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