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 \r
  33 public class SequenceFetcher\r
  34     extends JPanel implements Runnable\r
  35 {\r
  36   JInternalFrame frame;\r
  37   AlignFrame alignFrame;\r
  38   StringBuffer result;\r
  39   final String noDbSelected = "-- Select Database --";\r
  40   public SequenceFetcher(AlignFrame af)\r
  41   {\r
  42     alignFrame = af;\r
  43     database.addItem(noDbSelected);\r
  44     database.addItem("Uniprot");\r
  45     database.addItem("EMBL");\r
  46     database.addItem("EMBLCDS");\r
  47     database.addItem("PDB");\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, "Sequence Fetcher (WSDBfetch@EBI)", 400, 140);\r
  62     else\r
  63       Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 125);\r
  64   }\r
  65 \r
  66   private void jbInit()\r
  67       throws Exception\r
  68   {\r
  69     this.setLayout(gridBagLayout1);\r
  70 \r
  71     database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
  72     database.setMinimumSize(new Dimension(160, 21));\r
  73     database.setPreferredSize(new Dimension(160, 21));\r
  74     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
  75     jLabel1.setText(\r
  76         "Separate multiple accession ids with semi colon \";\"");\r
  77     ok.setText("OK");\r
  78     ok.addActionListener(new ActionListener()\r
  79     {\r
  80       public void actionPerformed(ActionEvent e)\r
  81       {\r
  82         ok_actionPerformed(e);\r
  83       }\r
  84     });\r
  85     cancel.setText("Cancel");\r
  86     cancel.addActionListener(new ActionListener()\r
  87     {\r
  88       public void actionPerformed(ActionEvent e)\r
  89       {\r
  90         cancel_actionPerformed(e);\r
  91       }\r
  92     });\r
  93     textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
  94     textfield.addActionListener(new ActionListener()\r
  95     {\r
  96       public void actionPerformed(ActionEvent e)\r
  97       {\r
  98         ok_actionPerformed(e);\r
  99       }\r
 100     });\r
 101     jPanel1.add(ok);\r
 102     jPanel1.add(cancel);\r
 103     this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
 104                                              , GridBagConstraints.WEST,\r
 105                                              GridBagConstraints.NONE,\r
 106                                              new Insets(7, 4, 0, 6), 77, 6));\r
 107     this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
 108                                              , GridBagConstraints.WEST,\r
 109                                              GridBagConstraints.BOTH,\r
 110                                              new Insets(7, -2, 7, 12), 241, -2));\r
 111     this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0\r
 112                                               , GridBagConstraints.WEST,\r
 113                                               GridBagConstraints.NONE,\r
 114                                               new Insets(0, 4, 0, 0), 1, 0));\r
 115     this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
 116                                                , GridBagConstraints.CENTER,\r
 117                                                GridBagConstraints.HORIZONTAL,\r
 118                                                new Insets(0, 0, 0, 6), 200, 1));\r
 119   }\r
 120 \r
 121   JComboBox database = new JComboBox();\r
 122   JLabel jLabel1 = new JLabel();\r
 123   JButton ok = new JButton();\r
 124   JButton cancel = new JButton();\r
 125   JPanel jPanel1 = new JPanel();\r
 126   JTextField textfield = new JTextField();\r
 127   GridBagLayout gridBagLayout1 = new GridBagLayout();\r
 128   public void cancel_actionPerformed(ActionEvent e)\r
 129   {\r
 130     try\r
 131     {\r
 132       frame.setClosed(true);\r
 133     }\r
 134     catch (Exception ex)\r
 135     {}\r
 136   }\r
 137 \r
 138   public void ok_actionPerformed(ActionEvent e)\r
 139   {\r
 140     frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");\r
 141     database.setEnabled(false);\r
 142     textfield.setEnabled(false);\r
 143     ok.setEnabled(false);\r
 144     cancel.setEnabled(false);\r
 145 \r
 146     Thread worker = new Thread(this);\r
 147     worker.start();\r
 148   }\r
 149 \r
 150   private void resetDialog() {\r
 151     database.setEnabled(true);\r
 152     textfield.setEnabled(true);\r
 153     ok.setEnabled(true);\r
 154     cancel.setEnabled(true);\r
 155     frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");\r
 156   }\r
 157 \r
 158   public void run()\r
 159   {\r
 160     String error = "";\r
 161     if (database.getSelectedItem().equals(noDbSelected))\r
 162       error += "Please select the source database\n";\r
 163     com.stevesoft.pat.Regex empty=new com.stevesoft.pat.Regex("\\s+","");\r
 164     textfield.setText(empty.replaceAll(textfield.getText()));\r
 165     if (textfield.getText().length()==0)\r
 166       error+="Please enter a (semi-colon separated list of) database id(s)";\r
 167     if (error.length()>0) {\r
 168       showErrorMessage(error);\r
 169       resetDialog();\r
 170       return;\r
 171     }\r
 172 \r
 173    result = new StringBuffer();\r
 174     if (database.getSelectedItem().equals("Uniprot"))\r
 175     {\r
 176       getUniprotFile(textfield.getText());\r
 177     }\r
 178     else if (database.getSelectedItem().equals("EMBL")\r
 179         || database.getSelectedItem().equals("EMBLCDS"))\r
 180     {\r
 181       EBIFetchClient dbFetch = new EBIFetchClient();\r
 182       String[] reply = dbFetch.fetchData(\r
 183           database.getSelectedItem().toString().toLowerCase(\r
 184           ) + ":" + textfield.getText(),\r
 185           "fasta", "raw");\r
 186 \r
 187       for (int i = 0; i < reply.length; i++)\r
 188         result.append(reply[i] + "\n");\r
 189 \r
 190       parseResult(result.toString());\r
 191     }\r
 192     else if (database.getSelectedItem().equals("PDB"))\r
 193     {\r
 194       result = getPDBFile(textfield.getText().toUpperCase());\r
 195       if (result!=null)\r
 196         parseResult(result.toString());\r
 197     }\r
 198 \r
 199 \r
 200     if (result == null || result.length() == 0)\r
 201       showErrorMessage("Error retrieving " + textfield.getText()\r
 202                        + " from " + database.getSelectedItem());\r
 203     else\r
 204       textfield.setText("");\r
 205     resetDialog();\r
 206   }\r
 207 \r
 208   void getUniprotFile(String id)\r
 209   {\r
 210     EBIFetchClient ebi = new EBIFetchClient();\r
 211     File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);\r
 212     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
 213     Vector entries = sff.getUniprotEntries(file);\r
 214 \r
 215     if(entries!=null)\r
 216     {\r
 217       //First, make the new sequences\r
 218       Enumeration en = entries.elements();\r
 219       while (en.hasMoreElements())\r
 220       {\r
 221         UniprotEntry entry = (UniprotEntry) en.nextElement();\r
 222         StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" );\r
 223         Enumeration en2 = entry.getAccession().elements();\r
 224         while(en2.hasMoreElements())\r
 225         {\r
 226           name.append("|");\r
 227           name.append(en2.nextElement());\r
 228         }\r
 229         en2 = entry.getName().elements();\r
 230         while(en2.hasMoreElements())\r
 231         {\r
 232           name.append("|");\r
 233           name.append(en2.nextElement());\r
 234         }\r
 235 \r
 236         if(entry.getProteinName()!=null)\r
 237           name.append(" "+entry.getProteinName().elementAt(0));\r
 238 \r
 239         result.append(name +"\n"+entry.getUniprotSequence().getContent());\r
 240 \r
 241       }\r
 242 \r
 243       //Then read in the features and apply them to the dataset\r
 244       SequenceI [] sequence = parseResult(result.toString());\r
 245       for(int i=0; i<entries.size(); i++)\r
 246       {\r
 247         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
 248         Enumeration e = entry.getDbReference().elements();\r
 249         Vector onlyPdbEntries = new Vector();\r
 250         while (e.hasMoreElements())\r
 251         {\r
 252           PDBEntry pdb = (PDBEntry) e.nextElement();\r
 253           if (!pdb.getType().equals("PDB"))\r
 254             continue;\r
 255 \r
 256           onlyPdbEntries.addElement(pdb);\r
 257         }\r
 258 \r
 259         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
 260         sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
 261 \r
 262       }\r
 263     }\r
 264   }\r
 265 \r
 266     StringBuffer getPDBFile(String id)\r
 267     {\r
 268       StringBuffer result = new StringBuffer();\r
 269       String chain = null;\r
 270       if (id.indexOf(":") > -1)\r
 271       {\r
 272         chain = id.substring(id.indexOf(":") + 1);\r
 273         id = id.substring(0, id.indexOf(":"));\r
 274       }\r
 275 \r
 276       EBIFetchClient ebi = new EBIFetchClient();\r
 277       String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
 278       if (reply==null)\r
 279         return null;\r
 280       try\r
 281       {\r
 282         PDBfile pdbfile = new PDBfile(reply);\r
 283         for (int i = 0; i < pdbfile.chains.size(); i++)\r
 284         {\r
 285           if (chain == null ||\r
 286               ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
 287               toUpperCase().equals(chain))\r
 288             result.append("\n>PDB|" + id + "|" +\r
 289                           ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 290                           getName() +\r
 291                           "\n"\r
 292                           +\r
 293                           ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 294                           getSequence());\r
 295         }\r
 296       }\r
 297       catch (Exception ex) // Problem parsing PDB file\r
 298       {\r
 299         jalview.bin.Cache.log.warn("Exception when retrieving " + textfield.getText() + " from " +\r
 300             database.getSelectedItem(), ex);\r
 301         return null;\r
 302       }\r
 303 \r
 304       return result;\r
 305     }\r
 306 \r
 307     SequenceI[] parseResult(String result)\r
 308     {\r
 309       String format = IdentifyFile.Identify(result, "Paste");\r
 310       SequenceI[] sequences = null;\r
 311 \r
 312       if (FormatAdapter.formats.contains(format))\r
 313       {\r
 314         sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);\r
 315         if (sequences != null && sequences.length>0)\r
 316         {\r
 317           if(alignFrame==null)\r
 318           {\r
 319             AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 320             af.currentFileFormat = format;\r
 321             Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),\r
 322                                      AlignFrame.NEW_WINDOW_WIDTH,\r
 323                                      AlignFrame.NEW_WINDOW_HEIGHT);\r
 324             af.statusBar.setText("Successfully pasted alignment file");\r
 325             try\r
 326             {\r
 327               af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
 328             }\r
 329             catch (Exception ex)\r
 330             {}\r
 331           }\r
 332           else\r
 333           {\r
 334             for (int i = 0; i < sequences.length; i++)\r
 335             {\r
 336               alignFrame.viewport.alignment.addSequence(sequences[i]);\r
 337 \r
 338               ////////////////////////////\r
 339               //Datset needs extension;\r
 340               /////////////////////////////\r
 341               Sequence ds = new Sequence(sequences[i].getName(),\r
 342                                          AlignSeq.extractGaps("-. ",\r
 343                   sequences[i].getSequence()),\r
 344                                          sequences[i].getStart(),\r
 345                                          sequences[i].getEnd());\r
 346               sequences[i].setDatasetSequence(ds);\r
 347               alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
 348             }\r
 349             alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
 350                                           getHeight());\r
 351             alignFrame.viewport.alignment.getWidth();\r
 352             alignFrame.viewport.firePropertyChange("alignment", null,\r
 353             alignFrame.viewport.getAlignment().getSequences());\r
 354 \r
 355           }\r
 356 \r
 357           if (database.getSelectedItem().equals("PDB"))\r
 358           {\r
 359             for (int i = 0; i < sequences.length; i++)\r
 360             {\r
 361               PDBEntry entry = new PDBEntry();\r
 362               entry.setId(textfield.getText());\r
 363               sequences[i].getDatasetSequence().addPDBId(entry);\r
 364             }\r
 365           }\r
 366 \r
 367         }\r
 368         else\r
 369           showErrorMessage( "Error retrieving "+textfield.getText()\r
 370                             +" from "+database.getSelectedItem());\r
 371       }\r
 372 \r
 373       return sequences;\r
 374 \r
 375   }\r
 376 \r
 377   void showErrorMessage(String error)\r
 378   {\r
 379     JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 380          error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);\r
 381   }\r
 382 }\r
 383 \r
 384 \r
 385 \r
 386 \r