package jalview.datamodel;
import jalview.util.Comparison;
+import jalview.util.ShiftList;
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
+public class HiddenColumns implements Iterable<int[]>
{
+ private static final ReentrantReadWriteLock lock = new ReentrantReadWriteLock();
+
/*
* list of hidden column [start, end] ranges; the list is maintained in
* ascending start column order
*/
public int getSize()
{
- int size = 0;
- if (hasHidden())
+ try
{
- for (int[] range : hiddenColumns)
+ lock.readLock().lock();
+ int size = 0;
+ if (hasHidden())
{
- size += range[1] - range[0] + 1;
+ for (int[] range : hiddenColumns)
+ {
+ size += range[1] - range[0] + 1;
+ }
}
+ return size;
+ }
+ finally
+ {
+ lock.readLock().unlock();
}
- return size;
}
/**
*/
public boolean hasHidden()
{
- return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
+ try
+ {
+ lock.readLock().lock();
+ return (hiddenColumns != null) && (!hiddenColumns.isEmpty());
+ } finally
+ {
+ lock.readLock().unlock();
+ }
+
}
@Override
public boolean equals(Object obj)
{
- if (!(obj instanceof HiddenColumns))
+ try
{
- return false;
- }
- HiddenColumns that = (HiddenColumns) obj;
+ lock.readLock().lock();
- /*
- * 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;
- }
- int i = 0;
- for (int[] thisRange : hiddenColumns)
- {
- int[] thatRange = that.hiddenColumns.get(i++);
- if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ 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;
}
+ int i = 0;
+ for (int[] thisRange : hiddenColumns)
+ {
+ int[] thatRange = that.hiddenColumns.get(i++);
+ if (thisRange[0] != thatRange[0] || thisRange[1] != thatRange[1])
+ {
+ return false;
+ }
+ }
+ return true;
+ } finally
+ {
+ lock.readLock().unlock();
}
- return true;
}
/**
*/
public int adjustForHiddenColumns(int column)
{
- int result = column;
- if (hiddenColumns != null)
+ try
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ lock.readLock().lock();
+ int result = column;
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.elementAt(i);
- if (result >= region[0])
+ for (int i = 0; i < hiddenColumns.size(); i++)
{
- result += region[1] - region[0] + 1;
+ int[] region = hiddenColumns.elementAt(i);
+ if (result >= region[0])
+ {
+ result += region[1] - region[0] + 1;
+ }
}
}
+ return result;
+ } finally
+ {
+ lock.readLock().unlock();
}
- return result;
}
/**
*/
public int findColumnPosition(int hiddenColumn)
{
- int result = hiddenColumn;
- if (hiddenColumns != null)
+ try
{
- int index = 0;
- int[] region;
- do
+ lock.readLock().lock();
+ int result = hiddenColumn;
+ if (hiddenColumns != null)
{
- region = hiddenColumns.elementAt(index++);
- if (hiddenColumn > region[1])
+ int index = 0;
+ int[] region;
+ do
{
- result -= region[1] + 1 - region[0];
- }
- } while ((hiddenColumn > region[1]) && (index < hiddenColumns.size()));
+ region = hiddenColumns.elementAt(index++);
+ if (hiddenColumn > region[1])
+ {
+ result -= region[1] + 1 - region[0];
+ }
+ } while ((hiddenColumn > region[1])
+ && (index < hiddenColumns.size()));
- if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
- {
- // Here the hidden column is within a region, so
- // we want to return the position of region[0]-1, adjusted for any
- // earlier hidden columns.
- // Calculate the difference between the actual hidden col position
- // and region[0]-1, and then subtract from result to convert result from
- // the adjusted hiddenColumn value to the adjusted region[0]-1 value
-
- // However, if the region begins at 0 we cannot return region[0]-1
- // just return 0
- if (region[0] == 0)
+ if (hiddenColumn >= region[0] && hiddenColumn <= region[1])
{
- return 0;
- }
- else
- {
- return result - (hiddenColumn - region[0] + 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
+
+ // However, if the region begins at 0 we cannot return region[0]-1
+ // just return 0
+ if (region[0] == 0)
+ {
+ return 0;
+ }
+ else
+ {
+ return result - (hiddenColumn - region[0] + 1);
+ }
}
}
+ return result; // return the shifted position after removing hidden
+ // columns.
+ } finally
+ {
+ lock.readLock().unlock();
}
- return result; // return the shifted position after removing hidden columns.
}
/**
*/
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
return nextstart - distance;
}
return start - distance;
+ } finally
+ {
+ lock.readLock().unlock();
+ }
}
/**
- * Use this method to determine where the next hiddenRegion starts
+ * Use this method to determine the set of hiddenRegion start positions
*
- * @param hiddenRegion
- * index of hidden region (counts from 0)
- * @return column number in visible view
+ * @return list of column number in visible view where hidden regions start
*/
- public int findHiddenRegionPosition(int hiddenRegion)
+ public List<Integer> findHiddenRegionPositions()
{
- int result = 0;
- if (hiddenColumns != null)
+ try
{
- int index = 0;
- int gaps = 0;
- do
+ lock.readLock().lock();
+ List<Integer> positions = new ArrayList<>(
+ hiddenColumns.size());
+
+ positions.add(hiddenColumns.elementAt(0)[0]);
+ for (int i = 1; i < hiddenColumns.size(); ++i)
{
- int[] region = hiddenColumns.elementAt(index);
- if (hiddenRegion == 0)
+
+ int result = 0;
+ if (hiddenColumns != null)
{
- return region[0];
- }
+ 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);
- gaps += region[1] + 1 - region[0];
- result = region[1] + 1;
- index++;
- } while (index <= hiddenRegion);
+ result -= gaps;
+ }
+ positions.add(result);
+ }
- result -= gaps;
+ return positions;
+ }
+ finally
+ {
+ lock.readLock().unlock();
}
-
- return result;
}
/**
*/
public int getHiddenBoundaryRight(int alPos)
{
- if (hiddenColumns != null)
+ try
{
- int index = 0;
- do
+ lock.readLock().lock();
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.elementAt(index);
- if (alPos < region[0])
+ int index = 0;
+ do
{
- return region[0];
- }
+ int[] region = hiddenColumns.elementAt(index);
+ if (alPos < region[0])
+ {
+ return region[0];
+ }
- index++;
- } while (index < hiddenColumns.size());
- }
+ index++;
+ } while (index < hiddenColumns.size());
+ }
- return alPos;
+ return alPos;
+ } finally
+ {
+ lock.readLock().unlock();
+ }
}
*/
public int getHiddenBoundaryLeft(int alPos)
{
+ try
+ {
+ lock.readLock().lock();
+
if (hiddenColumns != null)
{
int index = hiddenColumns.size() - 1;
}
return alPos;
-
+ } finally
+ {
+ lock.readLock().unlock();
+ }
}
/**
*/
private int getHiddenIndexLeft(int pos)
{
+ try
+ {
+
+ lock.readLock().lock();
if (hiddenColumns != null)
{
int index = hiddenColumns.size() - 1;
}
return -1;
+ } finally
+ {
+ lock.readLock().unlock();
+ }
}
*/
public void hideColumns(int start, int end)
{
+ hideColumns(start, end, false);
+ }
+
+ /**
+ * Adds the specified column range to the hidden columns
+ *
+ * @param start
+ * @param end
+ */
+ private void hideColumns(int start, int end, boolean alreadyLocked)
+ {
+ try
+ {
+
+ if (!alreadyLocked)
+ {
+ lock.writeLock().lock();
+ }
+
if (hiddenColumns == null)
{
- hiddenColumns = new Vector<int[]>();
+ hiddenColumns = new Vector<>();
}
/*
* remaining case is that the new range follows everything else
*/
hiddenColumns.addElement(new int[] { start, end });
+ } finally
+ {
+ if (!alreadyLocked)
+ {
+ lock.writeLock().unlock();
+ }
+ }
}
public boolean isVisible(int column)
{
+ try
+ {
+ lock.readLock().lock();
+
if (hiddenColumns != null)
{
for (int[] region : hiddenColumns)
}
return true;
+ } finally
+ {
+ lock.readLock().unlock();
+ }
}
/**
*/
public HiddenColumns(HiddenColumns copy)
{
- if (copy != null)
+ try
{
- if (copy.hiddenColumns != null)
+
+ lock.readLock().lock();
+ if (copy != null)
{
- hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
- for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
+ if (copy.hiddenColumns != null)
{
- int[] rh, cp;
- rh = copy.hiddenColumns.elementAt(i);
- if (rh != null)
- {
- cp = new int[rh.length];
- System.arraycopy(rh, 0, cp, 0, rh.length);
- hiddenColumns.addElement(cp);
- }
+ hiddenColumns = copy.copyHiddenRegions();
}
}
}
+ finally
+ {
+ lock.readLock().unlock();
+ }
+ }
+
+ private Vector<int[]> copyHiddenRegions()
+ {
+ Vector<int[]> copy = new Vector<>(hiddenColumns.size());
+ for (int i = 0, j = hiddenColumns.size(); i < j; i++)
+ {
+ int[] rh, cp;
+ rh = hiddenColumns.elementAt(i);
+ if (rh != null)
+ {
+ cp = new int[rh.length];
+ System.arraycopy(rh, 0, cp, 0, rh.length);
+ copy.addElement(cp);
+ }
+ }
+ return copy;
+ }
+
+ private ArrayList<int[]> copyHiddenRegionsToArrayList()
+ {
+ ArrayList<int[]> copy = new ArrayList<>(hiddenColumns.size());
+ for (int i = 0, j = hiddenColumns.size(); i < j; i++)
+ {
+ int[] rh, cp;
+ rh = hiddenColumns.elementAt(i);
+ if (rh != null)
+ {
+ cp = new int[rh.length];
+ System.arraycopy(rh, 0, cp, 0, rh.length);
+ copy.add(cp);
+ }
+ }
+ return copy;
+ }
+
+ public void getHiddenColumnsCopy(Vector<int[]> copy)
+ {
+ try
+ {
+ lock.readLock().lock();
+ copy = copyHiddenRegions();
+ } finally
+ {
+ lock.readLock().unlock();
+ }
+ }
+
+ public void getHiddenColumnsCopy(ArrayList<int[]> copy)
+ {
+ try
+ {
+ lock.readLock().lock();
+ copy = copyHiddenRegionsToArrayList();
+ } finally
+ {
+ lock.readLock().unlock();
+ }
}
/**
public List<int[]> compensateForEdit(int start, int change,
ColumnSelection sel)
{
- List<int[]> deletedHiddenColumns = null;
-
- if (hiddenColumns != null)
+ try
{
- deletedHiddenColumns = new ArrayList<int[]>();
- int hSize = hiddenColumns.size();
- for (int i = 0; i < hSize; i++)
+ lock.writeLock().lock();
+ List<int[]> deletedHiddenColumns = null;
+
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.elementAt(i);
- if (region[0] > start && start + change > region[1])
+ deletedHiddenColumns = new ArrayList<>();
+ int hSize = hiddenColumns.size();
+ for (int i = 0; i < hSize; i++)
{
- deletedHiddenColumns.add(region);
+ int[] region = hiddenColumns.elementAt(i);
+ if (region[0] > start && start + change > region[1])
+ {
+ deletedHiddenColumns.add(region);
- hiddenColumns.removeElementAt(i);
- i--;
- hSize--;
- continue;
- }
+ hiddenColumns.removeElementAt(i);
+ i--;
+ hSize--;
+ continue;
+ }
- if (region[0] > start)
- {
- region[0] -= change;
- region[1] -= change;
- }
+ if (region[0] > start)
+ {
+ region[0] -= change;
+ region[1] -= change;
+ }
+
+ if (region[0] < 0)
+ {
+ region[0] = 0;
+ }
- if (region[0] < 0)
- {
- region[0] = 0;
}
+ this.revealHiddenColumns(0, sel);
}
- this.revealHiddenColumns(0, sel);
+ return deletedHiddenColumns;
+ } finally
+ {
+ lock.writeLock().unlock();
}
-
- return deletedHiddenColumns;
}
/**
*/
public void compensateForDelEdits(int start, int change)
{
- if (hiddenColumns != null)
+ try
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ lock.writeLock().lock();
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.elementAt(i);
- if (region[0] >= start)
- {
- region[0] -= change;
- }
- if (region[1] >= start)
+ for (int i = 0; i < hiddenColumns.size(); i++)
{
- region[1] -= change;
- }
- if (region[1] < region[0])
- {
- hiddenColumns.removeElementAt(i--);
- }
+ int[] region = hiddenColumns.elementAt(i);
+ if (region[0] >= start)
+ {
+ region[0] -= change;
+ }
+ if (region[1] >= start)
+ {
+ region[1] -= change;
+ }
+ if (region[1] < region[0])
+ {
+ hiddenColumns.removeElementAt(i--);
+ }
- if (region[0] < 0)
- {
- region[0] = 0;
- }
- if (region[1] < 0)
- {
- region[1] = 0;
+ if (region[0] < 0)
+ {
+ region[0] = 0;
+ }
+ if (region[1] < 0)
+ {
+ region[1] = 0;
+ }
}
}
}
+ finally
+ {
+ lock.writeLock().unlock();
+ }
}
/**
*/
public int[] getVisibleContigs(int start, int end)
{
- if (hiddenColumns != null && hiddenColumns.size() > 0)
+ try
{
- List<int[]> visiblecontigs = new ArrayList<int[]>();
- List<int[]> regions = getHiddenRegions();
+ lock.readLock().lock();
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
+ {
+ List<int[]> visiblecontigs = new ArrayList<>();
+ List<int[]> regions = getHiddenRegions();
- int vstart = start;
- int[] region;
- int hideStart, hideEnd;
+ int vstart = start;
+ int[] region;
+ int hideStart, hideEnd;
- for (int j = 0; vstart < end && j < regions.size(); j++)
- {
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
+ for (int j = 0; vstart < end && j < regions.size(); j++)
+ {
+ region = regions.get(j);
+ hideStart = region[0];
+ hideEnd = region[1];
+
+ if (hideEnd < vstart)
+ {
+ continue;
+ }
+ if (hideStart > vstart)
+ {
+ visiblecontigs.add(new int[] { vstart, hideStart - 1 });
+ }
+ vstart = hideEnd + 1;
+ }
- if (hideEnd < vstart)
+ if (vstart < end)
{
- continue;
+ visiblecontigs.add(new int[] { vstart, end - 1 });
}
- if (hideStart > vstart)
+ int[] vcontigs = new int[visiblecontigs.size() * 2];
+ for (int i = 0, j = visiblecontigs.size(); i < j; i++)
{
- visiblecontigs.add(new int[] { vstart, hideStart - 1 });
+ int[] vc = visiblecontigs.get(i);
+ visiblecontigs.set(i, null);
+ vcontigs[i * 2] = vc[0];
+ vcontigs[i * 2 + 1] = vc[1];
}
- vstart = hideEnd + 1;
+ visiblecontigs.clear();
+ return vcontigs;
}
-
- if (vstart < end)
- {
- visiblecontigs.add(new int[] { vstart, end - 1 });
- }
- int[] vcontigs = new int[visiblecontigs.size() * 2];
- for (int i = 0, j = visiblecontigs.size(); i < j; i++)
+ else
{
- int[] vc = visiblecontigs.get(i);
- visiblecontigs.set(i, null);
- vcontigs[i * 2] = vc[0];
- vcontigs[i * 2 + 1] = vc[1];
+ return new int[] { start, end - 1 };
}
- visiblecontigs.clear();
- return vcontigs;
}
- else
+ finally
{
- return new int[] { start, end - 1 };
+ lock.readLock().unlock();
}
}
public String[] getVisibleSequenceStrings(int start, int end,
SequenceI[] seqs)
{
- int i, iSize = seqs.length;
- String selections[] = new String[iSize];
- if (hiddenColumns != null && hiddenColumns.size() > 0)
+ try
{
- for (i = 0; i < iSize; i++)
+ lock.readLock().lock();
+ int i, iSize = seqs.length;
+ String selections[] = new String[iSize];
+ if (hiddenColumns != null && hiddenColumns.size() > 0)
{
- StringBuffer visibleSeq = new StringBuffer();
- List<int[]> regions = getHiddenRegions();
-
- int blockStart = start, blockEnd = end;
- int[] region;
- int hideStart, hideEnd;
-
- for (int j = 0; j < regions.size(); j++)
+ for (i = 0; i < iSize; i++)
{
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
+ StringBuffer visibleSeq = new StringBuffer();
+ List<int[]> regions = getHiddenRegions();
- if (hideStart < start)
+ int blockStart = start, blockEnd = end;
+ int[] region;
+ int hideStart, hideEnd;
+
+ for (int j = 0; j < regions.size(); j++)
{
- continue;
- }
+ region = regions.get(j);
+ hideStart = region[0];
+ hideEnd = region[1];
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
+ if (hideStart < start)
+ {
+ continue;
+ }
- if (blockStart > blockEnd)
- {
- break;
+ blockStart = Math.min(blockStart, hideEnd + 1);
+ blockEnd = Math.min(blockEnd, hideStart);
+
+ if (blockStart > blockEnd)
+ {
+ break;
+ }
+
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+ blockStart = hideEnd + 1;
+ blockEnd = end;
}
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+ if (end > blockStart)
+ {
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));
+ }
- blockStart = hideEnd + 1;
- blockEnd = end;
+ selections[i] = visibleSeq.toString();
}
-
- if (end > blockStart)
+ }
+ else
+ {
+ for (i = 0; i < iSize; i++)
{
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
+ selections[i] = seqs[i].getSequenceAsString(start, end);
}
-
- selections[i] = visibleSeq.toString();
}
+
+ return selections;
}
- else
+ finally
{
- for (i = 0; i < iSize; i++)
- {
- selections[i] = seqs[i].getSequenceAsString(start, end);
- }
+ lock.readLock().unlock();
}
-
- return selections;
}
/**
*/
public int[] locateVisibleBoundsOfSequence(SequenceI seq)
{
- int fpos = seq.getStart(), lpos = seq.getEnd();
- int start = 0;
-
- if (hiddenColumns == null || hiddenColumns.size() == 0)
+ try
{
- int ifpos = seq.findIndex(fpos) - 1, ilpos = seq.findIndex(lpos) - 1;
- return new int[] { ifpos, ilpos, fpos, lpos, ifpos, ilpos };
- }
+ lock.readLock().lock();
+ int fpos = seq.getStart(), lpos = seq.getEnd();
+ int start = 0;
- // 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;
- boolean foundStart = false;
- for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
- && p < pLen; p++)
- {
- if (!Comparison.isGap(seq.getCharAt(p)))
+ if (hiddenColumns == null || hiddenColumns.size() == 0)
{
- // 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)
+ int ifpos = seq.findIndex(fpos) - 1,
+ 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;
+ boolean foundStart = false;
+ for (int p = 0, pLen = seq.getLength(); spos <= seq.getEnd()
+ && p < pLen; p++)
+ {
+ if (!Comparison.isGap(seq.getCharAt(p)))
{
- if (!foundStart)
+ // 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())
{
- fpos = spos;
- start = p;
- foundStart = true;
+ int[] region = regions.get(rcount++);
+ visPrev = visNext;
+ visNext += region[0] - visPrev;
+ hideStart = region[0];
+ hideEnd = region[1];
}
- lastvispos = p;
- lpos = spos;
+ if (hideEnd < p)
+ {
+ hideStart = seq.getLength();
+ }
+ // update visible boundary for sequence
+ if (p < hideStart)
+ {
+ if (!foundStart)
+ {
+ fpos = spos;
+ start = p;
+ foundStart = true;
+ }
+ lastvispos = p;
+ lpos = spos;
+ }
+ // look for next sequence position
+ spos++;
}
- // look for next sequence position
- spos++;
}
+ if (foundStart)
+ {
+ return new int[] { findColumnPosition(start),
+ findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+ }
+ // otherwise, sequence was completely hidden
+ return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
}
- if (foundStart)
+ finally
{
- return new int[] { findColumnPosition(start),
- findColumnPosition(lastvispos), fpos, lpos, firstP, lastP };
+ lock.readLock().unlock();
}
- // otherwise, sequence was completely hidden
- return new int[] { visPrev, visNext, 0, 0, firstP, lastP };
}
/**
public void makeVisibleAnnotation(int start, int end,
AlignmentAnnotation alignmentAnnotation)
{
- if (alignmentAnnotation.annotations == null)
- {
- return;
- }
- if (start == end && end == -1)
- {
- start = 0;
- end = alignmentAnnotation.annotations.length;
- }
- if (hiddenColumns != null && hiddenColumns.size() > 0)
+ try
{
- // then mangle the alignmentAnnotation annotation array
- Vector<Annotation[]> annels = new Vector<Annotation[]>();
- Annotation[] els = null;
- List<int[]> regions = getHiddenRegions();
- int blockStart = start, blockEnd = end;
- int[] region;
- int hideStart, hideEnd, w = 0;
-
- for (int j = 0; j < regions.size(); j++)
+ 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)
{
- region = regions.get(j);
- hideStart = region[0];
- hideEnd = region[1];
+ // then mangle the alignmentAnnotation annotation array
+ Vector<Annotation[]> annels = new Vector<>();
+ Annotation[] els = null;
+ List<int[]> regions = getHiddenRegions();
+ int blockStart = start, blockEnd = end;
+ int[] region;
+ int hideStart, hideEnd, w = 0;
- if (hideStart < start)
+ for (int j = 0; j < regions.size(); j++)
{
- continue;
- }
+ region = regions.get(j);
+ hideStart = region[0];
+ hideEnd = region[1];
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
+ if (hideStart < start)
+ {
+ continue;
+ }
- if (blockStart > blockEnd)
- {
- break;
- }
+ blockStart = Math.min(blockStart, hideEnd + 1);
+ blockEnd = Math.min(blockEnd, hideStart);
- annels.addElement(els = new Annotation[blockEnd - blockStart]);
- System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
- 0, els.length);
- w += els.length;
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
+ if (blockStart > blockEnd)
+ {
+ break;
+ }
- if (end > blockStart)
- {
- annels.addElement(els = new Annotation[end - blockStart + 1]);
- if ((els.length + blockStart) <= alignmentAnnotation.annotations.length)
+ annels.addElement(els = new Annotation[blockEnd - blockStart]);
+ System.arraycopy(alignmentAnnotation.annotations, blockStart, els,
+ 0, els.length);
+ w += els.length;
+ blockStart = hideEnd + 1;
+ blockEnd = end;
+ }
+
+ if (end > blockStart)
{
- // copy just the visible segment of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0, els.length);
+ annels.addElement(els = new Annotation[end - blockStart + 1]);
+ if ((els.length
+ + blockStart) <= alignmentAnnotation.annotations.length)
+ {
+ // copy just the visible segment of the annotation row
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,
+ els, 0, els.length);
+ }
+ else
+ {
+ // copy to the end of the annotation row
+ System.arraycopy(alignmentAnnotation.annotations, blockStart,
+ els, 0,
+ (alignmentAnnotation.annotations.length - blockStart));
+ }
+ w += els.length;
}
- else
+ if (w == 0)
{
- // copy to the end of the annotation row
- System.arraycopy(alignmentAnnotation.annotations, blockStart,
- els, 0,
- (alignmentAnnotation.annotations.length - blockStart));
+ return;
}
- w += els.length;
- }
- if (w == 0)
- {
- return;
- }
- alignmentAnnotation.annotations = new Annotation[w];
- w = 0;
+ alignmentAnnotation.annotations = new Annotation[w];
+ w = 0;
- for (Annotation[] chnk : annels)
+ for (Annotation[] chnk : annels)
+ {
+ System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
+ chnk.length);
+ w += chnk.length;
+ }
+ }
+ else
{
- System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
- chnk.length);
- w += chnk.length;
+ alignmentAnnotation.restrict(start, end);
}
}
- else
+ finally
{
- alignmentAnnotation.restrict(start, end);
+ lock.readLock().unlock();
}
}
*/
public boolean hasHiddenColumns()
{
- return hiddenColumns != null && hiddenColumns.size() > 0;
+ try
+ {
+ lock.readLock().lock();
+ return hiddenColumns != null && hiddenColumns.size() > 0;
+ } finally
+ {
+ lock.readLock().unlock();
+ }
}
/**
*/
public boolean hasManyHiddenColumns()
{
- return hiddenColumns != null && hiddenColumns.size() > 1;
+ try
+ {
+ lock.readLock().lock();
+ return hiddenColumns != null && hiddenColumns.size() > 1;
+ } finally
+ {
+ lock.readLock().unlock();
+ }
}
/**
*/
public void hideInsertionsFor(SequenceI sr)
{
- List<int[]> inserts = sr.getInsertions();
- for (int[] r : inserts)
+ try
+ {
+ lock.writeLock().lock();
+ List<int[]> inserts = sr.getInsertions();
+ for (int[] r : inserts)
+ {
+ hideColumns(r[0], r[1], true);
+ }
+ } finally
{
- hideColumns(r[0], r[1]);
+ lock.writeLock().unlock();
}
}
*/
public void revealAllHiddenColumns(ColumnSelection sel)
{
- if (hiddenColumns != null)
+ try
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ lock.writeLock().lock();
+ if (hiddenColumns != null)
{
- int[] region = hiddenColumns.elementAt(i);
- for (int j = region[0]; j < region[1] + 1; j++)
+ for (int i = 0; i < hiddenColumns.size(); i++)
{
- sel.addElement(j);
+ int[] region = hiddenColumns.elementAt(i);
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
}
}
- }
- hiddenColumns = null;
+ hiddenColumns = null;
+ }
+ finally
+ {
+ lock.writeLock().unlock();
+ }
}
/**
*/
public void revealHiddenColumns(int start, ColumnSelection sel)
{
- for (int i = 0; i < hiddenColumns.size(); i++)
+ try
{
- int[] region = hiddenColumns.elementAt(i);
- if (start == region[0])
+ lock.writeLock().lock();
+ for (int i = 0; i < hiddenColumns.size(); i++)
{
- for (int j = region[0]; j < region[1] + 1; j++)
+ int[] region = hiddenColumns.elementAt(i);
+ if (start == region[0])
{
- sel.addElement(j);
- }
+ for (int j = region[0]; j < region[1] + 1; j++)
+ {
+ sel.addElement(j);
+ }
- hiddenColumns.removeElement(region);
- break;
+ hiddenColumns.removeElement(region);
+ break;
+ }
+ }
+ if (hiddenColumns.size() == 0)
+ {
+ hiddenColumns = null;
}
}
- if (hiddenColumns.size() == 0)
+ finally
{
- hiddenColumns = null;
+ lock.writeLock().unlock();
}
}
*/
public void pruneDeletions(List<int[]> shifts)
{
- // delete any intervals intersecting.
- if (hiddenColumns != null)
+ try
{
- pruneIntervalVector(shifts, hiddenColumns);
- if (hiddenColumns != null && hiddenColumns.size() == 0)
+ lock.writeLock().lock();
+ // delete any intervals intersecting.
+ if (hiddenColumns != null)
{
- hiddenColumns = null;
+ pruneIntervalVector(shifts, hiddenColumns);
+ if (hiddenColumns != null && hiddenColumns.size() == 0)
+ {
+ hiddenColumns = null;
+ }
}
}
+ finally
+ {
+ lock.writeLock().unlock();
+ }
}
/**
- * Returns a hashCode built from selected columns and hidden column ranges
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * @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 int hashCode(int hc)
+ public static HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentI al, AlignmentView input)
{
- int hashCode = hc;
- if (hiddenColumns != null)
+ 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)
+ {
+ char gc = al.getGapCharacter();
+ // recover mapping between sequence's non-gap positions and positions
+ // mapping to view.
+ pruneDeletions(ShiftList.parseMap(origseq.gapMap()));
+ int[] viscontigs = al.getHiddenColumns().getVisibleContigs(0,
+ profileseq.getLength());
+ int spos = 0;
+ int offset = 0;
+
+ // add profile to visible contigs
+ for (int v = 0; v < viscontigs.length; v += 2)
+ {
+ if (viscontigs[v] > spos)
+ {
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = viscontigs[v] - spos; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ 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() <= spos + offset)
+ {
+ // pad sequence
+ int diff = spos + offset - sq.length() - 1;
+ if (diff > 0)
+ {
+ // pad gaps
+ sq = sq + sb;
+ while ((diff = spos + offset - sq.length() - 1) > 0)
+ {
+ // sq = sq
+ // + ((diff >= sb.length()) ? sb.toString() : sb
+ // .substring(0, diff));
+ 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, spos + offset) + sb.toString()
+ + sq.substring(spos + offset));
+ }
+ }
+ }
+ // offset+=sb.length();
+ }
+ spos = viscontigs[v + 1] + 1;
+ }
+ if ((offset + spos) < profileseq.getLength())
+ {
+ // pad the final region with gaps.
+ StringBuffer sb = new StringBuffer();
+ for (int s = 0, ns = profileseq.getLength() - spos - offset; s < ns; s++)
+ {
+ sb.append(gc);
+ }
+ for (int s = 0, ns = al.getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = al.getSequenceAt(s);
+ if (sqobj == profileseq)
+ {
+ continue;
+ }
+ String sq = sqobj.getSequenceAsString();
+ // pad sequence
+ int diff = origseq.getLength() - sq.length();
+ while (diff > 0)
+ {
+ // sq = sq
+ // + ((diff >= sb.length()) ? sb.toString() : sb
+ // .substring(0, diff));
+ if (diff >= sb.length())
+ {
+ sq += sb.toString();
+ }
+ else
+ {
+ char[] buf = new char[diff];
+ sb.getChars(0, diff, buf, 0);
+ sq += buf.toString();
+ }
+ diff = origseq.getLength() - sq.length();
+ }
+ }
+ }
+ }
+
+ /**
+ * remove any hiddenColumns or selected columns and shift remaining based on a
+ * series of position, range deletions.
+ *
+ * @param deletions
+ */
+ private void pruneDeletions(ShiftList deletions)
+ {
+ if (deletions != null)
+ {
+ final List<int[]> shifts = deletions.getShifts();
+ if (shifts != null && shifts.size() > 0)
+ {
+ pruneDeletions(shifts);
+
+ // and shift the rest.
+ this.compensateForEdits(deletions);
+ }
+ }
+ }
+
+ /**
+ * Adjust hidden column boundaries based on a series of column additions or
+ * deletions in visible regions.
+ *
+ * @param shiftrecord
+ * @return
+ */
+ private ShiftList compensateForEdits(ShiftList shiftrecord)
+ {
+ if (shiftrecord != null)
{
- for (int[] hidden : hiddenColumns)
+ final List<int[]> shifts = shiftrecord.getShifts();
+ if (shifts != null && shifts.size() > 0)
{
- hashCode = 31 * hashCode + hidden[0];
- hashCode = 31 * hashCode + hidden[1];
+ int shifted = 0;
+ for (int i = 0, j = shifts.size(); i < j; i++)
+ {
+ int[] sh = shifts.get(i);
+ compensateForDelEdits(shifted + sh[0], sh[1]);
+ shifted -= sh[1];
+ }
}
+ return shiftrecord.getInverse();
+ }
+ return null;
+ }
+
+ /**
+ * Returns a hashCode built from hidden column ranges
+ */
+ @Override
+ public int hashCode()
+ {
+ try
+ {
+ lock.readLock().lock();
+ int hashCode = 1;
+ if (hiddenColumns != null)
+ {
+ for (int[] hidden : hiddenColumns)
+ {
+ hashCode = 31 * hashCode + hidden[0];
+ hashCode = 31 * 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, true);
+ }
+ } 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;
+ }
+ for (int[] range : hiddenColumns)
+ {
+ inserts.set(range[0], range[1] + 1);
+ }
+ }
+ finally
+ {
+ lock.readLock().unlock();
+ }
+ }
+
+ @Override
+ public Iterator<int[]> iterator()
+ {
+ if (hiddenColumns == null)
+ {
+ return Collections.<int[]> emptyList().iterator();
}
- return hashCode;
+ return hiddenColumns.iterator();
}
}
git://source.jalview.org / jalview.git / blobdiff