src/jalview/gui/Jalview2XML_V1.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.binding.Annotation;
  24 import jalview.binding.AnnotationElement;
  25 import jalview.binding.Features;
  26 import jalview.binding.JGroup;
  27 import jalview.binding.JSeq;
  28 import jalview.binding.JalviewModel;
  29 import jalview.binding.JalviewModelSequence;
  30 import jalview.binding.Pdbids;
  31 import jalview.binding.Sequence;
  32 import jalview.binding.SequenceSet;
  33 import jalview.binding.Setting;
  34 import jalview.binding.Tree;
  35 import jalview.binding.UserColours;
  36 import jalview.binding.Viewport;
  37 import jalview.datamodel.PDBEntry;
  38 import jalview.schemes.ColourSchemeI;
  39 import jalview.schemes.ColourSchemeProperty;
  40 import jalview.schemes.ResidueProperties;
  41 import jalview.structure.StructureSelectionManager;
  42 import jalview.util.MessageManager;
  43 import jalview.util.jarInputStreamProvider;
  44 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
  45
  46 import java.io.InputStreamReader;
  47 import java.util.Hashtable;
  48 import java.util.Vector;
  49 import java.util.jar.JarEntry;
  50 import java.util.jar.JarInputStream;
  51
  52 import javax.swing.JOptionPane;
  53
  54 import org.exolab.castor.xml.IDResolver;
  55
  56 /**
  57  * DOCUMENT ME!
  58  *
  59  * @author $author$
  60  * @version $Revision$
  61  */
  62 public class Jalview2XML_V1
  63 {
  64   boolean raiseGUI = true;
  65
  66   public Jalview2XML_V1()
  67   {
  68
  69   };
  70
  71   public Jalview2XML_V1(boolean raiseGUI)
  72   {
  73     this.raiseGUI = raiseGUI;
  74   };
  75
  76   jalview.schemes.UserColourScheme GetUserColourScheme(
  77           JalviewModelSequence jms, String id)
  78   {
  79     UserColours[] uc = jms.getUserColours();
  80     UserColours colours = null;
  81
  82     for (int i = 0; i < uc.length; i++)
  83     {
  84       if (uc[i].getId().equals(id))
  85       {
  86         colours = uc[i];
  87
  88         break;
  89       }
  90     }
  91
  92     int csize = colours.getUserColourScheme().getColourCount();
  93     java.awt.Color[] newColours = new java.awt.Color[csize];
  94
  95     for (int i = 0; i < csize; i++)
  96     {
  97       newColours[i] = new java.awt.Color(Integer.parseInt(colours
  98               .getUserColourScheme().getColour(i).getRGB(), 16));
  99     }
 100
 101     return new jalview.schemes.UserColourScheme(newColours);
 102   }
 103
 104   /**
 105    * DOCUMENT ME!
 106    *
 107    * @param file
 108    *          DOCUMENT ME!
 109    */
 110   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
 111   {
 112     final String file = jprovider.getFilename();
 113     jalview.gui.AlignFrame af = null;
 114
 115     try
 116     {
 117       JarInputStream jin = null;
 118       JarEntry jarentry = null;
 119       int entryCount = 1;
 120
 121       do
 122       {
 123         jin = jprovider.getJarInputStream();
 124
 125         for (int i = 0; i < entryCount; i++)
 126         {
 127           jarentry = jin.getNextJarEntry();
 128         }
 129
 130         class NoDescIDResolver implements IDResolver
 131         {
 132           public Object resolve(String idref)
 133           {
 134             System.out.println(idref + " used");
 135             return null;
 136           }
 137         }
 138
 139         if (jarentry != null)
 140         {
 141           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 142           JalviewModel object = new JalviewModel();
 143
 144           object = object.unmarshal(in);
 145
 146           af = LoadFromObject(object, file);
 147           entryCount++;
 148         }
 149       } while (jarentry != null);
 150     } catch (final java.net.UnknownHostException ex)
 151     {
 152       ex.printStackTrace();
 153       if (raiseGUI)
 154       {
 155         javax.swing.SwingUtilities.invokeLater(new Runnable()
 156         {
 157           public void run()
 158           {
 159
 160             System.err.println("Couldn't locate Jalview XML file : " + ex
 161                     + "\n");
 162             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 163                     MessageManager.formatMessage("label.couldnt_locate",
 164                             new String[]
 165                             { file }), MessageManager
 166                             .getString("label.url_not_found"),
 167                     JOptionPane.WARNING_MESSAGE);
 168           }
 169         });
 170       }
 171       ;
 172     } catch (Exception ex)
 173     {
 174       System.err.println("Exception whilst loading jalview XML file : ");
 175       ex.printStackTrace();
 176       if (raiseGUI)
 177       {
 178         javax.swing.SwingUtilities.invokeLater(new Runnable()
 179         {
 180           public void run()
 181           {
 182
 183             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 184                     MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
 185                     JOptionPane.WARNING_MESSAGE);
 186           }
 187         });
 188       }
 189     }
 190
 191     return af;
 192   }
 193
 194   AlignFrame LoadFromObject(JalviewModel object, String file)
 195   {
 196     Vector seqids = new Vector();
 197     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 198     Sequence[] vamsasSeq = vamsasSet.getSequence();
 199
 200     JalviewModelSequence jms = object.getJalviewModelSequence();
 201
 202     // ////////////////////////////////
 203     // LOAD SEQUENCES
 204     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 205     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 206     for (int i = 0; i < vamsasSeq.length; i++)
 207     {
 208       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 209               vamsasSeq[i].getSequence());
 210       jseqs[i].setStart(JSEQ[i].getStart());
 211       jseqs[i].setEnd(JSEQ[i].getEnd());
 212       seqids.add(jseqs[i]);
 213     }
 214
 215     // /SequenceFeatures are added to the DatasetSequence,
 216     // so we must create the dataset before loading features
 217     // ///////////////////////////////
 218     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 219     al.setDataset(null);
 220     // ///////////////////////////////
 221
 222     for (int i = 0; i < vamsasSeq.length; i++)
 223     {
 224       if (JSEQ[i].getFeaturesCount() > 0)
 225       {
 226         Features[] features = JSEQ[i].getFeatures();
 227         for (int f = 0; f < features.length; f++)
 228         {
 229           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 230                   features[f].getType(), features[f].getDescription(),
 231                   features[f].getStatus(), features[f].getBegin(),
 232                   features[f].getEnd(), null);
 233
 234           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 235         }
 236       }
 237       if (JSEQ[i].getPdbidsCount() > 0)
 238       {
 239         Pdbids[] ids = JSEQ[i].getPdbids();
 240         for (int p = 0; p < ids.length; p++)
 241         {
 242           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 243           entry.setId(ids[p].getId());
 244           if (ids[p].getType() != null)
 245           {
 246             if (ids[p].getType().equalsIgnoreCase("PDB"))
 247             {
 248               entry.setType(PDBEntry.Type.PDB);
 249             }
 250             else
 251             {
 252               entry.setType(PDBEntry.Type.FILE);
 253             }
 254           }
 255           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 256           StructureSelectionManager.getStructureSelectionManager(
 257                   Desktop.instance).registerPDBEntry(entry);
 258         }
 259
 260       }
 261     }
 262
 263     // ///////////////////////////////
 264     // ////////////////////////////////
 265     // LOAD ANNOTATIONS
 266     if (vamsasSet.getAnnotation() != null)
 267     {
 268       Annotation[] an = vamsasSet.getAnnotation();
 269
 270       for (int i = 0; i < an.length; i++)
 271       {
 272         AnnotationElement[] ae = an[i].getAnnotationElement();
 273         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 274                 .getWidth()];
 275
 276         for (int aa = 0; aa < ae.length; aa++)
 277         {
 278           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 279                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 280                   ae[aa].getSecondaryStructure().charAt(0),
 281                   ae[aa].getValue());
 282         }
 283
 284         jalview.datamodel.AlignmentAnnotation jaa = null;
 285
 286         if (an[i].getGraph())
 287         {
 288           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 289                   an[i].getDescription(), anot, 0, 0,
 290                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 291         }
 292         else
 293         {
 294           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 295                   an[i].getDescription(), anot);
 296         }
 297
 298         al.addAnnotation(jaa);
 299       }
 300     }
 301
 302     // ///////////////////////////////
 303     // LOAD VIEWPORT
 304     Viewport[] views = jms.getViewport();
 305     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 306
 307     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 308
 309     af.setFileName(file, "Jalview");
 310
 311     for (int i = 0; i < JSEQ.length; i++)
 312     {
 313       af.viewport.setSequenceColour(af.viewport.getAlignment()
 314               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 315     }
 316
 317     // af.changeColour() );
 318     // ///////////////////////
 319     // LOAD GROUPS
 320     if (jms.getJGroupCount() > 0)
 321     {
 322       JGroup[] groups = jms.getJGroup();
 323
 324       for (int i = 0; i < groups.length; i++)
 325       {
 326         ColourSchemeI cs = null;
 327
 328         if (groups[i].getColour() != null)
 329         {
 330           if (groups[i].getColour().startsWith("ucs"))
 331           {
 332             cs = GetUserColourScheme(jms, groups[i].getColour());
 333           }
 334           else
 335           {
 336             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 337           }
 338
 339           if (cs != null)
 340           {
 341             cs.setThreshold(groups[i].getPidThreshold(), true);
 342           }
 343
 344         }
 345
 346         Vector seqs = new Vector();
 347         int[] ids = groups[i].getSeq();
 348
 349         for (int s = 0; s < ids.length; s++)
 350         {
 351           seqs.addElement(seqids
 352                   .elementAt(ids[s]));
 353         }
 354
 355         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 356                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 357                 groups[i].getDisplayText(), groups[i].getColourText(),
 358                 groups[i].getStart(), groups[i].getEnd());
 359
 360         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 361
 362         if (groups[i].getConsThreshold() != 0)
 363         {
 364           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 365                   "All", ResidueProperties.propHash, 3,
 366                   sg.getSequences(null), 0, sg.getWidth() - 1);
 367           c.calculate();
 368           c.verdict(false, 25);
 369           sg.cs.setConservation(c);
 370         }
 371
 372         al.addGroup(sg);
 373       }
 374     }
 375
 376     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 377             view.getHeight());
 378     af.viewport.setStartRes(view.getStartRes());
 379     af.viewport.setStartSeq(view.getStartSeq());
 380     af.viewport.setShowAnnotation(view.getShowAnnotation());
 381     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 382     af.viewport.setColourText(view.getShowColourText());
 383     af.viewport.setConservationSelected(view.getConservationSelected());
 384     af.viewport.setShowJVSuffix(view.getShowFullId());
 385     af.viewport.setFont(
 386             new java.awt.Font(view.getFontName(), view.getFontStyle(), view
 387                     .getFontSize()), true);
 388
 389     af.viewport.setRenderGaps(view.getRenderGaps());
 390     af.viewport.setWrapAlignment(view.getWrapAlignment());
 391
 392     af.viewport.setShowAnnotation(view.isShowAnnotation());
 393     af.viewport.setShowBoxes(view.getShowBoxes());
 394     af.viewport.setShowText(view.getShowText());
 395
 396     ColourSchemeI cs = null;
 397
 398     if (view.getBgColour() != null)
 399     {
 400       if (view.getBgColour().startsWith("ucs"))
 401       {
 402         cs = GetUserColourScheme(jms, view.getBgColour());
 403       }
 404       else
 405       {
 406         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 407       }
 408
 409       if (cs != null)
 410       {
 411         cs.setThreshold(view.getPidThreshold(), true);
 412         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 413       }
 414     }
 415
 416     af.viewport.setGlobalColourScheme(cs);
 417     af.viewport.setColourAppliesToAllGroups(false);
 418     af.alignPanel.updateLayout();
 419     af.changeColour(cs);
 420     if (view.getConservationSelected() && cs != null)
 421     {
 422       cs.setConservationInc(view.getConsThreshold());
 423     }
 424
 425     af.viewport.setColourAppliesToAllGroups(true);
 426     af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 427
 428     if (jms.getFeatureSettings() != null)
 429     {
 430       Hashtable featuresDisplayed = new Hashtable();
 431       Hashtable featureColours = new Hashtable();
 432       String[] renderOrder = new String[jms.getFeatureSettings()
 433               .getSettingCount()];
 434       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 435       {
 436         Setting setting = jms.getFeatureSettings().getSetting(fs);
 437
 438         featureColours.put(
 439                 setting.getType(), new java.awt.Color(setting.getColour()));
 440
 441         renderOrder[fs] = setting.getType();
 442
 443         if (setting.getDisplay())
 444         {
 445           featuresDisplayed.put(setting.getType(), new Integer(
 446                   setting.getColour()));
 447         }
 448       }
 449       FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
 450       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(frs);
 451     }
 452
 453     af.setMenusFromViewport(af.viewport);
 454
 455     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 456             view.getHeight());
 457
 458     // LOAD TREES
 459     // /////////////////////////////////////
 460     if (jms.getTreeCount() > 0)
 461     {
 462       try
 463       {
 464         for (int t = 0; t < jms.getTreeCount(); t++)
 465         {
 466
 467           Tree tree = jms.getTree(t);
 468
 469           TreePanel tp = af.ShowNewickTree(
 470                   new jalview.io.NewickFile(tree.getNewick()),
 471                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 472                   tree.getXpos(), tree.getYpos());
 473
 474           tp.fitToWindow.setState(tree.getFitToWindow());
 475           tp.fitToWindow_actionPerformed(null);
 476
 477           if (tree.getFontName() != null)
 478           {
 479             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 480                     .getFontStyle(), tree.getFontSize()));
 481           }
 482           else
 483           {
 484             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 485                     .getFontStyle(), tree.getFontSize()));
 486           }
 487
 488           tp.showPlaceholders(tree.getMarkUnlinked());
 489           tp.showBootstrap(tree.getShowBootstrap());
 490           tp.showDistances(tree.getShowDistances());
 491
 492           tp.treeCanvas.threshold = tree.getThreshold();
 493
 494           if (tree.getCurrentTree())
 495           {
 496             af.viewport.setCurrentTree(tp.getTree());
 497           }
 498         }
 499
 500       } catch (Exception ex)
 501       {
 502         ex.printStackTrace();
 503       }
 504
 505     }
 506
 507     return af;
 508   }
 509 }