2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
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3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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24 import java.util.jar.*;
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26 import javax.swing.*;
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28 import org.exolab.castor.xml.*;
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29 import jalview.binding.*;
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30 import jalview.schemes.*;
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36 * @version $Revision$
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38 public class Jalview2XML_V1
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40 boolean raiseGUI = true;
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42 public Jalview2XML_V1()
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47 public Jalview2XML_V1(boolean raiseGUI)
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49 this.raiseGUI = raiseGUI;
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52 jalview.schemes.UserColourScheme GetUserColourScheme(
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53 JalviewModelSequence jms, String id)
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55 UserColours[] uc = jms.getUserColours();
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56 UserColours colours = null;
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58 for (int i = 0; i < uc.length; i++)
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60 if (uc[i].getId().equals(id))
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68 int csize = colours.getUserColourScheme().getColourCount();
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69 java.awt.Color[] newColours = new java.awt.Color[csize];
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71 for (int i = 0; i < csize; i++)
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73 newColours[i] = new java.awt.Color(Integer.parseInt(colours
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74 .getUserColourScheme().getColour(i).getRGB(), 16));
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77 return new jalview.schemes.UserColourScheme(newColours);
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86 public AlignFrame LoadJalviewAlign(final String file)
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89 jalview.gui.AlignFrame af = null;
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93 // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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96 if (file.startsWith("http://"))
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98 url = new URL(file);
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101 JarInputStream jin = null;
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102 JarEntry jarentry = null;
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103 int entryCount = 1;
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109 jin = new JarInputStream(url.openStream());
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113 jin = new JarInputStream(new FileInputStream(file));
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116 for (int i = 0; i < entryCount; i++)
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118 jarentry = jin.getNextJarEntry();
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121 class NoDescIDResolver implements IDResolver
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123 public Object resolve(String idref)
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125 System.out.println(idref + " used");
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130 if (jarentry != null)
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132 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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133 JalviewModel object = new JalviewModel();
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135 object = (JalviewModel) object.unmarshal(in);
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137 af = LoadFromObject(object, file);
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140 } while (jarentry != null);
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141 } catch (final java.net.UnknownHostException ex)
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143 ex.printStackTrace();
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146 javax.swing.SwingUtilities.invokeLater(new Runnable()
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151 System.err.println("Couldn't locate Jalview XML file : " + ex
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153 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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154 "Couldn't locate " + file, "URL not found",
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155 JOptionPane.WARNING_MESSAGE);
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160 } catch (Exception ex)
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162 System.err.println("Exception whilst loading jalview XML file : ");
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163 ex.printStackTrace();
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166 javax.swing.SwingUtilities.invokeLater(new Runnable()
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171 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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172 "Error loading " + file, "Error loading Jalview file",
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173 JOptionPane.WARNING_MESSAGE);
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182 AlignFrame LoadFromObject(JalviewModel object, String file)
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184 Vector seqids = new Vector();
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185 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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186 Sequence[] vamsasSeq = vamsasSet.getSequence();
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188 JalviewModelSequence jms = object.getJalviewModelSequence();
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190 // ////////////////////////////////
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192 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
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193 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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194 for (int i = 0; i < vamsasSeq.length; i++)
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196 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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197 vamsasSeq[i].getSequence());
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198 jseqs[i].setStart(JSEQ[i].getStart());
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199 jseqs[i].setEnd(JSEQ[i].getEnd());
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200 seqids.add(jseqs[i]);
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203 // /SequenceFeatures are added to the DatasetSequence,
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204 // so we must create the dataset before loading features
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205 // ///////////////////////////////
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206 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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207 al.setDataset(null);
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208 // ///////////////////////////////
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210 for (int i = 0; i < vamsasSeq.length; i++)
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212 if (JSEQ[i].getFeaturesCount() > 0)
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214 Features[] features = JSEQ[i].getFeatures();
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215 for (int f = 0; f < features.length; f++)
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217 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
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218 features[f].getType(), features[f].getDescription(),
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219 features[f].getStatus(), features[f].getBegin(),
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220 features[f].getEnd(), null);
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222 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
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225 if (JSEQ[i].getPdbidsCount() > 0)
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227 Pdbids[] ids = JSEQ[i].getPdbids();
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228 for (int p = 0; p < ids.length; p++)
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230 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
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231 entry.setId(ids[p].getId());
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232 entry.setType(ids[p].getType());
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233 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
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239 // ///////////////////////////////
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240 // ////////////////////////////////
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241 // LOAD ANNOTATIONS
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242 if (vamsasSet.getAnnotation() != null)
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244 Annotation[] an = vamsasSet.getAnnotation();
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246 for (int i = 0; i < an.length; i++)
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248 AnnotationElement[] ae = an[i].getAnnotationElement();
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249 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
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252 for (int aa = 0; aa < ae.length; aa++)
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254 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
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255 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
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256 ae[aa].getSecondaryStructure().charAt(0), ae[aa]
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260 jalview.datamodel.AlignmentAnnotation jaa = null;
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262 if (an[i].getGraph())
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264 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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265 an[i].getDescription(), anot, 0, 0,
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266 jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
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270 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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271 an[i].getDescription(), anot);
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274 al.addAnnotation(jaa);
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278 // ///////////////////////////////
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280 Viewport[] views = jms.getViewport();
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281 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
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283 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
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285 af.setFileName(file, "Jalview");
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287 for (int i = 0; i < JSEQ.length; i++)
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289 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
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290 new java.awt.Color(JSEQ[i].getColour()));
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293 // af.changeColour() );
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294 // ///////////////////////
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296 if (jms.getJGroupCount() > 0)
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298 JGroup[] groups = jms.getJGroup();
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300 for (int i = 0; i < groups.length; i++)
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302 ColourSchemeI cs = null;
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304 if (groups[i].getColour() != null)
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306 if (groups[i].getColour().startsWith("ucs"))
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308 cs = GetUserColourScheme(jms, groups[i].getColour());
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312 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
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317 cs.setThreshold(groups[i].getPidThreshold(), true);
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322 Vector seqs = new Vector();
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323 int[] ids = groups[i].getSeq();
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325 for (int s = 0; s < ids.length; s++)
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327 seqs.addElement((jalview.datamodel.SequenceI) seqids
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328 .elementAt(ids[s]));
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331 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
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332 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
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333 groups[i].getDisplayText(), groups[i].getColourText(),
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334 groups[i].getStart(), groups[i].getEnd());
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337 .setOutlineColour(new java.awt.Color(groups[i]
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338 .getOutlineColour()));
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340 if (groups[i].getConsThreshold() != 0)
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342 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
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343 "All", ResidueProperties.propHash, 3, sg
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344 .getSequences(null), 0, sg.getWidth() - 1);
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346 c.verdict(false, 25);
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347 sg.cs.setConservation(c);
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354 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
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356 af.viewport.setStartRes(view.getStartRes());
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357 af.viewport.setStartSeq(view.getStartSeq());
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358 af.viewport.setShowAnnotation(view.getShowAnnotation());
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359 af.viewport.setAbovePIDThreshold(view.getPidSelected());
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360 af.viewport.setColourText(view.getShowColourText());
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361 af.viewport.setConservationSelected(view.getConservationSelected());
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362 af.viewport.setShowJVSuffix(view.getShowFullId());
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363 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
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364 .getFontStyle(), view.getFontSize()));
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365 af.alignPanel.fontChanged();
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367 af.viewport.setRenderGaps(view.getRenderGaps());
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368 af.viewport.setWrapAlignment(view.getWrapAlignment());
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369 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
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370 af.viewport.setShowAnnotation(view.getShowAnnotation());
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371 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
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372 af.viewport.setShowBoxes(view.getShowBoxes());
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373 af.viewport.setShowText(view.getShowText());
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375 ColourSchemeI cs = null;
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377 if (view.getBgColour() != null)
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379 if (view.getBgColour().startsWith("ucs"))
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381 cs = GetUserColourScheme(jms, view.getBgColour());
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385 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
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390 cs.setThreshold(view.getPidThreshold(), true);
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391 cs.setConsensus(af.viewport.hconsensus);
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395 af.viewport.setGlobalColourScheme(cs);
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396 af.viewport.setColourAppliesToAllGroups(false);
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397 af.changeColour(cs);
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398 if (view.getConservationSelected() && cs != null)
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400 cs.setConservationInc(view.getConsThreshold());
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403 af.viewport.setColourAppliesToAllGroups(true);
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404 af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
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406 if (jms.getFeatureSettings() != null)
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408 af.viewport.featuresDisplayed = new Hashtable();
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409 String[] renderOrder = new String[jms.getFeatureSettings()
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410 .getSettingCount()];
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411 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
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413 Setting setting = jms.getFeatureSettings().getSetting(fs);
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415 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
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416 setting.getType(), new java.awt.Color(setting.getColour()));
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418 renderOrder[fs] = setting.getType();
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420 if (setting.getDisplay())
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422 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
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423 setting.getColour()));
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426 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
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429 af.setMenusFromViewport(af.viewport);
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431 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
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435 // /////////////////////////////////////
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436 if (jms.getTreeCount() > 0)
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440 for (int t = 0; t < jms.getTreeCount(); t++)
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443 Tree tree = jms.getTree(t);
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445 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
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446 .getNewick()), tree.getTitle(), tree.getWidth(), tree
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447 .getHeight(), tree.getXpos(), tree.getYpos());
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449 tp.fitToWindow.setState(tree.getFitToWindow());
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450 tp.fitToWindow_actionPerformed(null);
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452 if (tree.getFontName() != null)
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454 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
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455 .getFontStyle(), tree.getFontSize()));
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459 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
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460 .getFontStyle(), tree.getFontSize()));
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463 tp.showPlaceholders(tree.getMarkUnlinked());
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464 tp.showBootstrap(tree.getShowBootstrap());
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465 tp.showDistances(tree.getShowDistances());
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467 tp.treeCanvas.threshold = tree.getThreshold();
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469 if (tree.getCurrentTree())
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471 af.viewport.setCurrentTree(tp.getTree());
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475 } catch (Exception ex)
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477 ex.printStackTrace();
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