src/jalview/gui/Jalview2XML_V1.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 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[] { file }), MessageManager
 165                             .getString("label.url_not_found"),
 166                     JOptionPane.WARNING_MESSAGE);
 167           }
 168         });
 169       }
 170       ;
 171     } catch (Exception ex)
 172     {
 173       System.err.println("Exception whilst loading jalview XML file : ");
 174       ex.printStackTrace();
 175       if (raiseGUI)
 176       {
 177         javax.swing.SwingUtilities.invokeLater(new Runnable()
 178         {
 179           public void run()
 180           {
 181
 182             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 183                     MessageManager.formatMessage(
 184                             "label.error_loading_file_params", new String[]
 185                             { file }), MessageManager
 186                             .getString("label.error_loading_jalview_file"),
 187                     JOptionPane.WARNING_MESSAGE);
 188           }
 189         });
 190       }
 191     }
 192
 193     return af;
 194   }
 195
 196   AlignFrame LoadFromObject(JalviewModel object, String file)
 197   {
 198     Vector seqids = new Vector();
 199     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 200     Sequence[] vamsasSeq = vamsasSet.getSequence();
 201
 202     JalviewModelSequence jms = object.getJalviewModelSequence();
 203
 204     // ////////////////////////////////
 205     // LOAD SEQUENCES
 206     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 207     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 208     for (int i = 0; i < vamsasSeq.length; i++)
 209     {
 210       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 211               vamsasSeq[i].getSequence());
 212       jseqs[i].setStart(JSEQ[i].getStart());
 213       jseqs[i].setEnd(JSEQ[i].getEnd());
 214       seqids.add(jseqs[i]);
 215     }
 216
 217     // /SequenceFeatures are added to the DatasetSequence,
 218     // so we must create the dataset before loading features
 219     // ///////////////////////////////
 220     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 221     al.setDataset(null);
 222     // ///////////////////////////////
 223
 224     for (int i = 0; i < vamsasSeq.length; i++)
 225     {
 226       if (JSEQ[i].getFeaturesCount() > 0)
 227       {
 228         Features[] features = JSEQ[i].getFeatures();
 229         for (int f = 0; f < features.length; f++)
 230         {
 231           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 232                   features[f].getType(), features[f].getDescription(),
 233                   features[f].getStatus(), features[f].getBegin(),
 234                   features[f].getEnd(), null);
 235
 236           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 237         }
 238       }
 239       if (JSEQ[i].getPdbidsCount() > 0)
 240       {
 241         Pdbids[] ids = JSEQ[i].getPdbids();
 242         for (int p = 0; p < ids.length; p++)
 243         {
 244           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 245           entry.setId(ids[p].getId());
 246           if (ids[p].getType() != null)
 247           {
 248             if (ids[p].getType().equalsIgnoreCase("PDB"))
 249             {
 250               entry.setType(PDBEntry.Type.PDB);
 251             }
 252             else
 253             {
 254               entry.setType(PDBEntry.Type.FILE);
 255             }
 256           }
 257           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 258           StructureSelectionManager.getStructureSelectionManager(
 259                   Desktop.instance).registerPDBEntry(entry);
 260         }
 261
 262       }
 263     }
 264
 265     // ///////////////////////////////
 266     // ////////////////////////////////
 267     // LOAD ANNOTATIONS
 268     if (vamsasSet.getAnnotation() != null)
 269     {
 270       Annotation[] an = vamsasSet.getAnnotation();
 271
 272       for (int i = 0; i < an.length; i++)
 273       {
 274         AnnotationElement[] ae = an[i].getAnnotationElement();
 275         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 276                 .getWidth()];
 277
 278         for (int aa = 0; aa < ae.length; aa++)
 279         {
 280           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 281                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 282                   ae[aa].getSecondaryStructure().charAt(0),
 283                   ae[aa].getValue());
 284         }
 285
 286         jalview.datamodel.AlignmentAnnotation jaa = null;
 287
 288         if (an[i].getGraph())
 289         {
 290           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 291                   an[i].getDescription(), anot, 0, 0,
 292                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 293         }
 294         else
 295         {
 296           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 297                   an[i].getDescription(), anot);
 298         }
 299
 300         al.addAnnotation(jaa);
 301       }
 302     }
 303
 304     // ///////////////////////////////
 305     // LOAD VIEWPORT
 306     Viewport[] views = jms.getViewport();
 307     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 308
 309     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 310
 311     af.setFileName(file, "Jalview");
 312
 313     for (int i = 0; i < JSEQ.length; i++)
 314     {
 315       af.viewport.setSequenceColour(af.viewport.getAlignment()
 316               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 317     }
 318
 319     // af.changeColour() );
 320     // ///////////////////////
 321     // LOAD GROUPS
 322     if (jms.getJGroupCount() > 0)
 323     {
 324       JGroup[] groups = jms.getJGroup();
 325
 326       for (int i = 0; i < groups.length; i++)
 327       {
 328         ColourSchemeI cs = null;
 329
 330         if (groups[i].getColour() != null)
 331         {
 332           if (groups[i].getColour().startsWith("ucs"))
 333           {
 334             cs = GetUserColourScheme(jms, groups[i].getColour());
 335           }
 336           else
 337           {
 338             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 339           }
 340
 341           if (cs != null)
 342           {
 343             cs.setThreshold(groups[i].getPidThreshold(), true);
 344           }
 345
 346         }
 347
 348         Vector seqs = new Vector();
 349         int[] ids = groups[i].getSeq();
 350
 351         for (int s = 0; s < ids.length; s++)
 352         {
 353           seqs.addElement(seqids.elementAt(ids[s]));
 354         }
 355
 356         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 357                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 358                 groups[i].getDisplayText(), groups[i].getColourText(),
 359                 groups[i].getStart(), groups[i].getEnd());
 360
 361         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 362
 363         if (groups[i].getConsThreshold() != 0)
 364         {
 365           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 366                   "All", ResidueProperties.propHash, 3,
 367                   sg.getSequences(null), 0, sg.getWidth() - 1);
 368           c.calculate();
 369           c.verdict(false, 25);
 370           sg.cs.setConservation(c);
 371         }
 372
 373         al.addGroup(sg);
 374       }
 375     }
 376
 377     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 378             view.getHeight());
 379     af.viewport.setStartRes(view.getStartRes());
 380     af.viewport.setStartSeq(view.getStartSeq());
 381     af.viewport.setShowAnnotation(view.getShowAnnotation());
 382     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 383     af.viewport.setColourText(view.getShowColourText());
 384     af.viewport.setConservationSelected(view.getConservationSelected());
 385     af.viewport.setShowJVSuffix(view.getShowFullId());
 386     af.viewport.setFont(
 387             new java.awt.Font(view.getFontName(), view.getFontStyle(), view
 388                     .getFontSize()), true);
 389
 390     af.viewport.setRenderGaps(view.getRenderGaps());
 391     af.viewport.setWrapAlignment(view.getWrapAlignment());
 392
 393     af.viewport.setShowAnnotation(view.isShowAnnotation());
 394     af.viewport.setShowBoxes(view.getShowBoxes());
 395     af.viewport.setShowText(view.getShowText());
 396
 397     ColourSchemeI cs = null;
 398
 399     if (view.getBgColour() != null)
 400     {
 401       if (view.getBgColour().startsWith("ucs"))
 402       {
 403         cs = GetUserColourScheme(jms, view.getBgColour());
 404       }
 405       else
 406       {
 407         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 408       }
 409
 410       if (cs != null)
 411       {
 412         cs.setThreshold(view.getPidThreshold(), true);
 413         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 414       }
 415     }
 416
 417     af.viewport.setGlobalColourScheme(cs);
 418     af.viewport.setColourAppliesToAllGroups(false);
 419     af.alignPanel.updateLayout();
 420     af.changeColour(cs);
 421     if (view.getConservationSelected() && cs != null)
 422     {
 423       cs.setConservationInc(view.getConsThreshold());
 424     }
 425
 426     af.viewport.setColourAppliesToAllGroups(true);
 427     af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 428
 429     if (jms.getFeatureSettings() != null)
 430     {
 431       Hashtable featuresDisplayed = new Hashtable();
 432       Hashtable featureColours = new Hashtable();
 433       String[] renderOrder = new String[jms.getFeatureSettings()
 434               .getSettingCount()];
 435       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 436       {
 437         Setting setting = jms.getFeatureSettings().getSetting(fs);
 438
 439         featureColours.put(setting.getType(),
 440                 new java.awt.Color(setting.getColour()));
 441
 442         renderOrder[fs] = setting.getType();
 443
 444         if (setting.getDisplay())
 445         {
 446           featuresDisplayed.put(setting.getType(),
 447                   new Integer(setting.getColour()));
 448         }
 449       }
 450       FeatureRendererSettings frs = new FeatureRendererSettings(
 451               renderOrder, new Hashtable(), featureColours, 1.0f, null);
 452       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 453               .transferSettings(frs);
 454     }
 455
 456     af.setMenusFromViewport(af.viewport);
 457
 458     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 459             view.getHeight());
 460
 461     // LOAD TREES
 462     // /////////////////////////////////////
 463     if (jms.getTreeCount() > 0)
 464     {
 465       try
 466       {
 467         for (int t = 0; t < jms.getTreeCount(); t++)
 468         {
 469
 470           Tree tree = jms.getTree(t);
 471
 472           TreePanel tp = af.ShowNewickTree(
 473                   new jalview.io.NewickFile(tree.getNewick()),
 474                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 475                   tree.getXpos(), tree.getYpos());
 476
 477           tp.fitToWindow.setState(tree.getFitToWindow());
 478           tp.fitToWindow_actionPerformed(null);
 479
 480           if (tree.getFontName() != null)
 481           {
 482             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 483                     .getFontStyle(), tree.getFontSize()));
 484           }
 485           else
 486           {
 487             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 488                     .getFontStyle(), tree.getFontSize()));
 489           }
 490
 491           tp.showPlaceholders(tree.getMarkUnlinked());
 492           tp.showBootstrap(tree.getShowBootstrap());
 493           tp.showDistances(tree.getShowDistances());
 494
 495           tp.treeCanvas.threshold = tree.getThreshold();
 496
 497           if (tree.getCurrentTree())
 498           {
 499             af.viewport.setCurrentTree(tp.getTree());
 500           }
 501         }
 502
 503       } catch (Exception ex)
 504       {
 505         ex.printStackTrace();
 506       }
 507
 508     }
 509
 510     return af;
 511   }
 512 }