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