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