;
- }
+ int startFrom = start;
+ int endAt = end;
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
- {
- break;
- }
-
- els = new Annotation[blockEnd - blockStart];
- annels.addElement(els);
- System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
- 0, els.length);
- w += els.length;
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
-
- if (end > blockStart)
+ if (alignmentAnnotation.annotations != null)
+ {
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- els = new Annotation[end - blockStart + 1];
- annels.addElement(els);
- 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,
+ 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
{
- 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;
+ }
}
}
try
{
LOCK.writeLock().lock();
- if (hiddenColumns != null)
+ Iterator<int[]> it = new RegionsIterator();
+ while (it.hasNext())
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ int[] region = it.next();
+ for (int j = region[0]; j < region[1] + 1; j++)
{
- int[] region = hiddenColumns.get(i);
- for (int j = region[0]; j < region[1] + 1; j++)
- {
- sel.addElement(j);
- }
+ sel.addElement(j);
}
}
try
{
LOCK.writeLock().lock();
- for (int i = 0; i < hiddenColumns.size(); i++)
+ Iterator<int[]> it = new RegionsIterator();
+ while (it.hasNext())
{
- int[] region = hiddenColumns.get(i);
+ int[] region = it.next();
if (start == region[0])
{
for (int j = region[0]; j < region[1] + 1; j++)
hiddenColumns.remove(region);
break;
}
+ else if (start < region[0])
+ {
+ break; // passed all possible matching regions
+ }
}
+
if (hiddenColumns.size() == 0)
{
hiddenColumns = null;
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
-
- // 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 = iterator();
- ArrayList<int[]> newhidden = new ArrayList<>();
-
- int numGapsBefore = 0;
- int gapPosition = 0;
- while (regions.hasNext())
- {
- // 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++;
- if (gaps.get(gapPosition))
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
+
+ // first get the gaps as a Bitset
+ BitSet gaps = origseq.gapBitset();
+
+ // now calculate hidden ^ not(gap)
+ BitSet hidden = new BitSet();
+ markHiddenRegions(hidden);
+ hidden.andNot(gaps);
+ hiddenColumns = null;
+ this.hideMarkedBits(hidden);
+
+ // for each sequence in the alignment, except the profile sequence,
+ // insert gaps corresponding to each hidden region
+ // but where each hidden column region is shifted backwards by the number
+ // of
+ // preceding visible gaps
+ // update hidden columns at the same time
+ Iterator<int[]> regions = new RegionsIterator();
+ ArrayList<int[]> newhidden = new ArrayList<>();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ while (regions.hasNext())
+ {
+ // 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;
+ } finally
+ {
+ LOCK.writeLock().unlock();
}
- hiddenColumns = newhidden;
}
/**
{
LOCK.readLock().lock();
int hashCode = 1;
- if (hiddenColumns != null)
+ Iterator<int[]> it = new RegionsIterator();
+ while (it.hasNext())
{
- for (int[] hidden : hiddenColumns)
- {
- hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
- hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
- }
+ int[] hidden = it.next();
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
+ hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
}
return hashCode;
} finally
{
return;
}
- for (int[] range : hiddenColumns)
+ Iterator<int[]> it = new RegionsIterator();
+ 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 = new RegionsIterator();
+ 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)
int adjres = adjustForHiddenColumns(res);
int[] reveal = null;
- if (hiddenColumns != null)
+ Iterator<int[]> it = new RegionsIterator(adjres - 2,
+ adjres + 2);
+ while (it.hasNext())
{
- for (int[] region : hiddenColumns)
+ int[] region = it.next();
+ if (adjres + 1 == region[0] || adjres - 1 == region[1])
{
- if (adjres + 1 == region[0] || adjres - 1 == region[1])
- {
- reveal = region;
- break;
- }
+ reveal = region;
+ break;
}
}
return reveal;
}
}
+ /**
+ * Return an iterator over the hidden regions
+ */
public Iterator<int[]> iterator()
{
- if (hiddenColumns != null)
- {
- int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
- return new BoundedHiddenColsIterator(0, last, true);
- }
- else
- {
- return new BoundedHiddenColsIterator(0, 0, true);
- }
+ return new BoundedHiddenColsIterator();
}
+ /**
+ * 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)
{
- return new BoundedHiddenColsIterator(start, end, true);
+ return new BoundedHiddenColsIterator(start, end);
}
+ /**
+ * 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);
}
+ /**
+ * 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, true);
+ return new VisibleColsIterator(start, end);
}
/**
- * An iterator which iterates over hidden column regions in a range.
+ * return an iterator over visible segments between the given start and end
+ * boundaries
*
- * @author kmourao
- *
+ * @param start
+ * (first column inclusive from 0)
+ * @param end
+ * (last column - not inclusive)
+ */
+ public Iterator<int[]> getVisContigsIterator(int start, int end)
+ {
+ // return new VisibleBlocksIterator(start, end, true)
+ return new VisibleContigsIterator(start, end, true);
+ }
+
+ /**
+ * 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
+ {
+ return new VisibleContigsIterator(start, end - 1, true);
+ }
+ }
+
+ /**
+ * 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).
*/
- class BoundedHiddenColsIterator implements Iterator<int[]>
+ private class RegionsIterator implements Iterator<int[]>
{
- private int start; // start position to iterate from
+ // start position to iterate from
+ private int start;
- private int end; // end position to iterate to
+ // end position to iterate to
+ private int end;
// current index in hiddenColumns
private int currentPosition = 0;
// current column in hiddenColumns
- private int[] currentRegion;
+ private int[] nextRegion = null;
+
+ // Constructor with bounds
+ RegionsIterator(int lowerBound, int upperBound)
+ {
+ init(lowerBound, upperBound);
+ }
+
+ // Unbounded constructor
+ RegionsIterator()
+ {
+ 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);
+ }
+ }
+
+ /**
+ * 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)
+ {
+ // iterate until a region overlaps with [start,end]
+ currentPosition = 0;
+ while ((currentPosition < hiddenColumns.size())
+ && (hiddenColumns.get(currentPosition)[1] < start))
+ {
+ currentPosition++;
+ }
+ if (currentPosition < hiddenColumns.size())
+ {
+ nextRegion = hiddenColumns.get(currentPosition);
+ }
+ }
+ }
+
+ @Override
+ public boolean hasNext()
+ {
+ return (hiddenColumns != null) && (nextRegion != null)
+ && (nextRegion[0] <= end);
+ }
+
+ @Override
+ public int[] next()
+ {
+ int[] region = nextRegion;
+ currentPosition++;
+ if (currentPosition < hiddenColumns.size())
+ {
+ nextRegion = hiddenColumns.get(currentPosition);
+ }
+ else
+ {
+ nextRegion = null;
+ }
+ return region;
+ }
+
+ }
+
+ /**
+ * 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).
+ */
+ private class ReverseRegionsIterator implements Iterator<int[]>
+ {
+ // start position to iterate to
+ private int start;
- // whether to make a local copy of hiddenColumns
- private final boolean useCopy;
+ // end position to iterate from
+ private int end;
+
+ // current index in hiddenColumns
+ private int currentPosition = 0;
+
+ // current column in hiddenColumns
+ private int[] nextRegion = null;
+
+ // Constructor with bounds
+ ReverseRegionsIterator(int lowerBound, int upperBound)
+ {
+ init(lowerBound, upperBound);
+ }
+
+ /**
+ * 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)
+ {
+ // iterate until a region overlaps with [start,end]
+ currentPosition = hiddenColumns.size() - 1;
+ while (currentPosition >= 0
+ && hiddenColumns.get(currentPosition)[1] > end)
+ {
+ currentPosition--;
+ }
+ if (currentPosition >= 0)
+ {
+ nextRegion = hiddenColumns.get(currentPosition);
+ }
+ }
+ }
+
+ @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
+ {
+ nextRegion = null;
+ }
+ return region;
+ }
+
+ }
+
+ /**
+ * 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.
+ */
+ private class BoundedHiddenColsIterator implements Iterator<int[]>
+ {
+ // start position to iterate from
+ private int start;
+
+ // end position to iterate to
+ private int end;
+
+ // current index in hiddenColumns
+ private int currentPosition = 0;
+
+ // current column in hiddenColumns
+ private int[] currentRegion;
// local copy or reference to hiddenColumns
private List<int[]> localHidden;
/**
+ * Unbounded constructor
+ */
+ BoundedHiddenColsIterator()
+ {
+ if (hiddenColumns != null)
+ {
+ int last = hiddenColumns.get(hiddenColumns.size() - 1)[1];
+ init(0, last);
+ }
+ else
+ {
+ init(0, 0);
+ }
+ }
+
+ /**
* Construct an iterator over hiddenColums bounded at
* [lowerBound,upperBound]
*
* 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)
*/
- BoundedHiddenColsIterator(int lowerBound, int upperBound,
- boolean useCopyCols)
+ 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;
- useCopy = useCopyCols;
try
{
- if (useCopy)
- {
- // assume that if useCopy is false the calling code has locked
- // hiddenColumns
- LOCK.readLock().lock();
- }
+ LOCK.readLock().lock();
if (hiddenColumns != null)
{
while (i < hiddenColumns.size()
&& (hiddenColumns.get(i)[0] <= end))
{
- int[] rh;
- int[] cp;
- rh = hiddenColumns.get(i);
- if (rh != null)
- {
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- localHidden.add(cp);
- }
+ int[] rh = hiddenColumns.get(i);
+ int[] cp = new int[2];
+ System.arraycopy(rh, 0, cp, 0, rh.length);
+ localHidden.add(cp);
i++;
}
}
}
finally
{
- if (useCopy)
- {
- LOCK.readLock().unlock();
- }
+ LOCK.readLock().unlock();
}
}
}
}
- class BoundedStartRegionIterator implements Iterator<Integer>
+ /**
+ * An iterator which iterates over visible start positions of hidden column
+ * regions in a range.
+ */
+ private class BoundedStartRegionIterator implements Iterator<Integer>
{
+ // start position to iterate from
+ private int start;
- private int start; // start position to iterate from
-
- private int end; // end position to iterate to
+ // end position to iterate to
+ private int end;
// current index in hiddenColumns
private int currentPosition = 0;
return (currentPosition < positions.size());
}
+ /**
+ * Get next hidden region start position
+ *
+ * @return the start position in *visible* coordinates
+ */
@Override
public Integer next()
{
}
}
- public class VisibleColsIterator implements Iterator<Integer>
+ /**
+ * Iterator over the visible *columns* (not regions) as determined by the set
+ * of hidden columns. Uses a local copy of hidden columns.
+ *
+ * @author kmourao
+ *
+ */
+ private class VisibleColsIterator implements Iterator<Integer>
{
private int last;
private List<int[]> localHidden = new ArrayList<>();
- private int lasthiddenregion;
+ private int nexthiddenregion;
- public VisibleColsIterator(int firstcol, int lastcol, boolean useCopy)
+ VisibleColsIterator(int firstcol, int lastcol)
{
last = lastcol;
current = firstcol;
next = firstcol;
- lasthiddenregion = -1;
+ nexthiddenregion = 0;
- try
- {
- if (useCopy)
- {
- // assume that if useCopy is false the calling code has locked
- // hiddenColumns
- LOCK.readLock().lock();
- }
+ LOCK.readLock().lock();
- if (hiddenColumns != null)
+ if (hiddenColumns != null)
+ {
+ int i = 0;
+ for (i = 0; i < hiddenColumns.size()
+ && (current <= hiddenColumns.get(i)[0]); ++i)
{
- int i = 0;
- for (i = 0; i < hiddenColumns.size(); ++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;
- }
- if (current < hiddenColumns.get(i)[0])
- {
- break;
- }
- }
-
- lasthiddenregion = i - 1;
-
- for (i = hiddenColumns.size() - 1; i >= 0; --i)
+ if (current >= hiddenColumns.get(i)[0]
+ && current <= hiddenColumns.get(i)[1])
{
- if (last >= hiddenColumns.get(i)[0]
- && last <= hiddenColumns.get(i)[1])
- {
- // last is hidden, move to left
- last = hiddenColumns.get(i)[0] - 1;
- }
- if (last > hiddenColumns.get(i)[1])
- {
- break;
- }
+ // current is hidden, move to right
+ current = hiddenColumns.get(i)[1] + 1;
+ next = current;
+ nexthiddenregion = i + 1;
}
+ }
- // make a local copy of the bit we need
- i = lasthiddenregion + 1;
- while (i < hiddenColumns.size()
- && hiddenColumns.get(i)[0] <= last)
+ for (i = hiddenColumns.size() - 1; i >= 0
+ && (last >= hiddenColumns.get(i)[1]); --i)
+ {
+ if (last >= hiddenColumns.get(i)[0]
+ && last <= hiddenColumns.get(i)[1])
{
- int[] region = new int[] { hiddenColumns.get(i)[0],
- hiddenColumns.get(i)[1] };
- localHidden.add(region);
- i++;
+ // last is hidden, move to left
+ last = hiddenColumns.get(i)[0] - 1;
}
- lasthiddenregion = -1;
}
- } finally
- {
- if (useCopy)
+
+ // make a local copy of the bit we need
+ i = nexthiddenregion;
+ while (i < hiddenColumns.size() && hiddenColumns.get(i)[0] <= last)
{
- LOCK.readLock().unlock();
+ int[] region = new int[] { hiddenColumns.get(i)[0],
+ hiddenColumns.get(i)[1] };
+ localHidden.add(region);
+ i++;
}
}
+
+ LOCK.readLock().unlock();
}
@Override
}
current = next;
if ((localHidden != null)
- && (lasthiddenregion + 1 < localHidden.size()))
+ && (nexthiddenregion < localHidden.size()))
{
// still some more hidden regions
- if (next + 1 < localHidden.get(lasthiddenregion + 1)[0])
+ if (next + 1 < localHidden.get(nexthiddenregion)[0])
{
// next+1 is still before the next hidden region
next++;
}
- else if ((next + 1 >= localHidden.get(lasthiddenregion + 1)[0])
- && (next + 1 <= localHidden.get(lasthiddenregion + 1)[1]))
+ 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(lasthiddenregion + 1)[1] + 1;
- lasthiddenregion++;
+ next = localHidden.get(nexthiddenregion)[1] + 1;
+ nexthiddenregion++;
}
}
else
throw new UnsupportedOperationException();
}
}
+
+ /**
+ * An iterator which iterates over visible regions in a range.
+ */
+ private class VisibleContigsIterator implements Iterator<int[]>
+ {
+ private List<int[]> vcontigs = new ArrayList<>();
+
+ private int currentPosition = 0;
+
+ VisibleContigsIterator(int start, int end, boolean usecopy)
+ {
+ 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;
+
+ // exit if we're past the end
+ if (vstart >= end)
+ {
+ break;
+ }
+ }
+
+ if (vstart < end)
+ {
+ int[] contig = new int[] { vstart, end - 1 };
+ vcontigs.add(contig);
+ }
+ }
+ else
+ {
+ int[] contig = new int[] { start, end - 1 };
+ vcontigs.add(contig);
+ }
+ } 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;
+ }
+ }
+
+ /**
+ * 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)
+ {
+ // 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