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     database.addItem("PFAM");\r
  48 \r
  49     try\r
  50     {\r
  51       jbInit();\r
  52     }\r
  53     catch (Exception ex)\r
  54     {\r
  55       ex.printStackTrace();\r
  56     }\r
  57 \r
  58     frame = new JInternalFrame();\r
  59     frame.setContentPane(this);\r
  60     if (System.getProperty("os.name").startsWith("Mac"))\r
  61       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);\r
  62     else\r
  63       Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);\r
  64   }\r
  65 \r
  66   private String getFrameTitle()\r
  67   {\r
  68     return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";\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     close.setText("Close");\r
  91     close.addActionListener(new ActionListener()\r
  92     {\r
  93       public void actionPerformed(ActionEvent e)\r
  94       {\r
  95         close_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(close);\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 close = new JButton();\r
 130   JPanel jPanel1 = new JPanel();\r
 131   JTextField textfield = new JTextField();\r
 132   GridBagLayout gridBagLayout1 = new GridBagLayout();\r
 133   public void close_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     database.setEnabled(false);\r
 146     textfield.setEnabled(false);\r
 147     ok.setEnabled(false);\r
 148     close.setEnabled(false);\r
 149 \r
 150     Thread worker = new Thread(this);\r
 151     worker.start();\r
 152   }\r
 153 \r
 154   private void resetDialog()\r
 155   {\r
 156     database.setEnabled(true);\r
 157     textfield.setEnabled(true);\r
 158     ok.setEnabled(true);\r
 159     close.setEnabled(true);\r
 160   }\r
 161 \r
 162   public void run()\r
 163   {\r
 164     String error = "";\r
 165     if (database.getSelectedItem().equals(noDbSelected))\r
 166       error += "Please select the source database\n";\r
 167     com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");\r
 168     textfield.setText(empty.replaceAll(textfield.getText()));\r
 169     if (textfield.getText().length() == 0)\r
 170       error += "Please enter a (semi-colon separated list of) database id(s)";\r
 171     if (error.length() > 0)\r
 172     {\r
 173       showErrorMessage(error);\r
 174       resetDialog();\r
 175       return;\r
 176     }\r
 177 \r
 178     result = new StringBuffer();\r
 179     if (database.getSelectedItem().equals("Uniprot"))\r
 180     {\r
 181       getUniprotFile(textfield.getText());\r
 182     }\r
 183     else if (database.getSelectedItem().equals("EMBL")\r
 184              || database.getSelectedItem().equals("EMBLCDS"))\r
 185     {\r
 186       EBIFetchClient dbFetch = new EBIFetchClient();\r
 187       String[] reply = dbFetch.fetchData(\r
 188           database.getSelectedItem().toString().toLowerCase(\r
 189           ) + ":" + textfield.getText(),\r
 190           "fasta", "raw");\r
 191 \r
 192       if(reply!=null)\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(), null);\r
 198       }\r
 199     }\r
 200     else if (database.getSelectedItem().equals("PDB"))\r
 201     {\r
 202       StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");\r
 203       String query;\r
 204       while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
 205       {\r
 206         StringBuffer respart = getPDBFile(query.toUpperCase());\r
 207         if(respart!=null)\r
 208           result.append(respart);\r
 209       }\r
 210 \r
 211 \r
 212       if (result.length()>0)\r
 213         parseResult(result.toString(), null);\r
 214     }\r
 215     else if( database.getSelectedItem().equals("PFAM"))\r
 216     {\r
 217       try{\r
 218         result.append(new FastaFile(\r
 219            "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="\r
 220            +  textfield.getText().toUpperCase(), "URL").print()\r
 221            );\r
 222 \r
 223          if(result.length()>0)\r
 224            parseResult( result.toString(), textfield.getText().toUpperCase() );\r
 225 \r
 226       }catch(java.io.IOException ex)\r
 227       {   result = null;    }\r
 228     }\r
 229 \r
 230     if (result == null || result.length() == 0)\r
 231       showErrorMessage("Error retrieving " + textfield.getText()\r
 232                        + " from " + database.getSelectedItem());\r
 233 \r
 234     resetDialog();\r
 235     return;\r
 236   }\r
 237 \r
 238   void getUniprotFile(String id)\r
 239   {\r
 240     EBIFetchClient ebi = new EBIFetchClient();\r
 241     File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
 242    // File file = new File("H:/jalview/classes/fer1.xml");\r
 243     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
 244     Vector entries = sff.getUniprotEntries(file);\r
 245 \r
 246     if (entries != null)\r
 247     {\r
 248       //First, make the new sequences\r
 249       Enumeration en = entries.elements();\r
 250       while (en.hasMoreElements())\r
 251       {\r
 252         UniprotEntry entry = (UniprotEntry) en.nextElement();\r
 253 \r
 254         StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
 255         Enumeration en2 = entry.getAccession().elements();\r
 256         while (en2.hasMoreElements())\r
 257         {\r
 258           name.append("|");\r
 259           name.append(en2.nextElement());\r
 260         }\r
 261         en2 = entry.getName().elements();\r
 262         while (en2.hasMoreElements())\r
 263         {\r
 264           name.append("|");\r
 265           name.append(en2.nextElement());\r
 266         }\r
 267 \r
 268         if (entry.getProtein() != null)\r
 269         {\r
 270            name.append(" " + entry.getProtein().getName().elementAt(0));\r
 271         }\r
 272 \r
 273         result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
 274                       "\n");\r
 275 \r
 276       }\r
 277 \r
 278       //Then read in the features and apply them to the dataset\r
 279       SequenceI[] sequence = parseResult(result.toString(), null);\r
 280       for (int i = 0; i < entries.size(); i++)\r
 281       {\r
 282         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
 283         Enumeration e = entry.getDbReference().elements();\r
 284         Vector onlyPdbEntries = new Vector();\r
 285         while (e.hasMoreElements())\r
 286         {\r
 287           PDBEntry pdb = (PDBEntry) e.nextElement();\r
 288           if (!pdb.getType().equals("PDB"))\r
 289             continue;\r
 290 \r
 291           onlyPdbEntries.addElement(pdb);\r
 292         }\r
 293 \r
 294         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
 295         if (entry.getFeature() != null)\r
 296         {\r
 297           e = entry.getFeature().elements();\r
 298           while (e.hasMoreElements())\r
 299           {\r
 300             SequenceFeature sf = (SequenceFeature) e.nextElement();\r
 301             sf.setFeatureGroup("Uniprot");\r
 302             sequence[i].getDatasetSequence().addSequenceFeature( sf );\r
 303           }\r
 304         }\r
 305       }\r
 306     }\r
 307   }\r
 308 \r
 309   StringBuffer getPDBFile(String id)\r
 310   {\r
 311     StringBuffer result = new StringBuffer();\r
 312     String chain = null;\r
 313     if (id.indexOf(":") > -1)\r
 314     {\r
 315       chain = id.substring(id.indexOf(":") + 1);\r
 316       id = id.substring(0, id.indexOf(":"));\r
 317     }\r
 318 \r
 319     EBIFetchClient ebi = new EBIFetchClient();\r
 320     String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
 321     if (reply == null)\r
 322       return null;\r
 323     try\r
 324     {\r
 325       PDBfile pdbfile = new PDBfile(reply);\r
 326       for (int i = 0; i < pdbfile.chains.size(); i++)\r
 327       {\r
 328         if (chain == null ||\r
 329             ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
 330             toUpperCase().equals(chain))\r
 331           result.append("\n>PDB|" + id + "|" +\r
 332                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 333                         getName() +\r
 334                         "\n"\r
 335                         +\r
 336                         ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 337                         getSequence());\r
 338       }\r
 339     }\r
 340     catch (Exception ex) // Problem parsing PDB file\r
 341     {\r
 342       jalview.bin.Cache.log.warn("Exception when retrieving " +\r
 343                                  textfield.getText() + " from " +\r
 344                                  database.getSelectedItem(), ex);\r
 345       return null;\r
 346     }\r
 347 \r
 348     return result;\r
 349   }\r
 350 \r
 351   SequenceI[] parseResult(String result, String title)\r
 352   {\r
 353     String format = new IdentifyFile().Identify(result, "Paste");\r
 354     SequenceI[] sequences = null;\r
 355 \r
 356     if (FormatAdapter.formats.contains(format))\r
 357     {\r
 358       sequences = null;\r
 359       try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
 360                                                format);}\r
 361       catch(Exception ex){}\r
 362 \r
 363       if (sequences != null && sequences.length > 0)\r
 364       {\r
 365         if (alignFrame == null)\r
 366         {\r
 367           AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 368           af.currentFileFormat = format;\r
 369           if(title==null)\r
 370             title = "Retrieved from " + database.getSelectedItem();\r
 371           Desktop.addInternalFrame(af,\r
 372                                    title,\r
 373                                    AlignFrame.NEW_WINDOW_WIDTH,\r
 374                                    AlignFrame.NEW_WINDOW_HEIGHT);\r
 375           af.statusBar.setText("Successfully pasted alignment file");\r
 376           try\r
 377           {\r
 378             af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
 379           }\r
 380           catch (Exception ex)\r
 381           {}\r
 382         }\r
 383         else\r
 384         {\r
 385           for (int i = 0; i < sequences.length; i++)\r
 386           {\r
 387             alignFrame.viewport.alignment.addSequence(sequences[i]);\r
 388 \r
 389             ////////////////////////////\r
 390             //Dataset needs extension;\r
 391             /////////////////////////////\r
 392             Sequence ds = new Sequence(sequences[i].getName(),\r
 393                                        AlignSeq.extractGaps("-. ",\r
 394                 sequences[i].getSequence()),\r
 395                                        sequences[i].getStart(),\r
 396                                        sequences[i].getEnd());\r
 397             sequences[i].setDatasetSequence(ds);\r
 398             alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
 399           }\r
 400           alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
 401                                         getHeight());\r
 402           alignFrame.viewport.alignment.getWidth();\r
 403           alignFrame.viewport.firePropertyChange("alignment", null,\r
 404                                                  alignFrame.viewport.\r
 405                                                  getAlignment().getSequences());\r
 406 \r
 407         }\r
 408 \r
 409         if (database.getSelectedItem().equals("PDB"))\r
 410         {\r
 411           // Parse out the ids from the structured names\r
 412           boolean errors = false;\r
 413           for (int i = 0; i < sequences.length; i++)\r
 414           {\r
 415             PDBEntry entry = new PDBEntry();\r
 416             com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(\r
 417                 "PDB\\|([0-9A-z]{4})\\|(.)");\r
 418             if (idbits.search(sequences[i].getName()))\r
 419             {\r
 420               String pdbid = idbits.substring(1);\r
 421               String pdbccode = idbits.substring(2);\r
 422               // Construct the PDBEntry\r
 423               entry.setId(pdbid);\r
 424               if (entry.getProperty() == null)\r
 425                 entry.setProperty(new Hashtable());\r
 426               entry.getProperty().put("chains",\r
 427                                       pdbccode\r
 428                                       + "=" + sequences[i].getStart()\r
 429                                       + "-" + sequences[i].getEnd());\r
 430               sequences[i].getDatasetSequence().addPDBId(entry);\r
 431 \r
 432               // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
 433               // JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
 434               DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);\r
 435               sequences[i].getDatasetSequence().addDBRef(dbentry);\r
 436             }\r
 437             else\r
 438             {\r
 439               // don't add an entry for this chain, but this is probably a bug\r
 440               // that the user should know about.\r
 441               jalview.bin.Cache.log.warn(\r
 442                   "No PDBEntry constructed for sequence " + i + " : " +\r
 443                   sequences[i].getName());\r
 444               errors = true;\r
 445             }\r
 446           }\r
 447           if (errors)\r
 448             jalview.bin.Cache.log.warn(\r
 449                 "Query string that resulted in PDBEntry construction failure was :\n" +\r
 450                 textfield.getText());\r
 451         }\r
 452 \r
 453       }\r
 454       else\r
 455         showErrorMessage("Error retrieving " + textfield.getText()\r
 456                          + " from " + database.getSelectedItem());\r
 457     }\r
 458 \r
 459     return sequences;\r
 460 \r
 461   }\r
 462 \r
 463   void showErrorMessage(String error)\r
 464   {\r
 465     resetDialog();\r
 466     JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 467                                           error, "Error Retrieving Data",\r
 468                                           JOptionPane.WARNING_MESSAGE);\r
 469     return;\r
 470   }\r
 471 }\r
 472 \r