package jalview.datamodel;
import jalview.analysis.AlignSeq;
+import jalview.api.DBRefEntryI;
import jalview.util.StringUtils;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
String vamsasId;
+ DBRefEntryI sourceDBRef;
+
DBRefEntry[] dbrefs;
RNA rna;
}
/**
- * Creates a new Sequence object with new features, DBRefEntries,
- * AlignmentAnnotations, and PDBIds but inherits any existing dataset sequence
- * reference.
+ * Creates a new Sequence object with new AlignmentAnnotations but inherits
+ * any existing dataset sequence reference. If non exists, everything is
+ * copied.
*
* @param seq
- * DOCUMENT ME!
+ * if seq is a dataset sequence, behaves like a plain old copy
+ * constructor
*/
public Sequence(SequenceI seq)
{
}
+ /**
+ * does the heavy lifting when cloning a dataset sequence, or coping data from
+ * dataset to a new derived sequence.
+ *
+ * @param seq
+ * - source of attributes.
+ * @param alAnnotation
+ * - alignment annotation present on seq that should be copied onto
+ * this sequence
+ */
protected void initSeqFrom(SequenceI seq,
AlignmentAnnotation[] alAnnotation)
{
- initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(),
+ {
+ char[] oseq = seq.getSequence();
+ initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
+ seq.getStart(),
seq.getEnd());
+ }
description = seq.getDescription();
- if (seq.getSequenceFeatures() != null)
+ sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
+ seq.getSourceDBRef());
+ if (seq != datasetSequence)
{
- SequenceFeature[] sf = seq.getSequenceFeatures();
- for (int i = 0; i < sf.length; i++)
- {
- addSequenceFeature(new SequenceFeature(sf[i]));
- }
+ setDatasetSequence(seq.getDatasetSequence());
}
- setDatasetSequence(seq.getDatasetSequence());
- if (datasetSequence == null && seq.getDBRef() != null)
+ if (datasetSequence == null && seq.getDBRefs() != null)
{
- // only copy DBRefs if we really are a dataset sequence
- DBRefEntry[] dbr = seq.getDBRef();
+ // only copy DBRefs and seqfeatures if we really are a dataset sequence
+ DBRefEntry[] dbr = seq.getDBRefs();
for (int i = 0; i < dbr.length; i++)
{
addDBRef(new DBRefEntry(dbr[i]));
}
+ if (seq.getSequenceFeatures() != null)
+ {
+ SequenceFeature[] sf = seq.getSequenceFeatures();
+ for (int i = 0; i < sf.length; i++)
+ {
+ addSequenceFeature(new SequenceFeature(sf[i]));
+ }
+ }
}
if (seq.getAnnotation() != null)
{
}
if (seq.getAllPDBEntries() != null)
{
- Vector ids = seq.getAllPDBEntries();
- Enumeration e = ids.elements();
- while (e.hasMoreElements())
+ Vector<PDBEntry> ids = seq.getAllPDBEntries();
+ for (PDBEntry pdb : ids)
{
- this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
+ this.addPDBId(new PDBEntry(pdb));
}
}
}
* @param v
* DOCUMENT ME!
*/
+ @Override
public void setSequenceFeatures(SequenceFeature[] features)
{
sequenceFeatures = features;
}
+ @Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
+ // TODO add to dataset sequence instead if there is one?
if (sequenceFeatures == null)
{
sequenceFeatures = new SequenceFeature[0];
sequenceFeatures = temp;
}
+ @Override
public void deleteFeature(SequenceFeature sf)
{
if (sequenceFeatures == null)
*
* @return
*/
+ @Override
public SequenceFeature[] getSequenceFeatures()
{
SequenceFeature[] features = sequenceFeatures;
return features;
}
+ @Override
public void addPDBId(PDBEntry entry)
{
if (pdbIds == null)
@Override
public Vector<PDBEntry> getAllPDBEntries()
{
- return pdbIds;
+ return pdbIds == null ? new Vector<PDBEntry>() : pdbIds;
}
/**
*
* @return DOCUMENT ME!
*/
+ @Override
public String getDisplayId(boolean jvsuffix)
{
StringBuffer result = new StringBuffer(name);
* @param name
* DOCUMENT ME!
*/
+ @Override
public void setName(String name)
{
this.name = name;
*
* @return DOCUMENT ME!
*/
+ @Override
public String getName()
{
return this.name;
* @param start
* DOCUMENT ME!
*/
+ @Override
public void setStart(int start)
{
this.start = start;
*
* @return DOCUMENT ME!
*/
+ @Override
public int getStart()
{
return this.start;
* @param end
* DOCUMENT ME!
*/
+ @Override
public void setEnd(int end)
{
this.end = end;
*
* @return DOCUMENT ME!
*/
+ @Override
public int getEnd()
{
return this.end;
*
* @return DOCUMENT ME!
*/
+ @Override
public int getLength()
{
return this.sequence.length;
* @param seq
* DOCUMENT ME!
*/
+ @Override
public void setSequence(String seq)
{
this.sequence = seq.toCharArray();
checkValidRange();
}
+ @Override
public String getSequenceAsString()
{
return new String(sequence);
}
+ @Override
public String getSequenceAsString(int start, int end)
{
return new String(getSequence(start, end));
}
+ @Override
public char[] getSequence()
{
return sequence;
*
* @see jalview.datamodel.SequenceI#getSequence(int, int)
*/
+ @Override
public char[] getSequence(int start, int end)
{
if (start < 0)
}
/**
- * DOCUMENT ME!
+ * Returns the character of the aligned sequence at the given position (base
+ * zero), or space if the position is not within the sequence's bounds
*
- * @param i
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return
*/
+ @Override
public char getCharAt(int i)
{
- if (i < sequence.length)
+ if (i >= 0 && i < sequence.length)
{
return sequence[i];
}
* @param desc
* DOCUMENT ME!
*/
+ @Override
public void setDescription(String desc)
{
this.description = desc;
*
* @return DOCUMENT ME!
*/
+ @Override
public String getDescription()
{
return this.description;
*
* @see jalview.datamodel.SequenceI#findIndex(int)
*/
+ @Override
public int findIndex(int pos)
{
// returns the alignment position for a residue
* @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
* residues in SequenceI object
*/
+ @Override
public int[] gapMap()
{
String seq = jalview.analysis.AlignSeq.extractGaps(
}
@Override
- public void setDBRef(DBRefEntry[] dbref)
+ public void setDBRefs(DBRefEntry[] dbref)
{
dbrefs = dbref;
}
@Override
- public DBRefEntry[] getDBRef()
+ public DBRefEntry[] getDBRefs()
{
if (dbrefs == null && datasetSequence != null
&& this != datasetSequence)
{
- return datasetSequence.getDBRef();
+ return datasetSequence.getDBRefs();
}
return dbrefs;
}
@Override
public void addDBRef(DBRefEntry entry)
{
+ // TODO add to dataset sequence instead if there is one?
if (dbrefs == null)
{
dbrefs = new DBRefEntry[0];
@Override
public void setDatasetSequence(SequenceI seq)
{
+ // TODO check for circular reference before setting?
datasetSequence = seq;
}
annotation.setSequenceRef(this);
}
+ @Override
public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
{
if (this.annotation != null)
*
* @see jalview.datamodel.SequenceI#createDatasetSequence()
*/
+ @Override
public SequenceI createDatasetSequence()
{
if (datasetSequence == null)
{
- datasetSequence = new Sequence(getName(), AlignSeq.extractGaps(
+ Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, getSequenceAsString()),
getStart(), getEnd());
- datasetSequence.setSequenceFeatures(getSequenceFeatures());
- datasetSequence.setDescription(getDescription());
- setSequenceFeatures(null);
- // move database references onto dataset sequence
- datasetSequence.setDBRef(getDBRef());
- setDBRef(null);
- datasetSequence.setPDBId(getAllPDBEntries());
- setPDBId(null);
+
+ datasetSequence = dsseq;
+
+ dsseq.setDescription(description);
+ // move features and database references onto dataset sequence
+ dsseq.sequenceFeatures = sequenceFeatures;
+ sequenceFeatures=null;
+ dsseq.dbrefs = dbrefs;
+ dbrefs=null;
+ // TODO: search and replace any references to this sequence with
+ // references to the dataset sequence in Mappings on dbref
+ dsseq.pdbIds = pdbIds;
+ pdbIds = null;
datasetSequence.updatePDBIds();
if (annotation != null)
{
+ // annotation is cloned rather than moved, to preserve what's currently
+ // on the alignment
for (AlignmentAnnotation aa : annotation)
{
AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
* jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
* annotations)
*/
+ @Override
public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
{
if (annotation != null)
}
}
// transfer database references
- DBRefEntry[] entryRefs = entry.getDBRef();
+ DBRefEntry[] entryRefs = entry.getDBRefs();
if (entryRefs != null)
{
for (int r = 0; r < entryRefs.length; r++)
* @return The index (zero-based) on this sequence in the MSA. It returns
* {@code -1} if this information is not available.
*/
+ @Override
public int getIndex()
{
return index;
* position for this sequence. This value is zero-based (zero for
* this first sequence)
*/
+ @Override
public void setIndex(int value)
{
index = value;
}
+ @Override
public void setRNA(RNA r)
{
rna = r;
}
+ @Override
public RNA getRNA()
{
return rna;
return result;
}
+ @Override
public String toString()
{
return getDisplayId(false);
return null;
}
+ @Override
+ public void setSourceDBRef(DBRefEntryI dbRef)
+ {
+ this.sourceDBRef = dbRef;
+ }
+
+ @Override
+ public DBRefEntryI getSourceDBRef()
+ {
+ return this.sourceDBRef;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff