* @param pdbId
* @return
*/
- String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
+ String origFile)
{
if (alreadyLoadedPDB.containsKey(pdbId))
{
return alreadyLoadedPDB.get(pdbId).toString();
}
- String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb");
+ String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
+ origFile);
if (tempFile != null)
{
alreadyLoadedPDB.put(pdbId, tempFile);
* @param prefix
* a prefix for the temporary file name, must be at least three
* characters long
+ * @param origFile
+ * null or original file - so new file can be given the same suffix
+ * as the old one
* @return
*/
protected String copyJarEntry(jarInputStreamProvider jprovider,
- String jarEntryName, String prefix)
+ String jarEntryName, String prefix, String origFile)
{
BufferedReader in = null;
PrintWriter out = null;
-
+ String suffix = ".tmp";
+ if (origFile == null)
+ {
+ origFile = jarEntryName;
+ }
+ int sfpos = origFile.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (origFile.length() - 3))
+ {
+ suffix = "." + origFile.substring(sfpos + 1);
+ }
try
{
JarInputStream jin = jprovider.getJarInputStream();
if (entry != null)
{
in = new BufferedReader(new InputStreamReader(jin, UTF_8));
- File outFile = File.createTempFile(prefix, ".tmp");
+ File outFile = File.createTempFile(prefix, suffix);
outFile.deleteOnExit();
out = new PrintWriter(new FileOutputStream(outFile));
String data;
} else {
incompleteSeqs.remove(seqId);
}
- if (vamsasSeq[vi].getId().equals(seqId))
+ if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId))
{
// most likely we are reading a dataset XML document so
// update from vamsasSeq section of XML for this sequence
entry.setId(ids[p].getId());
if (ids[p].getType() != null)
{
- if (ids[p].getType().equalsIgnoreCase("PDB"))
+ if (PDBEntry.Type.getType(ids[p].getType()) != null)
{
- entry.setType(PDBEntry.Type.PDB);
+ entry.setType(PDBEntry.Type.getType(ids[p].getType()));
}
else
{
{
if (!pdbloaded.containsKey(ids[p].getFile()))
{
- entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ entry.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
}
else
{
entry.setFile(pdbloaded.get(ids[p].getId()).toString());
}
}
+ if (ids[p].getPdbentryItem() != null)
+ {
+ entry.setProperty(new Hashtable());
+ for (PdbentryItem item : ids[p].getPdbentryItem())
+ {
+ for (Property pr : item.getProperty())
+ {
+ entry.getProperty().put(pr.getName(), pr.getValue());
+ }
+ }
+ }
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(entry);
// adds PDBEntry to datasequence's set (since Jalview 2.10)
String rnaTitle = ss.getTitle();
String sessionState = ss.getViewerState();
String tempStateFile = copyJarEntry(jprovider, sessionState,
- "varna");
+ "varna", null);
RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
appVarna.addModelSession(rna, rnaTitle, tempStateFile);
}
// Originally : ids[p].getFile()
// : TODO: verify external PDB file recovery still works in normal
// jalview project load
- jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile()));
jpdb.setId(ids[p].getId());
int x = structureState.getXpos();
// Probably don't need to do this anymore...
// Desktop.desktop.getComponentAt(x, y);
// TODO: NOW: check that this recovers the PDB file correctly.
- String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId(),
+ ids[p].getFile());
jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i]
.getId() + "");
if (sviewid == null)
*/
String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
- "chimera");
+ "chimera", null);
Set<Entry<File, StructureData>> fileData = data.getFileData()
.entrySet();
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
- ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i);
}
// create a new dataset
if (ds == null)
* dataset alignment
* @param dseqs
* vector to add new dataset sequence to
+ * @param ignoreUnrefed
+ * - when true, don't create new sequences from vamsasSeq if it's id
+ * doesn't already have an asssociated Jalview sequence.
+ * @param vseqpos
+ * - used to reorder the sequence in the alignment according to the
+ * vamsasSeq array ordering, to preserve ordering of dataset
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
SequenceI sq = seqRefIds.get(vamsasSeq.getId());
+ boolean reorder = false;
SequenceI dsq = null;
if (sq != null && sq.getDatasetSequence() != null)
{
dsq = sq.getDatasetSequence();
}
+ else
+ {
+ reorder = true;
+ }
if (sq == null && ignoreUnrefed)
{
return;
// + (post ? "appended" : ""));
}
}
+ else
+ {
+ // sequence refs are identical. We may need to update the existing dataset
+ // alignment with this one, though.
+ if (ds != null && dseqs == null)
+ {
+ int opos = ds.findIndex(dsq);
+ SequenceI tseq = null;
+ if (opos != -1 && vseqpos != opos)
+ {
+ // remove from old position
+ ds.deleteSequence(dsq);
+ }
+ if (vseqpos < ds.getHeight())
+ {
+ if (vseqpos != opos)
+ {
+ // save sequence at destination position
+ tseq = ds.getSequenceAt(vseqpos);
+ ds.replaceSequenceAt(vseqpos, dsq);
+ ds.addSequence(tseq);
+ }
+ }
+ else
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
}
/*