2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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25 import java.awt.event.*;
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26 import javax.swing.*;
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29 import jalview.datamodel.*;
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30 import jalview.datamodel.xdb.embl.*;
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31 import java.io.File;
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32 import jalview.io.*;
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33 import java.awt.Rectangle;
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34 import java.awt.BorderLayout;
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35 import java.awt.Dimension;
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37 public class SequenceFetcher
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38 extends JPanel implements Runnable
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40 JInternalFrame frame;
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41 AlignFrame alignFrame;
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42 StringBuffer result;
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43 final String noDbSelected = "-- Select Database --";
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44 public SequenceFetcher(AlignFrame af)
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47 database.addItem(noDbSelected);
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48 database.addItem("Uniprot");
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49 database.addItem("EMBL");
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50 database.addItem("EMBLCDS");
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51 database.addItem("PDB");
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52 database.addItem("PFAM");
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58 catch (Exception ex)
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60 ex.printStackTrace();
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63 frame = new JInternalFrame();
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64 frame.setContentPane(this);
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65 if (System.getProperty("os.name").startsWith("Mac"))
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67 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
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71 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
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75 private String getFrameTitle()
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77 return ( (alignFrame == null) ? "New " : "Additional ") +
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81 private void jbInit()
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84 this.setLayout(borderLayout2);
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86 database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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87 jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
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88 jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
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90 "Separate multiple accession ids with semi colon \";\"");
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92 ok.addActionListener(new ActionListener()
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94 public void actionPerformed(ActionEvent e)
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96 ok_actionPerformed();
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99 close.setText("Close");
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100 close.addActionListener(new ActionListener()
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102 public void actionPerformed(ActionEvent e)
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104 close_actionPerformed(e);
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107 textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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108 textArea.setLineWrap(true);
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109 textArea.addKeyListener(new KeyAdapter()
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111 public void keyPressed(KeyEvent e)
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113 System.out.println(e.getKeyCode()+" "+KeyEvent.VK_ENTER);
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114 if(e.getKeyCode()==KeyEvent.VK_ENTER)
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115 ok_actionPerformed();
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118 jPanel3.setLayout(borderLayout1);
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119 borderLayout1.setVgap(5);
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121 jPanel1.add(close);
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122 jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);
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123 jPanel2.add(database);
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124 jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
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125 jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);
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126 this.add(jPanel1, java.awt.BorderLayout.SOUTH);
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127 this.add(jPanel3, java.awt.BorderLayout.CENTER);
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128 jScrollPane1.getViewport().add(textArea);
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132 JComboBox database = new JComboBox();
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133 JLabel jLabel1 = new JLabel();
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134 JButton ok = new JButton();
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135 JButton close = new JButton();
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136 JPanel jPanel1 = new JPanel();
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137 JTextArea textArea = new JTextArea();
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138 JScrollPane jScrollPane1 = new JScrollPane();
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139 JPanel jPanel2 = new JPanel();
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140 JPanel jPanel3 = new JPanel();
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141 BorderLayout borderLayout1 = new BorderLayout();
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142 BorderLayout borderLayout2 = new BorderLayout();
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143 public void close_actionPerformed(ActionEvent e)
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147 frame.setClosed(true);
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149 catch (Exception ex)
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153 public void ok_actionPerformed()
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155 database.setEnabled(false);
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156 textArea.setEnabled(false);
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157 ok.setEnabled(false);
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158 close.setEnabled(false);
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160 Thread worker = new Thread(this);
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164 private void resetDialog()
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166 database.setEnabled(true);
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167 textArea.setEnabled(true);
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168 ok.setEnabled(true);
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169 close.setEnabled(true);
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175 if (database.getSelectedItem().equals(noDbSelected))
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177 error += "Please select the source database\n";
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179 com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
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180 textArea.setText(empty.replaceAll(textArea.getText()));
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181 if (textArea.getText().length() == 0)
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183 error += "Please enter a (semi-colon separated list of) database id(s)";
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185 if (error.length() > 0)
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187 showErrorMessage(error);
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192 result = new StringBuffer();
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193 if (database.getSelectedItem().equals("Uniprot"))
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195 getUniprotFile(textArea.getText());
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197 else if (database.getSelectedItem().equals("EMBL")
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198 || database.getSelectedItem().equals("EMBLCDS"))
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200 String DBRefSource = database.getSelectedItem().equals("EMBLCDS")
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201 ? jalview.datamodel.DBRefSource.EMBLCDS
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202 : jalview.datamodel.DBRefSource.EMBL;
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204 StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
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205 SequenceI[] seqs = null;
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206 while(st.hasMoreTokens())
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208 EBIFetchClient dbFetch = new EBIFetchClient();
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210 File reply = dbFetch.fetchDataAsFile(
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211 database.getSelectedItem().toString().toLowerCase(
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212 ) + ":" + st.nextToken(),
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215 jalview.datamodel.xdb.embl.EmblFile efile=null;
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216 if (reply != null && reply.exists())
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218 efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
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221 for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
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222 EmblEntry entry = (EmblEntry) i.next();
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223 SequenceI[] seqparts = entry.getSequences(false,true, DBRefSource);
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224 if (seqparts!=null) {
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225 SequenceI[] newseqs = null;
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228 newseqs = new SequenceI[seqparts.length];
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230 newseqs = new SequenceI[seqs.length+seqparts.length];
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232 for (;si<seqs.length; si++) {
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233 newseqs[si] = seqs[si];
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237 for (int j=0;j<seqparts.length; si++, j++) {
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238 newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer
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248 if (seqs!=null && seqs.length>0) {
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249 if (parseResult(new Alignment(seqs), null, null)!=null)
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250 result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
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253 else if (database.getSelectedItem().equals("PDB"))
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255 StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");
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257 SequenceI[] seqs = null;
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258 while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
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260 SequenceI[] seqparts = getPDBFile(query.toUpperCase());
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261 if (seqparts != null)
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269 SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];
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271 for (; i < seqs.length; i++)
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273 newseqs[i] = seqs[i];
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276 for (int j=0;j<seqparts.length; i++, j++)
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278 newseqs[i] = seqparts[j];
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282 result.append("# Success for "+query.toUpperCase()+"\n");
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285 if (seqs != null && seqs.length > 0)
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287 if (parseResult(new Alignment(seqs), null, null)!=null)
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290 "# Successfully parsed the PDB File Queries into an Alignment");
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294 else if( database.getSelectedItem().equals("PFAM"))
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298 result.append(new FastaFile(
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299 "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
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300 + textArea.getText().toUpperCase(), "URL").print()
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303 if(result.length()>0)
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305 parseResult( result.toString(), textArea.getText().toUpperCase() );
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309 catch (java.io.IOException ex)
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315 if (result == null || result.length() == 0)
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317 showErrorMessage("Error retrieving " + textArea.getText()
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318 + " from " + database.getSelectedItem());
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325 void getUniprotFile(String id)
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327 EBIFetchClient ebi = new EBIFetchClient();
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328 File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
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330 DBRefFetcher dbref = new DBRefFetcher();
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331 Vector entries = dbref.getUniprotEntries(file);
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333 if (entries != null)
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335 //First, make the new sequences
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336 Enumeration en = entries.elements();
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337 while (en.hasMoreElements())
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339 UniprotEntry entry = (UniprotEntry) en.nextElement();
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341 StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
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342 Enumeration en2 = entry.getAccession().elements();
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343 while (en2.hasMoreElements())
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346 name.append(en2.nextElement());
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348 en2 = entry.getName().elements();
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349 while (en2.hasMoreElements())
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352 name.append(en2.nextElement());
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355 if (entry.getProtein() != null)
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357 name.append(" " + entry.getProtein().getName().elementAt(0));
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360 result.append(name + "\n" + entry.getUniprotSequence().getContent() +
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365 //Then read in the features and apply them to the dataset
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366 Alignment al = parseResult(result.toString(), null);
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367 for (int i = 0; i < entries.size(); i++)
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369 UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
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370 Enumeration e = entry.getDbReference().elements();
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371 Vector onlyPdbEntries = new Vector();
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372 while (e.hasMoreElements())
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374 PDBEntry pdb = (PDBEntry) e.nextElement();
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375 if (!pdb.getType().equals("PDB"))
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380 onlyPdbEntries.addElement(pdb);
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383 Enumeration en2 = entry.getAccession().elements();
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384 while (en2.hasMoreElements())
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386 al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
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387 DBRefSource.UNIPROT,
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389 en2.nextElement().toString()));
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395 al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
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396 if (entry.getFeature() != null)
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398 e = entry.getFeature().elements();
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399 while (e.hasMoreElements())
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401 SequenceFeature sf = (SequenceFeature) e.nextElement();
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402 sf.setFeatureGroup("Uniprot");
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403 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
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410 SequenceI[] getPDBFile(String id)
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412 Vector result = new Vector();
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413 String chain = null;
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414 if (id.indexOf(":") > -1)
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416 chain = id.substring(id.indexOf(":") + 1);
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417 id = id.substring(0, id.indexOf(":"));
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420 EBIFetchClient ebi = new EBIFetchClient();
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421 String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").
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429 PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
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430 for (int i = 0; i < pdbfile.chains.size(); i++)
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432 if (chain == null ||
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433 ( (PDBChain) pdbfile.chains.elementAt(i)).id.
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434 toUpperCase().equals(chain))
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436 PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
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437 // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file
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438 SequenceI sq = pdbchain.sequence;
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439 // Specially formatted name for the PDB chain sequences retrieved from the PDB
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440 sq.setName("PDB|"+id+"|"+sq.getName());
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441 // Might need to add more metadata to the PDBEntry object
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444 * PDBEntry entry = new PDBEntry();
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445 // Construct the PDBEntry
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447 if (entry.getProperty() == null)
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448 entry.setProperty(new Hashtable());
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449 entry.getProperty().put("chains",
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451 + "=" + sq.getStart()
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452 + "-" + sq.getEnd());
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453 sq.getDatasetSequence().addPDBId(entry);
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456 // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
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457 // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
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458 DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,
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459 "0", id + pdbchain.id);
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460 sq.addDBRef(dbentry);
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461 // and add seuqence to the retrieved set
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462 result.addElement(sq.deriveSequence());
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466 if (result.size() < 1)
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468 throw new Exception("WsDBFetch for PDB id resulted in zero result size");
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471 catch (Exception ex) // Problem parsing PDB file
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473 jalview.bin.Cache.log.warn("Exception when retrieving " +
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474 textArea.getText() + " from " +
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475 database.getSelectedItem(), ex);
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480 SequenceI[] results = new SequenceI[result.size()];
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481 for (int i = 0, j = result.size(); i < j; i++)
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483 results[i] = (SequenceI) result.elementAt(i);
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484 result.setElementAt(null,i);
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488 Alignment parseResult(String result, String title)
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490 String format = new IdentifyFile().Identify(result, "Paste");
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491 Alignment sequences = null;
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492 if (FormatAdapter.isValidFormat(format))
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497 sequences = new FormatAdapter().readFile(result.toString(), "Paste",
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500 catch (Exception ex)
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503 if (sequences!=null)
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505 return parseResult(sequences, title, format);
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510 showErrorMessage("Error retrieving " + textArea.getText()
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511 + " from " + database.getSelectedItem());
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517 Alignment parseResult(Alignment al, String title, String currentFileFormat)
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520 if (al != null && al.getHeight() > 0)
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522 if (alignFrame == null)
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524 AlignFrame af = new AlignFrame(al,
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525 AlignFrame.DEFAULT_WIDTH,
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526 AlignFrame.DEFAULT_HEIGHT);
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527 if (currentFileFormat!=null)
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529 af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
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534 title = "Retrieved from " + database.getSelectedItem();
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537 Desktop.addInternalFrame(af,
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539 AlignFrame.DEFAULT_WIDTH,
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540 AlignFrame.DEFAULT_HEIGHT);
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542 af.statusBar.setText("Successfully pasted alignment file");
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546 af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
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548 catch (Exception ex)
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553 for (int i = 0; i < al.getHeight(); i++)
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555 alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
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557 alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
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559 alignFrame.viewport.alignment.getWidth();
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560 alignFrame.viewport.firePropertyChange("alignment", null,
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561 alignFrame.viewport.
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562 getAlignment().getSequences());
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568 void showErrorMessage(final String error)
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571 javax.swing.SwingUtilities.invokeLater(new Runnable()
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575 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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576 error, "Error Retrieving Data",
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577 JOptionPane.WARNING_MESSAGE);
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