2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
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3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.gui;
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23 import java.util.jar.*;
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25 import javax.swing.*;
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27 import org.exolab.castor.xml.*;
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28 import jalview.binding.*;
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29 import jalview.schemes.*;
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30 import jalview.util.jarInputStreamProvider;
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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 jarInputStreamProvider jprovider)
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88 final String file = jprovider.getFilename();
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89 jalview.gui.AlignFrame af = null;
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93 JarInputStream jin = null;
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94 JarEntry jarentry = null;
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99 jin = jprovider.getJarInputStream();
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101 for (int i = 0; i < entryCount; i++)
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103 jarentry = jin.getNextJarEntry();
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106 class NoDescIDResolver implements IDResolver
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108 public Object resolve(String idref)
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110 System.out.println(idref + " used");
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115 if (jarentry != null)
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117 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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118 JalviewModel object = new JalviewModel();
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120 object = (JalviewModel) object.unmarshal(in);
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122 af = LoadFromObject(object, file);
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125 } while (jarentry != null);
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126 } catch (final java.net.UnknownHostException ex)
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128 ex.printStackTrace();
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131 javax.swing.SwingUtilities.invokeLater(new Runnable()
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136 System.err.println("Couldn't locate Jalview XML file : " + ex
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138 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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139 "Couldn't locate " + file, "URL not found",
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140 JOptionPane.WARNING_MESSAGE);
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145 } catch (Exception ex)
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147 System.err.println("Exception whilst loading jalview XML file : ");
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148 ex.printStackTrace();
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151 javax.swing.SwingUtilities.invokeLater(new Runnable()
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156 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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157 "Error loading " + file, "Error loading Jalview file",
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158 JOptionPane.WARNING_MESSAGE);
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167 AlignFrame LoadFromObject(JalviewModel object, String file)
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169 Vector seqids = new Vector();
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170 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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171 Sequence[] vamsasSeq = vamsasSet.getSequence();
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173 JalviewModelSequence jms = object.getJalviewModelSequence();
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175 // ////////////////////////////////
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177 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
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178 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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179 for (int i = 0; i < vamsasSeq.length; i++)
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181 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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182 vamsasSeq[i].getSequence());
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183 jseqs[i].setStart(JSEQ[i].getStart());
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184 jseqs[i].setEnd(JSEQ[i].getEnd());
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185 seqids.add(jseqs[i]);
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188 // /SequenceFeatures are added to the DatasetSequence,
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189 // so we must create the dataset before loading features
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190 // ///////////////////////////////
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191 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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192 al.setDataset(null);
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193 // ///////////////////////////////
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195 for (int i = 0; i < vamsasSeq.length; i++)
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197 if (JSEQ[i].getFeaturesCount() > 0)
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199 Features[] features = JSEQ[i].getFeatures();
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200 for (int f = 0; f < features.length; f++)
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202 jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
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203 features[f].getType(), features[f].getDescription(),
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204 features[f].getStatus(), features[f].getBegin(),
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205 features[f].getEnd(), null);
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207 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
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210 if (JSEQ[i].getPdbidsCount() > 0)
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212 Pdbids[] ids = JSEQ[i].getPdbids();
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213 for (int p = 0; p < ids.length; p++)
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215 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
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216 entry.setId(ids[p].getId());
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217 entry.setType(ids[p].getType());
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218 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
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224 // ///////////////////////////////
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225 // ////////////////////////////////
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226 // LOAD ANNOTATIONS
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227 if (vamsasSet.getAnnotation() != null)
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229 Annotation[] an = vamsasSet.getAnnotation();
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231 for (int i = 0; i < an.length; i++)
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233 AnnotationElement[] ae = an[i].getAnnotationElement();
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234 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
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237 for (int aa = 0; aa < ae.length; aa++)
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239 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
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240 ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
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241 ae[aa].getSecondaryStructure().charAt(0), ae[aa]
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245 jalview.datamodel.AlignmentAnnotation jaa = null;
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247 if (an[i].getGraph())
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249 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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250 an[i].getDescription(), anot, 0, 0,
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251 jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
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255 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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256 an[i].getDescription(), anot);
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259 al.addAnnotation(jaa);
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263 // ///////////////////////////////
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265 Viewport[] views = jms.getViewport();
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266 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
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268 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
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270 af.setFileName(file, "Jalview");
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272 for (int i = 0; i < JSEQ.length; i++)
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274 af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
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275 new java.awt.Color(JSEQ[i].getColour()));
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278 // af.changeColour() );
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279 // ///////////////////////
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281 if (jms.getJGroupCount() > 0)
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283 JGroup[] groups = jms.getJGroup();
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285 for (int i = 0; i < groups.length; i++)
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287 ColourSchemeI cs = null;
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289 if (groups[i].getColour() != null)
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291 if (groups[i].getColour().startsWith("ucs"))
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293 cs = GetUserColourScheme(jms, groups[i].getColour());
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297 cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
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302 cs.setThreshold(groups[i].getPidThreshold(), true);
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307 Vector seqs = new Vector();
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308 int[] ids = groups[i].getSeq();
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310 for (int s = 0; s < ids.length; s++)
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312 seqs.addElement((jalview.datamodel.SequenceI) seqids
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313 .elementAt(ids[s]));
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316 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
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317 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
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318 groups[i].getDisplayText(), groups[i].getColourText(),
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319 groups[i].getStart(), groups[i].getEnd());
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322 .setOutlineColour(new java.awt.Color(groups[i]
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323 .getOutlineColour()));
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325 if (groups[i].getConsThreshold() != 0)
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327 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
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328 "All", ResidueProperties.propHash, 3, sg
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329 .getSequences(null), 0, sg.getWidth() - 1);
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331 c.verdict(false, 25);
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332 sg.cs.setConservation(c);
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339 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
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341 af.viewport.setStartRes(view.getStartRes());
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342 af.viewport.setStartSeq(view.getStartSeq());
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343 af.viewport.setShowAnnotation(view.getShowAnnotation());
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344 af.viewport.setAbovePIDThreshold(view.getPidSelected());
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345 af.viewport.setColourText(view.getShowColourText());
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346 af.viewport.setConservationSelected(view.getConservationSelected());
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347 af.viewport.setShowJVSuffix(view.getShowFullId());
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348 af.viewport.setFont(new java.awt.Font(view.getFontName(), view
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349 .getFontStyle(), view.getFontSize()));
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350 af.alignPanel.fontChanged();
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352 af.viewport.setRenderGaps(view.getRenderGaps());
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353 af.viewport.setWrapAlignment(view.getWrapAlignment());
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354 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
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355 af.viewport.setShowAnnotation(view.getShowAnnotation());
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356 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
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357 af.viewport.setShowBoxes(view.getShowBoxes());
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358 af.viewport.setShowText(view.getShowText());
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360 ColourSchemeI cs = null;
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362 if (view.getBgColour() != null)
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364 if (view.getBgColour().startsWith("ucs"))
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366 cs = GetUserColourScheme(jms, view.getBgColour());
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370 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
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375 cs.setThreshold(view.getPidThreshold(), true);
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376 cs.setConsensus(af.viewport.hconsensus);
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380 af.viewport.setGlobalColourScheme(cs);
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381 af.viewport.setColourAppliesToAllGroups(false);
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382 af.changeColour(cs);
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383 if (view.getConservationSelected() && cs != null)
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385 cs.setConservationInc(view.getConsThreshold());
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388 af.viewport.setColourAppliesToAllGroups(true);
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389 af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
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391 if (jms.getFeatureSettings() != null)
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393 af.viewport.featuresDisplayed = new Hashtable();
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394 String[] renderOrder = new String[jms.getFeatureSettings()
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395 .getSettingCount()];
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396 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
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398 Setting setting = jms.getFeatureSettings().getSetting(fs);
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400 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
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401 setting.getType(), new java.awt.Color(setting.getColour()));
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403 renderOrder[fs] = setting.getType();
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405 if (setting.getDisplay())
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407 af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
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408 setting.getColour()));
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411 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
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414 af.setMenusFromViewport(af.viewport);
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416 Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
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420 // /////////////////////////////////////
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421 if (jms.getTreeCount() > 0)
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425 for (int t = 0; t < jms.getTreeCount(); t++)
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428 Tree tree = jms.getTree(t);
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430 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
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431 .getNewick()), tree.getTitle(), tree.getWidth(), tree
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432 .getHeight(), tree.getXpos(), tree.getYpos());
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434 tp.fitToWindow.setState(tree.getFitToWindow());
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435 tp.fitToWindow_actionPerformed(null);
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437 if (tree.getFontName() != null)
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439 tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
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440 .getFontStyle(), tree.getFontSize()));
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444 tp.setTreeFont(new java.awt.Font(view.getFontName(), view
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445 .getFontStyle(), tree.getFontSize()));
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448 tp.showPlaceholders(tree.getMarkUnlinked());
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449 tp.showBootstrap(tree.getShowBootstrap());
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450 tp.showDistances(tree.getShowDistances());
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452 tp.treeCanvas.threshold = tree.getThreshold();
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454 if (tree.getCurrentTree())
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456 af.viewport.setCurrentTree(tp.getTree());
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460 } catch (Exception ex)
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462 ex.printStackTrace();
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