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;
*/
Vector<AlignmentAnnotation> annotation;
- /**
- * The index of the sequence in a MSA
- */
- int index = -1;
-
- private SequenceFeatures sequenceFeatureStore;
+ private SequenceFeaturesI sequenceFeatureStore;
/*
* A cursor holding the approximate current view position to the sequence,
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++;
}
}
/**
- * 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 AlignmentAnnotation[] getAnnotation()
{
- return annotation == null ? null : annotation
- .toArray(new AlignmentAnnotation[annotation.size()]);
+ return annotation == null ? null
+ : annotation
+ .toArray(new AlignmentAnnotation[annotation.size()]);
}
@Override
{
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)
{
}
}
- /**
- * @return The index (zero-based) on this sequence in the MSA. It returns
- * {@code -1} if this information is not available.
- */
- @Override
- public int getIndex()
- {
- return index;
- }
-
- /**
- * Defines the position of this sequence in the MSA. Use the value {@code -1}
- * if this information is undefined.
- *
- * @param The
- * position for this sequence. This value is zero-based (zero for
- * this first sequence)
- */
- @Override
- public void setIndex(int value)
- {
- index = value;
- }
-
@Override
public void setRNA(RNA r)
{
}
}
// 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
* 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[toColumn - 1]))
+ boolean endColumnIsGapped = toColumn > 0 && toColumn <= sequence.length
+ && Comparison.isGap(sequence[toColumn - 1]);
+ if (endPos > this.end || endColumnIsGapped)
{
ListIterator<SequenceFeature> it = result.listIterator();
while (it.hasNext())