import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.io.FastaFile;
import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
import jalview.util.MessageManager;
import java.util.ArrayList;
protected char gapCharacter = '-';
- protected int type = NUCLEOTIDE;
-
- public static final int PROTEIN = 0;
-
- public static final int NUCLEOTIDE = 1;
+ private boolean nucleotide = true;
public boolean hasRNAStructure = false;
hiddenSequences = new HiddenSequences(this);
codonFrameList = new ArrayList<AlignedCodonFrame>();
- if (Comparison.isNucleotide(seqs))
- {
- type = NUCLEOTIDE;
- }
- else
- {
- type = PROTEIN;
- }
+ nucleotide = Comparison.isNucleotide(seqs);
sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
}
/**
- * Adds a sequence to the alignment. Recalculates maxLength and size.
+ * Adds a sequence to the alignment. Recalculates maxLength and size. Note
+ * this currently does not recalculate whether or not the alignment is
+ * nucleotide, so mixed alignments may have undefined behaviour.
*
* @param snew
*/
{
if (dataset != null)
{
+
// maintain dataset integrity
- if (snew.getDatasetSequence() != null)
- {
- getDataset().addSequence(snew.getDatasetSequence());
- }
- else
+ SequenceI dsseq = snew.getDatasetSequence();
+ if (dsseq == null)
{
// derive new sequence
SequenceI adding = snew.deriveSequence();
- getDataset().addSequence(adding.getDatasetSequence());
snew = adding;
+ dsseq = snew.getDatasetSequence();
}
+ if (getDataset().findIndex(dsseq) == -1)
+ {
+ getDataset().addSequence(dsseq);
+ }
+
}
if (sequences == null)
{
}
@Override
- public void finalize()
+ public void finalize() throws Throwable
{
if (getDataset() != null)
{
getDataset().removeAlignmentRef();
}
+ nullReferences();
+ super.finalize();
+ }
+
+ /**
+ * Defensively nulls out references in case this object is not garbage
+ * collected
+ */
+ void nullReferences()
+ {
dataset = null;
sequences = null;
groups = null;
}
/**
- * decrement the alignmentRefs counter by one and call finalize if it goes to
- * zero.
+ * decrement the alignmentRefs counter by one and null references if it goes
+ * to zero.
+ *
+ * @throws Throwable
*/
- private void removeAlignmentRef()
+ private void removeAlignmentRef() throws Throwable
{
if (--alignmentRefs == 0)
{
- finalize();
+ nullReferences();
}
}
* @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
*/
@Override
- public SequenceGroup findGroup(SequenceI s)
+ public SequenceGroup findGroup(SequenceI seq, int position)
{
synchronized (groups)
{
- for (int i = 0; i < this.groups.size(); i++)
+ for (SequenceGroup sg : groups)
{
- SequenceGroup sg = groups.get(i);
-
- if (sg.getSequences(null).contains(s))
+ if (sg.getSequences(null).contains(seq))
{
- return sg;
+ if (position >= sg.getStartRes() && position <= sg.getEndRes())
+ {
+ return sg;
+ }
}
}
}
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
@Override
- public int findIndex(SearchResults results)
+ public int findIndex(SearchResultsI results)
{
int i = 0;
}
@Override
- public void setNucleotide(boolean b)
- {
- if (b)
- {
- type = NUCLEOTIDE;
- }
- else
- {
- type = PROTEIN;
- }
- }
-
- @Override
public boolean isNucleotide()
{
- if (type == NUCLEOTIDE)
- {
- return true;
- }
- else
- {
- return false;
- }
+ return nucleotide;
}
@Override
private void resolveAndAddDatasetSeq(SequenceI currentSeq,
Set<SequenceI> seqs, boolean createDatasetSequence)
{
+ SequenceI alignedSeq = currentSeq;
if (currentSeq.getDatasetSequence() != null)
{
currentSeq = currentSeq.getDatasetSequence();
{
if (dbr.getMap() != null && dbr.getMap().getTo() != null)
{
+ if (dbr.getMap().getTo() == alignedSeq)
+ {
+ /*
+ * update mapping to be to the newly created dataset sequence
+ */
+ dbr.getMap().setTo(currentSeq);
+ }
if (dbr.getMap().getTo().getDatasetSequence() != null)
{
- throw new Error("Implementation error: Map.getTo() for dbref"
- + dbr + " is not a dataset sequence.");
- // TODO: if this happens, could also rewrite the reference to
- // point to new dataset sequence
+ throw new Error(
+ "Implementation error: Map.getTo() for dbref " + dbr
+ + " from " + curDs.getName()
+ + " is not a dataset sequence.");
}
// we recurse to add all forward references to dataset sequences via
// DBRefs/etc
return;
}
// try to avoid using SequenceI.equals at this stage, it will be expensive
- Set<SequenceI> seqs = new jalview.util.LinkedIdentityHashSet<SequenceI>();
+ Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
for (int i = 0; i < getHeight(); i++)
{
String calcId, boolean autoCalc, SequenceI seqRef,
SequenceGroup groupRef)
{
- assert (name != null);
if (annotations != null)
{
for (AlignmentAnnotation annot : getAlignmentAnnotation())
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation a : getAlignmentAnnotation())
+ List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+ if (alignmentAnnotation != null)
{
- if (a.getCalcId() == calcId
- || (a.getCalcId() != null && calcId != null && a.getCalcId()
- .equals(calcId)))
+ for (AlignmentAnnotation a : alignmentAnnotation)
{
- aa.add(a);
+ if (a.getCalcId() == calcId
+ || (a.getCalcId() != null && calcId != null && a
+ .getCalcId().equals(calcId)))
+ {
+ aa.add(a);
+ }
}
}
return aa;
@Override
public String toString()
{
- return new FastaFile().print(getSequencesArray());
+ return new FastaFile().print(getSequencesArray(), true);
}
/**
git://source.jalview.org / jalview.git / blobdiff