src/jalview/gui/Jalview2XML_V1.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   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 org.exolab.castor.xml.IDResolver;
  53
  54 /**
  55  * DOCUMENT ME!
  56  *
  57  * @author $author$
  58  * @version $Revision$
  59  */
  60 public class Jalview2XML_V1
  61 {
  62   boolean raiseGUI = true;
  63
  64   public Jalview2XML_V1()
  65   {
  66
  67   };
  68
  69   public Jalview2XML_V1(boolean raiseGUI)
  70   {
  71     this.raiseGUI = raiseGUI;
  72   };
  73
  74   jalview.schemes.UserColourScheme GetUserColourScheme(
  75           JalviewModelSequence jms, String id)
  76   {
  77     UserColours[] uc = jms.getUserColours();
  78     UserColours colours = null;
  79
  80     for (int i = 0; i < uc.length; i++)
  81     {
  82       if (uc[i].getId().equals(id))
  83       {
  84         colours = uc[i];
  85
  86         break;
  87       }
  88     }
  89
  90     int csize = colours.getUserColourScheme().getColourCount();
  91     java.awt.Color[] newColours = new java.awt.Color[csize];
  92
  93     for (int i = 0; i < csize; i++)
  94     {
  95       newColours[i] = new java.awt.Color(Integer.parseInt(colours
  96               .getUserColourScheme().getColour(i).getRGB(), 16));
  97     }
  98
  99     return new jalview.schemes.UserColourScheme(newColours);
 100   }
 101
 102   /**
 103    * DOCUMENT ME!
 104    *
 105    * @param file
 106    *          DOCUMENT ME!
 107    */
 108   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
 109   {
 110     final String file = jprovider.getFilename();
 111     jalview.gui.AlignFrame af = null;
 112
 113     try
 114     {
 115       JarInputStream jin = null;
 116       JarEntry jarentry = null;
 117       int entryCount = 1;
 118
 119       do
 120       {
 121         jin = jprovider.getJarInputStream();
 122
 123         for (int i = 0; i < entryCount; i++)
 124         {
 125           jarentry = jin.getNextJarEntry();
 126         }
 127
 128         class NoDescIDResolver implements IDResolver
 129         {
 130           public Object resolve(String idref)
 131           {
 132             System.out.println(idref + " used");
 133             return null;
 134           }
 135         }
 136
 137         if (jarentry != null)
 138         {
 139           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 140           JalviewModel object = new JalviewModel();
 141
 142           object = object.unmarshal(in);
 143
 144           af = LoadFromObject(object, file);
 145           entryCount++;
 146         }
 147       } while (jarentry != null);
 148     } catch (final java.net.UnknownHostException ex)
 149     {
 150       ex.printStackTrace();
 151       if (raiseGUI)
 152       {
 153         javax.swing.SwingUtilities.invokeLater(new Runnable()
 154         {
 155           public void run()
 156           {
 157
 158             System.err.println("Couldn't locate Jalview XML file : " + ex
 159                     + "\n");
 160             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 161                     MessageManager.formatMessage("label.couldnt_locate",
 162                             new String[]
 163                             { file }), MessageManager
 164                             .getString("label.url_not_found"),
 165                     JOptionPane.WARNING_MESSAGE);
 166           }
 167         });
 168       }
 169       ;
 170     } catch (Exception ex)
 171     {
 172       System.err.println("Exception whilst loading jalview XML file : ");
 173       ex.printStackTrace();
 174       if (raiseGUI)
 175       {
 176         javax.swing.SwingUtilities.invokeLater(new Runnable()
 177         {
 178           public void run()
 179           {
 180
 181             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 182                     MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
 183                     JOptionPane.WARNING_MESSAGE);
 184           }
 185         });
 186       }
 187     }
 188
 189     return af;
 190   }
 191
 192   AlignFrame LoadFromObject(JalviewModel object, String file)
 193   {
 194     Vector seqids = new Vector();
 195     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 196     Sequence[] vamsasSeq = vamsasSet.getSequence();
 197
 198     JalviewModelSequence jms = object.getJalviewModelSequence();
 199
 200     // ////////////////////////////////
 201     // LOAD SEQUENCES
 202     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 203     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 204     for (int i = 0; i < vamsasSeq.length; i++)
 205     {
 206       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 207               vamsasSeq[i].getSequence());
 208       jseqs[i].setStart(JSEQ[i].getStart());
 209       jseqs[i].setEnd(JSEQ[i].getEnd());
 210       seqids.add(jseqs[i]);
 211     }
 212
 213     // /SequenceFeatures are added to the DatasetSequence,
 214     // so we must create the dataset before loading features
 215     // ///////////////////////////////
 216     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 217     al.setDataset(null);
 218     // ///////////////////////////////
 219
 220     for (int i = 0; i < vamsasSeq.length; i++)
 221     {
 222       if (JSEQ[i].getFeaturesCount() > 0)
 223       {
 224         Features[] features = JSEQ[i].getFeatures();
 225         for (int f = 0; f < features.length; f++)
 226         {
 227           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 228                   features[f].getType(), features[f].getDescription(),
 229                   features[f].getStatus(), features[f].getBegin(),
 230                   features[f].getEnd(), null);
 231
 232           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 233         }
 234       }
 235       if (JSEQ[i].getPdbidsCount() > 0)
 236       {
 237         Pdbids[] ids = JSEQ[i].getPdbids();
 238         for (int p = 0; p < ids.length; p++)
 239         {
 240           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 241           entry.setId(ids[p].getId());
 242           entry.setType(ids[p].getType());
 243           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 244           StructureSelectionManager.getStructureSelectionManager(
 245                   Desktop.instance).registerPDBEntry(entry);
 246         }
 247
 248       }
 249     }
 250
 251     // ///////////////////////////////
 252     // ////////////////////////////////
 253     // LOAD ANNOTATIONS
 254     if (vamsasSet.getAnnotation() != null)
 255     {
 256       Annotation[] an = vamsasSet.getAnnotation();
 257
 258       for (int i = 0; i < an.length; i++)
 259       {
 260         AnnotationElement[] ae = an[i].getAnnotationElement();
 261         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 262                 .getWidth()];
 263
 264         for (int aa = 0; aa < ae.length; aa++)
 265         {
 266           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 267                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 268                   ae[aa].getSecondaryStructure().charAt(0),
 269                   ae[aa].getValue());
 270         }
 271
 272         jalview.datamodel.AlignmentAnnotation jaa = null;
 273
 274         if (an[i].getGraph())
 275         {
 276           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 277                   an[i].getDescription(), anot, 0, 0,
 278                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 279         }
 280         else
 281         {
 282           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 283                   an[i].getDescription(), anot);
 284         }
 285
 286         al.addAnnotation(jaa);
 287       }
 288     }
 289
 290     // ///////////////////////////////
 291     // LOAD VIEWPORT
 292     Viewport[] views = jms.getViewport();
 293     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 294
 295     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 296
 297     af.setFileName(file, "Jalview");
 298
 299     for (int i = 0; i < JSEQ.length; i++)
 300     {
 301       af.viewport.setSequenceColour(af.viewport.getAlignment()
 302               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 303     }
 304
 305     // af.changeColour() );
 306     // ///////////////////////
 307     // LOAD GROUPS
 308     if (jms.getJGroupCount() > 0)
 309     {
 310       JGroup[] groups = jms.getJGroup();
 311
 312       for (int i = 0; i < groups.length; i++)
 313       {
 314         ColourSchemeI cs = null;
 315
 316         if (groups[i].getColour() != null)
 317         {
 318           if (groups[i].getColour().startsWith("ucs"))
 319           {
 320             cs = GetUserColourScheme(jms, groups[i].getColour());
 321           }
 322           else
 323           {
 324             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 325           }
 326
 327           if (cs != null)
 328           {
 329             cs.setThreshold(groups[i].getPidThreshold(), true);
 330           }
 331
 332         }
 333
 334         Vector seqs = new Vector();
 335         int[] ids = groups[i].getSeq();
 336
 337         for (int s = 0; s < ids.length; s++)
 338         {
 339           seqs.addElement(seqids
 340                   .elementAt(ids[s]));
 341         }
 342
 343         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 344                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 345                 groups[i].getDisplayText(), groups[i].getColourText(),
 346                 groups[i].getStart(), groups[i].getEnd());
 347
 348         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 349
 350         if (groups[i].getConsThreshold() != 0)
 351         {
 352           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 353                   "All", ResidueProperties.propHash, 3,
 354                   sg.getSequences(null), 0, sg.getWidth() - 1);
 355           c.calculate();
 356           c.verdict(false, 25);
 357           sg.cs.setConservation(c);
 358         }
 359
 360         al.addGroup(sg);
 361       }
 362     }
 363
 364     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 365             view.getHeight());
 366     af.viewport.setStartRes(view.getStartRes());
 367     af.viewport.setStartSeq(view.getStartSeq());
 368     af.viewport.setShowAnnotation(view.getShowAnnotation());
 369     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 370     af.viewport.setColourText(view.getShowColourText());
 371     af.viewport.setConservationSelected(view.getConservationSelected());
 372     af.viewport.setShowJVSuffix(view.getShowFullId());
 373     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
 374             .getFontStyle(), view.getFontSize()));
 375     af.alignPanel.fontChanged();
 376
 377     af.viewport.setRenderGaps(view.getRenderGaps());
 378     af.viewport.setWrapAlignment(view.getWrapAlignment());
 379     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
 380     af.viewport.setShowAnnotation(view.getShowAnnotation());
 381     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 382     af.viewport.setShowBoxes(view.getShowBoxes());
 383     af.viewport.setShowText(view.getShowText());
 384
 385     ColourSchemeI cs = null;
 386
 387     if (view.getBgColour() != null)
 388     {
 389       if (view.getBgColour().startsWith("ucs"))
 390       {
 391         cs = GetUserColourScheme(jms, view.getBgColour());
 392       }
 393       else
 394       {
 395         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 396       }
 397
 398       if (cs != null)
 399       {
 400         cs.setThreshold(view.getPidThreshold(), true);
 401         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 402       }
 403     }
 404
 405     af.viewport.setGlobalColourScheme(cs);
 406     af.viewport.setColourAppliesToAllGroups(false);
 407     af.changeColour(cs);
 408     if (view.getConservationSelected() && cs != null)
 409     {
 410       cs.setConservationInc(view.getConsThreshold());
 411     }
 412
 413     af.viewport.setColourAppliesToAllGroups(true);
 414     af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
 415
 416     if (jms.getFeatureSettings() != null)
 417     {
 418       af.viewport.featuresDisplayed = new Hashtable();
 419       String[] renderOrder = new String[jms.getFeatureSettings()
 420               .getSettingCount()];
 421       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 422       {
 423         Setting setting = jms.getFeatureSettings().getSetting(fs);
 424
 425         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
 426                 setting.getType(), new java.awt.Color(setting.getColour()));
 427
 428         renderOrder[fs] = setting.getType();
 429
 430         if (setting.getDisplay())
 431         {
 432           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
 433                   setting.getColour()));
 434         }
 435       }
 436       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
 437     }
 438
 439     af.setMenusFromViewport(af.viewport);
 440
 441     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 442             view.getHeight());
 443
 444     // LOAD TREES
 445     // /////////////////////////////////////
 446     if (jms.getTreeCount() > 0)
 447     {
 448       try
 449       {
 450         for (int t = 0; t < jms.getTreeCount(); t++)
 451         {
 452
 453           Tree tree = jms.getTree(t);
 454
 455           TreePanel tp = af.ShowNewickTree(
 456                   new jalview.io.NewickFile(tree.getNewick()),
 457                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 458                   tree.getXpos(), tree.getYpos());
 459
 460           tp.fitToWindow.setState(tree.getFitToWindow());
 461           tp.fitToWindow_actionPerformed(null);
 462
 463           if (tree.getFontName() != null)
 464           {
 465             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 466                     .getFontStyle(), tree.getFontSize()));
 467           }
 468           else
 469           {
 470             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 471                     .getFontStyle(), tree.getFontSize()));
 472           }
 473
 474           tp.showPlaceholders(tree.getMarkUnlinked());
 475           tp.showBootstrap(tree.getShowBootstrap());
 476           tp.showDistances(tree.getShowDistances());
 477
 478           tp.treeCanvas.threshold = tree.getThreshold();
 479
 480           if (tree.getCurrentTree())
 481           {
 482             af.viewport.setCurrentTree(tp.getTree());
 483           }
 484         }
 485
 486       } catch (Exception ex)
 487       {
 488         ex.printStackTrace();
 489       }
 490
 491     }
 492
 493     return af;
 494   }
 495 }