import jalview.analysis.AlignSeq;
import jalview.api.DBRefEntryI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
import jalview.util.StringUtils;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.Enumeration;
import java.util.List;
import java.util.Vector;
String vamsasId;
- DBRefEntryI sourceDBRef;
-
DBRefEntry[] dbrefs;
RNA rna;
seq.getEnd());
}
description = seq.getDescription();
- sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
- seq.getSourceDBRef());
if (seq != datasetSequence)
{
setDatasetSequence(seq.getDatasetSequence());
@Override
public void setSequenceFeatures(SequenceFeature[] features)
{
- sequenceFeatures = features;
+ if (datasetSequence == null)
+ {
+ sequenceFeatures = features;
+ }
+ else
+ {
+ if (datasetSequence.getSequenceFeatures() != features
+ && datasetSequence.getSequenceFeatures() != null
+ && datasetSequence.getSequenceFeatures().length > 0)
+ {
+ new Exception(
+ "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
+ .printStackTrace();
+ }
+ datasetSequence.setSequenceFeatures(features);
+ }
}
@Override
public synchronized void addSequenceFeature(SequenceFeature sf)
{
- // TODO add to dataset sequence instead if there is one?
+ if (sequenceFeatures==null && datasetSequence != null)
+ {
+ datasetSequence.addSequenceFeature(sf);
+ return;
+ }
if (sequenceFeatures == null)
{
sequenceFeatures = new SequenceFeature[0];
{
if (sequenceFeatures == null)
{
+ if (datasetSequence!=null) {
+ datasetSequence.deleteFeature(sf);
+ }
return;
}
dbrefs = new DBRefEntry[0];
}
- int i, iSize = dbrefs.length;
-
- for (i = 0; i < iSize; i++)
+ for (DBRefEntryI dbr : dbrefs)
{
- if (dbrefs[i].equalRef(entry))
+ if (dbr.updateFrom(entry))
{
- if (entry.getMap() != null)
- {
- if (dbrefs[i].getMap() == null)
- {
- // overwrite with 'superior' entry that contains a mapping.
- dbrefs[i] = entry;
- }
- }
+ /*
+ * found a dbref that either matched, or could be
+ * updated from, the new entry - no need to add it
+ */
return;
}
}
- DBRefEntry[] temp = new DBRefEntry[iSize + 1];
- System.arraycopy(dbrefs, 0, temp, 0, iSize);
+ /*
+ * extend the array to make room for one more
+ */
+ // TODO use an ArrayList instead
+ int j = dbrefs.length;
+ DBRefEntry[] temp = new DBRefEntry[j + 1];
+ System.arraycopy(dbrefs, 0, temp, 0, j);
temp[temp.length - 1] = entry;
dbrefs = temp;
return new Sequence(this);
}
+ private boolean _isNa;
+
+ private long _seqhash = 0;
+
+ @Override
+ public boolean isProtein()
+ {
+ if (datasetSequence != null)
+ {
+ return datasetSequence.isProtein();
+ }
+ if (_seqhash != sequence.hashCode())
+ {
+ _seqhash = sequence.hashCode();
+ _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
+ }
+ return !_isNa;
+ };
+
/*
* (non-Javadoc)
*
@Override
public PDBEntry getPDBEntry(String pdbIdStr)
{
- if (getDatasetSequence() == null
- || getDatasetSequence().getAllPDBEntries() == null)
+ if (getDatasetSequence() != null)
+ {
+ return getDatasetSequence().getPDBEntry(pdbIdStr);
+ }
+ if (pdbIds == null)
{
return null;
}
- List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+ List<PDBEntry> entries = getAllPDBEntries();
for (PDBEntry entry : entries)
{
if (entry.getId().equalsIgnoreCase(pdbIdStr))
return null;
}
- @Override
- public void setSourceDBRef(DBRefEntryI dbRef)
- {
- this.sourceDBRef = dbRef;
- }
@Override
- public DBRefEntryI getSourceDBRef()
+ public List<DBRefEntry> getPrimaryDBRefs()
{
- return this.sourceDBRef;
+ if (datasetSequence!=null)
+ {
+ return datasetSequence.getPrimaryDBRefs();
+ }
+ if (dbrefs==null || dbrefs.length==0)
+ {
+ return Collections.emptyList();
+ }
+ synchronized (dbrefs)
+ {
+ List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+ DBRefEntry[] tmp = new DBRefEntry[1];
+ for (DBRefEntry ref : dbrefs)
+ {
+ if (!ref.isPrimary())
+ {
+ continue;
+ }
+ if (ref.hasMap())
+ {
+ MapList mp = ref.getMap().getMap();
+ if (mp.getFromLowest() > start || mp.getFromHighest() < end)
+ {
+ // map only involves a subsequence, so cannot be primary
+ continue;
+ }
+ }
+ // whilst it looks like it is a primary ref, we also sanity check type
+ if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
+ DBRefUtils.getCanonicalName(ref.getSource())))
+ {
+ // PDB dbrefs imply there should be a PDBEntry associated
+ // TODO: tighten PDB dbrefs
+ // formally imply Jalview has actually downloaded and
+ // parsed the pdb file. That means there should be a cached file
+ // handle on the PDBEntry, and a real mapping between sequence and
+ // extracted sequence from PDB file
+ PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
+ if (pdbentry != null && pdbentry.getFile() != null)
+ {
+ primaries.add(ref);
+ }
+ continue;
+ }
+ // check standard protein or dna sources
+ tmp[0] = ref;
+ DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+ if (res != null && res[0] == tmp[0])
+ {
+ primaries.add(ref);
+ continue;
+ }
+ }
+ return primaries;
+ }
}
}