import java.util.ArrayList;
import java.util.BitSet;
-import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.NoSuchElementException;
}
/**
- * 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]
*
}
- /**
- * 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)
- {
- positions = new ArrayList<>(hiddenColumns.size());
- // 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))
- {
- int[] region = hiddenColumns.get(i);
- positions.add(region[0] - hiddenSoFar);
- hiddenSoFar += region[1] - region[0] + 1;
- i++;
- }
- }
- else
- {
- positions = new ArrayList<>();
- }
-
- return positions;
- } finally
- {
- LOCK.readLock().unlock();
- }
- }
/**
* This method returns the rightmost limit of a region of an alignment with
// Simply walk along the sequence whilst watching for hidden column
// boundaries
- List<int[]> regions = getHiddenRegions();
+ Iterator<int[]> regions = iterator();
int spos = fpos;
- int rcount = 0;
int hideStart = seq.getLength();
int hideEnd = -1;
int visPrev = 0;
}
lastP = p;
// update hidden region start/end
- while (hideEnd < p && rcount < regions.size())
+ while (hideEnd < p && regions.hasNext())
{
- int[] region = regions.get(rcount++);
+ int[] region = regions.next();
visPrev = visNext;
visNext += region[0] - visPrev;
hideStart = region[0];
*/
public void makeVisibleAnnotation(AlignmentAnnotation alignmentAnnotation)
{
- makeVisibleAnnotation(-1, -1, alignmentAnnotation);
+ makeVisibleAnnotation(0, alignmentAnnotation.annotations.length,
+ alignmentAnnotation);
}
/**
if (alignmentAnnotation.annotations != null)
{
- if (start == end && end == -1)
- {
- startFrom = 0;
- endAt = alignmentAnnotation.annotations.length;
- }
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
removeHiddenAnnotation(startFrom, endAt, alignmentAnnotation);
private void propagateInsertions(SequenceI profileseq, AlignmentI al,
SequenceI origseq)
{
- 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())
+ try
{
- // 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))
+ 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])
{
- 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;
}
/**
if (hiddenColumns != null)
{
int i = 0;
- for (i = 0; i < hiddenColumns.size(); ++i)
+ for (i = 0; i < hiddenColumns.size()
+ && (current < hiddenColumns.get(i)[0]); ++i)
{
if (current >= hiddenColumns.get(i)[0]
&& current <= hiddenColumns.get(i)[1])
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)
+ for (i = hiddenColumns.size() - 1; i >= 0
+ && (last > hiddenColumns.get(i)[1]); --i)
{
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;
- }
}
// make a local copy of the bit we need
import java.util.Arrays;
import java.util.BitSet;
import java.util.Iterator;
-import java.util.List;
import java.util.Random;
import org.testng.annotations.BeforeClass;
}
@Test(groups = { "Functional" })
- public void testFindHiddenRegionPositions()
- {
- HiddenColumns hc = new HiddenColumns();
-
- List<Integer> positions = hc.findHiddenRegionPositions(0, 20);
- assertTrue(positions.isEmpty());
-
- hc.hideColumns(3, 7);
- hc.hideColumns(10, 10);
- hc.hideColumns(14, 15);
-
- positions = hc.findHiddenRegionPositions(0, 20);
- assertEquals(3, positions.size());
- assertEquals(3, positions.get(0).intValue());
- assertEquals(5, positions.get(1).intValue());
- assertEquals(8, positions.get(2).intValue());
-
- positions = hc.findHiddenRegionPositions(7, 20);
- assertEquals(2, positions.size());
- assertEquals(5, positions.get(0).intValue());
- assertEquals(8, positions.get(1).intValue());
-
- positions = hc.findHiddenRegionPositions(11, 13);
- assertEquals(0, positions.size());
-
- positions = hc.findHiddenRegionPositions(7, 20);
- assertEquals(2, positions.size());
- assertEquals(5, positions.get(0).intValue());
- assertEquals(8, positions.get(1).intValue());
-
- positions = hc.findHiddenRegionPositions(0, 1);
- assertEquals(0, positions.size());
-
- positions = hc.findHiddenRegionPositions(17, 20);
- assertEquals(0, positions.size());
-
- positions = hc.findHiddenRegionPositions(10, 15);
- assertEquals(2, positions.size());
- assertEquals(5, positions.get(0).intValue());
- assertEquals(8, positions.get(1).intValue());
- }
-
- @Test(groups = { "Functional" })
public void testRegionsToString()
{
HiddenColumns hc = new HiddenColumns();
git://source.jalview.org / jalview.git / commitdiff