From 9749ae4861ba174e80afe4de8bd2dd039e5334ba Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 2 May 2007 13:03:14 +0000 Subject: [PATCH] Allow expansion of textarea for many sequence input --- src/jalview/gui/SequenceFetcher.java | 1162 +++++++++++++++++----------------- 1 file changed, 582 insertions(+), 580 deletions(-) diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 0ea13a2..4d21506 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,580 +1,582 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import java.io.*; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; -import javax.swing.*; - -import MCview.*; -import jalview.datamodel.*; -import jalview.datamodel.xdb.embl.*; -import jalview.analysis.*; -import java.io.File; -import jalview.io.*; - -public class SequenceFetcher -extends JPanel implements Runnable -{ - JInternalFrame frame; - AlignFrame alignFrame; - StringBuffer result; - final String noDbSelected = "-- Select Database --"; - public SequenceFetcher(AlignFrame af) - { - alignFrame = af; - database.addItem(noDbSelected); - database.addItem("Uniprot"); - database.addItem("EMBL"); - database.addItem("EMBLCDS"); - database.addItem("PDB"); - database.addItem("PFAM"); - - try - { - jbInit(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - - frame = new JInternalFrame(); - frame.setContentPane(this); - if (System.getProperty("os.name").startsWith("Mac")) - { - Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140); - } - else - { - Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125); - } - } - - private String getFrameTitle() - { - return ( (alignFrame == null) ? "New " : "Additional ") + - "Sequence Fetcher"; - } - - private void jbInit() - throws Exception - { - this.setLayout(gridBagLayout1); - - database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - database.setMinimumSize(new Dimension(160, 21)); - database.setPreferredSize(new Dimension(160, 21)); - jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); - jLabel1.setText( - "Separate multiple accession ids with semi colon \";\""); - ok.setText("OK"); - ok.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - ok_actionPerformed(e); - } - }); - close.setText("Close"); - close.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - close_actionPerformed(e); - } - }); - textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - textfield.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - ok_actionPerformed(e); - } - }); - jPanel1.add(ok); - jPanel1.add(close); - this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0 - , GridBagConstraints.WEST, - GridBagConstraints.NONE, - new Insets(7, 4, 0, 6), 77, 6)); - this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0 - , GridBagConstraints.WEST, - GridBagConstraints.BOTH, - new Insets(7, -2, 7, 12), 241, -2)); - this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0 - , GridBagConstraints.WEST, - GridBagConstraints.NONE, - new Insets(0, 4, 0, 0), 1, 0)); - this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0 - , GridBagConstraints.CENTER, - GridBagConstraints.NONE, - new Insets(0, 0, 0, 6), 211, 1)); - } - - JComboBox database = new JComboBox(); - JLabel jLabel1 = new JLabel(); - JButton ok = new JButton(); - JButton close = new JButton(); - JPanel jPanel1 = new JPanel(); - JTextField textfield = new JTextField(); - GridBagLayout gridBagLayout1 = new GridBagLayout(); - public void close_actionPerformed(ActionEvent e) - { - try - { - frame.setClosed(true); - } - catch (Exception ex) - {} - } - - public void ok_actionPerformed(ActionEvent e) - { - database.setEnabled(false); - textfield.setEnabled(false); - ok.setEnabled(false); - close.setEnabled(false); - - Thread worker = new Thread(this); - worker.start(); - } - - private void resetDialog() - { - database.setEnabled(true); - textfield.setEnabled(true); - ok.setEnabled(true); - close.setEnabled(true); - } - - public void run() - { - String error = ""; - if (database.getSelectedItem().equals(noDbSelected)) - { - error += "Please select the source database\n"; - } - com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", ""); - textfield.setText(empty.replaceAll(textfield.getText())); - if (textfield.getText().length() == 0) - { - error += "Please enter a (semi-colon separated list of) database id(s)"; - } - if (error.length() > 0) - { - showErrorMessage(error); - resetDialog(); - return; - } - - result = new StringBuffer(); - if (database.getSelectedItem().equals("Uniprot")) - { - getUniprotFile(textfield.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(textfield.getText(), ";"); - SequenceI[] seqs = null; - while(st.hasMoreTokens()) - { - EBIFetchClient dbFetch = new EBIFetchClient(); - - File reply = dbFetch.fetchDataAsFile( - database.getSelectedItem().toString().toLowerCase( - ) + ":" + st.nextToken(), - "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(textfield.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=" - + textfield.getText().toUpperCase(), "URL").print() - ); - - if(result.length()>0) - { - parseResult( result.toString(), textfield.getText().toUpperCase() ); - } - - } - catch (java.io.IOException ex) - { - result = null; - } - } - - if (result == null || result.length() == 0) - { - showErrorMessage("Error retrieving " + textfield.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 " + - textfield.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; - } - Alignment parseResult(String result, String title) - { - 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); - 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 - { - af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); - } - catch (Exception ex) - {} - } - else - { - for (int i = 0; i < al.getHeight(); i++) - { - alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries - } - alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment. - getHeight()); - alignFrame.viewport.alignment.getWidth(); - alignFrame.viewport.firePropertyChange("alignment", null, - alignFrame.viewport. - getAlignment().getSequences()); - } - } - return al; - } - - void showErrorMessage(final String error) - { - resetDialog(); - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - error, "Error Retrieving Data", - JOptionPane.WARNING_MESSAGE); - } - }); - } -} - +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.gui; + +import java.io.*; +import java.util.*; + +import java.awt.*; +import java.awt.event.*; +import javax.swing.*; + +import MCview.*; +import jalview.datamodel.*; +import jalview.datamodel.xdb.embl.*; +import java.io.File; +import jalview.io.*; +import java.awt.Rectangle; +import java.awt.BorderLayout; +import java.awt.Dimension; + +public class SequenceFetcher +extends JPanel implements Runnable +{ + JInternalFrame frame; + AlignFrame alignFrame; + StringBuffer result; + final String noDbSelected = "-- Select Database --"; + public SequenceFetcher(AlignFrame af) + { + alignFrame = af; + database.addItem(noDbSelected); + database.addItem("Uniprot"); + database.addItem("EMBL"); + database.addItem("EMBLCDS"); + database.addItem("PDB"); + database.addItem("PFAM"); + + try + { + jbInit(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + + frame = new JInternalFrame(); + frame.setContentPane(this); + if (System.getProperty("os.name").startsWith("Mac")) + { + Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140); + } + else + { + Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125); + } + } + + private String getFrameTitle() + { + return ( (alignFrame == null) ? "New " : "Additional ") + + "Sequence Fetcher"; + } + + private void jbInit() + throws Exception + { + this.setLayout(borderLayout2); + + database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); + jLabel1.setHorizontalAlignment(SwingConstants.CENTER); + jLabel1.setText( + "Separate multiple accession ids with semi colon \";\""); + ok.setText("OK"); + ok.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ok_actionPerformed(); + } + }); + close.setText("Close"); + close.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + close_actionPerformed(e); + } + }); + textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + textArea.setLineWrap(true); + textArea.addKeyListener(new KeyAdapter() + { + public void keyPressed(KeyEvent e) + { + System.out.println(e.getKeyCode()+" "+KeyEvent.VK_ENTER); + if(e.getKeyCode()==KeyEvent.VK_ENTER) + ok_actionPerformed(); + } + }); + jPanel3.setLayout(borderLayout1); + borderLayout1.setVgap(5); + jPanel1.add(ok); + jPanel1.add(close); + jPanel3.add(jPanel2, java.awt.BorderLayout.WEST); + jPanel2.add(database); + jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER); + jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH); + this.add(jPanel1, java.awt.BorderLayout.SOUTH); + this.add(jPanel3, java.awt.BorderLayout.CENTER); + jScrollPane1.getViewport().add(textArea); + + } + + JComboBox database = new JComboBox(); + JLabel jLabel1 = new JLabel(); + JButton ok = new JButton(); + JButton close = new JButton(); + JPanel jPanel1 = new JPanel(); + JTextArea textArea = new JTextArea(); + JScrollPane jScrollPane1 = new JScrollPane(); + JPanel jPanel2 = new JPanel(); + JPanel jPanel3 = new JPanel(); + BorderLayout borderLayout1 = new BorderLayout(); + BorderLayout borderLayout2 = new BorderLayout(); + public void close_actionPerformed(ActionEvent e) + { + try + { + frame.setClosed(true); + } + catch (Exception ex) + {} + } + + public void ok_actionPerformed() + { + database.setEnabled(false); + textArea.setEnabled(false); + ok.setEnabled(false); + close.setEnabled(false); + + Thread worker = new Thread(this); + worker.start(); + } + + private void resetDialog() + { + database.setEnabled(true); + textArea.setEnabled(true); + ok.setEnabled(true); + close.setEnabled(true); + } + + public void run() + { + String error = ""; + if (database.getSelectedItem().equals(noDbSelected)) + { + error += "Please select the source database\n"; + } + com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", ""); + textArea.setText(empty.replaceAll(textArea.getText())); + if (textArea.getText().length() == 0) + { + error += "Please enter a (semi-colon separated list of) database id(s)"; + } + if (error.length() > 0) + { + showErrorMessage(error); + resetDialog(); + return; + } + + 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(); + + File reply = dbFetch.fetchDataAsFile( + database.getSelectedItem().toString().toLowerCase( + ) + ":" + st.nextToken(), + "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; + } + Alignment parseResult(String result, String title) + { + 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 " + textArea.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); + 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 + { + af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); + } + catch (Exception ex) + {} + } + else + { + for (int i = 0; i < al.getHeight(); i++) + { + alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries + } + alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment. + getHeight()); + alignFrame.viewport.alignment.getWidth(); + alignFrame.viewport.firePropertyChange("alignment", null, + alignFrame.viewport. + getAlignment().getSequences()); + } + } + return al; + } + + void showErrorMessage(final String error) + { + resetDialog(); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + error, "Error Retrieving Data", + JOptionPane.WARNING_MESSAGE); + } + }); + } +} + -- 1.7.10.2