src/jalview/gui/Jalview2XML_V1.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.schemes.ColourSchemeI;
  38 import jalview.schemes.ColourSchemeProperty;
  39 import jalview.schemes.ResidueProperties;
  40 import jalview.structure.StructureSelectionManager;
  41 import jalview.util.MessageManager;
  42 import jalview.util.jarInputStreamProvider;
  43
  44 import java.io.InputStreamReader;
  45 import java.util.Hashtable;
  46 import java.util.Vector;
  47 import java.util.jar.JarEntry;
  48 import java.util.jar.JarInputStream;
  49
  50 import javax.swing.JOptionPane;
  51
  52 import jalview.util.MessageManager;
  53 import jalview.util.jarInputStreamProvider;
  54 import org.exolab.castor.xml.IDResolver;
  55 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
  56
  57 /**
  58  * DOCUMENT ME!
  59  *
  60  * @author $author$
  61  * @version $Revision$
  62  */
  63 public class Jalview2XML_V1
  64 {
  65   boolean raiseGUI = true;
  66
  67   public Jalview2XML_V1()
  68   {
  69
  70   };
  71
  72   public Jalview2XML_V1(boolean raiseGUI)
  73   {
  74     this.raiseGUI = raiseGUI;
  75   };
  76
  77   jalview.schemes.UserColourScheme GetUserColourScheme(
  78           JalviewModelSequence jms, String id)
  79   {
  80     UserColours[] uc = jms.getUserColours();
  81     UserColours colours = null;
  82
  83     for (int i = 0; i < uc.length; i++)
  84     {
  85       if (uc[i].getId().equals(id))
  86       {
  87         colours = uc[i];
  88
  89         break;
  90       }
  91     }
  92
  93     int csize = colours.getUserColourScheme().getColourCount();
  94     java.awt.Color[] newColours = new java.awt.Color[csize];
  95
  96     for (int i = 0; i < csize; i++)
  97     {
  98       newColours[i] = new java.awt.Color(Integer.parseInt(colours
  99               .getUserColourScheme().getColour(i).getRGB(), 16));
 100     }
 101
 102     return new jalview.schemes.UserColourScheme(newColours);
 103   }
 104
 105   /**
 106    * DOCUMENT ME!
 107    *
 108    * @param file
 109    *          DOCUMENT ME!
 110    */
 111   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
 112   {
 113     final String file = jprovider.getFilename();
 114     jalview.gui.AlignFrame af = null;
 115
 116     try
 117     {
 118       JarInputStream jin = null;
 119       JarEntry jarentry = null;
 120       int entryCount = 1;
 121
 122       do
 123       {
 124         jin = jprovider.getJarInputStream();
 125
 126         for (int i = 0; i < entryCount; i++)
 127         {
 128           jarentry = jin.getNextJarEntry();
 129         }
 130
 131         class NoDescIDResolver implements IDResolver
 132         {
 133           public Object resolve(String idref)
 134           {
 135             System.out.println(idref + " used");
 136             return null;
 137           }
 138         }
 139
 140         if (jarentry != null)
 141         {
 142           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 143           JalviewModel object = new JalviewModel();
 144
 145           object = object.unmarshal(in);
 146
 147           af = LoadFromObject(object, file);
 148           entryCount++;
 149         }
 150       } while (jarentry != null);
 151     } catch (final java.net.UnknownHostException ex)
 152     {
 153       ex.printStackTrace();
 154       if (raiseGUI)
 155       {
 156         javax.swing.SwingUtilities.invokeLater(new Runnable()
 157         {
 158           public void run()
 159           {
 160
 161             System.err.println("Couldn't locate Jalview XML file : " + ex
 162                     + "\n");
 163             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 164                     MessageManager.formatMessage("label.couldnt_locate",
 165                             new String[]
 166                             { file }), MessageManager
 167                             .getString("label.url_not_found"),
 168                     JOptionPane.WARNING_MESSAGE);
 169           }
 170         });
 171       }
 172       ;
 173     } catch (Exception ex)
 174     {
 175       System.err.println("Exception whilst loading jalview XML file : ");
 176       ex.printStackTrace();
 177       if (raiseGUI)
 178       {
 179         javax.swing.SwingUtilities.invokeLater(new Runnable()
 180         {
 181           public void run()
 182           {
 183
 184             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 185                     MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
 186                     JOptionPane.WARNING_MESSAGE);
 187           }
 188         });
 189       }
 190     }
 191
 192     return af;
 193   }
 194
 195   AlignFrame LoadFromObject(JalviewModel object, String file)
 196   {
 197     Vector seqids = new Vector();
 198     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 199     Sequence[] vamsasSeq = vamsasSet.getSequence();
 200
 201     JalviewModelSequence jms = object.getJalviewModelSequence();
 202
 203     // ////////////////////////////////
 204     // LOAD SEQUENCES
 205     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 206     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 207     for (int i = 0; i < vamsasSeq.length; i++)
 208     {
 209       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 210               vamsasSeq[i].getSequence());
 211       jseqs[i].setStart(JSEQ[i].getStart());
 212       jseqs[i].setEnd(JSEQ[i].getEnd());
 213       seqids.add(jseqs[i]);
 214     }
 215
 216     // /SequenceFeatures are added to the DatasetSequence,
 217     // so we must create the dataset before loading features
 218     // ///////////////////////////////
 219     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 220     al.setDataset(null);
 221     // ///////////////////////////////
 222
 223     for (int i = 0; i < vamsasSeq.length; i++)
 224     {
 225       if (JSEQ[i].getFeaturesCount() > 0)
 226       {
 227         Features[] features = JSEQ[i].getFeatures();
 228         for (int f = 0; f < features.length; f++)
 229         {
 230           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 231                   features[f].getType(), features[f].getDescription(),
 232                   features[f].getStatus(), features[f].getBegin(),
 233                   features[f].getEnd(), null);
 234
 235           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 236         }
 237       }
 238       if (JSEQ[i].getPdbidsCount() > 0)
 239       {
 240         Pdbids[] ids = JSEQ[i].getPdbids();
 241         for (int p = 0; p < ids.length; p++)
 242         {
 243           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 244           entry.setId(ids[p].getId());
 245           entry.setType(ids[p].getType());
 246           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 247           StructureSelectionManager.getStructureSelectionManager(
 248                   Desktop.instance).registerPDBEntry(entry);
 249         }
 250
 251       }
 252     }
 253
 254     // ///////////////////////////////
 255     // ////////////////////////////////
 256     // LOAD ANNOTATIONS
 257     if (vamsasSet.getAnnotation() != null)
 258     {
 259       Annotation[] an = vamsasSet.getAnnotation();
 260
 261       for (int i = 0; i < an.length; i++)
 262       {
 263         AnnotationElement[] ae = an[i].getAnnotationElement();
 264         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 265                 .getWidth()];
 266
 267         for (int aa = 0; aa < ae.length; aa++)
 268         {
 269           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 270                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 271                   ae[aa].getSecondaryStructure().charAt(0),
 272                   ae[aa].getValue());
 273         }
 274
 275         jalview.datamodel.AlignmentAnnotation jaa = null;
 276
 277         if (an[i].getGraph())
 278         {
 279           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 280                   an[i].getDescription(), anot, 0, 0,
 281                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 282         }
 283         else
 284         {
 285           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 286                   an[i].getDescription(), anot);
 287         }
 288
 289         al.addAnnotation(jaa);
 290       }
 291     }
 292
 293     // ///////////////////////////////
 294     // LOAD VIEWPORT
 295     Viewport[] views = jms.getViewport();
 296     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 297
 298     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 299
 300     af.setFileName(file, "Jalview");
 301
 302     for (int i = 0; i < JSEQ.length; i++)
 303     {
 304       af.viewport.setSequenceColour(af.viewport.getAlignment()
 305               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 306     }
 307
 308     // af.changeColour() );
 309     // ///////////////////////
 310     // LOAD GROUPS
 311     if (jms.getJGroupCount() > 0)
 312     {
 313       JGroup[] groups = jms.getJGroup();
 314
 315       for (int i = 0; i < groups.length; i++)
 316       {
 317         ColourSchemeI cs = null;
 318
 319         if (groups[i].getColour() != null)
 320         {
 321           if (groups[i].getColour().startsWith("ucs"))
 322           {
 323             cs = GetUserColourScheme(jms, groups[i].getColour());
 324           }
 325           else
 326           {
 327             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 328           }
 329
 330           if (cs != null)
 331           {
 332             cs.setThreshold(groups[i].getPidThreshold(), true);
 333           }
 334
 335         }
 336
 337         Vector seqs = new Vector();
 338         int[] ids = groups[i].getSeq();
 339
 340         for (int s = 0; s < ids.length; s++)
 341         {
 342           seqs.addElement(seqids
 343                   .elementAt(ids[s]));
 344         }
 345
 346         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 347                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 348                 groups[i].getDisplayText(), groups[i].getColourText(),
 349                 groups[i].getStart(), groups[i].getEnd());
 350
 351         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 352
 353         if (groups[i].getConsThreshold() != 0)
 354         {
 355           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 356                   "All", ResidueProperties.propHash, 3,
 357                   sg.getSequences(null), 0, sg.getWidth() - 1);
 358           c.calculate();
 359           c.verdict(false, 25);
 360           sg.cs.setConservation(c);
 361         }
 362
 363         al.addGroup(sg);
 364       }
 365     }
 366
 367     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 368             view.getHeight());
 369     af.viewport.setStartRes(view.getStartRes());
 370     af.viewport.setStartSeq(view.getStartSeq());
 371     af.viewport.setShowAnnotation(view.getShowAnnotation());
 372     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 373     af.viewport.setColourText(view.getShowColourText());
 374     af.viewport.setConservationSelected(view.getConservationSelected());
 375     af.viewport.setShowJVSuffix(view.getShowFullId());
 376     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
 377             .getFontStyle(), view.getFontSize()));
 378     af.alignPanel.fontChanged();
 379
 380     af.viewport.setRenderGaps(view.getRenderGaps());
 381     af.viewport.setWrapAlignment(view.getWrapAlignment());
 382     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
 383     af.viewport.setShowAnnotation(view.getShowAnnotation());
 384     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 385     af.viewport.setShowBoxes(view.getShowBoxes());
 386     af.viewport.setShowText(view.getShowText());
 387
 388     ColourSchemeI cs = null;
 389
 390     if (view.getBgColour() != null)
 391     {
 392       if (view.getBgColour().startsWith("ucs"))
 393       {
 394         cs = GetUserColourScheme(jms, view.getBgColour());
 395       }
 396       else
 397       {
 398         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 399       }
 400
 401       if (cs != null)
 402       {
 403         cs.setThreshold(view.getPidThreshold(), true);
 404         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 405       }
 406     }
 407
 408     af.viewport.setGlobalColourScheme(cs);
 409     af.viewport.setColourAppliesToAllGroups(false);
 410     af.changeColour(cs);
 411     if (view.getConservationSelected() && cs != null)
 412     {
 413       cs.setConservationInc(view.getConsThreshold());
 414     }
 415
 416     af.viewport.setColourAppliesToAllGroups(true);
 417     af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 418
 419     if (jms.getFeatureSettings() != null)
 420     {
 421       Hashtable featuresDisplayed = new Hashtable();
 422       Hashtable featureColours = new Hashtable();
 423       String[] renderOrder = new String[jms.getFeatureSettings()
 424               .getSettingCount()];
 425       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 426       {
 427         Setting setting = jms.getFeatureSettings().getSetting(fs);
 428
 429         featureColours.put(
 430                 setting.getType(), new java.awt.Color(setting.getColour()));
 431
 432         renderOrder[fs] = setting.getType();
 433
 434         if (setting.getDisplay())
 435         {
 436           featuresDisplayed.put(setting.getType(), new Integer(
 437                   setting.getColour()));
 438         }
 439       }
 440       FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
 441       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(frs);
 442     }
 443
 444     af.setMenusFromViewport(af.viewport);
 445
 446     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 447             view.getHeight());
 448
 449     // LOAD TREES
 450     // /////////////////////////////////////
 451     if (jms.getTreeCount() > 0)
 452     {
 453       try
 454       {
 455         for (int t = 0; t < jms.getTreeCount(); t++)
 456         {
 457
 458           Tree tree = jms.getTree(t);
 459
 460           TreePanel tp = af.ShowNewickTree(
 461                   new jalview.io.NewickFile(tree.getNewick()),
 462                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 463                   tree.getXpos(), tree.getYpos());
 464
 465           tp.fitToWindow.setState(tree.getFitToWindow());
 466           tp.fitToWindow_actionPerformed(null);
 467
 468           if (tree.getFontName() != null)
 469           {
 470             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 471                     .getFontStyle(), tree.getFontSize()));
 472           }
 473           else
 474           {
 475             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 476                     .getFontStyle(), tree.getFontSize()));
 477           }
 478
 479           tp.showPlaceholders(tree.getMarkUnlinked());
 480           tp.showBootstrap(tree.getShowBootstrap());
 481           tp.showDistances(tree.getShowDistances());
 482
 483           tp.treeCanvas.threshold = tree.getThreshold();
 484
 485           if (tree.getCurrentTree())
 486           {
 487             af.viewport.setCurrentTree(tp.getTree());
 488           }
 489         }
 490
 491       } catch (Exception ex)
 492       {
 493         ex.printStackTrace();
 494       }
 495
 496     }
 497
 498     return af;
 499   }
 500 }