+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
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 implements Iterable<int[]>
+public class HiddenColumns
{
- private static final ReentrantReadWriteLock lock = new ReentrantReadWriteLock();
+ private static final ReentrantReadWriteLock LOCK = new ReentrantReadWriteLock();
/*
* list of hidden column [start, end] ranges; the list is maintained in
*
* @return empty list or List of hidden column intervals
*/
- public List<int[]> getHiddenRegions()
+ private List<int[]> getHiddenRegions()
{
return hiddenColumns == null ? Collections.<int[]> emptyList()
: hiddenColumns;
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
StringBuilder regionBuilder = new StringBuilder();
- for (int[] range : hiddenColumns)
+ if (hiddenColumns != null)
{
- regionBuilder.append(delimiter).append(range[0]).append(between)
- .append(range[1]);
- }
+ for (int[] range : hiddenColumns)
+ {
+ regionBuilder.append(delimiter).append(range[0]).append(between)
+ .append(range[1]);
+ }
- regionBuilder.deleteCharAt(0);
+ regionBuilder.deleteCharAt(0);
+ }
return regionBuilder.toString();
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
int size = 0;
if (hasHidden())
{
}
finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
if (!(obj instanceof HiddenColumns))
{
return true;
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
int result = column;
if (hiddenColumns != null)
{
return result;
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
int result = hiddenColumn;
if (hiddenColumns != null)
{
// columns.
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
int distance = visibleDistance;
// in case startColumn is in a hidden region, move it to the left
return start - distance;
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
- List<Integer> positions = new ArrayList<>(
- hiddenColumns.size());
+ LOCK.readLock().lock();
+ List<Integer> positions = null;
- positions.add(hiddenColumns.elementAt(0)[0]);
- for (int i = 1; i < hiddenColumns.size(); ++i)
+ if (hiddenColumns != null)
{
+ positions = new ArrayList<>(hiddenColumns.size());
- int result = 0;
- if (hiddenColumns != null)
+ positions.add(hiddenColumns.elementAt(0)[0]);
+ for (int i = 1; i < hiddenColumns.size(); ++i)
{
- int index = 0;
- int gaps = 0;
- do
+
+ int result = 0;
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.elementAt(index);
- gaps += region[1] + 1 - region[0];
- result = region[1] + 1;
- index++;
- } while (index <= i);
+ int index = 0;
+ int gaps = 0;
+ do
+ {
+ int[] region = hiddenColumns.elementAt(index);
+ gaps += region[1] + 1 - region[0];
+ result = region[1] + 1;
+ index++;
+ } while (index <= i);
- result -= gaps;
+ result -= gaps;
+ }
+ positions.add(result);
}
- positions.add(result);
+ }
+ else
+ {
+ positions = new ArrayList<>();
}
return positions;
}
finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
if (hiddenColumns != null)
{
int index = 0;
return alPos;
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
if (hiddenColumns != null)
{
return alPos;
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
if (hiddenColumns != null)
{
int index = hiddenColumns.size() - 1;
return -1;
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
if (!alreadyLocked)
{
- lock.writeLock().lock();
+ LOCK.writeLock().lock();
}
- if (hiddenColumns == null)
- {
- hiddenColumns = new Vector<>();
- }
-
- /*
- * traverse existing hidden ranges and insert / amend / append as
- * appropriate
- */
- for (int i = 0; i < hiddenColumns.size(); i++)
- {
- int[] region = hiddenColumns.elementAt(i);
-
- if (end < region[0] - 1)
+ if (hiddenColumns == null)
{
- /*
- * insert discontiguous preceding range
- */
- hiddenColumns.insertElementAt(new int[] { start, end }, i);
- return;
+ hiddenColumns = new Vector<>();
}
- if (end <= region[1])
+ /*
+ * traverse existing hidden ranges and insert / amend / append as
+ * appropriate
+ */
+ for (int i = 0; i < hiddenColumns.size(); i++)
{
- /*
- * new range overlaps existing, or is contiguous preceding it - adjust
- * start column
- */
- region[0] = Math.min(region[0], start);
- return;
- }
+ int[] region = hiddenColumns.elementAt(i);
- 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)
+ if (end < region[0] - 1)
+ {
+ /*
+ * insert discontiguous preceding range
+ */
+ hiddenColumns.insertElementAt(new int[] { start, end }, i);
+ return;
+ }
+
+ if (end <= region[1])
{
- int[] nextRegion = hiddenColumns.get(i + 1);
- if (nextRegion[0] > end + 1)
+ /*
+ * new range overlaps existing, or is contiguous preceding it - adjust
+ * start column
+ */
+ region[0] = Math.min(region[0], start);
+ return;
+ }
+
+ if (start <= region[1] + 1)
+ {
+ /*
+ * new range overlaps existing, or is contiguous following it - adjust
+ * start and end columns
+ */
+ region[0] = Math.min(region[0], start);
+ region[1] = Math.max(region[1], end);
+
+ /*
+ * also update or remove any subsequent ranges
+ * that are overlapped
+ */
+ while (i < hiddenColumns.size() - 1)
{
- /*
- * gap to next hidden range - no more to update
- */
- break;
+ 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);
}
- region[1] = Math.max(nextRegion[1], end);
- hiddenColumns.remove(i + 1);
+ return;
}
- return;
- }
}
/*
{
if (!alreadyLocked)
{
- lock.writeLock().unlock();
+ LOCK.writeLock().unlock();
}
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
if (hiddenColumns != null)
{
return true;
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
if (copy != null)
{
if (copy.hiddenColumns != null)
}
finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
Vector<int[]> copy = new Vector<>(hiddenColumns.size());
for (int i = 0, j = hiddenColumns.size(); i < j; i++)
{
- int[] rh, cp;
+ int[] rh;
+ int[] cp;
rh = hiddenColumns.elementAt(i);
if (rh != null)
{
private ArrayList<int[]> copyHiddenRegionsToArrayList()
{
- ArrayList<int[]> copy = new ArrayList<>(hiddenColumns.size());
- for (int i = 0, j = hiddenColumns.size(); i < j; i++)
+ int size = 0;
+ if (hiddenColumns != null)
{
- int[] rh, cp;
+ size = hiddenColumns.size();
+ }
+ ArrayList<int[]> copy = new ArrayList<>(size);
+
+ for (int i = 0, j = size; i < j; i++)
+ {
+ int[] rh;
+ int[] cp;
rh = hiddenColumns.elementAt(i);
if (rh != null)
{
copy.add(cp);
}
}
+
return copy;
}
- public void getHiddenColumnsCopy(Vector<int[]> copy)
+ /**
+ * Returns a copy of the vector of hidden regions, as a vector. 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.
+ *
+ * @return hidden regions as vector of [start,end] pairs
+ */
+ public Vector<int[]> getHiddenColumnsCopy()
{
try
{
- lock.readLock().lock();
- copy = copyHiddenRegions();
+ LOCK.readLock().lock();
+ return copyHiddenRegions();
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
- public void getHiddenColumnsCopy(ArrayList<int[]> 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.
+ *
+ * @return hidden regions as an ArrayList of [start,end] pairs
+ */
+ public ArrayList<int[]> getHiddenColumnsCopyAsList()
{
try
{
- lock.readLock().lock();
- copy = copyHiddenRegionsToArrayList();
+ LOCK.readLock().lock();
+ return copyHiddenRegionsToArrayList();
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.writeLock().lock();
+ LOCK.writeLock().lock();
List<int[]> deletedHiddenColumns = null;
if (hiddenColumns != null)
return deletedHiddenColumns;
} finally
{
- lock.writeLock().unlock();
+ LOCK.writeLock().unlock();
}
}
{
try
{
- lock.writeLock().lock();
+ LOCK.writeLock().lock();
if (hiddenColumns != null)
{
for (int i = 0; i < hiddenColumns.size(); i++)
}
finally
{
- lock.writeLock().unlock();
+ LOCK.writeLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
List<int[]> visiblecontigs = new ArrayList<>();
int vstart = start;
int[] region;
- int hideStart, hideEnd;
+ int hideStart;
+ int hideEnd;
for (int j = 0; vstart < end && j < regions.size(); j++)
{
}
finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
- int i, iSize = seqs.length;
+ LOCK.readLock().lock();
+ int iSize = seqs.length;
String selections[] = new String[iSize];
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- for (i = 0; i < iSize; i++)
+ for (int i = 0; i < iSize; i++)
{
StringBuffer visibleSeq = new StringBuffer();
List<int[]> regions = getHiddenRegions();
- int blockStart = start, blockEnd = end;
+ int blockStart = start;
+ int blockEnd = end;
int[] region;
- int hideStart, hideEnd;
+ int hideStart;
+ int hideEnd;
for (int j = 0; j < regions.size(); j++)
{
}
else
{
- for (i = 0; i < iSize; i++)
+ for (int i = 0; i < iSize; i++)
{
selections[i] = seqs[i].getSequenceAsString(start, end);
}
}
finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
- int fpos = seq.getStart(), lpos = seq.getEnd();
+ 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,
- ilpos = seq.findIndex(lpos) - 1;
+ int ifpos = seq.findIndex(fpos) - 1;
+ int ilpos = seq.findIndex(lpos) - 1;
return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
}
// Simply walk along the sequence whilst watching for hidden column
// boundaries
List<int[]> regions = getHiddenRegions();
- int spos = fpos, lastvispos = -1, rcount = 0,
- hideStart = seq.getLength(), hideEnd = -1;
- int visPrev = 0, visNext = 0, firstP = -1, lastP = -1;
+ int spos = fpos;
+ int lastvispos = -1;
+ int rcount = 0;
+ int hideStart = seq.getLength();
+ int hideEnd = -1;
+ int visPrev = 0;
+ int visNext = 0;
+ int firstP = -1;
+ int lastP = -1;
boolean foundStart = false;
for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
&& p < pLen; p++)
}
finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
if (alignmentAnnotation.annotations == null)
{
return;
Vector<Annotation[]> annels = new Vector<>();
Annotation[] els = null;
List<int[]> regions = getHiddenRegions();
- int blockStart = start, blockEnd = end;
+ int blockStart = start;
+ int blockEnd = end;
int[] region;
- int hideStart, hideEnd, w = 0;
+ int hideStart;
+ int hideEnd;
+ int w = 0;
for (int j = 0; j < regions.size(); j++)
{
}
finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
return hiddenColumns != null && hiddenColumns.size() > 0;
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
return hiddenColumns != null && hiddenColumns.size() > 1;
} finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.writeLock().lock();
+ LOCK.writeLock().lock();
List<int[]> inserts = sr.getInsertions();
for (int[] r : inserts)
{
}
} finally
{
- lock.writeLock().unlock();
+ LOCK.writeLock().unlock();
}
}
{
try
{
- lock.writeLock().lock();
+ LOCK.writeLock().lock();
if (hiddenColumns != null)
{
for (int i = 0; i < hiddenColumns.size(); i++)
}
finally
{
- lock.writeLock().unlock();
+ LOCK.writeLock().unlock();
}
}
{
try
{
- lock.writeLock().lock();
+ LOCK.writeLock().lock();
for (int i = 0; i < hiddenColumns.size(); i++)
{
int[] region = hiddenColumns.elementAt(i);
}
finally
{
- lock.writeLock().unlock();
+ LOCK.writeLock().unlock();
}
}
Vector<int[]> intervals)
{
boolean pruned = false;
- int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
+ int i = 0;
+ int j = intervals.size() - 1;
+ int s = 0;
+ int t = shifts.size() - 1;
int hr[] = intervals.elementAt(i);
int sr[] = shifts.get(s);
while (i <= j && s <= t)
{
try
{
- lock.writeLock().lock();
+ LOCK.writeLock().lock();
// delete any intervals intersecting.
if (hiddenColumns != null)
{
}
finally
{
- lock.writeLock().unlock();
+ LOCK.writeLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
int hashCode = 1;
if (hiddenColumns != null)
{
}
finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
{
try
{
- lock.writeLock().lock();
+ LOCK.writeLock().lock();
for (int firstSet = inserts
.nextSetBit(0), lastSet = 0; firstSet >= 0; firstSet = inserts
.nextSetBit(lastSet))
}
} finally
{
- lock.writeLock().unlock();
+ LOCK.writeLock().unlock();
}
}
{
try
{
- lock.readLock().lock();
+ LOCK.readLock().lock();
if (hiddenColumns == null)
{
return;
}
finally
{
- lock.readLock().unlock();
+ LOCK.readLock().unlock();
}
}
- @Override
- public Iterator<int[]> iterator()
+ /**
+ * 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 };
+ }
+
+ for (int[] hiddenCol : hiddenColumns)
+ {
+ lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+ higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+ }
+
+ if (lowestRange[0] == -1 && lowestRange[1] == -1)
+ {
+ startPos = alignmentStartEnd[0];
+ }
+ else
+ {
+ startPos = lowestRange[1] + 1;
+ }
+
+ if (higestRange[0] == -1 && 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)
{
- if (hiddenColumns == null)
+ try
+ {
+ LOCK.readLock().lock();
+ int adjres = adjustForHiddenColumns(res);
+
+ int[] reveal = null;
+ if (hiddenColumns != null)
+ {
+ for (int[] region : hiddenColumns)
+ {
+ if (adjres + 1 == region[0] || adjres - 1 == region[1])
+ {
+ reveal = region;
+ break;
+ }
+ }
+ }
+ return reveal;
+ } finally
{
- return Collections.<int[]> emptyList().iterator();
+ LOCK.readLock().unlock();
}
- return hiddenColumns.iterator();
}
}
git://source.jalview.org / jalview.git / blobdiff