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