import jalview.util.MessageManager;
import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
cs.hideList(repseq.getInsertions());
setHiddenColumns(cs);
}
+
+ @Override
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ char gc = getGapCharacter();
+ Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+ HiddenColumns nview = (HiddenColumns) alandhidden[1];
+ SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+ return propagateInsertions(profileseq, origseq, 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 HiddenColumns propagateInsertions(SequenceI profileseq,
+ SequenceI origseq, HiddenColumns hc)
+ {
+ // 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
+ // then calculate hidden ^ not(gap)
+ BitSet gaps = origseq.gapBitset();
+ hc.andNot(gaps);
+
+ // 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
+ HiddenColumns newhidden = new HiddenColumns();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ Iterator<int[]> it = hc.iterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+
+ // get region coordinates accounting for gaps
+ // we can rely on gaps not being *in* hidden regions because we already
+ // removed those
+ while (gapPosition < region[0])
+ {
+ gapPosition++;
+ if (gaps.get(gapPosition))
+ {
+ numGapsBefore++;
+ }
+ }
+
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+
+ newhidden.hideColumns(left, right);
+ padGaps(left, right, profileseq);
+ }
+ return newhidden;
+ }
+
+ /**
+ * Pad gaps in all sequences in alignment except profileseq
+ *
+ * @param left
+ * position of first gap to insert
+ * @param right
+ * position of last gap to insert
+ * @param profileseq
+ * sequence not to pad
+ */
+ private void padGaps(int left, int right, SequenceI profileseq)
+ {
+ char gc = getGapCharacter();
+
+ // make a string with number of gaps = length of hidden region
+ StringBuilder sb = new StringBuilder();
+ for (int g = 0; g < right - left + 1; g++)
+ {
+ sb.append(gc);
+ }
+
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = getSequenceAt(s);
+ if ((sqobj != profileseq) && (sqobj.getLength() >= left))
+ {
+ String sq = sqobj.getSequenceAsString();
+ sqobj.setSequence(
+ sq.substring(0, left) + sb.toString() + sq.substring(left));
+ }
+ }
+ }
+
}
*/
public void setupJPredAlignment();
+ /**
+ * Add gaps into the sequences aligned to profileseq under the given
+ * AlignmentView
+ *
+ * @param profileseq
+ * sequence in al which sequences are aligned to
+ * @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 HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input);
+
}
*/
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;
- }
+ LOCK.writeLock().lock();
int previndex = 0;
int prevHiddenCount = 0;
} finally
{
- if (!wasAlreadyLocked)
- {
- LOCK.writeLock().unlock();
- }
+ 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 non-gaps as a Bitset
- // then calculate hidden ^ not(gap)
- BitSet gaps = origseq.gapBitset();
- this.andNot(gaps);
-
- // 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
- List<int[]> newhidden = new ArrayList<>();
-
- int numGapsBefore = 0;
- int gapPosition = 0;
- for (int[] region : hiddenColumns)
- {
- // get region coordinates accounting for gaps
- // we can rely on gaps not being *in* hidden regions because we already
- // removed those
- 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
- StringBuilder sb = new StringBuilder();
- 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(StringBuilder 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.
/**
*
- * @param inserts
+ * @param updates
* BitSet where hidden columns will be marked
*/
- private void andNot(BitSet updates)
+ protected void andNot(BitSet updates)
{
try
{
- LOCK.readLock().lock();
+ LOCK.writeLock().lock();
BitSet hiddenBitSet = new BitSet();
for (int[] range : hiddenColumns)
hideColumns(hiddenBitSet);
} finally
{
- LOCK.readLock().unlock();
+ LOCK.writeLock().unlock();
}
}
{
// Adjust input view for gaps
// propagate insertions into profile
- alhidden = HiddenColumns.propagateInsertions(profileseq, al,
- input);
+ alhidden = al.propagateInsertions(profileseq, input);
}
}
}
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
+import jalview.util.Comparison;
import jalview.util.MapList;
import java.io.IOException;
// todo test coverage for annotations, mappings, groups,
// hidden sequences, properties
}
+
+ @Test(groups = "Functional")
+ public void testPropagateInsertions()
+ {
+ // create an alignment with no gaps - this will be the profile seq and other
+ // JPRED seqs
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
+
+ // get the profileseq
+ SequenceI profileseq = al.getSequenceAt(0);
+ SequenceI gappedseq = new Sequence(profileseq);
+ gappedseq.insertCharAt(5, al.getGapCharacter());
+ gappedseq.insertCharAt(6, al.getGapCharacter());
+ gappedseq.insertCharAt(7, al.getGapCharacter());
+ gappedseq.insertCharAt(8, al.getGapCharacter());
+
+ // force different kinds of padding
+ al.getSequenceAt(3).deleteChars(2, 23);
+ al.getSequenceAt(4).deleteChars(2, 27);
+ al.getSequenceAt(5).deleteChars(10, 27);
+
+ // create an alignment view with the gapped sequence
+ SequenceI[] seqs = new SequenceI[1];
+ seqs[0] = gappedseq;
+ AlignmentI newal = new Alignment(seqs);
+ HiddenColumns hidden = new HiddenColumns();
+ hidden.hideColumns(15, 17);
+
+ AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+ false);
+
+ // confirm that original contigs are as expected
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
+ int[] region = visible.next();
+ assertEquals("[0, 14]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[18, 24]", Arrays.toString(region));
+
+ // propagate insertions
+ HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+ // confirm that the contigs have changed to account for the gaps
+ visible = result.getVisContigsIterator(0, 25, false);
+ region = visible.next();
+ assertEquals("[0, 10]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[14, 24]", Arrays.toString(region));
+
+ // confirm the alignment has been changed so that the other sequences have
+ // gaps inserted where the columns are hidden
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
+
+ }
+
+ @Test(groups = "Functional")
+ public void testPropagateInsertionsOverlap()
+ {
+ // test propagateInsertions where gaps and hiddenColumns overlap
+
+ // create an alignment with no gaps - this will be the profile seq and other
+ // JPRED seqs
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
+
+ // get the profileseq
+ SequenceI profileseq = al.getSequenceAt(0);
+ SequenceI gappedseq = new Sequence(profileseq);
+ gappedseq.insertCharAt(5, al.getGapCharacter());
+ gappedseq.insertCharAt(6, al.getGapCharacter());
+ gappedseq.insertCharAt(7, al.getGapCharacter());
+ gappedseq.insertCharAt(8, al.getGapCharacter());
+
+ // create an alignment view with the gapped sequence
+ SequenceI[] seqs = new SequenceI[1];
+ seqs[0] = gappedseq;
+ AlignmentI newal = new Alignment(seqs);
+
+ // hide columns so that some overlap with the gaps
+ HiddenColumns hidden = new HiddenColumns();
+ hidden.hideColumns(7, 10);
+
+ AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
+ false);
+
+ // confirm that original contigs are as expected
+ Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
+ int[] region = visible.next();
+ assertEquals("[0, 6]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[11, 19]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // propagate insertions
+ HiddenColumns result = al.propagateInsertions(profileseq, view);
+
+ // confirm that the contigs have changed to account for the gaps
+ visible = result.getVisContigsIterator(0, 20, false);
+ region = visible.next();
+ assertEquals("[0, 4]", Arrays.toString(region));
+ region = visible.next();
+ assertEquals("[7, 19]", Arrays.toString(region));
+ assertFalse(visible.hasNext());
+
+ // confirm the alignment has been changed so that the other sequences have
+ // gaps inserted where the columns are hidden
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
+ assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
+ assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
+ }
}
import static org.testng.AssertJUnit.assertTrue;
import jalview.analysis.AlignmentGenerator;
-import jalview.util.Comparison;
import java.util.Arrays;
import java.util.BitSet;
}
@Test(groups = "Functional")
- public void testPropagateInsertions()
- {
- // create an alignment with no gaps - this will be the profile seq and other
- // JPRED seqs
- AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(25, 10, 1234, 0, 0);
-
- // get the profileseq
- SequenceI profileseq = al.getSequenceAt(0);
- SequenceI gappedseq = new Sequence(profileseq);
- gappedseq.insertCharAt(5, al.getGapCharacter());
- gappedseq.insertCharAt(6, al.getGapCharacter());
- gappedseq.insertCharAt(7, al.getGapCharacter());
- gappedseq.insertCharAt(8, al.getGapCharacter());
-
- // force different kinds of padding
- al.getSequenceAt(3).deleteChars(2, 23);
- al.getSequenceAt(4).deleteChars(2, 27);
- al.getSequenceAt(5).deleteChars(10, 27);
-
- // create an alignment view with the gapped sequence
- SequenceI[] seqs = new SequenceI[1];
- seqs[0] = gappedseq;
- AlignmentI newal = new Alignment(seqs);
- HiddenColumns hidden = new HiddenColumns();
- hidden.hideColumns(15, 17);
-
- AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
- false);
-
- // confirm that original contigs are as expected
- Iterator<int[]> visible = hidden.getVisContigsIterator(0, 25, false);
- int[] region = visible.next();
- assertEquals("[0, 14]", Arrays.toString(region));
- region = visible.next();
- assertEquals("[18, 24]", Arrays.toString(region));
-
- // propagate insertions
- HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
- view);
-
- // confirm that the contigs have changed to account for the gaps
- visible = result.getVisContigsIterator(0, 25, false);
- region = visible.next();
- assertEquals("[0, 10]", Arrays.toString(region));
- region = visible.next();
- assertEquals("[14, 24]", Arrays.toString(region));
-
- // confirm the alignment has been changed so that the other sequences have
- // gaps inserted where the columns are hidden
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[10]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[11]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[12]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[13]));
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[14]));
-
- }
-
- @Test(groups = "Functional")
- public void testPropagateInsertionsOverlap()
- {
- // test propagateInsertions where gaps and hiddenColumns overlap
-
- // create an alignment with no gaps - this will be the profile seq and other
- // JPRED seqs
- AlignmentGenerator gen = new AlignmentGenerator(false);
- AlignmentI al = gen.generate(20, 10, 1234, 0, 0);
-
- // get the profileseq
- SequenceI profileseq = al.getSequenceAt(0);
- SequenceI gappedseq = new Sequence(profileseq);
- gappedseq.insertCharAt(5, al.getGapCharacter());
- gappedseq.insertCharAt(6, al.getGapCharacter());
- gappedseq.insertCharAt(7, al.getGapCharacter());
- gappedseq.insertCharAt(8, al.getGapCharacter());
-
- // create an alignment view with the gapped sequence
- SequenceI[] seqs = new SequenceI[1];
- seqs[0] = gappedseq;
- AlignmentI newal = new Alignment(seqs);
-
- // hide columns so that some overlap with the gaps
- HiddenColumns hidden = new HiddenColumns();
- hidden.hideColumns(7, 10);
-
- AlignmentView view = new AlignmentView(newal, hidden, null, true, false,
- false);
-
- // confirm that original contigs are as expected
- Iterator<int[]> visible = hidden.getVisContigsIterator(0, 20, false);
- int[] region = visible.next();
- assertEquals("[0, 6]", Arrays.toString(region));
- region = visible.next();
- assertEquals("[11, 19]", Arrays.toString(region));
- assertFalse(visible.hasNext());
-
- // propagate insertions
- HiddenColumns result = HiddenColumns.propagateInsertions(profileseq, al,
- view);
-
- // confirm that the contigs have changed to account for the gaps
- visible = result.getVisContigsIterator(0, 20, false);
- region = visible.next();
- assertEquals("[0, 4]", Arrays.toString(region));
- region = visible.next();
- assertEquals("[7, 19]", Arrays.toString(region));
- assertFalse(visible.hasNext());
-
- // confirm the alignment has been changed so that the other sequences have
- // gaps inserted where the columns are hidden
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[4]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[5]));
- assertTrue(Comparison.isGap(al.getSequenceAt(1).getSequence()[6]));
- assertFalse(Comparison.isGap(al.getSequenceAt(1).getSequence()[7]));
- }
-
- @Test(groups = "Functional")
public void testHasHiddenColumns()
{
HiddenColumns h = new HiddenColumns();
git://source.jalview.org / jalview.git / commitdiff