3 import javax.swing.*;
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5 import java.awt.event.*;
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6 import jalview.io.EBIFetchClient;
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8 import jalview.datamodel.*;
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9 import jalview.analysis.AlignSeq;
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10 import java.io.File;
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11 import jalview.io.*;
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15 public class SequenceFetcher
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16 extends JPanel implements Runnable
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18 JInternalFrame frame;
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19 AlignFrame alignFrame;
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20 StringBuffer result;
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21 public SequenceFetcher(AlignFrame af)
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24 database.addItem("-- Select Database --");
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25 database.addItem("Uniprot");
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26 database.addItem("EMBL");
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27 database.addItem("EMBLCDS");
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28 database.addItem("PDB");
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34 catch (Exception ex)
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36 ex.printStackTrace();
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39 frame = new JInternalFrame();
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40 frame.setContentPane(this);
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41 if(System.getProperty("os.name").startsWith("Mac"))
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42 Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 390, 140);
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44 Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 390, 120);
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47 private void jbInit()
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50 this.setLayout(gridBagLayout1);
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51 database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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52 jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
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54 "Separate multiple accession ids with semi colon \";\"");
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56 ok.addActionListener(new ActionListener()
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58 public void actionPerformed(ActionEvent e)
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60 ok_actionPerformed(e);
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63 cancel.setText("Cancel");
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64 cancel.addActionListener(new ActionListener()
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66 public void actionPerformed(ActionEvent e)
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68 cancel_actionPerformed(e);
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71 textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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72 textfield.addActionListener(new ActionListener()
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74 public void actionPerformed(ActionEvent e)
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76 ok_actionPerformed(e);
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80 jPanel1.add(cancel);
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81 this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
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82 , GridBagConstraints.WEST,
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83 GridBagConstraints.NONE,
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84 new Insets(7, 4, 0, 6), 77, 6));
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85 this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
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86 , GridBagConstraints.WEST,
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87 GridBagConstraints.HORIZONTAL,
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88 new Insets(0, 0, 0, 6), 221, 1));
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89 this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
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90 , GridBagConstraints.WEST,
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91 GridBagConstraints.BOTH,
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92 new Insets(7, -2, 7, 12), 241, -2));
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93 this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0
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94 , GridBagConstraints.CENTER,
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95 GridBagConstraints.NONE,
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96 new Insets(0, 4, 0, 0), 1, 0));
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99 JComboBox database = new JComboBox();
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100 JLabel jLabel1 = new JLabel();
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101 JButton ok = new JButton();
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102 JButton cancel = new JButton();
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103 JPanel jPanel1 = new JPanel();
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104 JTextField textfield = new JTextField();
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105 GridBagLayout gridBagLayout1 = new GridBagLayout();
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106 public void cancel_actionPerformed(ActionEvent e)
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110 frame.setClosed(true);
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112 catch (Exception ex)
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116 public void ok_actionPerformed(ActionEvent e)
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118 frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");
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119 database.setEnabled(false);
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120 textfield.setEnabled(false);
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121 ok.setEnabled(false);
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122 cancel.setEnabled(false);
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124 Thread worker = new Thread(this);
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130 result = new StringBuffer();
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131 if (database.getSelectedItem().equals("Uniprot"))
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133 getUniprotFile(textfield.getText());
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135 else if (database.getSelectedItem().equals("EMBL")
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136 || database.getSelectedItem().equals("EMBLCDS"))
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138 EBIFetchClient dbFetch = new EBIFetchClient();
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139 String[] reply = dbFetch.fetchData(
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140 database.getSelectedItem().toString().toLowerCase(
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141 ) + ":" + textfield.getText(),
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144 for (int i = 0; i < reply.length; i++)
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145 result.append(reply[i] + "\n");
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147 parseResult(result.toString());
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149 else if (database.getSelectedItem().equals("PDB"))
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151 result = getPDBFile(textfield.getText().toUpperCase());
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152 parseResult(result.toString());
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156 if (result == null || result.length() == 0)
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157 showErrorMessage("Error retrieving " + textfield.getText()
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158 + " from " + database.getSelectedItem());
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161 database.setEnabled(true);
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162 textfield.setEnabled(true);
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163 ok.setEnabled(true);
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164 cancel.setEnabled(true);
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165 frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");
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168 void getUniprotFile(String id)
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170 EBIFetchClient ebi = new EBIFetchClient();
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171 File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);
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172 SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
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173 Vector entries = sff.getUniprotEntries(file);
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177 //First, make the new sequences
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178 Enumeration en = entries.elements();
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179 while (en.hasMoreElements())
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181 UniprotEntry entry = (UniprotEntry) en.nextElement();
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182 StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" );
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183 Enumeration en2 = entry.getAccession().elements();
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184 while(en2.hasMoreElements())
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187 name.append(en2.nextElement());
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189 en2 = entry.getName().elements();
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190 while(en2.hasMoreElements())
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193 name.append(en2.nextElement());
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196 if(entry.getProteinName()!=null)
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197 name.append(" "+entry.getProteinName().elementAt(0));
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199 result.append(name +"\n"+entry.getUniprotSequence().getContent());
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203 //Then read in the features and apply them to the dataset
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204 SequenceI [] sequence = parseResult(result.toString());
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205 for(int i=0; i<entries.size(); i++)
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207 UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
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208 Enumeration e = entry.getDbReference().elements();
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209 Vector onlyPdbEntries = new Vector();
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210 while (e.hasMoreElements())
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212 PDBEntry pdb = (PDBEntry) e.nextElement();
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213 if (!pdb.getType().equals("PDB"))
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216 onlyPdbEntries.addElement(pdb);
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219 sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
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220 sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());
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226 StringBuffer getPDBFile(String id)
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228 StringBuffer result = new StringBuffer();
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229 String chain = null;
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230 if (id.indexOf(":") > -1)
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232 chain = id.substring(id.indexOf(":") + 1);
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233 id = id.substring(0, id.indexOf(":"));
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236 EBIFetchClient ebi = new EBIFetchClient();
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237 String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
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240 PDBfile pdbfile = new PDBfile(reply);
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241 for (int i = 0; i < pdbfile.chains.size(); i++)
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243 if (chain == null ||
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244 ( (PDBChain) pdbfile.chains.elementAt(i)).id.
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245 toUpperCase().equals(chain))
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246 result.append("\n>PDB|" + id + "|" +
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247 ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
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251 ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
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255 catch (Exception ex) // Problem parsing PDB file
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257 showErrorMessage("Error retrieving " + textfield.getText() + " from " +
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258 database.getSelectedItem());
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265 SequenceI[] parseResult(String result)
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267 String format = IdentifyFile.Identify(result, "Paste");
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268 SequenceI[] sequences = null;
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270 if (FormatAdapter.formats.contains(format))
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272 sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);
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273 if (sequences != null && sequences.length>0)
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275 if(alignFrame==null)
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277 AlignFrame af = new AlignFrame(new Alignment(sequences));
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278 af.currentFileFormat = format;
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279 Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),
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280 AlignFrame.NEW_WINDOW_WIDTH,
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281 AlignFrame.NEW_WINDOW_HEIGHT);
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282 af.statusBar.setText("Successfully pasted alignment file");
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285 af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
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287 catch (Exception ex)
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292 for (int i = 0; i < sequences.length; i++)
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294 alignFrame.viewport.alignment.addSequence(sequences[i]);
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296 ////////////////////////////
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297 //Datset needs extension;
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298 /////////////////////////////
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299 Sequence ds = new Sequence(sequences[i].getName(),
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300 AlignSeq.extractGaps("-. ",
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301 sequences[i].getSequence()),
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302 sequences[i].getStart(),
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303 sequences[i].getEnd());
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304 sequences[i].setDatasetSequence(ds);
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305 alignFrame.viewport.alignment.getDataset().addSequence(ds);
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307 alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
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309 alignFrame.viewport.alignment.getWidth();
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310 alignFrame.viewport.firePropertyChange("alignment", null,
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311 alignFrame.viewport.getAlignment().getSequences());
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315 if (database.getSelectedItem().equals("PDB"))
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317 for (int i = 0; i < sequences.length; i++)
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319 PDBEntry entry = new PDBEntry();
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320 entry.setId(textfield.getText());
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321 sequences[i].getDatasetSequence().addPDBId(entry);
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327 showErrorMessage( "Error retrieving "+textfield.getText()
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328 +" from "+database.getSelectedItem());
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335 void showErrorMessage(String error)
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337 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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338 error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
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