clean up old commented code

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 5ea5768..49511ad 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -572,149 +572,6 @@ public class SequenceFetcher extends JPanel implements Runnable
     resetDialog();
   }
 
-  /*
-   * 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)
   {
     String format = new IdentifyFile().Identify(result, "Paste");