+ /*
+ * result = new StringBuffer(); if
+ * (database.getSelectedItem().equals("Uniprot")) {
+ * getUniprotFile(textArea.getText()); } else if
+ * (database.getSelectedItem().equals("EMBL") ||
+ * database.getSelectedItem().equals("EMBLCDS")) { String DBRefSource =
+ * database.getSelectedItem().equals("EMBLCDS") ?
+ * jalview.datamodel.DBRefSource.EMBLCDS : jalview.datamodel.DBRefSource.EMBL;
+ *
+ * StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
+ * SequenceI[] seqs = null; while(st.hasMoreTokens()) { EBIFetchClient dbFetch =
+ * new EBIFetchClient(); String qry =
+ * database.getSelectedItem().toString().toLowerCase( ) + ":" +
+ * st.nextToken(); File reply = dbFetch.fetchDataAsFile( qry, "emblxml",null);
+ *
+ * jalview.datamodel.xdb.embl.EmblFile efile=null; if (reply != null &&
+ * reply.exists()) { efile =
+ * jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply); } if (efile!=null) {
+ * for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) { EmblEntry
+ * entry = (EmblEntry) i.next(); SequenceI[] seqparts =
+ * entry.getSequences(false,true, DBRefSource); if (seqparts!=null) {
+ * SequenceI[] newseqs = null; int si=0; if (seqs==null) { newseqs = new
+ * SequenceI[seqparts.length]; } else { newseqs = new
+ * SequenceI[seqs.length+seqparts.length];
+ *
+ * for (;si<seqs.length; si++) { newseqs[si] = seqs[si]; seqs[si] = null; } }
+ * for (int j=0;j<seqparts.length; si++, j++) { newseqs[si] =
+ * seqparts[j].deriveSequence(); // place DBReferences on dataset and refer }
+ * seqs=newseqs;
+ * } } } else { result.append("# no response for "+qry); } } if (seqs!=null &&
+ * seqs.length>0) { if (parseResult(new Alignment(seqs), null, null)!=null) {
+ * result.append("# Successfully parsed the "+database.getSelectedItem()+"
+ * Queries into an Alignment"); } } } else if
+ * (database.getSelectedItem().equals("PDB")) { StringTokenizer qset = new
+ * StringTokenizer(textArea.getText(), ";"); String query; SequenceI[] seqs =
+ * null; while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null)) {
+ * 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"); } } } else if( database.getSelectedItem().equals("PFAM")) {
+ * try { result.append(new FastaFile(
+ * "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc=" +
+ * textArea.getText().toUpperCase(), "URL").print() );
+ *
+ * if(result.length()>0) { parseResult( result.toString(),
+ * textArea.getText().toUpperCase() ); }
+ * } catch (java.io.IOException ex) { result = null; } }
+ *
+ * if (result == null || result.length() == 0) { showErrorMessage("Error
+ * retrieving " + textArea.getText() + " from " + database.getSelectedItem()); }
+ *
+ * resetDialog(); return; }
+ *
+ * void getUniprotFile(String id) { EBIFetchClient ebi = new EBIFetchClient();
+ * File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
+ *
+ * DBRefFetcher dbref = new DBRefFetcher(); Vector entries =
+ * dbref.getUniprotEntries(file);
+ *
+ * if (entries != null) { //First, make the new sequences Enumeration en =
+ * entries.elements(); while (en.hasMoreElements()) { UniprotEntry entry =
+ * (UniprotEntry) en.nextElement();
+ *
+ * StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot"); Enumeration
+ * en2 = entry.getAccession().elements(); while (en2.hasMoreElements()) {
+ * name.append("|"); name.append(en2.nextElement()); } en2 =
+ * entry.getName().elements(); while (en2.hasMoreElements()) {
+ * name.append("|"); name.append(en2.nextElement()); }
+ *
+ * if (entry.getProtein() != null) { name.append(" " +
+ * entry.getProtein().getName().elementAt(0)); }
+ *
+ * result.append(name + "\n" + entry.getUniprotSequence().getContent() +
+ * "\n");
+ * }
+ *
+ * //Then read in the features and apply them to the dataset Alignment al =
+ * parseResult(result.toString(), null); for (int i = 0; i < entries.size();
+ * i++) { UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
+ * Enumeration e = entry.getDbReference().elements(); Vector onlyPdbEntries =
+ * new Vector(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry)
+ * e.nextElement(); if (!pdb.getType().equals("PDB")) { continue; }
+ *
+ * onlyPdbEntries.addElement(pdb); }
+ *
+ * Enumeration en2 = entry.getAccession().elements(); while
+ * (en2.hasMoreElements()) {
+ * al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
+ * DBRefSource.UNIPROT, "0", en2.nextElement().toString())); }
+ *
+ *
+ *
+ *
+ * al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries); if
+ * (entry.getFeature() != null) { e = entry.getFeature().elements(); while
+ * (e.hasMoreElements()) { SequenceFeature sf = (SequenceFeature)
+ * e.nextElement(); sf.setFeatureGroup("Uniprot");
+ * al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf ); } } } } }
+ *
+ * SequenceI[] getPDBFile(String id) { Vector result = new Vector(); String
+ * chain = null; if (id.indexOf(":") > -1) { chain =
+ * id.substring(id.indexOf(":") + 1); id = id.substring(0, id.indexOf(":")); }
+ *
+ * EBIFetchClient ebi = new EBIFetchClient(); String file =
+ * ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw"). getAbsolutePath(); if (file ==
+ * null) { return null; } try { PDBfile pdbfile = new PDBfile(file,
+ * jalview.io.AppletFormatAdapter.FILE); for (int i = 0; i <
+ * pdbfile.chains.size(); i++) { if (chain == null || ( (PDBChain)
+ * pdbfile.chains.elementAt(i)).id. 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()); } }
+ *
+ * if (result.size() < 1) { throw new Exception("WsDBFetch for PDB id resulted
+ * in zero result size"); } } catch (Exception ex) // Problem parsing PDB file {
+ * jalview.bin.Cache.log.warn("Exception when retrieving " +
+ * textArea.getText() + " from " + database.getSelectedItem(), ex); return
+ * null; }
+ *
+ *
+ * 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; }
+ */
+ AlignmentI parseResult(String result, String title)