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.ActionListener;\r
   6 import java.awt.event.ActionEvent;\r
   7 import MCview.PDBfile;\r
   8 import jalview.io.EBIFetchClient;\r
   9 import MCview.PDBChain;\r
  10 import jalview.datamodel.Alignment;\r
  11 import jalview.io.FormatAdapter;\r
  12 import jalview.datamodel.SequenceI;\r
  13 import jalview.io.IdentifyFile;\r
  14 import jalview.analysis.AlignSeq;\r
  15 import jalview.datamodel.*;\r
  16 \r
  17 public class SequenceFetcher\r
  18     extends JPanel implements Runnable\r
  19 {\r
  20   JInternalFrame frame;\r
  21   AlignFrame alignFrame;\r
  22   public SequenceFetcher(AlignFrame af)\r
  23   {\r
  24     alignFrame = af;\r
  25     database.addItem("-- Select Database --");\r
  26     database.addItem("Uniprot");\r
  27     database.addItem("EMBL");\r
  28     database.addItem("EMBLCDS");\r
  29     database.addItem("PDB");\r
  30 \r
  31     try\r
  32     {\r
  33       jbInit();\r
  34     }\r
  35     catch (Exception ex)\r
  36     {\r
  37       ex.printStackTrace();\r
  38     }\r
  39 \r
  40     frame = new JInternalFrame();\r
  41     frame.setContentPane(this);\r
  42     if(System.getProperty("os.name").startsWith("Mac"))\r
  43       Desktop.addInternalFrame(frame, "Sequence Fetcher", 390, 135);\r
  44     else\r
  45       Desktop.addInternalFrame(frame, "Sequence Fetcher", 390, 120);\r
  46   }\r
  47 \r
  48   private void jbInit()\r
  49       throws Exception\r
  50   {\r
  51     this.setLayout(gridBagLayout1);\r
  52     database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
  53     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
  54     jLabel1.setText(\r
  55         "Separate multiple accession ids with semi colon \";\"");\r
  56     ok.setText("OK");\r
  57     ok.addActionListener(new ActionListener()\r
  58     {\r
  59       public void actionPerformed(ActionEvent e)\r
  60       {\r
  61         ok_actionPerformed(e);\r
  62       }\r
  63     });\r
  64     cancel.setText("Cancel");\r
  65     cancel.addActionListener(new ActionListener()\r
  66     {\r
  67       public void actionPerformed(ActionEvent e)\r
  68       {\r
  69         cancel_actionPerformed(e);\r
  70       }\r
  71     });\r
  72     textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
  73     textfield.addActionListener(new ActionListener()\r
  74     {\r
  75       public void actionPerformed(ActionEvent e)\r
  76       {\r
  77         ok_actionPerformed(e);\r
  78       }\r
  79     });\r
  80     jPanel1.add(ok);\r
  81     jPanel1.add(cancel);\r
  82     this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
  83                                              , GridBagConstraints.WEST,\r
  84                                              GridBagConstraints.NONE,\r
  85                                              new Insets(7, 4, 0, 6), 77, 6));\r
  86     this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
  87                                                , GridBagConstraints.WEST,\r
  88                                                GridBagConstraints.HORIZONTAL,\r
  89                                                new Insets(0, 0, 0, 6), 221, 1));\r
  90     this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
  91                                              , GridBagConstraints.WEST,\r
  92                                              GridBagConstraints.BOTH,\r
  93                                              new Insets(7, -2, 7, 12), 241, -2));\r
  94     this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0\r
  95                                               , GridBagConstraints.CENTER,\r
  96                                               GridBagConstraints.NONE,\r
  97                                               new Insets(0, 4, 0, 0), 1, 0));\r
  98   }\r
  99 \r
 100   JComboBox database = new JComboBox();\r
 101   JLabel jLabel1 = new JLabel();\r
 102   JButton ok = new JButton();\r
 103   JButton cancel = new JButton();\r
 104   JPanel jPanel1 = new JPanel();\r
 105   JTextField textfield = new JTextField();\r
 106   GridBagLayout gridBagLayout1 = new GridBagLayout();\r
 107   public void cancel_actionPerformed(ActionEvent e)\r
 108   {\r
 109     try\r
 110     {\r
 111       frame.setClosed(true);\r
 112     }\r
 113     catch (Exception ex)\r
 114     {}\r
 115   }\r
 116 \r
 117   public void ok_actionPerformed(ActionEvent e)\r
 118   {\r
 119     frame.setTitle("WSDBfetch@EBI Sequence Fetcher - Fetching Sequence...");\r
 120     database.setEnabled(false);\r
 121     textfield.setEnabled(false);\r
 122     ok.setEnabled(false);\r
 123     cancel.setEnabled(false);\r
 124 \r
 125     Thread worker = new Thread(this);\r
 126     worker.start();\r
 127   }\r
 128 \r
 129   public void run()\r
 130   {\r
 131     String error = null;\r
 132     StringBuffer result = new StringBuffer();\r
 133       if (database.getSelectedItem().equals("Uniprot")\r
 134           || database.getSelectedItem().equals("EMBL")\r
 135           || database.getSelectedItem().equals("EMBLCDS"))\r
 136       {\r
 137         EBIFetchClient dbFetch = new EBIFetchClient();\r
 138         String[] reply = dbFetch.fetchData(\r
 139             database.getSelectedItem().toString().toLowerCase(\r
 140             ) + ":" + textfield.getText(),\r
 141             "fasta", "raw");\r
 142 \r
 143         for (int i = 0; i < reply.length; i++)\r
 144           result.append(reply[i] + "\n");\r
 145       }\r
 146       else if (database.getSelectedItem().equals("PDB"))\r
 147       {\r
 148         String id = textfield.getText().toUpperCase();\r
 149         String chain=null;\r
 150         if(id.indexOf(":")>-1)\r
 151         {\r
 152           chain = id.substring(id.indexOf(":")+1);\r
 153           id = id.substring(0,id.indexOf(":"));\r
 154           System.out.println(id+" "+chain);\r
 155         }\r
 156 \r
 157         EBIFetchClient ebi = new EBIFetchClient();\r
 158         String[] reply = ebi.fetchData("pdb:" + id, "pdb",\r
 159                                        "raw");\r
 160         try{\r
 161           PDBfile pdbfile = new PDBfile(reply);\r
 162           for (int i = 0; i < pdbfile.chains.size(); i++)\r
 163           {\r
 164             if( chain == null || ((PDBChain)pdbfile.chains.elementAt(i)).id.toUpperCase().equals(chain))\r
 165             result.append("\n>PDB|" + id+"|"+\r
 166                           ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 167                           getName() +\r
 168                           "\n"\r
 169                           +\r
 170                           ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
 171                           getSequence());\r
 172           }\r
 173         }catch(Exception ex)// Problem parsing PDB file\r
 174         {\r
 175           error = "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem();\r
 176         }\r
 177       }\r
 178 \r
 179     if (result.length() > 0 && error==null)\r
 180     {\r
 181       String format = IdentifyFile.Identify(result.toString(), "Paste");\r
 182       SequenceI[] sequences = null;\r
 183 \r
 184       if (FormatAdapter.formats.contains(format))\r
 185       {\r
 186         sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);\r
 187         if (sequences != null && sequences.length>0)\r
 188         {\r
 189           if(alignFrame==null)\r
 190           {\r
 191             AlignFrame af = new AlignFrame(new Alignment(sequences));\r
 192             af.currentFileFormat = format;\r
 193             Desktop.addInternalFrame(af, "Cut & Paste input - " + format,\r
 194                                      AlignFrame.NEW_WINDOW_WIDTH,\r
 195                                      AlignFrame.NEW_WINDOW_HEIGHT);\r
 196             af.statusBar.setText("Successfully pasted alignment file");\r
 197             try\r
 198             {\r
 199               af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
 200             }\r
 201             catch (Exception ex)\r
 202             {}\r
 203           }\r
 204           else\r
 205           {\r
 206             for (int i = 0; i < sequences.length; i++)\r
 207             {\r
 208               alignFrame.viewport.alignment.addSequence(sequences[i]);\r
 209 \r
 210               ////////////////////////////\r
 211               //Datset needs extension;\r
 212               /////////////////////////////\r
 213               Sequence ds = new Sequence(sequences[i].getName(),\r
 214                                          AlignSeq.extractGaps("-. ",\r
 215                   sequences[i].getSequence()),\r
 216                                          sequences[i].getStart(),\r
 217                                          sequences[i].getEnd());\r
 218               sequences[i].setDatasetSequence(ds);\r
 219               alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
 220             }\r
 221             alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
 222                                           getHeight());\r
 223             alignFrame.viewport.alignment.getWidth();\r
 224             alignFrame.viewport.firePropertyChange("alignment", null,\r
 225                 alignFrame.viewport.getAlignment().getSequences());\r
 226 \r
 227           }\r
 228 \r
 229           if (database.getSelectedItem().equals("PDB"))\r
 230           {\r
 231             for (int i = 0; i < sequences.length; i++)\r
 232             {\r
 233               PDBEntry entry = new PDBEntry();\r
 234               entry.setId(textfield.getText());\r
 235               sequences[i].getDatasetSequence().addPDBId(entry);\r
 236             }\r
 237           }\r
 238 \r
 239         }\r
 240         else\r
 241           error = "Error retrieving "+textfield.getText()+" from "+database.getSelectedItem();\r
 242 \r
 243 \r
 244 \r
 245       }\r
 246     }\r
 247 \r
 248     if(error!=null)\r
 249           showErrorMessage(error);\r
 250 \r
 251     database.setEnabled(true);\r
 252     textfield.setEnabled(true);\r
 253     ok.setEnabled(true);\r
 254     cancel.setEnabled(true);\r
 255     frame.setTitle("WSDBfetch@EBI Sequence Fetcher");\r
 256   }\r
 257 \r
 258   void showErrorMessage(String error)\r
 259   {\r
 260     JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 261          error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);\r
 262   }\r
 263 }\r
 264 \r
 265 \r
 266 \r
 267 \r