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