{
StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");
String query;
+ SequenceI[] seqs = null;
while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
{
- StringBuffer respart = getPDBFile(query.toUpperCase());
- if(respart!=null)
- result.append(respart);
+ SequenceI[] seqparts = getPDBFile(query.toUpperCase());
+ if (seqparts!=null) {
+ if (seqs==null) {
+ seqs = seqparts;
+ } else {
+ SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];
+ int i=0;
+ for (;i<seqs.length; i++) {
+ newseqs[i] = seqs[i];
+ seqs[i] = null;
+ }
+ for (int j=0;j<seqparts.length; i++, j++)
+ newseqs[i] = seqparts[j];
+ seqs=newseqs;
+ }
+ result.append("# Success for "+query.toUpperCase()+"\n");
+ }
+ }
+ if (seqs!=null && seqs.length>0) {
+ if (parseResult(new Alignment(seqs), null, null)!=null)
+ result.append("# Successfully parsed the PDB File Queries into an Alignment");
}
-
-
- if (result.length()>0)
- parseResult(result.toString(), null);
}
else if( database.getSelectedItem().equals("PFAM"))
{
}
}
- StringBuffer getPDBFile(String id)
+ SequenceI[] getPDBFile(String id)
{
- StringBuffer result = new StringBuffer();
+ Vector result = new Vector();
String chain = null;
if (id.indexOf(":") > -1)
{
{
if (chain == null ||
( (PDBChain) pdbfile.chains.elementAt(i)).id.
- toUpperCase().equals(chain))
-
- result.append("\n>PDB|" + id + "|" +
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
- getName() +
- "\n"
- +
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
- getSequenceAsString());
+ toUpperCase().equals(chain)) {
+ PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
+ // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file
+ SequenceI sq = pdbchain.sequence;
+ // Specially formatted name for the PDB chain sequences retrieved from the PDB
+ sq.setName("PDB|"+id+"|"+sq.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry();
+ // Construct the PDBEntry
+ entry.setId(id);
+ if (entry.getProperty() == null)
+ entry.setProperty(new Hashtable());
+ entry.getProperty().put("chains",
+ pdbchain.id
+ + "=" + sq.getStart()
+ + "-" + sq.getEnd());
+ sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
+ DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",id+pdbchain.id);
+ sq.addDBRef(dbentry);
+ // and add seuqence to the retrieved set
+ result.addElement(sq.deriveSequence());
+ }
}
}
catch (Exception ex) // Problem parsing PDB file
database.getSelectedItem(), ex);
return null;
}
-
- return result;
+ SequenceI[] results = new SequenceI[result.size()];
+ for (int i=0,j=result.size();i<j; i++) {
+ results[i] = (SequenceI) result.elementAt(i);
+ result.setElementAt(null,i);
+ }
+ return results;
}
-
Alignment parseResult(String result, String title)
{
- String format = new IdentifyFile().Identify(result, "Paste");
- Alignment al = null;
-
- if (FormatAdapter.isValidFormat(format))
- {
-
- try{ al = new FormatAdapter().readFile(result.toString(), "Paste",
- format);}
- catch(Exception ex){}
+ String format = new IdentifyFile().Identify(result, "Paste");
+ Alignment sequences = null;
+ if (FormatAdapter.isValidFormat(format))
+ {
+ sequences = null;
+ try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
+ format);}
+ catch(Exception ex){}
+
+ if (sequences!=null)
+ return parseResult(sequences, title, format);
+ } else {
+ showErrorMessage("Error retrieving " + textfield.getText()
+ + " from " + database.getSelectedItem());
+ }
+ return null;
+ }
+ Alignment parseResult(Alignment al, String title, String currentFileFormat) {
+
if (al != null && al.getHeight() > 0)
{
if (alignFrame == null)
{
AlignFrame af = new AlignFrame(al,
AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT
-);
- af.currentFileFormat = format;
+ AlignFrame.DEFAULT_HEIGHT);
+ if (currentFileFormat!=null)
+ af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
+
if(title==null)
title = "Retrieved from " + database.getSelectedItem();
+
Desktop.addInternalFrame(af,
title,
AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
+
af.statusBar.setText("Successfully pasted alignment file");
try
{
for (int i = 0; i < al.getHeight(); i++)
{
- alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i));
-
- ////////////////////////////
- //Dataset needs extension;
- /////////////////////////////
- Sequence ds = new Sequence(al.getSequenceAt(i).getName(),
- AlignSeq.extractGaps("-. ",
- al.getSequenceAt(i).getSequenceAsString()),
- al.getSequenceAt(i).getStart(),
- al.getSequenceAt(i).getEnd());
- al.getSequenceAt(i).setDatasetSequence(ds);
- alignFrame.viewport.alignment.getDataset().addSequence(ds);
+ alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
}
alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
getHeight());
alignFrame.viewport.firePropertyChange("alignment", null,
alignFrame.viewport.
getAlignment().getSequences());
-
- }
-
- if (database.getSelectedItem().equals("PDB"))
- {
- // Parse out the ids from the structured names
- boolean errors = false;
- for (int i = 0; i < al.getHeight(); i++)
- {
- PDBEntry entry = new PDBEntry();
- com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(
- "PDB\\|([0-9A-z]{4})\\|(.)");
- if (idbits.search(al.getSequenceAt(i).getName()))
- {
- String pdbid = idbits.substring(1);
- String pdbccode = idbits.substring(2);
- // Construct the PDBEntry
- entry.setId(pdbid);
- if (entry.getProperty() == null)
- entry.setProperty(new Hashtable());
- entry.getProperty().put("chains",
- pdbccode
- + "=" + al.getSequenceAt(i).getStart()
- + "-" + al.getSequenceAt(i).getEnd());
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
-
- // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
- DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",pdbid);
- al.getSequenceAt(i).getDatasetSequence().addDBRef(dbentry);
- }
- else
- {
- // don't add an entry for this chain, but this is probably a bug
- // that the user should know about.
- jalview.bin.Cache.log.warn(
- "No PDBEntry constructed for sequence " + i + " : " +
- al.getSequenceAt(i).getName());
- errors = true;
- }
- }
- if (errors)
- jalview.bin.Cache.log.warn(
- "Query string that resulted in PDBEntry construction failure was :\n" +
- textfield.getText());
}
-
}
- else
- showErrorMessage("Error retrieving " + textfield.getText()
- + " from " + database.getSelectedItem());
- }
-
return al;
-
}
void showErrorMessage(final String error)
git://source.jalview.org / jalview.git / blobdiff