/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
import java.util.concurrent.locks.ReentrantReadWriteLock;
/**
* This class manages the collection of hidden columns associated with an
* alignment. To iterate over the collection, or over visible columns/regions,
* use an iterator obtained from one of:
*
* - getBoundedIterator: iterates over the hidden regions, within some bounds,
* returning absolute positions
*
* - getBoundedStartIterator: iterates over the start positions of hidden
* regions, within some bounds, returning visible positions
*
* - getVisContigsIterator: iterates over visible regions in a range, returning
* absolute positions
*
* - getVisibleColsIterator: iterates over the visible *columns*
*
* For performance reasons, provide bounds where possible.
*
* @author kmourao
*
*/
public class HiddenColumns
{
private static final int HASH_MULTIPLIER = 31;
private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
/*
* Cursor which tracks the last used hidden columns region, and the number
* of hidden columns up to (but not including) that region.
*/
private HiddenColumnsCursor cursor = new HiddenColumnsCursor();
/*
* cache of the number of hidden columns
*/
private int numColumns = 0;
/*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
*/
private ArrayList hiddenColumns;
/**
* Constructor
*/
public HiddenColumns()
{
}
/*
* Methods which change the hiddenColumns collection. These methods should
* use a writeLock to prevent other threads accessing the hiddenColumns
* collection while changes are being made. They should also reset the hidden
* columns cursor, and either update the hidden columns count, or set it to 0
* (so that it will later be updated when needed).
*/
/**
* Copy constructor
*
* @param copy
* the HiddenColumns object to copy from
*/
public HiddenColumns(HiddenColumns copy)
{
try
{
LOCK.writeLock().lock();
numColumns = 0;
if (copy != null)
{
if (copy.hiddenColumns != null)
{
hiddenColumns = new ArrayList<>();
Iterator it = copy.iterator();
while (it.hasNext())
{
int[] region = it.next();
hiddenColumns.add(region);
numColumns += region[1] - region[0] + 1;
}
cursor.resetCursor(hiddenColumns);
}
}
} finally
{
LOCK.writeLock().unlock();
}
}
/**
* 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
*
*/
public HiddenColumns(HiddenColumns copy, int start, int end, int offset)
{
try
{
LOCK.writeLock().lock();
if (copy != null)
{
hiddenColumns = new ArrayList<>();
numColumns = 0;
Iterator 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();
}
}
/**
* 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;
}
int previndex = 0;
int prevHiddenCount = 0;
int regionindex = 0;
if (hiddenColumns == null)
{
hiddenColumns = new ArrayList<>();
}
else
{
// set up cursor reset values
HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
regionindex = cursorPos.getRegionIndex();
if (regionindex > 0)
{
// get previous index and hidden count for updating the cursor later
previndex = regionindex - 1;
int[] prevRegion = hiddenColumns.get(previndex);
prevHiddenCount = cursorPos.getHiddenSoFar()
- (prevRegion[1] - prevRegion[0] + 1);
}
}
/*
* 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;
if (regionindex > 0)
{
added = insertRangeAtRegion(regionindex - 1, start, end);
}
if (!added && regionindex < hiddenColumns.size())
{
insertRangeAtRegion(regionindex, start, end);
}
}
// 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
{
if (!wasAlreadyLocked)
{
LOCK.writeLock().unlock();
}
}
}
/**
* Insert [start, range] at the region at index i in hiddenColumns, if
* feasible
*
* @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
*/
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);
// in theory this is faster than hiddenColumns.remove(i+1)
// benchmarking results a bit ambivalent
hiddenColumns.subList(i + 1, i + 2).clear();
}
added = true;
}
return added;
}
/**
* 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 inserts = sr.getInsertions();
for (int[] r : inserts)
{
hideColumns(r[0], r[1]);
}
cursor.resetCursor(hiddenColumns);
numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
}
}
/**
* Unhides, and adds to the selection list, all hidden columns
*/
public void revealAllHiddenColumns(ColumnSelection sel)
{
try
{
LOCK.writeLock().lock();
if (hiddenColumns != null)
{
Iterator it = hiddenColumns.iterator();
while (it.hasNext())
{
int[] region = it.next();
for (int j = region[0]; j < region[1] + 1; j++)
{
sel.addElement(j);
}
}
hiddenColumns = null;
cursor.resetCursor(hiddenColumns);
numColumns = 0;
}
} finally
{
LOCK.writeLock().unlock();
}
}
/**
* Reveals, and marks as selected, the hidden column range with the given
* start column
*
* @param start
* the start column to look for
* @param sel
* the column selection to add the hidden column range to
*/
public void revealHiddenColumns(int start, ColumnSelection sel)
{
try
{
LOCK.writeLock().lock();
if (hiddenColumns != null)
{
int regionIndex = cursor.findRegionForColumn(start)
.getRegionIndex();
if (regionIndex != -1 && regionIndex != hiddenColumns.size())
{
// regionIndex is the region which either contains start
// or lies to the right of start
int[] region = hiddenColumns.get(regionIndex);
if (start == region[0])
{
for (int j = region[0]; j < region[1] + 1; j++)
{
sel.addElement(j);
}
int colsToRemove = region[1] - region[0] + 1;
hiddenColumns.remove(regionIndex);
if (hiddenColumns.isEmpty())
{
hiddenColumns = null;
numColumns = 0;
}
else
{
numColumns -= colsToRemove;
}
cursor.updateForDeletedRegion(hiddenColumns);
}
}
}
} finally
{
LOCK.writeLock().unlock();
}
}
/**
* 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
* @param input
* alignment view where sequence corresponding to profileseq is first
* entry
* @return new HiddenColumns for new alignment view, with insertions into
* profileseq marked as hidden.
*/
public static HiddenColumns propagateInsertions(SequenceI profileseq,
AlignmentI al, AlignmentView input)
{
int profsqpos = 0;
char gc = al.getGapCharacter();
Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
HiddenColumns nview = (HiddenColumns) alandhidden[1];
SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
nview.propagateInsertions(profileseq, al, origseq);
return nview;
}
/**
*
* @param profileseq
* sequence in al which corresponds to origseq
* @param al
* alignment which is to have gaps inserted into it
* @param origseq
* sequence corresponding to profileseq which defines gap map for
* modifying al
*/
private void propagateInsertions(SequenceI profileseq, AlignmentI al,
SequenceI origseq)
{
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 regions = hiddenColumns.iterator();
ArrayList 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))
{
numGapsBefore++;
}
}
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);
}
hiddenColumns = newhidden;
cursor.resetCursor(hiddenColumns);
numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
}
}
/**
* Pad gaps in all sequences in alignment except profileseq
*
* @param sb
* gap string to insert
* @param left
* position to insert at
* @param profileseq
* sequence not to pad
* @param al
* alignment to pad sequences in
*/
private void padGaps(StringBuffer sb, int pos, SequenceI profileseq,
AlignmentI al)
{
// loop over the sequences and pad with gaps where required
for (int s = 0, ns = al.getHeight(); s < ns; s++)
{
SequenceI sqobj = al.getSequenceAt(s);
if (sqobj != profileseq)
{
String sq = al.getSequenceAt(s).getSequenceAsString();
if (sq.length() <= pos)
{
// pad sequence
int diff = pos - sq.length() - 1;
if (diff > 0)
{
// pad gaps
sq = sq + sb;
while ((diff = pos - sq.length() - 1) > 0)
{
if (diff >= sb.length())
{
sq += sb.toString();
}
else
{
char[] buf = new char[diff];
sb.getChars(0, diff, buf, 0);
sq += buf.toString();
}
}
}
sq += sb.toString();
}
else
{
al.getSequenceAt(s).setSequence(
sq.substring(0, pos) + sb.toString() + sq.substring(pos));
}
}
}
}
/*
* 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.
*/
/**
* Output regions data as a string. String is in the format:
* reg0[0]reg0[1]reg1[0]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
*/
public String regionsToString(String delimiter, String between)
{
try
{
LOCK.readLock().lock();
StringBuilder regionBuilder = new StringBuilder();
if (hiddenColumns != null)
{
Iterator it = hiddenColumns.iterator();
while (it.hasNext())
{
int[] range = it.next();
regionBuilder.append(delimiter).append(range[0]).append(between)
.append(range[1]);
if (!it.hasNext())
{
regionBuilder.deleteCharAt(0);
}
}
}
return regionBuilder.toString();
} finally
{
LOCK.readLock().unlock();
}
}
/**
* Find the number of hidden columns
*
* @return number of hidden columns
*/
public int getSize()
{
try
{
LOCK.readLock().lock();
if (numColumns == 0 && hiddenColumns != null)
{
// numColumns is out of date, so recalculate
int size = 0;
Iterator it = hiddenColumns.iterator();
while (it.hasNext())
{
int[] range = it.next();
size += range[1] - range[0] + 1;
}
numColumns = 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();
}
}
@Override
public boolean equals(Object obj)
{
try
{
LOCK.readLock().lock();
if (!(obj instanceof HiddenColumns))
{
return false;
}
HiddenColumns that = (HiddenColumns) obj;
/*
* check hidden columns are either both null, or match
*/
if (this.hiddenColumns == null)
{
return (that.hiddenColumns == null);
}
if (that.hiddenColumns == null
|| that.hiddenColumns.size() != this.hiddenColumns.size())
{
return false;
}
Iterator it = hiddenColumns.iterator();
Iterator thatit = that.iterator();
while (it.hasNext())
{
int[] thisRange = it.next();
int[] thatRange = thatit.next();
if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
{
return false;
}
}
return true;
} finally
{
LOCK.readLock().unlock();
}
}
/**
* Return absolute column index for a visible column index
*
* @param column
* int column index in alignment view (count from zero)
* @return alignment column index for column
*/
public int adjustForHiddenColumns(int column)
{
try
{
LOCK.readLock().lock();
int result = column;
if (hiddenColumns != null)
{
result += cursor.getHiddenOffset(column).getHiddenSoFar();
}
return result;
} finally
{
LOCK.readLock().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
*/
public int findColumnPosition(int hiddenColumn)
{
try
{
LOCK.readLock().lock();
int result = hiddenColumn;
if (hiddenColumns != null)
{
HiddenCursorPosition cursorPos = cursor
.findRegionForColumn(hiddenColumn);
int index = cursorPos.getRegionIndex();
int hiddenBeforeCol = cursorPos.getHiddenSoFar();
// just subtract hidden cols count - this works fine if column is
// visible
result = hiddenColumn - hiddenBeforeCol;
// now check in case column is hidden - it will be in the returned
// hidden region
if (index < hiddenColumns.size())
{
int[] region = hiddenColumns.get(index);
if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
{
// actually col is hidden, return region[0]-1
// unless region[0]==0 in which case return 0
if (region[0] == 0)
{
result = 0;
}
else
{
result = region[0] - 1 - hiddenBeforeCol;
}
}
}
}
return result; // return the shifted position after removing hidden
// columns.
} finally
{
LOCK.readLock().unlock();
}
}
/**
* Find the visible column which is a given visible number of columns to the
* left of another visible column. i.e. for a startColumn x, the column which
* is distance 1 away will be column x-1.
*
* @param visibleDistance
* the number of visible columns to offset by
* @param startColumn
* the column to start from
* @return the position of the column in the visible alignment
*/
public int subtractVisibleColumns(int visibleDistance, int startColumn)
{
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 it = new ReverseRegionsIterator(0, start,
hiddenColumns);
while (it.hasNext() && (distance > 0))
{
int[] region = it.next();
if (start > region[1])
{
// subtract the gap to right of region from distance
if (start - region[1] <= distance)
{
distance -= start - region[1];
start = region[0] - 1;
}
else
{
start = start - distance;
distance = 0;
}
}
}
return start - distance;
} 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 alPos
* the absolute (visible) alignmentPosition to find the next hidden
* column for
*/
public int getHiddenBoundaryRight(int alPos)
{
try
{
LOCK.readLock().lock();
if (hiddenColumns != null)
{
int index = cursor.findRegionForColumn(alPos).getRegionIndex();
if (index < hiddenColumns.size())
{
int[] region = hiddenColumns.get(index);
if (alPos < region[0])
{
return region[0];
}
else if ((alPos <= region[1])
&& (index + 1 < hiddenColumns.size()))
{
// alPos is within a hidden region, return the next one
// if there is one
region = hiddenColumns.get(index + 1);
return region[0];
}
}
}
return alPos;
} finally
{
LOCK.readLock().unlock();
}
}
/**
* This method returns the leftmost limit of a region of an alignment with
* hidden columns. In otherwords, the previous hidden column.
*
* @param alPos
* the absolute (visible) alignmentPosition to find the previous
* hidden column for
*/
public int getHiddenBoundaryLeft(int alPos)
{
try
{
LOCK.readLock().lock();
if (hiddenColumns != null)
{
int index = cursor.findRegionForColumn(alPos).getRegionIndex();
if (index > 0)
{
int[] region = hiddenColumns.get(index - 1);
return region[1];
}
}
return alPos;
} finally
{
LOCK.readLock().unlock();
}
}
/**
* 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();
int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
if (regionindex > -1 && regionindex < 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])
{
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 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
{
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 regions = hiddenColumns.iterator();
int hideStart = seq.getLength();
int hideEnd = -1;
int visPrev = 0;
int visNext = 0;
boolean foundStart = false;
// step through the non-gapped positions of the sequence
for (int i = seq.getStart(); i <= seq.getEnd() && (!foundStart); i++)
{
// get alignment position of this residue in the sequence
int p = seq.findIndex(i) - 1;
// update hidden region start/end
while (hideEnd < p && regions.hasNext())
{
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)
{
if (alignmentAnnotation != null
&& alignmentAnnotation.annotations != null)
{
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 != null
&& 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 annels = new ArrayList<>();
Annotation[] els = null;
int w = 0;
Iterator 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
{
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();
}
}
/**
* Returns a hashCode built from hidden column ranges
*/
@Override
public int hashCode()
{
try
{
LOCK.readLock().lock();
int hashCode = 1;
Iterator it = hiddenColumns.iterator();
while (it.hasNext())
{
int[] hidden = it.next();
hashCode = HASH_MULTIPLIER * hashCode + hidden[0];
hashCode = HASH_MULTIPLIER * hashCode + hidden[1];
}
return hashCode;
} finally
{
LOCK.readLock().unlock();
}
}
/**
* Hide columns corresponding to the marked bits
*
* @param inserts
* - columns map to bits starting from zero
*/
public void hideMarkedBits(BitSet inserts)
{
try
{
LOCK.writeLock().lock();
for (int firstSet = inserts
.nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
.nextSetBit(lastSet))
{
lastSet = inserts.nextClearBit(firstSet);
hideColumns(firstSet, lastSet - 1);
}
cursor.resetCursor(hiddenColumns);
numColumns = 0;
} finally
{
LOCK.writeLock().unlock();
}
}
/**
*
* @param inserts
* BitSet where hidden columns will be marked
*/
public void markHiddenRegions(BitSet inserts)
{
try
{
LOCK.readLock().lock();
if (hiddenColumns == null)
{
return;
}
Iterator it = hiddenColumns.iterator();
while (it.hasNext())
{
int[] range = it.next();
inserts.set(range[0], range[1] + 1);
}
} 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)
{
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)
{
return new int[] { startPos, endPos };
}
Iterator it = hiddenColumns.iterator();
while (it.hasNext())
{
int[] range = it.next();
lowestRange = (range[0] <= startPos) ? range : lowestRange;
higestRange = (range[1] >= endPos) ? range : higestRange;
}
if (lowestRange[0] == -1) // includes (lowestRange[1] == -1)
{
startPos = alignmentStartEnd[0];
}
else
{
startPos = lowestRange[1] + 1;
}
if (higestRange[0] == -1) // includes (higestRange[1] == -1)
{
endPos = alignmentStartEnd[1];
}
else
{
endPos = higestRange[0] - 1;
}
return new int[] { startPos, endPos };
} finally
{
LOCK.readLock().unlock();
}
}
/**
* 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
*/
public int[] getRegionWithEdgeAtRes(int res)
{
try
{
LOCK.readLock().lock();
int adjres = adjustForHiddenColumns(res);
int[] reveal = null;
if (hiddenColumns != null)
{
// 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)
{
reveal = hiddenColumns.get(regionindex);
}
}
return reveal;
} finally
{
LOCK.readLock().unlock();
}
}
/**
* Return an iterator over the hidden regions
*/
public Iterator 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 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 getBoundedStartIterator(int start, int end)
{
try
{
LOCK.readLock().lock();
// get absolute position of column in alignment
int absoluteStart = adjustForHiddenColumns(start);
// Get cursor position and supply it to the iterator:
// Since we want visible region start, we look for a cursor for the
// (absoluteStart-1), then if absoluteStart is the start of a visible
// region we'll get the cursor pointing to the region before, which is
// what we want
HiddenCursorPosition pos = cursor
.findRegionForColumn(absoluteStart - 1);
return new BoundedStartRegionIterator(pos, start, end,
hiddenColumns);
} finally
{
LOCK.readLock().unlock();
}
}
/**
* Return an iterator over visible *columns* (not regions) between the given
* start and end boundaries
*
* @param start
* first column (inclusive)
* @param end
* last column (inclusive)
*/
public Iterator getVisibleColsIterator(int start, int end)
{
try
{
LOCK.readLock().lock();
return new VisibleColsIterator(start, end, hiddenColumns);
} finally
{
LOCK.readLock().unlock();
}
}
/**
* return an iterator over visible segments between the given start and end
* boundaries
*
* @param start
* first column, inclusive from 0
* @param end
* last column - not inclusive
* @param useVisibleCoords
* if true, start and end are visible column positions, not absolute
* positions*
*/
public Iterator getVisContigsIterator(int start, int end,
boolean useVisibleCoords)
{
int adjstart = start;
int adjend = end;
if (useVisibleCoords)
{
adjstart = adjustForHiddenColumns(start);
adjend = adjustForHiddenColumns(end);
}
try
{
LOCK.readLock().lock();
return new VisibleContigsIterator(adjstart, adjend, hiddenColumns);
} finally
{
LOCK.readLock().unlock();
}
}
}