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.io.Reader;
  48 import java.net.UnknownHostException;
  49 import java.util.Hashtable;
  50 import java.util.Vector;
  51 import java.util.jar.JarEntry;
  52 import java.util.jar.JarInputStream;
  53
  54 import javax.swing.JOptionPane;
  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         if (jarentry != null)
 131         {
 132           entryCount++;
 133           if (jarentry.getName().endsWith(".xml"))
 134           {
 135             Reader in = new InputStreamReader(jin, "UTF-8");
 136             JalviewModel object = new JalviewModel();
 137
 138             object = object.unmarshal(in);
 139
 140             af = LoadFromObject(object, file);
 141           }
 142         }
 143         jin.close();
 144       } while (jarentry != null);
 145     } catch (final UnknownHostException ex)
 146     {
 147       ex.printStackTrace();
 148       if (raiseGUI)
 149       {
 150         javax.swing.SwingUtilities.invokeLater(new Runnable()
 151         {
 152           @Override
 153           public void run()
 154           {
 155
 156             System.err.println("Couldn't locate Jalview XML file : " + ex
 157                     + "\n");
 158             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 159                     MessageManager.formatMessage("label.couldnt_locate",
 160                             new String[] { file }), MessageManager
 161                             .getString("label.url_not_found"),
 162                     JOptionPane.WARNING_MESSAGE);
 163           }
 164         });
 165       }
 166       ;
 167     } catch (Exception ex)
 168     {
 169       System.err.println("Exception whilst loading jalview XML file : ");
 170       ex.printStackTrace();
 171       if (raiseGUI)
 172       {
 173         javax.swing.SwingUtilities.invokeLater(new Runnable()
 174         {
 175           @Override
 176           public void run()
 177           {
 178
 179             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 180                     MessageManager.formatMessage(
 181                             "label.error_loading_file_params", new String[]
 182                             { file }), MessageManager
 183                             .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           if (ids[p].getType() != null)
 244           {
 245             if (ids[p].getType().equalsIgnoreCase("PDB"))
 246             {
 247               entry.setType(PDBEntry.Type.PDB);
 248             }
 249             else
 250             {
 251               entry.setType(PDBEntry.Type.FILE);
 252             }
 253           }
 254           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 255           StructureSelectionManager.getStructureSelectionManager(
 256                   Desktop.instance).registerPDBEntry(entry);
 257         }
 258
 259       }
 260     }
 261
 262     // ///////////////////////////////
 263     // ////////////////////////////////
 264     // LOAD ANNOTATIONS
 265     if (vamsasSet.getAnnotation() != null)
 266     {
 267       Annotation[] an = vamsasSet.getAnnotation();
 268
 269       for (int i = 0; i < an.length; i++)
 270       {
 271         AnnotationElement[] ae = an[i].getAnnotationElement();
 272         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 273                 .getWidth()];
 274
 275         for (int aa = 0; aa < ae.length; aa++)
 276         {
 277           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 278                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 279                   ae[aa].getSecondaryStructure().charAt(0),
 280                   ae[aa].getValue());
 281         }
 282
 283         jalview.datamodel.AlignmentAnnotation jaa = null;
 284
 285         if (an[i].getGraph())
 286         {
 287           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 288                   an[i].getDescription(), anot, 0, 0,
 289                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 290         }
 291         else
 292         {
 293           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 294                   an[i].getDescription(), anot);
 295         }
 296
 297         al.addAnnotation(jaa);
 298       }
 299     }
 300
 301     // ///////////////////////////////
 302     // LOAD VIEWPORT
 303     Viewport[] views = jms.getViewport();
 304     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 305
 306     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 307
 308     af.setFileName(file, "Jalview");
 309
 310     for (int i = 0; i < JSEQ.length; i++)
 311     {
 312       af.viewport.setSequenceColour(af.viewport.getAlignment()
 313               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 314     }
 315
 316     // af.changeColour() );
 317     // ///////////////////////
 318     // LOAD GROUPS
 319     if (jms.getJGroupCount() > 0)
 320     {
 321       JGroup[] groups = jms.getJGroup();
 322
 323       for (int i = 0; i < groups.length; i++)
 324       {
 325         ColourSchemeI cs = null;
 326
 327         if (groups[i].getColour() != null)
 328         {
 329           if (groups[i].getColour().startsWith("ucs"))
 330           {
 331             cs = GetUserColourScheme(jms, groups[i].getColour());
 332           }
 333           else
 334           {
 335             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 336           }
 337
 338           if (cs != null)
 339           {
 340             cs.setThreshold(groups[i].getPidThreshold(), true);
 341           }
 342
 343         }
 344
 345         Vector seqs = new Vector();
 346         int[] ids = groups[i].getSeq();
 347
 348         for (int s = 0; s < ids.length; s++)
 349         {
 350           seqs.addElement(seqids.elementAt(ids[s]));
 351         }
 352
 353         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 354                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 355                 groups[i].getDisplayText(), groups[i].getColourText(),
 356                 groups[i].getStart(), groups[i].getEnd());
 357
 358         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 359
 360         if (groups[i].getConsThreshold() != 0)
 361         {
 362           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 363                   "All", ResidueProperties.propHash, 3,
 364                   sg.getSequences(null), 0, sg.getWidth() - 1);
 365           c.calculate();
 366           c.verdict(false, 25);
 367           sg.cs.setConservation(c);
 368         }
 369
 370         al.addGroup(sg);
 371       }
 372     }
 373
 374     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 375             view.getHeight());
 376     af.viewport.setStartRes(view.getStartRes());
 377     af.viewport.setStartSeq(view.getStartSeq());
 378     af.viewport.setShowAnnotation(view.getShowAnnotation());
 379     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 380     af.viewport.setColourText(view.getShowColourText());
 381     af.viewport.setConservationSelected(view.getConservationSelected());
 382     af.viewport.setShowJVSuffix(view.getShowFullId());
 383     af.viewport.setFont(
 384             new java.awt.Font(view.getFontName(), view.getFontStyle(), view
 385                     .getFontSize()), true);
 386
 387     af.viewport.setRenderGaps(view.getRenderGaps());
 388     af.viewport.setWrapAlignment(view.getWrapAlignment());
 389
 390     af.viewport.setShowAnnotation(view.isShowAnnotation());
 391     af.viewport.setShowBoxes(view.getShowBoxes());
 392     af.viewport.setShowText(view.getShowText());
 393
 394     ColourSchemeI cs = null;
 395
 396     if (view.getBgColour() != null)
 397     {
 398       if (view.getBgColour().startsWith("ucs"))
 399       {
 400         cs = GetUserColourScheme(jms, view.getBgColour());
 401       }
 402       else
 403       {
 404         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 405       }
 406
 407       if (cs != null)
 408       {
 409         cs.setThreshold(view.getPidThreshold(), true);
 410         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 411       }
 412     }
 413
 414     af.viewport.setGlobalColourScheme(cs);
 415     af.viewport.setColourAppliesToAllGroups(false);
 416     af.alignPanel.updateLayout();
 417     af.changeColour(cs);
 418     if (view.getConservationSelected() && cs != null)
 419     {
 420       cs.setConservationInc(view.getConsThreshold());
 421     }
 422
 423     af.viewport.setColourAppliesToAllGroups(true);
 424     af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 425
 426     if (jms.getFeatureSettings() != null)
 427     {
 428       Hashtable featuresDisplayed = new Hashtable();
 429       Hashtable featureColours = new Hashtable();
 430       String[] renderOrder = new String[jms.getFeatureSettings()
 431               .getSettingCount()];
 432       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 433       {
 434         Setting setting = jms.getFeatureSettings().getSetting(fs);
 435
 436         featureColours.put(setting.getType(),
 437                 new java.awt.Color(setting.getColour()));
 438
 439         renderOrder[fs] = setting.getType();
 440
 441         if (setting.getDisplay())
 442         {
 443           featuresDisplayed.put(setting.getType(),
 444                   new Integer(setting.getColour()));
 445         }
 446       }
 447       FeatureRendererSettings frs = new FeatureRendererSettings(
 448               renderOrder, new Hashtable(), featureColours, 1.0f, null);
 449       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 450               .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 }