package jalview.datamodel;
import jalview.analysis.AlignmentUtils;
+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;
+import java.util.Collections;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Hashtable;
-import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
*/
public class Alignment implements AlignmentI
{
- protected Alignment dataset;
+ private Alignment dataset;
protected List<SequenceI> sequences;
- protected List<SequenceGroup> groups = java.util.Collections
- .synchronizedList(new ArrayList<SequenceGroup>());
+ protected List<SequenceGroup> groups;
protected char gapCharacter = '-';
public boolean hasRNAStructure = false;
- /** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
- HiddenSequences hiddenSequences = new HiddenSequences(this);
+ HiddenSequences hiddenSequences;
public Hashtable alignmentProperties;
- private Set<AlignedCodonFrame> codonFrameList = new LinkedHashSet<AlignedCodonFrame>();
+ private List<AlignedCodonFrame> codonFrameList;
private void initAlignment(SequenceI[] seqs)
{
- int i = 0;
+ groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
+ hiddenSequences = new HiddenSequences(this);
+ codonFrameList = new ArrayList<AlignedCodonFrame>();
- if (jalview.util.Comparison.isNucleotide(seqs))
+ if (Comparison.isNucleotide(seqs))
{
type = NUCLEOTIDE;
}
type = PROTEIN;
}
- sequences = java.util.Collections
- .synchronizedList(new ArrayList<SequenceI>());
+ sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
- for (i = 0; i < seqs.length; i++)
+ for (int i = 0; i < seqs.length; i++)
{
sequences.add(seqs[i]);
}
seqs[i] = new Sequence(seqs[i]);
}
+ initAlignment(seqs);
+
/*
- * Share the same dataset sequence mappings (if any). TODO: find a better
- * place for these to live (alignment dataset?).
+ * Share the same dataset sequence mappings (if any).
*/
- this.codonFrameList = ((Alignment) al).codonFrameList;
-
- initAlignment(seqs);
+ if (dataset == null && al.getDataset() == null)
+ {
+ this.setCodonFrames(al.getCodonFrames());
+ }
}
/**
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
- throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented"));
+ throw new Error(
+ MessageManager
+ .getString("error.alignment_cigararray_not_implemented"));
// this(compactAlignment.refCigars);
}
{
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)
{
- initAlignment(new SequenceI[]
- { snew });
+ initAlignment(new SequenceI[] { snew });
}
else
{
}
}
- /**
- * Adds a sequence to the alignment. Recalculates maxLength and size.
- *
- * @param snew
- */
@Override
- public void setSequenceAt(int i, SequenceI snew)
+ public SequenceI replaceSequenceAt(int i, SequenceI snew)
{
synchronized (sequences)
{
- deleteSequence(i);
- sequences.set(i, snew);
+ if (sequences.size() > i)
+ {
+ return sequences.set(i, snew);
+
+ }
+ else
+ {
+ sequences.add(snew);
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+ return 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();
}
}
}
@Override
- public void setDataset(Alignment data)
+ public void setDataset(AlignmentI data)
{
if (dataset == null && data == null)
{
- // Create a new dataset for this alignment.
- // Can only be done once, if dataset is not null
- // This will not be performed
- SequenceI[] seqs = new SequenceI[getHeight()];
- SequenceI currentSeq;
- for (int i = 0; i < getHeight(); i++)
- {
- currentSeq = getSequenceAt(i);
- if (currentSeq.getDatasetSequence() != null)
- {
- seqs[i] = currentSeq.getDatasetSequence();
- }
- else
- {
- seqs[i] = currentSeq.createDatasetSequence();
- }
- }
-
- dataset = new Alignment(seqs);
+ createDatasetAlignment();
}
else if (dataset == null && data != null)
{
- dataset = data;
+ if (!(data instanceof Alignment))
+ {
+ throw new Error(
+ "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference");
+ }
+ dataset = (Alignment) data;
for (int i = 0; i < getHeight(); i++)
{
SequenceI currentSeq = getSequenceAt(i);
}
/**
+ * add dataset sequences to seq for currentSeq and any sequences it references
+ */
+ private void resolveAndAddDatasetSeq(SequenceI currentSeq,
+ Set<SequenceI> seqs, boolean createDatasetSequence)
+ {
+ SequenceI alignedSeq = currentSeq;
+ if (currentSeq.getDatasetSequence() != null)
+ {
+ currentSeq = currentSeq.getDatasetSequence();
+ }
+ else
+ {
+ if (createDatasetSequence)
+ {
+ currentSeq = currentSeq.createDatasetSequence();
+ }
+ }
+ if (seqs.contains(currentSeq))
+ {
+ return;
+ }
+ List<SequenceI> toProcess = new ArrayList<SequenceI>();
+ toProcess.add(currentSeq);
+ while (toProcess.size() > 0)
+ {
+ // use a queue ?
+ SequenceI curDs = toProcess.remove(0);
+ if (seqs.contains(curDs))
+ {
+ continue;
+ }
+ seqs.add(curDs);
+ // iterate over database references, making sure we add forward referenced
+ // sequences
+ if (curDs.getDBRefs() != null)
+ {
+ for (DBRefEntry dbr : curDs.getDBRefs())
+ {
+ 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
+ + " from " + curDs.getName()
+ + " is not a dataset sequence.");
+ }
+ // we recurse to add all forward references to dataset sequences via
+ // DBRefs/etc
+ toProcess.add(dbr.getMap().getTo());
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Creates a new dataset for this alignment. Can only be done once - if
+ * dataset is not null this will not be performed.
+ */
+ public void createDatasetAlignment()
+ {
+ if (dataset != null)
+ {
+ return;
+ }
+ // try to avoid using SequenceI.equals at this stage, it will be expensive
+ Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
+
+ for (int i = 0; i < getHeight(); i++)
+ {
+ SequenceI currentSeq = getSequenceAt(i);
+ resolveAndAddDatasetSeq(currentSeq, seqs, true);
+ }
+
+ // verify all mappings are in dataset
+ for (AlignedCodonFrame cf : codonFrameList)
+ {
+ for (SequenceToSequenceMapping ssm : cf.getMappings())
+ {
+ if (!seqs.contains(ssm.getFromSeq()))
+ {
+ resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false);
+ }
+ if (!seqs.contains(ssm.getMapping().getTo()))
+ {
+ resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false);
+ }
+ }
+ }
+ // finally construct dataset
+ dataset = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+ // move mappings to the dataset alignment
+ dataset.codonFrameList = this.codonFrameList;
+ this.codonFrameList = null;
+ }
+
+ /**
* reference count for number of alignments referencing this one.
*/
int alignmentRefs = 0;
return alignmentProperties;
}
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
- * )
+ /**
+ * Adds the given mapping to the stored set. Note this may be held on the
+ * dataset alignment.
*/
@Override
public void addCodonFrame(AlignedCodonFrame codons)
{
- if (codons != null)
+ List<AlignedCodonFrame> acfs = getCodonFrames();
+ if (codons != null && acfs != null && !acfs.contains(codons))
{
- codonFrameList.add(codons);
+ acfs.add(codons);
}
}
return null;
}
List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
- for (AlignedCodonFrame acf : codonFrameList)
+ for (AlignedCodonFrame acf : getCodonFrames())
{
if (acf.involvesSequence(seq))
{
}
/**
- * Sets the codon frame mappings (replacing any existing mappings).
+ * Sets the codon frame mappings (replacing any existing mappings). Note the
+ * mappings are set on the dataset alignment instead if there is one.
*
* @see jalview.datamodel.AlignmentI#setCodonFrames()
*/
@Override
- public void setCodonFrames(Set<AlignedCodonFrame> acfs)
+ public void setCodonFrames(List<AlignedCodonFrame> acfs)
{
- this.codonFrameList = acfs;
+ if (dataset != null)
+ {
+ dataset.setCodonFrames(acfs);
+ }
+ else
+ {
+ this.codonFrameList = acfs;
+ }
}
/**
* Returns the set of codon frame mappings. Any changes to the returned set
- * will affect the alignment.
+ * will affect the alignment. The mappings are held on (and read from) the
+ * dataset alignment if there is one.
*
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
@Override
- public Set<AlignedCodonFrame> getCodonFrames()
+ public List<AlignedCodonFrame> getCodonFrames()
{
- return codonFrameList;
+ // TODO: Fix this method to fix failing AlignedCodonFrame tests
+ // this behaviour is currently incorrect. method should return codon frames
+ // for just the alignment,
+ // selected from dataset
+ return dataset != null ? dataset.getCodonFrames() : codonFrameList;
}
- /*
- * (non-Javadoc)
- *
- * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
- * AlignedCodonFrame)
+ /**
+ * Removes the given mapping from the stored set. Note that the mappings are
+ * held on the dataset alignment if there is one.
*/
@Override
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
- if (codons == null || codonFrameList == null)
+ List<AlignedCodonFrame> acfs = getCodonFrames();
+ if (codons == null || acfs == null)
{
return false;
}
- return codonFrameList.remove(codons);
+ return acfs.remove(codons);
}
@Override
public void append(AlignmentI toappend)
{
- if (toappend == this)
- {
- System.err.println("Self append may cause a deadlock.");
- }
- // TODO test this method for a future 2.5 release
+ // TODO JAL-1270 needs test coverage
// currently tested for use in jalview.gui.SequenceFetcher
boolean samegap = toappend.getGapCharacter() == getGapCharacter();
char oldc = toappend.getGapCharacter();
.getFullAlignment().getSequences() : toappend.getSequences();
if (sqs != null)
{
+ // avoid self append deadlock by
+ List<SequenceI> toappendsq = new ArrayList<SequenceI>();
synchronized (sqs)
{
for (SequenceI addedsq : sqs)
}
}
}
- addSequence(addedsq);
+ toappendsq.add(addedsq);
}
}
+ for (SequenceI addedsq : toappendsq)
+ {
+ addSequence(addedsq);
+ }
}
AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
for (int a = 0; alan != null && a < alan.length; a++)
addAnnotation(alan[a]);
}
- this.codonFrameList.addAll(toappend.getCodonFrames());
+ // use add method
+ getCodonFrames().addAll(toappend.getCodonFrames());
List<SequenceGroup> sg = toappend.getGroups();
if (sg != null)
}
}
+ private SequenceI seqrep = null;
- private SequenceI seqrep=null;
-
- /**
- *
- * @return the representative sequence for this group
- */
- public SequenceI getSeqrep()
- {
- return seqrep;
- }
+ /**
+ *
+ * @return the representative sequence for this group
+ */
+ @Override
+ public SequenceI getSeqrep()
+ {
+ return seqrep;
+ }
- /**
- * set the representative sequence for this group. Note - this affects the
- * interpretation of the Hidereps attribute.
- *
- * @param seqrep
- * the seqrep to set (null means no sequence representative)
- */
- public void setSeqrep(SequenceI seqrep)
- {
- this.seqrep = seqrep;
- }
+ /**
+ * set the representative sequence for this group. Note - this affects the
+ * interpretation of the Hidereps attribute.
+ *
+ * @param seqrep
+ * the seqrep to set (null means no sequence representative)
+ */
+ @Override
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
- /**
- *
- * @return true if group has a sequence representative
- */
- public boolean hasSeqrep()
- {
- return seqrep != null;
- }
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ @Override
+ public boolean hasSeqrep()
+ {
+ return seqrep != null;
+ }
@Override
public int getEndRes()
* identically. If this is nucleotide and the other is protein, make 3 gaps
* for each gap in the protein sequences. If this is protein and the other is
* nucleotide, insert a gap for each 3 gaps (or part thereof) between
- * nucleotide bases. Does nothing if alignment of protein from cDNA is
- * requested (not yet implemented).
+ * nucleotide bases. If this is protein and the other is nucleotide, gaps
+ * protein to match the relative ordering of codons in the nucleotide.
*
* Parameters control whether gaps in exon (mapped) and intron (unmapped)
* regions are preserved. Gaps that connect introns to exons are treated
* conservatively, i.e. only preserved if both intron and exon gaps are
- * preserved.
+ * preserved. TODO: check caveats below where the implementation fails
*
* @param al
+ * - must have same dataset, and sequences in al must have equivalent
+ * dataset sequence and start/end bounds under given mapping
* @param preserveMappedGaps
* if true, gaps within and between mapped codons are preserved
* @param preserveUnmappedGaps
* if true, gaps within and between unmapped codons are preserved
*/
-// @Override
+ // @Override
public int alignAs(AlignmentI al, boolean preserveMappedGaps,
boolean preserveUnmappedGaps)
{
// TODO should this method signature be the one in the interface?
- int count = 0;
+ // JBPComment - yes - neither flag is used, so should be deleted.
boolean thisIsNucleotide = this.isNucleotide();
boolean thatIsProtein = !al.isNucleotide();
if (!thatIsProtein && !thisIsNucleotide)
{
return AlignmentUtils.alignProteinAsDna(this, al);
}
-
- char thisGapChar = this.getGapCharacter();
- String gap = thisIsNucleotide && thatIsProtein ? String
- .valueOf(new char[]
- { thisGapChar, thisGapChar, thisGapChar }) : String
- .valueOf(thisGapChar);
-
- /*
- * Get mappings from 'that' alignment's sequences to this.
- */
- for (SequenceI alignTo : getSequences())
+ else if (thatIsProtein && thisIsNucleotide)
{
- count += AlignmentUtils.alignSequenceAs(alignTo, al, gap, preserveMappedGaps,
- preserveUnmappedGaps) ? 1 : 0;
+ return AlignmentUtils.alignCdsAsProtein(this, al);
}
- return count;
+ return AlignmentUtils.alignAs(this, al);
}
/**
}
return names;
}
+
+ @Override
+ public boolean hasValidSequence()
+ {
+ boolean hasValidSeq = false;
+ for (SequenceI seq : getSequences())
+ {
+ if ((seq.getEnd() - seq.getStart()) > 0)
+ {
+ hasValidSeq = true;
+ break;
+ }
+ }
+ return hasValidSeq;
+ }
+
+ /**
+ * Update any mappings to 'virtual' sequences to compatible real ones, if
+ * present in the added sequences. Returns a count of mappings updated.
+ *
+ * @param seqs
+ * @return
+ */
+ @Override
+ public int realiseMappings(List<SequenceI> seqs)
+ {
+ int count = 0;
+ for (SequenceI seq : seqs)
+ {
+ for (AlignedCodonFrame mapping : getCodonFrames())
+ {
+ count += mapping.realiseWith(seq);
+ }
+ }
+ return count;
+ }
+
+ /**
+ * Returns the first AlignedCodonFrame that has a mapping between the given
+ * dataset sequences
+ *
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ @Override
+ public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo)
+ {
+ for (AlignedCodonFrame acf : getCodonFrames())
+ {
+ if (acf.getAaForDnaSeq(mapFrom) == mapTo)
+ {
+ return acf;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+ {
+ int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 };
+ int startPos = alignmentStartEnd[0];
+ int endPos = alignmentStartEnd[1];
+
+ int[] lowestRange = new int[] { -1, -1 };
+ int[] higestRange = new int[] { -1, -1 };
+
+ for (int[] hiddenCol : hiddenCols)
+ {
+ lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
+ higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
+ }
+
+ if (lowestRange[0] == -1 && lowestRange[1] == -1)
+ {
+ startPos = alignmentStartEnd[0];
+ }
+ else
+ {
+ startPos = lowestRange[1] + 1;
+ }
+
+ if (higestRange[0] == -1 && higestRange[1] == -1)
+ {
+ endPos = alignmentStartEnd[1];
+ }
+ else
+ {
+ endPos = higestRange[0] - 1;
+ }
+ return new int[] { startPos, endPos };
+ }
}
git://source.jalview.org / jalview.git / blobdiff