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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33 public class SequenceFetcher
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34 extends JPanel implements Runnable
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36 JInternalFrame frame;
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37 AlignFrame alignFrame;
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38 StringBuffer result;
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39 public SequenceFetcher(AlignFrame af)
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42 database.addItem("-- Select Database --");
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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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52 catch (Exception ex)
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54 ex.printStackTrace();
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57 frame = new JInternalFrame();
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58 frame.setContentPane(this);
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59 if(System.getProperty("os.name").startsWith("Mac"))
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60 Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 140);
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62 Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 125);
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65 private void jbInit()
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68 this.setLayout(gridBagLayout1);
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70 database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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71 database.setMinimumSize(new Dimension(160, 21));
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72 database.setPreferredSize(new Dimension(160, 21));
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73 jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
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75 "Separate multiple accession ids with semi colon \";\"");
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77 ok.addActionListener(new ActionListener()
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79 public void actionPerformed(ActionEvent e)
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81 ok_actionPerformed(e);
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84 cancel.setText("Cancel");
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85 cancel.addActionListener(new ActionListener()
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87 public void actionPerformed(ActionEvent e)
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89 cancel_actionPerformed(e);
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92 textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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93 textfield.addActionListener(new ActionListener()
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95 public void actionPerformed(ActionEvent e)
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97 ok_actionPerformed(e);
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101 jPanel1.add(cancel);
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102 this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
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103 , GridBagConstraints.WEST,
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104 GridBagConstraints.NONE,
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105 new Insets(7, 4, 0, 6), 77, 6));
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106 this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
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107 , GridBagConstraints.WEST,
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108 GridBagConstraints.BOTH,
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109 new Insets(7, -2, 7, 12), 241, -2));
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110 this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0
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111 , GridBagConstraints.WEST,
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112 GridBagConstraints.NONE,
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113 new Insets(0, 4, 0, 0), 1, 0));
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114 this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
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115 , GridBagConstraints.CENTER,
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116 GridBagConstraints.HORIZONTAL,
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117 new Insets(0, 0, 0, 6), 200, 1));
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120 JComboBox database = new JComboBox();
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121 JLabel jLabel1 = new JLabel();
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122 JButton ok = new JButton();
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123 JButton cancel = new JButton();
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124 JPanel jPanel1 = new JPanel();
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125 JTextField textfield = new JTextField();
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126 GridBagLayout gridBagLayout1 = new GridBagLayout();
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127 public void cancel_actionPerformed(ActionEvent e)
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131 frame.setClosed(true);
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133 catch (Exception ex)
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137 public void ok_actionPerformed(ActionEvent e)
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139 frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");
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140 database.setEnabled(false);
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141 textfield.setEnabled(false);
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142 ok.setEnabled(false);
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143 cancel.setEnabled(false);
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145 Thread worker = new Thread(this);
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151 result = new StringBuffer();
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152 if (database.getSelectedItem().equals("Uniprot"))
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154 getUniprotFile(textfield.getText());
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156 else if (database.getSelectedItem().equals("EMBL")
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157 || database.getSelectedItem().equals("EMBLCDS"))
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159 EBIFetchClient dbFetch = new EBIFetchClient();
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160 String[] reply = dbFetch.fetchData(
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161 database.getSelectedItem().toString().toLowerCase(
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162 ) + ":" + textfield.getText(),
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165 for (int i = 0; i < reply.length; i++)
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166 result.append(reply[i] + "\n");
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168 parseResult(result.toString());
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170 else if (database.getSelectedItem().equals("PDB"))
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172 result = getPDBFile(textfield.getText().toUpperCase());
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173 parseResult(result.toString());
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177 if (result == null || result.length() == 0)
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178 showErrorMessage("Error retrieving " + textfield.getText()
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179 + " from " + database.getSelectedItem());
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182 database.setEnabled(true);
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183 textfield.setEnabled(true);
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184 ok.setEnabled(true);
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185 cancel.setEnabled(true);
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186 frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");
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189 void getUniprotFile(String id)
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191 EBIFetchClient ebi = new EBIFetchClient();
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192 File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);
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193 SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
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194 Vector entries = sff.getUniprotEntries(file);
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198 //First, make the new sequences
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199 Enumeration en = entries.elements();
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200 while (en.hasMoreElements())
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202 UniprotEntry entry = (UniprotEntry) en.nextElement();
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203 StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" );
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204 Enumeration en2 = entry.getAccession().elements();
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205 while(en2.hasMoreElements())
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208 name.append(en2.nextElement());
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210 en2 = entry.getName().elements();
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211 while(en2.hasMoreElements())
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214 name.append(en2.nextElement());
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217 if(entry.getProteinName()!=null)
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218 name.append(" "+entry.getProteinName().elementAt(0));
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220 result.append(name +"\n"+entry.getUniprotSequence().getContent());
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224 //Then read in the features and apply them to the dataset
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225 SequenceI [] sequence = parseResult(result.toString());
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226 for(int i=0; i<entries.size(); i++)
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228 UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
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229 Enumeration e = entry.getDbReference().elements();
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230 Vector onlyPdbEntries = new Vector();
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231 while (e.hasMoreElements())
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233 PDBEntry pdb = (PDBEntry) e.nextElement();
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234 if (!pdb.getType().equals("PDB"))
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237 onlyPdbEntries.addElement(pdb);
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240 sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
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241 sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());
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247 StringBuffer getPDBFile(String id)
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249 StringBuffer result = new StringBuffer();
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250 String chain = null;
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251 if (id.indexOf(":") > -1)
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253 chain = id.substring(id.indexOf(":") + 1);
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254 id = id.substring(0, id.indexOf(":"));
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257 EBIFetchClient ebi = new EBIFetchClient();
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258 String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
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261 PDBfile pdbfile = new PDBfile(reply);
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262 for (int i = 0; i < pdbfile.chains.size(); i++)
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264 if (chain == null ||
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265 ( (PDBChain) pdbfile.chains.elementAt(i)).id.
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266 toUpperCase().equals(chain))
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267 result.append("\n>PDB|" + id + "|" +
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268 ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
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272 ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
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276 catch (Exception ex) // Problem parsing PDB file
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278 showErrorMessage("Error retrieving " + textfield.getText() + " from " +
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279 database.getSelectedItem());
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286 SequenceI[] parseResult(String result)
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288 String format = IdentifyFile.Identify(result, "Paste");
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289 SequenceI[] sequences = null;
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291 if (FormatAdapter.formats.contains(format))
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293 sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);
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294 if (sequences != null && sequences.length>0)
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296 if(alignFrame==null)
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298 AlignFrame af = new AlignFrame(new Alignment(sequences));
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299 af.currentFileFormat = format;
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300 Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),
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301 AlignFrame.NEW_WINDOW_WIDTH,
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302 AlignFrame.NEW_WINDOW_HEIGHT);
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303 af.statusBar.setText("Successfully pasted alignment file");
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306 af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
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308 catch (Exception ex)
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313 for (int i = 0; i < sequences.length; i++)
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315 alignFrame.viewport.alignment.addSequence(sequences[i]);
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317 ////////////////////////////
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318 //Datset needs extension;
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319 /////////////////////////////
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320 Sequence ds = new Sequence(sequences[i].getName(),
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321 AlignSeq.extractGaps("-. ",
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322 sequences[i].getSequence()),
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323 sequences[i].getStart(),
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324 sequences[i].getEnd());
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325 sequences[i].setDatasetSequence(ds);
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326 alignFrame.viewport.alignment.getDataset().addSequence(ds);
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328 alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
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330 alignFrame.viewport.alignment.getWidth();
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331 alignFrame.viewport.firePropertyChange("alignment", null,
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332 alignFrame.viewport.getAlignment().getSequences());
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336 if (database.getSelectedItem().equals("PDB"))
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338 for (int i = 0; i < sequences.length; i++)
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340 PDBEntry entry = new PDBEntry();
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341 entry.setId(textfield.getText());
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342 sequences[i].getDatasetSequence().addPDBId(entry);
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348 showErrorMessage( "Error retrieving "+textfield.getText()
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349 +" from "+database.getSelectedItem());
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356 void showErrorMessage(String error)
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358 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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359 error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
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