*/
package jalview.datamodel;
+import jalview.analysis.AlignSeq;
+import jalview.util.StringUtils;
+
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.
}
}
}
- if (seq.getPDBId() != null)
+ if (seq.getAllPDBEntries() != null)
{
- Vector ids = seq.getPDBId();
+ Vector ids = seq.getAllPDBEntries();
Enumeration e = ids.elements();
while (e.hasMoreElements())
{
* @return DOCUMENT ME!
*/
@Override
- public Vector<PDBEntry> getPDBId()
+ public Vector<PDBEntry> getAllPDBEntries()
{
return pdbIds;
}
{
if (lastj != -1)
{
- map.add(new int[]
- { lastj, j - 1 });
+ map.add(new int[] { lastj, j - 1 });
lastj = -1;
}
}
}
if (lastj != -1)
{
- map.add(new int[]
- { lastj, j - 1 });
+ map.add(new int[] { lastj, j - 1 });
lastj = -1;
}
return map;
public void deleteChars(int i, int j)
{
int newstart = start, newend = end;
- if (i >= sequence.length)
+ if (i >= sequence.length || i < 0)
{
return;
}
.toArray(new AlignmentAnnotation[annotation.size()]);
}
-
@Override
public boolean hasAnnotation(AlignmentAnnotation ann)
{
// move database references onto dataset sequence
datasetSequence.setDBRef(getDBRef());
setDBRef(null);
- datasetSequence.setPDBId(getPDBId());
+ datasetSequence.setPDBId(getAllPDBEntries());
setPDBId(null);
datasetSequence.updatePDBIds();
if (annotation != null)
for (int si = 0; si < sfs.length; si++)
{
SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si])
- : new SequenceFeature[]
- { new SequenceFeature(sfs[si]) };
+ : new SequenceFeature[] { new SequenceFeature(sfs[si]) };
if (sf != null && sf.length > 0)
{
for (int sfi = 0; sfi < sf.length; sfi++)
}
// transfer PDB entries
- if (entry.getPDBId() != null)
+ if (entry.getAllPDBEntries() != null)
{
- Enumeration e = entry.getPDBId().elements();
+ Enumeration e = entry.getAllPDBEntries().elements();
while (e.hasMoreElements())
{
PDBEntry pdb = (PDBEntry) e.nextElement();
return result;
}
+ public String toString()
+ {
+ return getDisplayId(false);
+ }
+
+ @Override
+ public PDBEntry getPDBEntry(String pdbIdStr)
+ {
+ if (getDatasetSequence() == null
+ || getDatasetSequence().getAllPDBEntries() == null)
+ {
+ return null;
+ }
+ List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+ for (PDBEntry entry : entries)
+ {
+ if (entry.getId().equalsIgnoreCase(pdbIdStr))
+ {
+ return entry;
+ }
+ }
+ return null;
+ }
+
}