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       if(reply!=null)\r
 195       {\r
 196         for (int i = 0; i < reply.length; i++)\r
 197           result.append(reply[i] + "\n");\r
 198 \r
 199         parseResult(result.toString());\r
 200       }\r
 201     }\r
 202     else if (database.getSelectedItem().equals("PDB"))\r
 203     {\r
 204       StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");\r
 205       String query;\r
 206       while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
 207       {\r
 208         StringBuffer respart = getPDBFile(query.toUpperCase());\r
 209         if(respart!=null)\r
 210           result.append(respart);\r
 211       }\r
 212 \r
 213 \r
 214       if (result.length()>0)\r
 215         parseResult(result.toString());\r
 216     }\r
 217 \r
 218     if (result == null || result.length() == 0)\r
 219       showErrorMessage("Error retrieving " + textfield.getText()\r
 220                        + " from " + database.getSelectedItem());\r
 221     else\r
 222       textfield.setText("");\r
 223     resetDialog();\r
 224   }\r
 225 \r
 226   void getUniprotFile(String id)\r
 227   {\r
 228     EBIFetchClient ebi = new EBIFetchClient();\r
 229     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
 230     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
 231     Vector entries = sff.getUniprotEntries(file);\r
 232 \r
 233     if (entries != null)\r
 234     {\r
 235       //First, make the new sequences\r
 236       Enumeration en = entries.elements();\r
 237       while (en.hasMoreElements())\r
 238       {\r
 239         UniprotEntry entry = (UniprotEntry) en.nextElement();\r
 240         StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");\r
 241         Enumeration en2 = entry.getAccession().elements();\r
 242         while (en2.hasMoreElements())\r
 243         {\r
 244           name.append("|");\r
 245           name.append(en2.nextElement());\r
 246         }\r
 247         en2 = entry.getName().elements();\r
 248         while (en2.hasMoreElements())\r
 249         {\r
 250           name.append("|");\r
 251           name.append(en2.nextElement());\r
 252         }\r
 253 \r
 254         if (entry.getProteinName() != null)\r
 255           name.append(" " + entry.getProteinName().elementAt(0));\r
 256 \r
 257         result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
 258                       "\n");\r
 259 \r
 260       }\r
 261 \r
 262       //Then read in the features and apply them to the dataset\r
 263       SequenceI[] sequence = parseResult(result.toString());\r
 264       for (int i = 0; i < entries.size(); i++)\r
 265       {\r
 266         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
 267         Enumeration e = entry.getDbReference().elements();\r
 268         Vector onlyPdbEntries = new Vector();\r
 269         while (e.hasMoreElements())\r
 270         {\r
 271           PDBEntry pdb = (PDBEntry) e.nextElement();\r
 272           if (!pdb.getType().equals("PDB"))\r
 273             continue;\r
 274 \r
 275           onlyPdbEntries.addElement(pdb);\r
 276         }\r
 277 \r
 278         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
 279         sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
 280 \r
 281       }\r
 282     }\r
 283   }\r
 284 \r
 285   StringBuffer getPDBFile(String id)\r
 286   {\r
 287     StringBuffer result = new StringBuffer();\r
 288     String chain = null;\r
 289     if (id.indexOf(":") > -1)\r
 290     {\r
 291       chain = id.substring(id.indexOf(":") + 1);\r
 292       id = id.substring(0, id.indexOf(":"));\r
 293     }\r
 294 \r
 295     EBIFetchClient ebi = new EBIFetchClient();\r
 296     String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
 297     if (reply == null)\r
 298       return null;\r
 299     try\r
 300     {\r
 301       PDBfile pdbfile = new PDBfile(reply);\r
 302       for (int i = 0; i < pdbfile.chains.size(); i++)\r
 303       {\r
 304         if (chain == null ||\r
 305             ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
 306             toUpperCase().equals(chain))\r
 307           result.append("\n>PDB|" + id + "|" +\r
 308                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 309                         getName() +\r
 310                         "\n"\r
 311                         +\r
 312                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 313                         getSequence());\r
 314       }\r
 315     }\r
 316     catch (Exception ex) // Problem parsing PDB file\r
 317     {\r
 318       jalview.bin.Cache.log.warn("Exception when retrieving " +\r
 319                                  textfield.getText() + " from " +\r
 320                                  database.getSelectedItem(), ex);\r
 321       return null;\r
 322     }\r
 323 \r
 324     return result;\r
 325   }\r
 326 \r
 327   SequenceI[] parseResult(String result)\r
 328   {\r
 329     String format = IdentifyFile.Identify(result, "Paste");\r
 330     SequenceI[] sequences = null;\r
 331 \r
 332     if (FormatAdapter.formats.contains(format))\r
 333     {\r
 334       sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
 335                                                format);\r
 336       if (sequences != null && sequences.length > 0)\r
 337       {\r
 338         if (alignFrame == null)\r
 339         {\r
 340           AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 341           af.currentFileFormat = format;\r
 342           Desktop.addInternalFrame(af,\r
 343                                    "Retrieved from " + database.getSelectedItem(),\r
 344                                    AlignFrame.NEW_WINDOW_WIDTH,\r
 345                                    AlignFrame.NEW_WINDOW_HEIGHT);\r
 346           af.statusBar.setText("Successfully pasted alignment file");\r
 347           try\r
 348           {\r
 349             af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
 350           }\r
 351           catch (Exception ex)\r
 352           {}\r
 353         }\r
 354         else\r
 355         {\r
 356           for (int i = 0; i < sequences.length; i++)\r
 357           {\r
 358             alignFrame.viewport.alignment.addSequence(sequences[i]);\r
 359 \r
 360             ////////////////////////////\r
 361             //Datset needs extension;\r
 362             /////////////////////////////\r
 363             Sequence ds = new Sequence(sequences[i].getName(),\r
 364                                        AlignSeq.extractGaps("-. ",\r
 365                 sequences[i].getSequence()),\r
 366                                        sequences[i].getStart(),\r
 367                                        sequences[i].getEnd());\r
 368             sequences[i].setDatasetSequence(ds);\r
 369             alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
 370           }\r
 371           alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
 372                                         getHeight());\r
 373           alignFrame.viewport.alignment.getWidth();\r
 374           alignFrame.viewport.firePropertyChange("alignment", null,\r
 375                                                  alignFrame.viewport.\r
 376                                                  getAlignment().getSequences());\r
 377 \r
 378         }\r
 379 \r
 380         if (database.getSelectedItem().equals("PDB"))\r
 381         {\r
 382           // Parse out the ids from the structured names\r
 383           boolean errors = false;\r
 384           for (int i = 0; i < sequences.length; i++)\r
 385           {\r
 386             PDBEntry entry = new PDBEntry();\r
 387             com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(\r
 388                 "PDB\\|([0-9A-z]{4})\\|(.)");\r
 389             if (idbits.search(sequences[i].getName()))\r
 390             {\r
 391               String pdbid = idbits.substring(1);\r
 392               String pdbccode = idbits.substring(2);\r
 393               // Construct the PDBEntry\r
 394               entry.setId(pdbid);\r
 395               if (entry.getProperty() == null)\r
 396                 entry.setProperty(new Hashtable());\r
 397               entry.getProperty().put("chains",\r
 398                                       pdbccode\r
 399                                       + "=" + sequences[i].getStart()\r
 400                                       + "-" + sequences[i].getEnd());\r
 401               sequences[i].getDatasetSequence().addPDBId(entry);\r
 402               // JBPNote - should add a PDB DBRefEntry too since we\r
 403               // have obtained the PDB file from a verifiable source\r
 404               DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);\r
 405               sequences[i].getDatasetSequence().addDBRef(dbentry);\r
 406             }\r
 407             else\r
 408             {\r
 409               // don't add an entry for this chain, but this is probably a bug\r
 410               // that the user should know about.\r
 411               jalview.bin.Cache.log.warn(\r
 412                   "No PDBEntry constructed for sequence " + i + " : " +\r
 413                   sequences[i].getName());\r
 414               errors = true;\r
 415             }\r
 416           }\r
 417           if (errors)\r
 418             jalview.bin.Cache.log.warn(\r
 419                 "Query string that resulted in PDBEntry construction failure was :\n" +\r
 420                 textfield.getText());\r
 421         }\r
 422 \r
 423       }\r
 424       else\r
 425         showErrorMessage("Error retrieving " + textfield.getText()\r
 426                          + " from " + database.getSelectedItem());\r
 427     }\r
 428 \r
 429     return sequences;\r
 430 \r
 431   }\r
 432 \r
 433   void showErrorMessage(String error)\r
 434   {\r
 435     JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 436                                           error, "Error Retrieving Data",\r
 437                                           JOptionPane.WARNING_MESSAGE);\r
 438   }\r
 439 }\r
 440 \r