import java.util.ListIterator;
import java.util.Vector;
-import com.stevesoft.pat.Regex;
-
import fr.orsay.lri.varna.models.rna.RNA;
/**
*/
public class Sequence extends ASequence implements SequenceI
{
- private static final Regex limitrx = new Regex(
- "[/][0-9]{1,}[-][0-9]{1,}$");
-
- private static final Regex endrx = new Regex("[0-9]{1,}$");
-
SequenceI datasetSequence;
String name;
checkValidRange();
}
+ /**
+ * If 'name' ends in /i-j, where i >= j > 0 are integers, extracts i and j as
+ * start and end respectively and removes the suffix from the name
+ */
void parseId()
{
if (name == null)
{
- System.err
- .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+ System.err.println(
+ "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
- // Does sequence have the /start-end signature?
- if (limitrx.search(name))
+ int slashPos = name.lastIndexOf('/');
+ if (slashPos > -1 && slashPos < name.length() - 1)
{
- name = limitrx.left();
- endrx.search(limitrx.stringMatched());
- setStart(Integer.parseInt(limitrx.stringMatched().substring(1,
- endrx.matchedFrom() - 1)));
- setEnd(Integer.parseInt(endrx.stringMatched()));
+ String suffix = name.substring(slashPos + 1);
+ String[] range = suffix.split("-");
+ if (range.length == 2)
+ {
+ try
+ {
+ int from = Integer.valueOf(range[0]);
+ int to = Integer.valueOf(range[1]);
+ if (from > 0 && to >= from)
+ {
+ name = name.substring(0, slashPos);
+ setStart(from);
+ setEnd(to);
+ checkValidRange();
+ }
+ } catch (NumberFormatException e)
+ {
+ // leave name unchanged if suffix is invalid
+ }
+ }
}
}
+ /**
+ * Ensures that 'end' is not before the end of the sequence, that is,
+ * (end-start+1) is at least as long as the count of ungapped positions. Note
+ * that end is permitted to be beyond the end of the sequence data.
+ */
void checkValidRange()
{
// Note: JAL-774 :
int endRes = 0;
for (int j = 0; j < sequence.length; j++)
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
endRes++;
}
protected void initSeqFrom(SequenceI seq,
AlignmentAnnotation[] alAnnotation)
{
- char[] oseq = seq.getSequence();
- initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
- seq.getStart(), seq.getEnd());
+ char[] oseq = seq.getSequence(); // returns a copy of the array
+ initSeqAndName(seq.getName(), oseq, seq.getStart(), seq.getEnd());
description = seq.getDescription();
if (seq != datasetSequence)
}
/**
- * DOCUMENT ME!
+ * Sets the sequence name. If the name ends in /start-end, then the start-end
+ * values are parsed out and set, and the suffix is removed from the name.
*
- * @param name
- * DOCUMENT ME!
+ * @param theName
*/
@Override
- public void setName(String name)
+ public void setName(String theName)
{
- this.name = name;
+ this.name = theName;
this.parseId();
}
@Override
public char[] getSequence()
{
- return sequence;
+ // return sequence;
+ return sequence == null ? null : Arrays.copyOf(sequence,
+ sequence.length);
}
/*
int j = start;
int i = 0;
- // Rely on end being at least as long as the length of the sequence.
+ int startColumn = 0;
+
+ /*
+ * traverse sequence from the start counting gaps; make a note of
+ * the column of the first residue to save in the cursor
+ */
while ((i < sequence.length) && (j <= end) && (j <= pos))
{
if (!Comparison.isGap(sequence[i]))
{
+ if (j == start)
+ {
+ startColumn = i;
+ }
j++;
}
i++;
return end + 1;
}
- updateCursor(pos, i);
+ updateCursor(pos, i, startColumn);
return i;
}
* (start..)
* @param column
* (1..)
+ * @param startColumn
+ * column position of the first sequence residue
*/
- protected void updateCursor(int residuePos, int column)
+ protected void updateCursor(int residuePos, int column, int startColumn)
{
- cursor = new SequenceCursor(this, residuePos, column, this.changeCount);
+ /*
+ * preserve end residue column provided cursor was valid
+ */
+ int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0;
+ if (residuePos == this.end)
+ {
+ endColumn = column;
+ }
+
+ cursor = new SequenceCursor(this, residuePos, column, startColumn,
+ endColumn, this.changeCount);
}
/**
}
col++; // convert back to base 1
- updateCursor(pos, col);
+ updateCursor(pos, col, curs.firstColumnPosition);
return col;
}
{
return findPosition(column + 1, cursor);
}
-
+
// TODO recode this more naturally i.e. count residues only
// as they are found, not 'in anticipation'
+ /*
+ * traverse the sequence counting gaps; note the column position
+ * of the first residue, to save in the cursor
+ */
+ int firstResidueColumn = 0;
int lastPosFound = 0;
int lastPosFoundColumn = 0;
int seqlen = sequence.length;
+
if (seqlen > 0 && !Comparison.isGap(sequence[0]))
{
lastPosFound = start;
{
lastPosFound = pos;
lastPosFoundColumn = j;
+ if (pos == this.start)
+ {
+ firstResidueColumn = j;
+ }
pos++;
}
j++;
{
lastPosFound = pos;
lastPosFoundColumn = j;
+ if (pos == this.start)
+ {
+ firstResidueColumn = j;
+ }
}
/*
*/
if (lastPosFound != 0)
{
- updateCursor(lastPosFound, lastPosFoundColumn + 1);
+ updateCursor(lastPosFound, lastPosFoundColumn + 1,
+ firstResidueColumn + 1);
}
return pos;
return curs.residuePosition; // easy case :-)
}
+ if (curs.lastColumnPosition > 0 && curs.lastColumnPosition < col)
+ {
+ /*
+ * sequence lies entirely to the left of col
+ * - return last residue + 1
+ */
+ return end + 1;
+ }
+
+ if (curs.firstColumnPosition > 0 && curs.firstColumnPosition > col)
+ {
+ /*
+ * sequence lies entirely to the right of col
+ * - return first residue
+ */
+ return start;
+ }
+
+ // todo could choose closest to col out of column,
+ // firstColumnPosition, lastColumnPosition as a start point
+
/*
* move left or right to find pos from cursor position
*/
+ int firstResidueColumn = curs.firstColumnPosition;
int column = curs.columnPosition - 1; // to base 0
int newPos = curs.residuePosition;
int delta = curs.columnPosition > col ? -1 : 1;
newPos += delta;
lastFoundPosition = newPos;
lastFoundPositionColumn = column + 1;
+ if (lastFoundPosition == this.start)
+ {
+ firstResidueColumn = column + 1;
+ }
}
}
if (cursor == null || lastFoundPosition != cursor.residuePosition)
{
- updateCursor(lastFoundPosition, lastFoundPositionColumn);
+ updateCursor(lastFoundPosition, lastFoundPositionColumn,
+ firstResidueColumn);
}
/*
}
/**
+ * {@inheritDoc}
+ */
+ @Override
+ public Range findPositions(int fromColumn, int toColumn)
+ {
+ if (toColumn < fromColumn || fromColumn < 1)
+ {
+ return null;
+ }
+
+ /*
+ * find the first non-gapped position, if any
+ */
+ int firstPosition = 0;
+ int col = fromColumn - 1;
+ int length = sequence.length;
+ while (col < length && col < toColumn)
+ {
+ if (!Comparison.isGap(sequence[col]))
+ {
+ firstPosition = findPosition(col++);
+ break;
+ }
+ col++;
+ }
+
+ if (firstPosition == 0)
+ {
+ return null;
+ }
+
+ /*
+ * find the last non-gapped position
+ */
+ int lastPosition = firstPosition;
+ while (col < length && col < toColumn)
+ {
+ if (!Comparison.isGap(sequence[col++]))
+ {
+ lastPosition++;
+ }
+ }
+
+ return new Range(firstPosition, lastPosition);
+ }
+
+ /**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
@Override
public AlignmentAnnotation[] getAnnotation()
{
- return annotation == null ? null : annotation
- .toArray(new AlignmentAnnotation[annotation.size()]);
+ return annotation == null ? null
+ : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
}
@Override
private boolean _isNa;
- private long _seqhash = 0;
+ private int _seqhash = 0;
/**
* Answers false if the sequence is more than 85% nucleotide (ACGTU), else
{
if (datasetSequence == null)
{
- Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars, getSequenceAsString()),
+ Sequence dsseq = new Sequence(getName(),
+ AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
+ getSequenceAsString()),
getStart(), getEnd());
datasetSequence = dsseq;
List<SequenceFeature> sfs = entry.getSequenceFeatures();
for (SequenceFeature feature : sfs)
{
- SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
+ SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
: new SequenceFeature[] { new SequenceFeature(feature) };
if (sf != null)
{
}
}
// whilst it looks like it is a primary ref, we also sanity check type
- if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
- DBRefUtils.getCanonicalName(ref.getSource())))
+ if (DBRefUtils.getCanonicalName(DBRefSource.PDB)
+ .equals(DBRefUtils.getCanonicalName(ref.getSource())))
{
// PDB dbrefs imply there should be a PDBEntry associated
// TODO: tighten PDB dbrefs
String... types)
{
int startPos = findPosition(fromColumn - 1); // convert base 1 to base 0
- int endPos = findPosition(toColumn - 1);
+ int endPos = fromColumn == toColumn ? startPos
+ : findPosition(toColumn - 1);
- List<SequenceFeature> result = new ArrayList<>();
- if (datasetSequence != null)
- {
- result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
- types);
- }
- else
- {
- result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
- }
+ List<SequenceFeature> result = getFeatures().findFeatures(startPos,
+ endPos, types);
/*
- * if the start or end column is gapped, startPos or endPos may be to the
- * left or right, and we may have included adjacent or enclosing features;
+ * if end column is gapped, endPos may be to the right,
+ * and we may have included adjacent or enclosing features;
* remove any that are not enclosing, non-contact features
*/
- if (endPos > this.end || Comparison.isGap(sequence[fromColumn - 1])
- || Comparison.isGap(sequence[toColumn - 1]))
+ if (endPos > this.end || Comparison.isGap(sequence[toColumn - 1]))
{
ListIterator<SequenceFeature> it = result.listIterator();
while (it.hasNext())
{
SequenceFeature sf = it.next();
- int featureStartColumn = findIndex(sf.getBegin());
- int featureEndColumn = findIndex(sf.getEnd());
- boolean noOverlap = featureStartColumn > toColumn
- || featureEndColumn < fromColumn;
-
- /*
- * reject an 'enclosing' feature if it is actually a contact feature
- */
- if (sf.isContactFeature() && featureStartColumn < fromColumn
- && featureEndColumn > toColumn)
+ int sfBegin = sf.getBegin();
+ int sfEnd = sf.getEnd();
+ int featureStartColumn = findIndex(sfBegin);
+ if (featureStartColumn > toColumn)
{
- noOverlap = true;
+ it.remove();
}
- if (noOverlap)
+ else if (featureStartColumn < fromColumn)
{
- it.remove();
+ int featureEndColumn = sfEnd == sfBegin ? featureStartColumn
+ : findIndex(sfEnd);
+ if (featureEndColumn < fromColumn)
+ {
+ it.remove();
+ }
+ else if (featureEndColumn > toColumn && sf.isContactFeature())
+ {
+ /*
+ * remove an enclosing feature if it is a contact feature
+ */
+ it.remove();
+ }
}
}
}
{
changeCount++;
}
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public int replace(char c1, char c2)
+ {
+ if (c1 == c2)
+ {
+ return 0;
+ }
+ int count = 0;
+ synchronized (sequence)
+ {
+ for (int c = 0; c < sequence.length; c++)
+ {
+ if (sequence[c] == c1)
+ {
+ sequence[c] = c2;
+ count++;
+ }
+ }
+ }
+ if (count > 0)
+ {
+ sequenceChanged();
+ }
+
+ return count;
+ }
}
git://source.jalview.org / jalview.git / blobdiff