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.Arrays;
+import java.util.BitSet;
+import java.util.Collections;
import java.util.Enumeration;
import java.util.HashSet;
import java.util.Hashtable;
-import java.util.LinkedHashSet;
+import java.util.Iterator;
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;
+ private List<SequenceI> sequences;
- protected List<SequenceGroup> groups = java.util.Collections
- .synchronizedList(new ArrayList<SequenceGroup>());
+ protected List<SequenceGroup> groups;
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;
- /** DOCUMENT ME!! */
public AlignmentAnnotation[] annotations;
- HiddenSequences hiddenSequences = new HiddenSequences(this);
+ HiddenSequences hiddenSequences;
+
+ HiddenColumns hiddenCols;
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);
+ hiddenCols = new HiddenColumns();
+ codonFrameList = new ArrayList<>();
- if (jalview.util.Comparison.isNucleotide(seqs))
- {
- type = NUCLEOTIDE;
- }
- else
- {
- type = PROTEIN;
- }
+ nucleotide = Comparison.isNucleotide(seqs);
- 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.setCodonFrames(al.getCodonFrames());
-
- initAlignment(seqs);
+ if (dataset == null && al.getDataset() == null)
+ {
+ this.setCodonFrames(al.getCodonFrames());
+ }
}
/**
public Alignment(SeqCigar[] alseqs)
{
SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
- gapCharacter, new ColumnSelection(), null);
+ gapCharacter, new HiddenColumns(), null);
initAlignment(seqs);
}
*/
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);
}
return AlignmentUtils.getSequencesByName(this);
}
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
@Override
public SequenceI getSequenceAt(int i)
{
return sequences.get(i);
}
}
+
return null;
}
+ @Override
+ public SequenceI getSequenceAtAbsoluteIndex(int i)
+ {
+ SequenceI seq = null;
+ if (getHiddenSequences().getSize() > 0)
+ {
+ seq = getHiddenSequences().getHiddenSequence(i);
+ if (seq == null)
+ {
+ // didn't find the sequence in the hidden sequences, get it from the
+ // alignment
+ int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i);
+ seq = getSequenceAt(index);
+ }
+ }
+ else
+ {
+ seq = getSequenceAt(i);
+ }
+ return seq;
+ }
+
/**
- * 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)
{
}
}
- /**
- * 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();
}
}
- /**
- * DOCUMENT ME!
- *
- * @param s
- * DOCUMENT ME!
- */
@Override
public void deleteSequence(SequenceI s)
{
- deleteSequence(findIndex(s));
+ synchronized (sequences)
+ {
+ deleteSequence(findIndex(s));
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- */
@Override
public void deleteSequence(int i)
{
- if (i > -1 && i < getHeight())
+ synchronized (sequences)
{
- synchronized (sequences)
+ if (i > -1 && i < getHeight())
{
sequences.remove(i);
hiddenSequences.adjustHeightSequenceDeleted(i);
}
}
+ @Override
+ public void deleteHiddenSequence(int i)
+ {
+ synchronized (sequences)
+ {
+ if (i > -1 && i < getHeight())
+ {
+ sequences.remove(i);
+ }
+ }
+ }
+
/*
* (non-Javadoc)
*
* @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;
+ }
}
}
}
@Override
public SequenceGroup[] findAllGroups(SequenceI s)
{
- ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
+ ArrayList<SequenceGroup> temp = new ArrayList<>();
synchronized (groups)
{
return;
}
}
- sg.setContext(this);
+ sg.setContext(this, true);
groups.add(sg);
}
}
return;
}
// remove annotation very quickly
- AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+ AlignmentAnnotation[] t,
+ todelete = new AlignmentAnnotation[annotations.length],
+ tokeep = new AlignmentAnnotation[annotations.length];
int i, p, k;
if (gp == null)
{
}
for (SequenceGroup sg : groups)
{
- sg.setContext(null);
+ sg.setContext(null, false);
}
groups.clear();
}
{
removeAnnotationForGroup(g);
groups.remove(g);
- g.setContext(null);
+ g.setContext(null, false);
}
}
}
sqname = sq.getName();
if (sqname.equals(token) // exact match
|| (b && // allow imperfect matches - case varies
- (sqname.equalsIgnoreCase(token))))
+ (sqname.equalsIgnoreCase(token))))
{
return getSequenceAt(i);
}
* jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
@Override
- public int findIndex(SearchResults results)
+ public int findIndex(SearchResultsI results)
{
int i = 0;
return -1;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
@Override
public int getHeight()
{
return sequences.size();
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
+ @Override
+ public int getAbsoluteHeight()
+ {
+ return sequences.size() + getHiddenSequences().getSize();
+ }
+
@Override
public int getWidth()
{
int maxLength = -1;
-
+
for (int i = 0; i < sequences.size(); i++)
{
if (getSequenceAt(i).getLength() > maxLength)
maxLength = getSequenceAt(i).getLength();
}
}
-
+
return maxLength;
}
+ /*
+ @Override
+ public int getWidth()
+ {
+ final Wrapper temp = new Wrapper();
+
+ forEachSequence(new Consumer<SequenceI>()
+ {
+ @Override
+ public void accept(SequenceI s)
+ {
+ if (s.getLength() > temp.inner)
+ {
+ temp.inner = s.getLength();
+ }
+ }
+ }, 0, sequences.size() - 1);
+
+ return temp.inner;
+ }
+
+ public static class Wrapper
+ {
+ public int inner;
+ }*/
/**
* DOCUMENT ME!
return true;
}
+ @Override
+ public boolean isHidden(int alignmentIndex)
+ {
+ return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null);
+ }
+
/**
* Delete all annotations, including auto-calculated if the flag is set true.
* Returns true if at least one annotation was deleted, else false.
}
@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
}
@Override
- public void setDataset(Alignment data)
+ public void setDataset(AlignmentI data)
{
if (dataset == null && data == null)
{
}
else if (dataset == null && data != null)
{
- dataset = data;
+ if (data == this)
+ {
+ throw new IllegalArgumentException("Circular dataset reference");
+ }
+ 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();
+ }
+ }
+
+ List<SequenceI> toProcess = new ArrayList<>();
+ toProcess.add(currentSeq);
+ while (toProcess.size() > 0)
+ {
+ // use a queue ?
+ SequenceI curDs = toProcess.remove(0);
+
+ if (!seqs.add(curDs))
+ {
+ continue;
+ }
+ // 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.
*/
{
return;
}
- SequenceI[] seqs = new SequenceI[getHeight()];
- SequenceI currentSeq;
+ // try to avoid using SequenceI.equals at this stage, it will be expensive
+ Set<SequenceI> seqs = new LinkedIdentityHashSet<>();
+
for (int i = 0; i < getHeight(); i++)
{
- currentSeq = getSequenceAt(i);
- if (currentSeq.getDatasetSequence() != null)
- {
- seqs[i] = currentSeq.getDatasetSequence();
- }
- else
+ SequenceI currentSeq = getSequenceAt(i);
+ resolveAndAddDatasetSeq(currentSeq, seqs, true);
+ }
+
+ // verify all mappings are in dataset
+ for (AlignedCodonFrame cf : codonFrameList)
+ {
+ for (SequenceToSequenceMapping ssm : cf.getMappings())
{
- seqs[i] = currentSeq.createDatasetSequence();
+ if (!seqs.contains(ssm.getFromSeq()))
+ {
+ resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false);
+ }
+ if (!seqs.contains(ssm.getMapping().getTo()))
+ {
+ resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false);
+ }
}
}
-
- dataset = new Alignment(seqs);
+ // 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;
current = getSequenceAt(i);
// This should really be a sequence method
ends[i * 2] = current.findIndex(current.getStart());
- ends[i * 2 + 1] = current.findIndex(current.getStart()
- + current.getLength());
+ ends[i * 2 + 1] = current
+ .findIndex(current.getStart() + current.getLength());
boolean hitres = false;
for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
{
}
@Override
+ public HiddenColumns getHiddenColumns()
+ {
+ return hiddenCols;
+ }
+
+ @Override
public CigarArray getCompactAlignment()
{
synchronized (sequences)
@Override
public void addCodonFrame(AlignedCodonFrame codons)
{
- Set<AlignedCodonFrame> acfs = getCodonFrames();
- if (codons != null && acfs != null)
+ List<AlignedCodonFrame> acfs = getCodonFrames();
+ if (codons != null && acfs != null && !acfs.contains(codons))
{
acfs.add(codons);
}
{
return null;
}
- List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> cframes = new ArrayList<>();
for (AlignedCodonFrame acf : getCodonFrames())
{
if (acf.involvesSequence(seq))
* @see jalview.datamodel.AlignmentI#setCodonFrames()
*/
@Override
- public void setCodonFrames(Set<AlignedCodonFrame> acfs)
+ public void setCodonFrames(List<AlignedCodonFrame> acfs)
{
if (dataset != null)
{
* @see jalview.datamodel.AlignmentI#getCodonFrames()
*/
@Override
- public Set<AlignedCodonFrame> getCodonFrames()
+ public List<AlignedCodonFrame> getCodonFrames()
{
+ // 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;
}
@Override
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
- Set<AlignedCodonFrame> acfs = getCodonFrames();
+ List<AlignedCodonFrame> acfs = getCodonFrames();
if (codons == null || acfs == null)
{
return false;
@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();
+ boolean samegap = oldc == getGapCharacter();
boolean hashidden = toappend.getHiddenSequences() != null
&& toappend.getHiddenSequences().hiddenSequences != null;
// get all sequences including any hidden ones
- List<SequenceI> sqs = (hashidden) ? toappend.getHiddenSequences()
- .getFullAlignment().getSequences() : toappend.getSequences();
+ List<SequenceI> sqs = (hashidden)
+ ? toappend.getHiddenSequences().getFullAlignment()
+ .getSequences()
+ : toappend.getSequences();
if (sqs != null)
{
+ // avoid self append deadlock by
+ List<SequenceI> toappendsq = new ArrayList<>();
synchronized (sqs)
{
for (SequenceI addedsq : sqs)
{
if (!samegap)
{
- char[] oldseq = addedsq.getSequence();
- for (int c = 0; c < oldseq.length; c++)
- {
- if (oldseq[c] == oldc)
- {
- oldseq[c] = gapCharacter;
- }
- }
+ addedsq.replace(oldc, gapCharacter);
}
- 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]);
}
+ // use add method
getCodonFrames().addAll(toappend.getCodonFrames());
List<SequenceGroup> sg = toappend.getGroups();
if (ourval instanceof String)
{
// append strings
- this.setProperty(k, ((String) ourval) + "; "
- + ((String) toapprop));
+ this.setProperty(k,
+ ((String) ourval) + "; " + ((String) toapprop));
}
else
{
String calcId, boolean autoCalc, SequenceI seqRef,
SequenceGroup groupRef)
{
- assert (name != null);
if (annotations != null)
{
for (AlignmentAnnotation annot : getAlignmentAnnotation())
AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
annot.hasText = false;
- annot.setCalcId(new String(calcId));
+ if (calcId != null)
+ {
+ annot.setCalcId(new String(calcId));
+ }
annot.autoCalculated = autoCalc;
if (seqRef != null)
{
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation a : getAlignmentAnnotation())
+ AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+ if (alignmentAnnotation != null)
{
- if (a.getCalcId() == calcId
- || (a.getCalcId() != null && calcId != null && a.getCalcId()
- .equals(calcId)))
- {
- aa.add(a);
- }
+ return AlignmentAnnotation.findAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), calcId);
}
- return aa;
+ return Arrays.asList(new AlignmentAnnotation[] {});
}
- /**
- * Returns an iterable collection of any annotations that match on given
- * sequence ref, calcId and label (ignoring null values).
- */
@Override
public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
String calcId, String label)
{
- ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
- for (AlignmentAnnotation ann : getAlignmentAnnotation())
- {
- if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
- && ann.sequenceRef != null && ann.sequenceRef == seq
- && ann.label != null && ann.label.equals(label))
- {
- aa.add(ann);
- }
- }
- return aa;
+ return AlignmentAnnotation.findAnnotations(
+ Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
}
@Override
* 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
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);
-
- // TODO handle intron regions? Needs a 'holistic' alignment of dna,
- // not just sequence by sequence. But how to 'gap' intron regions?
-
- /*
- * 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);
}
/**
@Override
public String toString()
{
- return new FastaFile().print(getSequencesArray());
+ return new FastaFile().print(getSequencesArray(), true);
}
/**
@Override
public Set<String> getSequenceNames()
{
- Set<String> names = new HashSet<String>();
+ Set<String> names = new HashSet<>();
for (SequenceI seq : getSequences())
{
names.add(seq.getName());
}
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 void setHiddenColumns(HiddenColumns cols)
+ {
+ hiddenCols = cols;
+ }
+
+ @Override
+ public void setupJPredAlignment()
+ {
+ SequenceI repseq = getSequenceAt(0);
+ setSeqrep(repseq);
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideList(repseq.getInsertions());
+ setHiddenColumns(cs);
+ }
+
+ @Override
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ char gc = getGapCharacter();
+ Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+ HiddenColumns nview = (HiddenColumns) alandhidden[1];
+ SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+ return propagateInsertions(profileseq, origseq, nview);
+ }
+
+ /**
+ *
+ * @param profileseq
+ * sequence in al which corresponds to origseq
+ * @param al
+ * alignment which is to have gaps inserted into it
+ * @param origseq
+ * sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ private HiddenColumns propagateInsertions(SequenceI profileseq,
+ SequenceI origseq, HiddenColumns hc)
+ {
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
+
+ // first get the gaps as a Bitset
+ // then calculate hidden ^ not(gap)
+ BitSet gaps = origseq.gapBitset();
+ hc.andNot(gaps);
+
+ // for each sequence in the alignment, except the profile sequence,
+ // insert gaps corresponding to each hidden region but where each hidden
+ // column region is shifted backwards by the number of preceding visible
+ // gaps update hidden columns at the same time
+ HiddenColumns newhidden = new HiddenColumns();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ Iterator<int[]> it = hc.iterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+
+ // get region coordinates accounting for gaps
+ // we can rely on gaps not being *in* hidden regions because we already
+ // removed those
+ while (gapPosition < region[0])
+ {
+ gapPosition++;
+ if (gaps.get(gapPosition))
+ {
+ numGapsBefore++;
+ }
+ }
+
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+
+ newhidden.hideColumns(left, right);
+ padGaps(left, right, profileseq);
+ }
+ return newhidden;
+ }
+
+ /**
+ * Pad gaps in all sequences in alignment except profileseq
+ *
+ * @param left
+ * position of first gap to insert
+ * @param right
+ * position of last gap to insert
+ * @param profileseq
+ * sequence not to pad
+ */
+ private void padGaps(int left, int right, SequenceI profileseq)
+ {
+ char gc = getGapCharacter();
+
+ // make a string with number of gaps = length of hidden region
+ StringBuilder sb = new StringBuilder();
+ for (int g = 0; g < right - left + 1; g++)
+ {
+ sb.append(gc);
+ }
+
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = getSequenceAt(s);
+ if ((sqobj != profileseq) && (sqobj.getLength() >= left))
+ {
+ String sq = sqobj.getSequenceAsString();
+ sqobj.setSequence(
+ sq.substring(0, left) + sb.toString() + sq.substring(left));
+ }
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff