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