src/jalview/gui/SequenceFetcher.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  *\r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  *\r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  *\r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import javax.swing.*;\r
  22 import java.awt.*;\r
  23 import java.awt.event.*;\r
  24 import jalview.io.EBIFetchClient;\r
  25 import MCview.*;\r
  26 import jalview.datamodel.*;\r
  27 import jalview.analysis.AlignSeq;\r
  28 import java.io.File;\r
  29 import jalview.io.*;\r
  30 import java.util.*;\r
  31 \r
  32 public class SequenceFetcher\r
  33     extends JPanel implements Runnable\r
  34 {\r
  35   JInternalFrame frame;\r
  36   AlignFrame alignFrame;\r
  37   StringBuffer result;\r
  38   final String noDbSelected = "-- Select Database --";\r
  39   public SequenceFetcher(AlignFrame af)\r
  40   {\r
  41     alignFrame = af;\r
  42     database.addItem(noDbSelected);\r
  43     database.addItem("Uniprot");\r
  44     database.addItem("EMBL");\r
  45     database.addItem("EMBLCDS");\r
  46     database.addItem("PDB");\r
  47 \r
  48     try\r
  49     {\r
  50       jbInit();\r
  51     }\r
  52     catch (Exception ex)\r
  53     {\r
  54       ex.printStackTrace();\r
  55     }\r
  56 \r
  57     frame = new JInternalFrame();\r
  58     frame.setContentPane(this);\r
  59     if (System.getProperty("os.name").startsWith("Mac"))\r
  60       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);\r
  61     else\r
  62       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);\r
  63   }\r
  64 \r
  65   private String getFrameTitle()\r
  66   {\r
  67     return ( (alignFrame == null) ? "New " : "Additional ") +\r
  68         "Sequence Fetcher (WSDBfetch@EBI)";\r
  69   }\r
  70 \r
  71   private void jbInit()\r
  72       throws Exception\r
  73   {\r
  74     this.setLayout(gridBagLayout1);\r
  75 \r
  76     database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
  77     database.setMinimumSize(new Dimension(160, 21));\r
  78     database.setPreferredSize(new Dimension(160, 21));\r
  79     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
  80     jLabel1.setText(\r
  81         "Separate multiple accession ids with semi colon \";\"");\r
  82     ok.setText("OK");\r
  83     ok.addActionListener(new ActionListener()\r
  84     {\r
  85       public void actionPerformed(ActionEvent e)\r
  86       {\r
  87         ok_actionPerformed(e);\r
  88       }\r
  89     });\r
  90     cancel.setText("Cancel");\r
  91     cancel.addActionListener(new ActionListener()\r
  92     {\r
  93       public void actionPerformed(ActionEvent e)\r
  94       {\r
  95         cancel_actionPerformed(e);\r
  96       }\r
  97     });\r
  98     textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
  99     textfield.addActionListener(new ActionListener()\r
 100     {\r
 101       public void actionPerformed(ActionEvent e)\r
 102       {\r
 103         ok_actionPerformed(e);\r
 104       }\r
 105     });\r
 106     jPanel1.add(ok);\r
 107     jPanel1.add(cancel);\r
 108     this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
 109                                              , GridBagConstraints.WEST,\r
 110                                              GridBagConstraints.NONE,\r
 111                                              new Insets(7, 4, 0, 6), 77, 6));\r
 112     this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
 113                                              , GridBagConstraints.WEST,\r
 114                                              GridBagConstraints.BOTH,\r
 115                                              new Insets(7, -2, 7, 12), 241, -2));\r
 116     this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0\r
 117                                               , GridBagConstraints.WEST,\r
 118                                               GridBagConstraints.NONE,\r
 119                                               new Insets(0, 4, 0, 0), 1, 0));\r
 120     this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
 121                                                , GridBagConstraints.CENTER,\r
 122                                                GridBagConstraints.HORIZONTAL,\r
 123                                                new Insets(0, 0, 0, 6), 200, 1));\r
 124   }\r
 125 \r
 126   JComboBox database = new JComboBox();\r
 127   JLabel jLabel1 = new JLabel();\r
 128   JButton ok = new JButton();\r
 129   JButton cancel = new JButton();\r
 130   JPanel jPanel1 = new JPanel();\r
 131   JTextField textfield = new JTextField();\r
 132   GridBagLayout gridBagLayout1 = new GridBagLayout();\r
 133   public void cancel_actionPerformed(ActionEvent e)\r
 134   {\r
 135     try\r
 136     {\r
 137       frame.setClosed(true);\r
 138     }\r
 139     catch (Exception ex)\r
 140     {}\r
 141   }\r
 142 \r
 143   public void ok_actionPerformed(ActionEvent e)\r
 144   {\r
 145     frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");\r
 146     database.setEnabled(false);\r
 147     textfield.setEnabled(false);\r
 148     ok.setEnabled(false);\r
 149     cancel.setEnabled(false);\r
 150 \r
 151     Thread worker = new Thread(this);\r
 152     worker.start();\r
 153   }\r
 154 \r
 155   private void resetDialog()\r
 156   {\r
 157     database.setEnabled(true);\r
 158     textfield.setEnabled(true);\r
 159     ok.setEnabled(true);\r
 160     cancel.setEnabled(true);\r
 161     frame.setTitle(getFrameTitle());\r
 162   }\r
 163 \r
 164   public void run()\r
 165   {\r
 166     String error = "";\r
 167     if (database.getSelectedItem().equals(noDbSelected))\r
 168       error += "Please select the source database\n";\r
 169     com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");\r
 170     textfield.setText(empty.replaceAll(textfield.getText()));\r
 171     if (textfield.getText().length() == 0)\r
 172       error += "Please enter a (semi-colon separated list of) database id(s)";\r
 173     if (error.length() > 0)\r
 174     {\r
 175       showErrorMessage(error);\r
 176       resetDialog();\r
 177       return;\r
 178     }\r
 179 \r
 180     result = new StringBuffer();\r
 181     if (database.getSelectedItem().equals("Uniprot"))\r
 182     {\r
 183       getUniprotFile(textfield.getText());\r
 184     }\r
 185     else if (database.getSelectedItem().equals("EMBL")\r
 186              || database.getSelectedItem().equals("EMBLCDS"))\r
 187     {\r
 188       EBIFetchClient dbFetch = new EBIFetchClient();\r
 189       String[] reply = dbFetch.fetchData(\r
 190           database.getSelectedItem().toString().toLowerCase(\r
 191           ) + ":" + textfield.getText(),\r
 192           "fasta", "raw");\r
 193 \r
 194       for (int i = 0; i < reply.length; i++)\r
 195         result.append(reply[i] + "\n");\r
 196 \r
 197       parseResult(result.toString());\r
 198     }\r
 199     else if (database.getSelectedItem().equals("PDB"))\r
 200     {\r
 201       StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");\r
 202       String query;\r
 203       while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
 204       {\r
 205         StringBuffer respart = getPDBFile(query.toUpperCase());\r
 206         result.append(respart);\r
 207 \r
 208       }\r
 209 \r
 210       if (result != null)\r
 211         parseResult(result.toString());\r
 212     }\r
 213 \r
 214     if (result == null || result.length() == 0)\r
 215       showErrorMessage("Error retrieving " + textfield.getText()\r
 216                        + " from " + database.getSelectedItem());\r
 217     else\r
 218       textfield.setText("");\r
 219     resetDialog();\r
 220   }\r
 221 \r
 222   void getUniprotFile(String id)\r
 223   {\r
 224     EBIFetchClient ebi = new EBIFetchClient();\r
 225     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
 226     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
 227     Vector entries = sff.getUniprotEntries(file);\r
 228 \r
 229     if (entries != null)\r
 230     {\r
 231       //First, make the new sequences\r
 232       Enumeration en = entries.elements();\r
 233       while (en.hasMoreElements())\r
 234       {\r
 235         UniprotEntry entry = (UniprotEntry) en.nextElement();\r
 236         StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");\r
 237         Enumeration en2 = entry.getAccession().elements();\r
 238         while (en2.hasMoreElements())\r
 239         {\r
 240           name.append("|");\r
 241           name.append(en2.nextElement());\r
 242         }\r
 243         en2 = entry.getName().elements();\r
 244         while (en2.hasMoreElements())\r
 245         {\r
 246           name.append("|");\r
 247           name.append(en2.nextElement());\r
 248         }\r
 249 \r
 250         if (entry.getProteinName() != null)\r
 251           name.append(" " + entry.getProteinName().elementAt(0));\r
 252 \r
 253         result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
 254                       "\n");\r
 255 \r
 256       }\r
 257 \r
 258       //Then read in the features and apply them to the dataset\r
 259       SequenceI[] sequence = parseResult(result.toString());\r
 260       for (int i = 0; i < entries.size(); i++)\r
 261       {\r
 262         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
 263         Enumeration e = entry.getDbReference().elements();\r
 264         Vector onlyPdbEntries = new Vector();\r
 265         while (e.hasMoreElements())\r
 266         {\r
 267           PDBEntry pdb = (PDBEntry) e.nextElement();\r
 268           if (!pdb.getType().equals("PDB"))\r
 269             continue;\r
 270 \r
 271           onlyPdbEntries.addElement(pdb);\r
 272         }\r
 273 \r
 274         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
 275         sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
 276 \r
 277       }\r
 278     }\r
 279   }\r
 280 \r
 281   StringBuffer getPDBFile(String id)\r
 282   {\r
 283     StringBuffer result = new StringBuffer();\r
 284     String chain = null;\r
 285     if (id.indexOf(":") > -1)\r
 286     {\r
 287       chain = id.substring(id.indexOf(":") + 1);\r
 288       id = id.substring(0, id.indexOf(":"));\r
 289     }\r
 290 \r
 291     EBIFetchClient ebi = new EBIFetchClient();\r
 292     String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
 293     if (reply == null)\r
 294       return null;\r
 295     try\r
 296     {\r
 297       PDBfile pdbfile = new PDBfile(reply);\r
 298       for (int i = 0; i < pdbfile.chains.size(); i++)\r
 299       {\r
 300         if (chain == null ||\r
 301             ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
 302             toUpperCase().equals(chain))\r
 303           result.append("\n>PDB|" + id + "|" +\r
 304                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 305                         getName() +\r
 306                         "\n"\r
 307                         +\r
 308                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 309                         getSequence());\r
 310       }\r
 311     }\r
 312     catch (Exception ex) // Problem parsing PDB file\r
 313     {\r
 314       jalview.bin.Cache.log.warn("Exception when retrieving " +\r
 315                                  textfield.getText() + " from " +\r
 316                                  database.getSelectedItem(), ex);\r
 317       return null;\r
 318     }\r
 319 \r
 320     return result;\r
 321   }\r
 322 \r
 323   SequenceI[] parseResult(String result)\r
 324   {\r
 325     String format = IdentifyFile.Identify(result, "Paste");\r
 326     SequenceI[] sequences = null;\r
 327 \r
 328     if (FormatAdapter.formats.contains(format))\r
 329     {\r
 330       sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
 331                                                format);\r
 332       if (sequences != null && sequences.length > 0)\r
 333       {\r
 334         if (alignFrame == null)\r
 335         {\r
 336           AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 337           af.currentFileFormat = format;\r
 338           Desktop.addInternalFrame(af,\r
 339                                    "Retrieved from " + database.getSelectedItem(),\r
 340                                    AlignFrame.NEW_WINDOW_WIDTH,\r
 341                                    AlignFrame.NEW_WINDOW_HEIGHT);\r
 342           af.statusBar.setText("Successfully pasted alignment file");\r
 343           try\r
 344           {\r
 345             af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
 346           }\r
 347           catch (Exception ex)\r
 348           {}\r
 349         }\r
 350         else\r
 351         {\r
 352           for (int i = 0; i < sequences.length; i++)\r
 353           {\r
 354             alignFrame.viewport.alignment.addSequence(sequences[i]);\r
 355 \r
 356             ////////////////////////////\r
 357             //Datset needs extension;\r
 358             /////////////////////////////\r
 359             Sequence ds = new Sequence(sequences[i].getName(),\r
 360                                        AlignSeq.extractGaps("-. ",\r
 361                 sequences[i].getSequence()),\r
 362                                        sequences[i].getStart(),\r
 363                                        sequences[i].getEnd());\r
 364             sequences[i].setDatasetSequence(ds);\r
 365             alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
 366           }\r
 367           alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
 368                                         getHeight());\r
 369           alignFrame.viewport.alignment.getWidth();\r
 370           alignFrame.viewport.firePropertyChange("alignment", null,\r
 371                                                  alignFrame.viewport.\r
 372                                                  getAlignment().getSequences());\r
 373 \r
 374         }\r
 375 \r
 376         if (database.getSelectedItem().equals("PDB"))\r
 377         {\r
 378           // Parse out the ids from the structured names\r
 379           boolean errors = false;\r
 380           for (int i = 0; i < sequences.length; i++)\r
 381           {\r
 382             PDBEntry entry = new PDBEntry();\r
 383             com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(\r
 384                 "PDB\\|([0-9A-z]{4})\\|(.)");\r
 385             if (idbits.search(sequences[i].getName()))\r
 386             {\r
 387               String pdbid = idbits.substring(1);\r
 388               String pdbccode = idbits.substring(2);\r
 389               // Construct the PDBEntry\r
 390               entry.setId(pdbid);\r
 391               if (entry.getProperty() == null)\r
 392                 entry.setProperty(new Hashtable());\r
 393               entry.getProperty().put("chains",\r
 394                                       pdbccode\r
 395                                       + "=" + sequences[i].getStart()\r
 396                                       + "-" + sequences[i].getEnd());\r
 397               sequences[i].getDatasetSequence().addPDBId(entry);\r
 398             }\r
 399             else\r
 400             {\r
 401               // don't add an entry for this chain, but this is probably a bug\r
 402               // that the user should know about.\r
 403               jalview.bin.Cache.log.warn(\r
 404                   "No PDBEntry constructed for sequence " + i + " : " +\r
 405                   sequences[i].getName());\r
 406               errors = true;\r
 407             }\r
 408           }\r
 409           if (errors)\r
 410             jalview.bin.Cache.log.warn(\r
 411                 "Query string that resulted in PDBEntry construction failure was :\n" +\r
 412                 textfield.getText());\r
 413         }\r
 414 \r
 415       }\r
 416       else\r
 417         showErrorMessage("Error retrieving " + textfield.getText()\r
 418                          + " from " + database.getSelectedItem());\r
 419     }\r
 420 \r
 421     return sequences;\r
 422 \r
 423   }\r
 424 \r
 425   void showErrorMessage(String error)\r
 426   {\r
 427     JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 428                                           error, "Error Retrieving Data",\r
 429                                           JOptionPane.WARNING_MESSAGE);\r
 430   }\r
 431 }\r
 432 \r