From e7a39cabfa0ee4eaf45fc999ceed3ed4674b8e46 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 14 May 2012 11:10:57 +0100 Subject: [PATCH] clean up old commented code --- src/jalview/gui/SequenceFetcher.java | 143 ---------------------------------- 1 file changed, 143 deletions(-) diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 5ea5768..49511ad 100755 --- 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 (;si0) { 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 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"); -- 1.7.10.2