{
private Alignment dataset;
- protected List<SequenceI> sequences;
+ private List<SequenceI> sequences;
protected List<SequenceGroup> groups;
HiddenSequences hiddenSequences;
+ HiddenColumns hiddenCols;
+
public Hashtable alignmentProperties;
private List<AlignedCodonFrame> codonFrameList;
{
groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
hiddenSequences = new HiddenSequences(this);
- codonFrameList = new ArrayList<AlignedCodonFrame>();
+ hiddenCols = new HiddenColumns();
+ codonFrameList = new ArrayList<>();
nucleotide = Comparison.isNucleotide(seqs);
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. Note
* this currently does not recalculate whether or not the alignment is
}
}
- /**
- * 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)
*
@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);
}
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.
}
else if (dataset == null && data != null)
{
+ if (data == this)
+ {
+ throw new IllegalArgumentException("Circular dataset reference");
+ }
if (!(data instanceof Alignment))
{
throw new Error(
currentSeq = currentSeq.createDatasetSequence();
}
}
- if (seqs.contains(currentSeq))
- {
- return;
- }
- List<SequenceI> toProcess = new ArrayList<SequenceI>();
+
+ List<SequenceI> toProcess = new ArrayList<>();
toProcess.add(currentSeq);
while (toProcess.size() > 0)
{
// use a queue ?
SequenceI curDs = toProcess.remove(0);
- if (seqs.contains(curDs))
+
+ if (!seqs.add(curDs))
{
continue;
}
- seqs.add(curDs);
// iterate over database references, making sure we add forward referenced
// sequences
if (curDs.getDBRefs() != null)
}
if (dbr.getMap().getTo().getDatasetSequence() != null)
{
- throw new Error(
- "Implementation error: Map.getTo() for dbref " + dbr
- + " from " + curDs.getName()
- + " is not a 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 LinkedIdentityHashSet<SequenceI>();
+ Set<SequenceI> seqs = new LinkedIdentityHashSet<>();
for (int i = 0; i < getHeight(); i++)
{
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)
{
return null;
}
- List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> cframes = new ArrayList<>();
for (AlignedCodonFrame acf : getCodonFrames())
{
if (acf.involvesSequence(seq))
{
// 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<SequenceI>();
+ 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);
}
toappendsq.add(addedsq);
}
if (ourval instanceof String)
{
// append strings
- this.setProperty(k, ((String) ourval) + "; "
- + ((String) toapprop));
+ this.setProperty(k,
+ ((String) ourval) + "; " + ((String) toapprop));
}
else
{
@Override
public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
{
- List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> aa = new ArrayList<>();
AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
if (alignmentAnnotation != null)
{
for (AlignmentAnnotation a : alignmentAnnotation)
{
- if (a.getCalcId() == calcId
- || (a.getCalcId() != null && calcId != null && a
- .getCalcId().equals(calcId)))
+ if (a.getCalcId() == calcId || (a.getCalcId() != null
+ && calcId != null && a.getCalcId().equals(calcId)))
{
aa.add(a);
}
return aa;
}
- /**
- * 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>();
+ ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
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))
+ if ((calcId == null || (ann.getCalcId() != null
+ && ann.getCalcId().equals(calcId)))
+ && (seq == null || (ann.sequenceRef != null
+ && ann.sequenceRef == seq))
+ && (label == null
+ || (ann.label != null && ann.label.equals(label))))
{
aa.add(ann);
}
@Override
public Set<String> getSequenceNames()
{
- Set<String> names = new HashSet<String>();
+ Set<String> names = new HashSet<>();
for (SequenceI seq : getSequences())
{
names.add(seq.getName());
}
@Override
- public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols)
+ public void setHiddenColumns(HiddenColumns cols)
{
- 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 };
+ hiddenCols = cols;
}
}
git://source.jalview.org / jalview.git / blobdiff