src/jalview/gui/SequenceFetcher.java

   1 package jalview.gui;\r
   2 \r
   3 import javax.swing.*;\r
   4 import java.awt.*;\r
   5 import java.awt.event.*;\r
   6 import jalview.io.EBIFetchClient;\r
   7 import MCview.*;\r
   8 import jalview.datamodel.*;\r
   9 import jalview.analysis.AlignSeq;\r
  10 import java.io.File;\r
  11 import jalview.io.*;\r
  12 import java.util.*;\r
  13 \r
  14 \r
  15 public class SequenceFetcher\r
  16     extends JPanel implements Runnable\r
  17 {\r
  18   JInternalFrame frame;\r
  19   AlignFrame alignFrame;\r
  20   StringBuffer result;\r
  21   public SequenceFetcher(AlignFrame af)\r
  22   {\r
  23     alignFrame = af;\r
  24     database.addItem("-- Select Database --");\r
  25     database.addItem("Uniprot");\r
  26     database.addItem("EMBL");\r
  27     database.addItem("EMBLCDS");\r
  28     database.addItem("PDB");\r
  29 \r
  30     try\r
  31     {\r
  32       jbInit();\r
  33     }\r
  34     catch (Exception ex)\r
  35     {\r
  36       ex.printStackTrace();\r
  37     }\r
  38 \r
  39     frame = new JInternalFrame();\r
  40     frame.setContentPane(this);\r
  41     if(System.getProperty("os.name").startsWith("Mac"))\r
  42       Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 390, 135);\r
  43     else\r
  44       Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 390, 120);\r
  45   }\r
  46 \r
  47   private void jbInit()\r
  48       throws Exception\r
  49   {\r
  50     this.setLayout(gridBagLayout1);\r
  51     database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
  52     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
  53     jLabel1.setText(\r
  54         "Separate multiple accession ids with semi colon \";\"");\r
  55     ok.setText("OK");\r
  56     ok.addActionListener(new ActionListener()\r
  57     {\r
  58       public void actionPerformed(ActionEvent e)\r
  59       {\r
  60         ok_actionPerformed(e);\r
  61       }\r
  62     });\r
  63     cancel.setText("Cancel");\r
  64     cancel.addActionListener(new ActionListener()\r
  65     {\r
  66       public void actionPerformed(ActionEvent e)\r
  67       {\r
  68         cancel_actionPerformed(e);\r
  69       }\r
  70     });\r
  71     textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
  72     textfield.addActionListener(new ActionListener()\r
  73     {\r
  74       public void actionPerformed(ActionEvent e)\r
  75       {\r
  76         ok_actionPerformed(e);\r
  77       }\r
  78     });\r
  79     jPanel1.add(ok);\r
  80     jPanel1.add(cancel);\r
  81     this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
  82                                              , GridBagConstraints.WEST,\r
  83                                              GridBagConstraints.NONE,\r
  84                                              new Insets(7, 4, 0, 6), 77, 6));\r
  85     this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
  86                                                , GridBagConstraints.WEST,\r
  87                                                GridBagConstraints.HORIZONTAL,\r
  88                                                new Insets(0, 0, 0, 6), 221, 1));\r
  89     this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
  90                                              , GridBagConstraints.WEST,\r
  91                                              GridBagConstraints.BOTH,\r
  92                                              new Insets(7, -2, 7, 12), 241, -2));\r
  93     this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0\r
  94                                               , GridBagConstraints.CENTER,\r
  95                                               GridBagConstraints.NONE,\r
  96                                               new Insets(0, 4, 0, 0), 1, 0));\r
  97   }\r
  98 \r
  99   JComboBox database = new JComboBox();\r
 100   JLabel jLabel1 = new JLabel();\r
 101   JButton ok = new JButton();\r
 102   JButton cancel = new JButton();\r
 103   JPanel jPanel1 = new JPanel();\r
 104   JTextField textfield = new JTextField();\r
 105   GridBagLayout gridBagLayout1 = new GridBagLayout();\r
 106   public void cancel_actionPerformed(ActionEvent e)\r
 107   {\r
 108     try\r
 109     {\r
 110       frame.setClosed(true);\r
 111     }\r
 112     catch (Exception ex)\r
 113     {}\r
 114   }\r
 115 \r
 116   public void ok_actionPerformed(ActionEvent e)\r
 117   {\r
 118     frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");\r
 119     database.setEnabled(false);\r
 120     textfield.setEnabled(false);\r
 121     ok.setEnabled(false);\r
 122     cancel.setEnabled(false);\r
 123 \r
 124     Thread worker = new Thread(this);\r
 125     worker.start();\r
 126   }\r
 127 \r
 128   public void run()\r
 129   {\r
 130    result = new StringBuffer();\r
 131     if (database.getSelectedItem().equals("Uniprot"))\r
 132     {\r
 133       getUniprotFile(textfield.getText());\r
 134     }\r
 135     else if (database.getSelectedItem().equals("EMBL")\r
 136         || database.getSelectedItem().equals("EMBLCDS"))\r
 137     {\r
 138       EBIFetchClient dbFetch = new EBIFetchClient();\r
 139       String[] reply = dbFetch.fetchData(\r
 140           database.getSelectedItem().toString().toLowerCase(\r
 141           ) + ":" + textfield.getText(),\r
 142           "fasta", "raw");\r
 143 \r
 144       for (int i = 0; i < reply.length; i++)\r
 145         result.append(reply[i] + "\n");\r
 146 \r
 147       parseResult(result.toString());\r
 148     }\r
 149     else if (database.getSelectedItem().equals("PDB"))\r
 150     {\r
 151       result = getPDBFile(textfield.getText().toUpperCase());\r
 152       parseResult(result.toString());\r
 153     }\r
 154 \r
 155 \r
 156     if (result == null || result.length() == 0)\r
 157       showErrorMessage("Error retrieving " + textfield.getText()\r
 158                        + " from " + database.getSelectedItem());\r
 159 \r
 160 \r
 161       database.setEnabled(true);\r
 162       textfield.setEnabled(true);\r
 163       ok.setEnabled(true);\r
 164       cancel.setEnabled(true);\r
 165       frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");\r
 166   }\r
 167 \r
 168   void getUniprotFile(String id)\r
 169   {\r
 170     EBIFetchClient ebi = new EBIFetchClient();\r
 171     File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);\r
 172     SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
 173     Vector entries = sff.getUniprotEntries(file);\r
 174 \r
 175     if(entries!=null)\r
 176     {\r
 177       //First, make the new sequences\r
 178       Enumeration en = entries.elements();\r
 179       while (en.hasMoreElements())\r
 180       {\r
 181         UniprotEntry entry = (UniprotEntry) en.nextElement();\r
 182         StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" );\r
 183         Enumeration en2 = entry.getAccession().elements();\r
 184         while(en2.hasMoreElements())\r
 185         {\r
 186           name.append("|");\r
 187           name.append(en2.nextElement());\r
 188         }\r
 189         en2 = entry.getName().elements();\r
 190         while(en2.hasMoreElements())\r
 191         {\r
 192           name.append("|");\r
 193           name.append(en2.nextElement());\r
 194         }\r
 195 \r
 196         if(entry.getProteinName()!=null)\r
 197           name.append(" "+entry.getProteinName().elementAt(0));\r
 198 \r
 199         result.append(name +"\n"+entry.getUniprotSequence().getContent());\r
 200 \r
 201       }\r
 202 \r
 203       //Then read in the features and apply them to the dataset\r
 204       SequenceI [] sequence = parseResult(result.toString());\r
 205       for(int i=0; i<entries.size(); i++)\r
 206       {\r
 207         UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
 208         Enumeration e = entry.getDbReference().elements();\r
 209         Vector onlyPdbEntries = new Vector();\r
 210         while (e.hasMoreElements())\r
 211         {\r
 212           PDBEntry pdb = (PDBEntry) e.nextElement();\r
 213           if (!pdb.getType().equals("PDB"))\r
 214             continue;\r
 215 \r
 216           onlyPdbEntries.addElement(pdb);\r
 217         }\r
 218 \r
 219         sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
 220         sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
 221 \r
 222       }\r
 223     }\r
 224   }\r
 225 \r
 226     StringBuffer getPDBFile(String id)\r
 227     {\r
 228       StringBuffer result = new StringBuffer();\r
 229       String chain = null;\r
 230       if (id.indexOf(":") > -1)\r
 231       {\r
 232         chain = id.substring(id.indexOf(":") + 1);\r
 233         id = id.substring(0, id.indexOf(":"));\r
 234       }\r
 235 \r
 236       EBIFetchClient ebi = new EBIFetchClient();\r
 237       String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
 238       try\r
 239       {\r
 240         PDBfile pdbfile = new PDBfile(reply);\r
 241         for (int i = 0; i < pdbfile.chains.size(); i++)\r
 242         {\r
 243           if (chain == null ||\r
 244               ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
 245               toUpperCase().equals(chain))\r
 246             result.append("\n>PDB|" + id + "|" +\r
 247                           ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 248                           getName() +\r
 249                           "\n"\r
 250                           +\r
 251                           ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 252                           getSequence());\r
 253         }\r
 254       }\r
 255       catch (Exception ex) // Problem parsing PDB file\r
 256       {\r
 257         showErrorMessage("Error retrieving " + textfield.getText() + " from " +\r
 258             database.getSelectedItem());\r
 259         return null;\r
 260       }\r
 261 \r
 262       return result;\r
 263     }\r
 264 \r
 265     SequenceI[] parseResult(String result)\r
 266     {\r
 267       String format = IdentifyFile.Identify(result, "Paste");\r
 268       SequenceI[] sequences = null;\r
 269 \r
 270       if (FormatAdapter.formats.contains(format))\r
 271       {\r
 272         sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);\r
 273         if (sequences != null && sequences.length>0)\r
 274         {\r
 275           if(alignFrame==null)\r
 276           {\r
 277             AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 278             af.currentFileFormat = format;\r
 279             Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),\r
 280                                      AlignFrame.NEW_WINDOW_WIDTH,\r
 281                                      AlignFrame.NEW_WINDOW_HEIGHT);\r
 282             af.statusBar.setText("Successfully pasted alignment file");\r
 283             try\r
 284             {\r
 285               af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
 286             }\r
 287             catch (Exception ex)\r
 288             {}\r
 289           }\r
 290           else\r
 291           {\r
 292             for (int i = 0; i < sequences.length; i++)\r
 293             {\r
 294               alignFrame.viewport.alignment.addSequence(sequences[i]);\r
 295 \r
 296               ////////////////////////////\r
 297               //Datset needs extension;\r
 298               /////////////////////////////\r
 299               Sequence ds = new Sequence(sequences[i].getName(),\r
 300                                          AlignSeq.extractGaps("-. ",\r
 301                   sequences[i].getSequence()),\r
 302                                          sequences[i].getStart(),\r
 303                                          sequences[i].getEnd());\r
 304               sequences[i].setDatasetSequence(ds);\r
 305               alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
 306             }\r
 307             alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
 308                                           getHeight());\r
 309             alignFrame.viewport.alignment.getWidth();\r
 310             alignFrame.viewport.firePropertyChange("alignment", null,\r
 311             alignFrame.viewport.getAlignment().getSequences());\r
 312 \r
 313           }\r
 314 \r
 315           if (database.getSelectedItem().equals("PDB"))\r
 316           {\r
 317             for (int i = 0; i < sequences.length; i++)\r
 318             {\r
 319               PDBEntry entry = new PDBEntry();\r
 320               entry.setId(textfield.getText());\r
 321               sequences[i].getDatasetSequence().addPDBId(entry);\r
 322             }\r
 323           }\r
 324 \r
 325         }\r
 326         else\r
 327           showErrorMessage( "Error retrieving "+textfield.getText()\r
 328                             +" from "+database.getSelectedItem());\r
 329       }\r
 330 \r
 331       return sequences;\r
 332 \r
 333   }\r
 334 \r
 335   void showErrorMessage(String error)\r
 336   {\r
 337     JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 338          error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);\r
 339   }\r
 340 }\r
 341 \r
 342 \r
 343 \r
 344 \r