/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.datamodel;
-import jalview.analysis.AlignSeq;
-
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.List;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
+
/**
*
* Implements the SequenceI interface for a char[] based sequence object.
int end;
- Vector pdbIds;
+ Vector<PDBEntry> pdbIds;
String vamsasId;
.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
name = "";
}
- // Does sequence have the /start-end signiature?
+ // Does sequence have the /start-end signature?
if (limitrx.search(name))
{
name = limitrx.left();
}
/**
- * DOCUMENT ME!
+ * 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).
*
- * @return DOCUMENT ME!
+ * @return
*/
public SequenceFeature[] getSequenceFeatures()
{
- return sequenceFeatures;
+ SequenceFeature[] features = sequenceFeatures;
+
+ SequenceI seq = this;
+ int count = 0; // failsafe against loop in sequence.datasetsequence...
+ while (features == null && seq.getDatasetSequence() != null
+ && count++ < 10)
+ {
+ seq = seq.getDatasetSequence();
+ features = ((Sequence) seq).sequenceFeatures;
+ }
+ return features;
}
public void addPDBId(PDBEntry entry)
{
if (pdbIds == null)
{
- pdbIds = new Vector();
+ pdbIds = new Vector<PDBEntry>();
}
- if (!pdbIds.contains(entry))
+ if (pdbIds.contains(entry))
+ {
+ updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
+ }
+ else
{
pdbIds.addElement(entry);
}
}
+ private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
+ {
+ if (newEntry.getFile() != null)
+ {
+ oldEntry.setFile(newEntry.getFile());
+ }
+ }
+
/**
* DOCUMENT ME!
*
* @param id
* DOCUMENT ME!
*/
- public void setPDBId(Vector id)
+ @Override
+ public void setPDBId(Vector<PDBEntry> id)
{
pdbIds = id;
}
*
* @return DOCUMENT ME!
*/
- public Vector getPDBId()
+ @Override
+ public Vector<PDBEntry> getPDBId()
{
return pdbIds;
}
return map;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#findPositionMap()
- */
+ @Override
public int[] findPositionMap()
{
int map[] = new int[sequence.length];
return map;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#deleteChars(int, int)
- */
+ @Override
+ public List<int[]> getInsertions()
+ {
+ ArrayList<int[]> map = new ArrayList<int[]>();
+ int lastj = -1, j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
+ {
+ if (jalview.util.Comparison.isGap(sequence[j]))
+ {
+ if (lastj == -1)
+ {
+ lastj = j;
+ }
+ }
+ else
+ {
+ if (lastj != -1)
+ {
+ map.add(new int[]
+ { lastj, j - 1 });
+ lastj = -1;
+ }
+ }
+ j++;
+ }
+ if (lastj != -1)
+ {
+ map.add(new int[]
+ { lastj, j - 1 });
+ lastj = -1;
+ }
+ return map;
+ }
+
+ @Override
public void deleteChars(int i, int j)
{
int newstart = start, newend = end;
return;
}
- char[] tmp;
-
- if (j >= sequence.length)
- {
- tmp = new char[i];
- System.arraycopy(sequence, 0, tmp, 0, i);
- j = sequence.length;
- }
- else
- {
- tmp = new char[sequence.length - j + i];
- System.arraycopy(sequence, 0, tmp, 0, i);
- System.arraycopy(sequence, j, tmp, i, sequence.length - j);
- }
+ char[] tmp = StringUtils.deleteChars(sequence, i, j);
boolean createNewDs = false;
- // TODO: take a look at the new dataset creation validation method below -
- // this could become time comsuming for large sequences - consider making it
- // more efficient
+ // TODO: take a (second look) at the dataset creation validation method for
+ // the very large sequence case
+ int eindex = -1, sindex = -1;
+ boolean ecalc = false, scalc = false;
for (int s = i; s < j; s++)
{
if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
}
else
{
- int sindex = findIndex(start) - 1;
+ if (!scalc)
+ {
+ sindex = findIndex(start) - 1;
+ scalc = true;
+ }
if (sindex == s)
{
// delete characters including start of sequence
else
{
// delete characters after start.
- int eindex = findIndex(end) - 1;
+ if (!ecalc)
+ {
+ eindex = findIndex(end) - 1;
+ ecalc = true;
+ }
if (eindex < j)
{
// delete characters at end of sequence
sequence = tmp;
}
- /**
- * DOCUMENT ME!
- *
- * @param i
- * DOCUMENT ME!
- * @param c
- * DOCUMENT ME!
- * @param chop
- * DOCUMENT ME!
- */
+ @Override
public void insertCharAt(int i, int length, char c)
{
char[] tmp = new char[sequence.length + length];
sequence = tmp;
}
+ @Override
public void insertCharAt(int i, char c)
{
insertCharAt(i, 1, c);
}
+ @Override
public String getVamsasId()
{
return vamsasId;
}
+ @Override
public void setVamsasId(String id)
{
vamsasId = id;
}
+ @Override
public void setDBRef(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
+ @Override
public DBRefEntry[] getDBRef()
{
if (dbrefs == null && datasetSequence != null
return dbrefs;
}
+ @Override
public void addDBRef(DBRefEntry entry)
{
if (dbrefs == null)
dbrefs = temp;
}
+ @Override
public void setDatasetSequence(SequenceI seq)
{
datasetSequence = seq;
}
+ @Override
public SequenceI getDatasetSequence()
{
return datasetSequence;
}
- /**
- * Returns a new array containing this sequence's annotations, or null.
- */
+ @Override
public AlignmentAnnotation[] getAnnotation()
{
return annotation == null ? null : annotation
.toArray(new AlignmentAnnotation[annotation.size()]);
}
- /**
- * Returns true if this sequence has the given annotation (by object
- * identity).
- */
+
@Override
public boolean hasAnnotation(AlignmentAnnotation ann)
{
return annotation == null ? false : annotation.contains(ann);
}
- /**
- * Add the given annotation, if not already added, and set its sequence ref to
- * be this sequence. Does nothing if this sequence's annotations already
- * include this annotation (by identical object reference).
- */
+ @Override
public void addAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation == null)
{
- this.annotation = new Vector();
+ this.annotation = new Vector<AlignmentAnnotation>();
}
if (!this.annotation.contains(annotation))
{
return true;
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#deriveSequence()
- */
+ @Override
public SequenceI deriveSequence()
{
SequenceI seq = new Sequence(this);
AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
_aa.sequenceRef = datasetSequence;
_aa.adjustForAlignment(); // uses annotation's own record of
- // sequence-column mapping
+ // sequence-column mapping
datasetSequence.addAlignmentAnnotation(_aa);
}
}
}
}
- /*
- * (non-Javadoc)
- *
- * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
- */
+ @Override
public AlignmentAnnotation[] getAnnotation(String label)
{
if (annotation == null || annotation.size() == 0)
return anns;
}
+ @Override
public boolean updatePDBIds()
{
if (datasetSequence != null)
return false;
}
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
- * jalview.datamodel.Mapping)
- */
+ @Override
public void transferAnnotation(SequenceI entry, Mapping mp)
{
if (datasetSequence != null)
return rna;
}
- /**
- * Returns a (possibly empty) list of any annotations that match on given
- * calcId (source) and label (type). Null values do not match.
- *
- * @param calcId
- * @param label
- */
@Override
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label)
{
List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
- if (this.annotation != null) {
- for (AlignmentAnnotation ann : annotation) {
+ if (this.annotation != null)
+ {
+ for (AlignmentAnnotation ann : annotation)
+ {
if (ann.calcId != null && ann.calcId.equals(calcId)
&& ann.label != null && ann.label.equals(label))
{
git://source.jalview.org / jalview.git / blobdiff