*/
int index = -1;
- /** array of sequence features - may not be null for a valid sequence object */
- public SequenceFeature[] sequenceFeatures;
-
private SequenceFeatures sequenceFeatureStore;
/**
*/
public Sequence(String name, String sequence, int start, int end)
{
+ this();
initSeqAndName(name, sequence.toCharArray(), start, end);
}
public Sequence(String name, char[] sequence, int start, int end)
{
+ this();
initSeqAndName(name, sequence, start, end);
}
this.sequence = sequence2;
this.start = start2;
this.end = end2;
- sequenceFeatureStore = new SequenceFeatures();
parseId();
checkValidRange();
}
}
/**
+ * default constructor
+ */
+ private Sequence()
+ {
+ sequenceFeatureStore = new SequenceFeatures();
+ }
+
+ /**
* Creates a new Sequence object.
*
* @param name
*/
public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
{
+ this();
initSeqFrom(seq, alAnnotation);
-
}
/**
addDBRef(new DBRefEntry(dbr[i]));
}
}
- if (seq.getSequenceFeatures() != null)
+
+ /*
+ * make copies of any sequence features
+ */
+ for (SequenceFeature sf : seq.getSequenceFeatures())
{
- SequenceFeature[] sf = seq.getSequenceFeatures();
- for (int i = 0; i < sf.length; i++)
- {
- addSequenceFeature(new SequenceFeature(sf[i]));
- }
+ addSequenceFeature(new SequenceFeature(sf));
}
}
}
@Override
- public void setSequenceFeatures(SequenceFeature[] features)
+ public void setSequenceFeatures(List<SequenceFeature> features)
{
- if (datasetSequence == null)
- {
- sequenceFeatures = features;
- }
- else
+ if (datasetSequence != null)
{
- if (datasetSequence.getSequenceFeatures() != features
- && datasetSequence.getSequenceFeatures() != null
- && datasetSequence.getSequenceFeatures().length > 0)
- {
- new Exception(
- "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
- .printStackTrace();
- }
datasetSequence.setSequenceFeatures(features);
+ return;
}
+ sequenceFeatureStore = new SequenceFeatures(features);
}
@Override
return false;
}
- if (sequenceFeatures == null && datasetSequence != null)
+ if (datasetSequence != null)
{
return datasetSequence.addSequenceFeature(sf);
}
- if (sequenceFeatures == null)
- {
- sequenceFeatures = new SequenceFeature[0];
- }
-
- for (int i = 0; i < sequenceFeatures.length; i++)
- {
- if (sequenceFeatures[i].equals(sf))
- {
- return false;
- }
- }
-
- SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1];
- System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
- temp[sequenceFeatures.length] = sf;
- sequenceFeatures = temp;
-
- sequenceFeatureStore.add(sf);
- return true;
+ return sequenceFeatureStore.add(sf);
}
@Override
public void deleteFeature(SequenceFeature sf)
{
- if (sequenceFeatures == null)
- {
- if (datasetSequence != null)
- {
- datasetSequence.deleteFeature(sf);
- }
- return;
- }
-
- /*
- * new way
- */
- sequenceFeatureStore.delete(sf);
-
- /*
- * old way - to be removed
- */
- int index = 0;
- for (index = 0; index < sequenceFeatures.length; index++)
- {
- if (sequenceFeatures[index].equals(sf))
- {
- break;
- }
- }
-
- if (index == sequenceFeatures.length)
- {
- return;
- }
-
- int sfLength = sequenceFeatures.length;
- if (sfLength < 2)
+ if (datasetSequence != null)
{
- sequenceFeatures = null;
+ datasetSequence.deleteFeature(sf);
}
else
{
- SequenceFeature[] temp = new SequenceFeature[sfLength - 1];
- System.arraycopy(sequenceFeatures, 0, temp, 0, index);
-
- if (index < sfLength)
- {
- System.arraycopy(sequenceFeatures, index + 1, temp, index,
- sequenceFeatures.length - index - 1);
- }
-
- sequenceFeatures = temp;
+ sequenceFeatureStore.delete(sf);
}
}
/**
- * Returns the sequence features (if any), looking first on the sequence, then
- * on its dataset sequence, and so on until a non-null value is found (or
- * none). This supports retrieval of sequence features stored on the sequence
- * (as in the applet) or on the dataset sequence (as in the Desktop version).
+ * {@inheritDoc}
*
* @return
*/
@Override
- public SequenceFeature[] getSequenceFeatures()
+ public List<SequenceFeature> getSequenceFeatures()
{
- SequenceFeature[] features = sequenceFeatures;
-
- SequenceI seq = this;
- int count = 0; // failsafe against loop in sequence.datasetsequence...
- while (features == null && seq.getDatasetSequence() != null
- && count++ < 10)
+ if (datasetSequence != null)
{
- seq = seq.getDatasetSequence();
- features = ((Sequence) seq).sequenceFeatures;
+ return datasetSequence.getSequenceFeatures();
}
- return features;
+ return sequenceFeatureStore.getAllFeatures();
}
@Override
// Rely on end being at least as long as the length of the sequence.
while ((i < sequence.length) && (j <= end) && (j <= pos))
{
- if (!jalview.util.Comparison.isGap(sequence[i]))
+ if (!Comparison.isGap(sequence[i]))
{
j++;
}
int seqlen = sequence.length;
while ((j < i) && (j < seqlen))
{
- if (!jalview.util.Comparison.isGap(sequence[j]))
+ if (!Comparison.isGap(sequence[j]))
{
pos++;
}
}
/**
+ * {@inheritDoc}
+ */
+ @Override
+ public Range findPositions(int fromCol, int toCol)
+ {
+ /*
+ * count residues before fromCol
+ */
+ int j = 0;
+ int count = 0;
+ int seqlen = sequence.length;
+ while (j < fromCol && j < seqlen)
+ {
+ if (!Comparison.isGap(sequence[j]))
+ {
+ count++;
+ }
+ j++;
+ }
+
+ /*
+ * find first and last residues between fromCol and toCol
+ */
+ int firstPos = 0;
+ int lastPos = 0;
+ int firstPosCol = 0;
+ boolean foundFirst = false;
+
+ while (j <= toCol && j < seqlen)
+ {
+ if (!Comparison.isGap(sequence[j]))
+ {
+ count++;
+ if (!foundFirst)
+ {
+ firstPos = count;
+ firstPosCol = j;
+ foundFirst = true;
+ }
+ lastPos = count;
+ }
+ j++;
+ }
+
+ if (firstPos == 0)
+ {
+ /*
+ * no residues in this range
+ */
+ return null;
+ }
+
+ /*
+ * adjust for sequence start coordinate
+ */
+ firstPos += start - 1;
+ lastPos += start - 1;
+
+ return new Range(firstPos, lastPos);
+ }
+
+ /**
* Returns an int array where indices correspond to each residue in the
* sequence and the element value gives its position in the alignment
*
dsseq.setDescription(description);
// move features and database references onto dataset sequence
- dsseq.sequenceFeatures = sequenceFeatures;
- sequenceFeatures = null;
dsseq.sequenceFeatureStore = sequenceFeatureStore;
sequenceFeatureStore = null;
dsseq.dbrefs = dbrefs;
if (entry.getSequenceFeatures() != null)
{
- SequenceFeature[] sfs = entry.getSequenceFeatures();
- for (int si = 0; si < sfs.length; si++)
+ List<SequenceFeature> sfs = entry.getSequenceFeatures();
+ for (SequenceFeature feature : sfs)
{
- SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
- : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
- if (sf != null && sf.length > 0)
+ SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
+ : new SequenceFeature[] { new SequenceFeature(feature) };
+ if (sf != null)
{
for (int sfi = 0; sfi < sf.length; sfi++)
{
git://source.jalview.org / jalview.git / blobdiff