2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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21 import javax.swing.*;
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23 import java.awt.event.*;
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24 import jalview.io.EBIFetchClient;
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26 import jalview.datamodel.*;
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27 import jalview.analysis.AlignSeq;
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28 import java.io.File;
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29 import jalview.io.*;
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32 public class SequenceFetcher
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33 extends JPanel implements Runnable
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35 JInternalFrame frame;
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36 AlignFrame alignFrame;
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37 StringBuffer result;
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38 final String noDbSelected = "-- Select Database --";
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39 public SequenceFetcher(AlignFrame af)
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42 database.addItem(noDbSelected);
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43 database.addItem("Uniprot");
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44 database.addItem("EMBL");
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45 database.addItem("EMBLCDS");
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46 database.addItem("PDB");
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47 database.addItem("PFAM");
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53 catch (Exception ex)
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55 ex.printStackTrace();
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58 frame = new JInternalFrame();
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59 frame.setContentPane(this);
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60 if (System.getProperty("os.name").startsWith("Mac"))
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61 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
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63 Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
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66 private String getFrameTitle()
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68 return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";
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71 private void jbInit()
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74 this.setLayout(gridBagLayout1);
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76 database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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77 database.setMinimumSize(new Dimension(160, 21));
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78 database.setPreferredSize(new Dimension(160, 21));
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79 jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
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81 "Separate multiple accession ids with semi colon \";\"");
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83 ok.addActionListener(new ActionListener()
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85 public void actionPerformed(ActionEvent e)
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87 ok_actionPerformed(e);
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90 close.setText("Close");
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91 close.addActionListener(new ActionListener()
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93 public void actionPerformed(ActionEvent e)
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95 close_actionPerformed(e);
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98 textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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99 textfield.addActionListener(new ActionListener()
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101 public void actionPerformed(ActionEvent e)
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103 ok_actionPerformed(e);
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107 jPanel1.add(close);
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108 this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
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109 , GridBagConstraints.WEST,
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110 GridBagConstraints.NONE,
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111 new Insets(7, 4, 0, 6), 77, 6));
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112 this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
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113 , GridBagConstraints.WEST,
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114 GridBagConstraints.BOTH,
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115 new Insets(7, -2, 7, 12), 241, -2));
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116 this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0
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117 , GridBagConstraints.WEST,
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118 GridBagConstraints.NONE,
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119 new Insets(0, 4, 0, 0), 1, 0));
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120 this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
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121 , GridBagConstraints.CENTER,
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122 GridBagConstraints.HORIZONTAL,
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123 new Insets(0, 0, 0, 6), 200, 1));
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126 JComboBox database = new JComboBox();
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127 JLabel jLabel1 = new JLabel();
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128 JButton ok = new JButton();
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129 JButton close = new JButton();
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130 JPanel jPanel1 = new JPanel();
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131 JTextField textfield = new JTextField();
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132 GridBagLayout gridBagLayout1 = new GridBagLayout();
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133 public void close_actionPerformed(ActionEvent e)
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137 frame.setClosed(true);
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139 catch (Exception ex)
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143 public void ok_actionPerformed(ActionEvent e)
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145 database.setEnabled(false);
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146 textfield.setEnabled(false);
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147 ok.setEnabled(false);
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148 close.setEnabled(false);
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150 Thread worker = new Thread(this);
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154 private void resetDialog()
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156 database.setEnabled(true);
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157 textfield.setEnabled(true);
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158 ok.setEnabled(true);
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159 close.setEnabled(true);
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165 if (database.getSelectedItem().equals(noDbSelected))
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166 error += "Please select the source database\n";
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167 com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
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168 textfield.setText(empty.replaceAll(textfield.getText()));
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169 if (textfield.getText().length() == 0)
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170 error += "Please enter a (semi-colon separated list of) database id(s)";
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171 if (error.length() > 0)
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173 showErrorMessage(error);
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178 result = new StringBuffer();
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179 if (database.getSelectedItem().equals("Uniprot"))
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181 getUniprotFile(textfield.getText());
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183 else if (database.getSelectedItem().equals("EMBL")
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184 || database.getSelectedItem().equals("EMBLCDS"))
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186 EBIFetchClient dbFetch = new EBIFetchClient();
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187 String[] reply = dbFetch.fetchData(
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188 database.getSelectedItem().toString().toLowerCase(
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189 ) + ":" + textfield.getText(),
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194 for (int i = 0; i < reply.length; i++)
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195 result.append(reply[i] + "\n");
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197 parseResult(result.toString(), null);
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200 else if (database.getSelectedItem().equals("PDB"))
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202 StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");
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204 while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
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206 StringBuffer respart = getPDBFile(query.toUpperCase());
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208 result.append(respart);
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212 if (result.length()>0)
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213 parseResult(result.toString(), null);
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215 else if( database.getSelectedItem().equals("PFAM"))
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218 result.append(new FastaFile(
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219 "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
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220 + textfield.getText().toUpperCase(), "URL").print()
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223 if(result.length()>0)
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224 parseResult( result.toString(), textfield.getText().toUpperCase() );
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226 }catch(java.io.IOException ex)
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230 if (result == null || result.length() == 0)
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231 showErrorMessage("Error retrieving " + textfield.getText()
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232 + " from " + database.getSelectedItem());
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238 void getUniprotFile(String id)
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240 EBIFetchClient ebi = new EBIFetchClient();
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241 File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
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242 SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
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243 Vector entries = sff.getUniprotEntries(file);
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245 if (entries != null)
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247 //First, make the new sequences
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248 Enumeration en = entries.elements();
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249 while (en.hasMoreElements())
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251 UniprotEntry entry = (UniprotEntry) en.nextElement();
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252 StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
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253 Enumeration en2 = entry.getAccession().elements();
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254 while (en2.hasMoreElements())
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257 name.append(en2.nextElement());
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259 en2 = entry.getName().elements();
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260 while (en2.hasMoreElements())
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263 name.append(en2.nextElement());
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266 if (entry.getProteinName() != null)
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267 name.append(" " + entry.getProteinName().elementAt(0));
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269 result.append(name + "\n" + entry.getUniprotSequence().getContent() +
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274 //Then read in the features and apply them to the dataset
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275 SequenceI[] sequence = parseResult(result.toString(), null);
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276 for (int i = 0; i < entries.size(); i++)
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278 UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
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279 Enumeration e = entry.getDbReference().elements();
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280 Vector onlyPdbEntries = new Vector();
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281 while (e.hasMoreElements())
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283 PDBEntry pdb = (PDBEntry) e.nextElement();
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284 if (!pdb.getType().equals("PDB"))
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287 onlyPdbEntries.addElement(pdb);
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290 sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
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291 if (entry.getFeature() != null)
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293 e = entry.getFeature().elements();
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294 while (e.hasMoreElements())
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296 sequence[i].getDatasetSequence().addSequenceFeature( (
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297 SequenceFeature) e.nextElement());
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304 StringBuffer getPDBFile(String id)
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306 StringBuffer result = new StringBuffer();
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307 String chain = null;
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308 if (id.indexOf(":") > -1)
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310 chain = id.substring(id.indexOf(":") + 1);
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311 id = id.substring(0, id.indexOf(":"));
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314 EBIFetchClient ebi = new EBIFetchClient();
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315 String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
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320 PDBfile pdbfile = new PDBfile(reply);
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321 for (int i = 0; i < pdbfile.chains.size(); i++)
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323 if (chain == null ||
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324 ( (PDBChain) pdbfile.chains.elementAt(i)).id.
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325 toUpperCase().equals(chain))
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326 result.append("\n>PDB|" + id + "|" +
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327 ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
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331 ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
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335 catch (Exception ex) // Problem parsing PDB file
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337 jalview.bin.Cache.log.warn("Exception when retrieving " +
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338 textfield.getText() + " from " +
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339 database.getSelectedItem(), ex);
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346 SequenceI[] parseResult(String result, String title)
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348 String format = new IdentifyFile().Identify(result, "Paste");
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349 SequenceI[] sequences = null;
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351 if (FormatAdapter.formats.contains(format))
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354 try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
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356 catch(Exception ex){}
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358 if (sequences != null && sequences.length > 0)
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360 if (alignFrame == null)
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362 AlignFrame af = new AlignFrame(new Alignment(sequences));
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363 af.currentFileFormat = format;
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365 title = "Retrieved from " + database.getSelectedItem();
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366 Desktop.addInternalFrame(af,
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368 AlignFrame.NEW_WINDOW_WIDTH,
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369 AlignFrame.NEW_WINDOW_HEIGHT);
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370 af.statusBar.setText("Successfully pasted alignment file");
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373 af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
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375 catch (Exception ex)
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380 for (int i = 0; i < sequences.length; i++)
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382 alignFrame.viewport.alignment.addSequence(sequences[i]);
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384 ////////////////////////////
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385 //Dataset needs extension;
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386 /////////////////////////////
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387 Sequence ds = new Sequence(sequences[i].getName(),
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388 AlignSeq.extractGaps("-. ",
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389 sequences[i].getSequence()),
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390 sequences[i].getStart(),
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391 sequences[i].getEnd());
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392 sequences[i].setDatasetSequence(ds);
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393 alignFrame.viewport.alignment.getDataset().addSequence(ds);
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395 alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
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397 alignFrame.viewport.alignment.getWidth();
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398 alignFrame.viewport.firePropertyChange("alignment", null,
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399 alignFrame.viewport.
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400 getAlignment().getSequences());
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404 if (database.getSelectedItem().equals("PDB"))
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406 // Parse out the ids from the structured names
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407 boolean errors = false;
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408 for (int i = 0; i < sequences.length; i++)
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410 PDBEntry entry = new PDBEntry();
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411 com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(
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412 "PDB\\|([0-9A-z]{4})\\|(.)");
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413 if (idbits.search(sequences[i].getName()))
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415 String pdbid = idbits.substring(1);
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416 String pdbccode = idbits.substring(2);
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417 // Construct the PDBEntry
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418 entry.setId(pdbid);
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419 if (entry.getProperty() == null)
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420 entry.setProperty(new Hashtable());
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421 entry.getProperty().put("chains",
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423 + "=" + sequences[i].getStart()
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424 + "-" + sequences[i].getEnd());
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425 sequences[i].getDatasetSequence().addPDBId(entry);
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427 // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
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428 // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
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429 DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);
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430 sequences[i].getDatasetSequence().addDBRef(dbentry);
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434 // don't add an entry for this chain, but this is probably a bug
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435 // that the user should know about.
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436 jalview.bin.Cache.log.warn(
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437 "No PDBEntry constructed for sequence " + i + " : " +
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438 sequences[i].getName());
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443 jalview.bin.Cache.log.warn(
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444 "Query string that resulted in PDBEntry construction failure was :\n" +
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445 textfield.getText());
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450 showErrorMessage("Error retrieving " + textfield.getText()
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451 + " from " + database.getSelectedItem());
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458 void showErrorMessage(String error)
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461 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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462 error, "Error Retrieving Data",
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463 JOptionPane.WARNING_MESSAGE);
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