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.analysis.Conservation;
  24 import jalview.binding.Annotation;
  25 import jalview.binding.AnnotationElement;
  26 import jalview.binding.Features;
  27 import jalview.binding.JGroup;
  28 import jalview.binding.JSeq;
  29 import jalview.binding.JalviewModel;
  30 import jalview.binding.JalviewModelSequence;
  31 import jalview.binding.Pdbids;
  32 import jalview.binding.Sequence;
  33 import jalview.binding.SequenceSet;
  34 import jalview.binding.Setting;
  35 import jalview.binding.Tree;
  36 import jalview.binding.UserColours;
  37 import jalview.binding.Viewport;
  38 import jalview.datamodel.PDBEntry;
  39 import jalview.datamodel.SequenceFeature;
  40 import jalview.io.FileFormat;
  41 import jalview.schemes.ColourSchemeI;
  42 import jalview.schemes.ColourSchemeProperty;
  43 import jalview.structure.StructureSelectionManager;
  44 import jalview.util.MessageManager;
  45 import jalview.util.jarInputStreamProvider;
  46 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
  47
  48 import java.io.InputStreamReader;
  49 import java.io.Reader;
  50 import java.net.UnknownHostException;
  51 import java.util.Hashtable;
  52 import java.util.Vector;
  53 import java.util.jar.JarEntry;
  54 import java.util.jar.JarInputStream;
  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             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 159                     MessageManager.formatMessage("label.couldnt_locate",
 160                             new String[] { file }), MessageManager
 161                             .getString("label.url_not_found"),
 162                     JvOptionPane.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             JvOptionPane.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                     JvOptionPane.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           SequenceFeature sf = new SequenceFeature(features[f].getType(),
 229                   features[f].getDescription(), features[f].getBegin(),
 230                   features[f].getEnd(), null);
 231           sf.setStatus(features[f].getStatus());
 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           if (ids[p].getType() != null)
 243           {
 244             if (ids[p].getType().equalsIgnoreCase("PDB"))
 245             {
 246               entry.setType(PDBEntry.Type.PDB);
 247             }
 248             else
 249             {
 250               entry.setType(PDBEntry.Type.FILE);
 251             }
 252           }
 253           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 254           StructureSelectionManager.getStructureSelectionManager(
 255                   Desktop.instance).registerPDBEntry(entry);
 256         }
 257
 258       }
 259     }
 260
 261     // ///////////////////////////////
 262     // ////////////////////////////////
 263     // LOAD ANNOTATIONS
 264     if (vamsasSet.getAnnotation() != null)
 265     {
 266       Annotation[] an = vamsasSet.getAnnotation();
 267
 268       for (int i = 0; i < an.length; i++)
 269       {
 270         AnnotationElement[] ae = an[i].getAnnotationElement();
 271         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 272                 .getWidth()];
 273
 274         for (int aa = 0; aa < ae.length; aa++)
 275         {
 276           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 277                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 278                   ae[aa].getSecondaryStructure().charAt(0),
 279                   ae[aa].getValue());
 280         }
 281
 282         jalview.datamodel.AlignmentAnnotation jaa = null;
 283
 284         if (an[i].getGraph())
 285         {
 286           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 287                   an[i].getDescription(), anot, 0, 0,
 288                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 289         }
 290         else
 291         {
 292           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 293                   an[i].getDescription(), anot);
 294         }
 295
 296         al.addAnnotation(jaa);
 297       }
 298     }
 299
 300     // ///////////////////////////////
 301     // LOAD VIEWPORT
 302     Viewport[] views = jms.getViewport();
 303     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 304
 305     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 306
 307     af.setFileName(file, FileFormat.Jalview);
 308
 309     for (int i = 0; i < JSEQ.length; i++)
 310     {
 311       af.viewport.setSequenceColour(af.viewport.getAlignment()
 312               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 313     }
 314
 315     // af.changeColour() );
 316     // ///////////////////////
 317     // LOAD GROUPS
 318     if (jms.getJGroupCount() > 0)
 319     {
 320       JGroup[] groups = jms.getJGroup();
 321
 322       for (int i = 0; i < groups.length; i++)
 323       {
 324         ColourSchemeI cs = null;
 325
 326         if (groups[i].getColour() != null)
 327         {
 328           if (groups[i].getColour().startsWith("ucs"))
 329           {
 330             cs = GetUserColourScheme(jms, groups[i].getColour());
 331           }
 332           else
 333           {
 334             cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
 335           }
 336         }
 337         int pidThreshold = groups[i].getPidThreshold();
 338
 339         Vector seqs = new Vector();
 340         int[] ids = groups[i].getSeq();
 341
 342         for (int s = 0; s < ids.length; s++)
 343         {
 344           seqs.addElement(seqids.elementAt(ids[s]));
 345         }
 346
 347         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 348                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 349                 groups[i].getDisplayText(), groups[i].getColourText(),
 350                 groups[i].getStart(), groups[i].getEnd());
 351         sg.getGroupColourScheme().setThreshold(pidThreshold, true);
 352
 353         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 354
 355         if (groups[i].getConsThreshold() != 0)
 356         {
 357           Conservation c = new Conservation("All", sg.getSequences(null),
 358                   0, sg.getWidth() - 1);
 359           c.calculate();
 360           c.verdict(false, 25);
 361           sg.cs.setConservation(c);
 362         }
 363
 364         al.addGroup(sg);
 365       }
 366     }
 367
 368     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 369             view.getHeight());
 370     af.viewport.getRanges().setStartRes(view.getStartRes());
 371     // startSeq set in af.alignPanel.updateLayout below
 372     af.viewport.setShowAnnotation(view.getShowAnnotation());
 373     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 374     af.viewport.setColourText(view.getShowColourText());
 375     af.viewport.setConservationSelected(view.getConservationSelected());
 376     af.viewport.setShowJVSuffix(view.getShowFullId());
 377     af.viewport.setFont(
 378             new java.awt.Font(view.getFontName(), view.getFontStyle(), view
 379                     .getFontSize()), true);
 380
 381     af.viewport.setRenderGaps(view.getRenderGaps());
 382     af.viewport.setWrapAlignment(view.getWrapAlignment());
 383
 384     af.viewport.setShowAnnotation(view.isShowAnnotation());
 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.getColourScheme(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.getResidueShading().setThreshold(
 409             view.getPidThreshold(), true);
 410     af.viewport.getResidueShading().setConsensus(
 411             af.viewport.getSequenceConsensusHash());
 412     af.viewport.setColourAppliesToAllGroups(false);
 413     af.alignPanel.updateLayout();
 414     af.changeColour(cs);
 415     if (view.getConservationSelected() && cs != null)
 416     {
 417       af.viewport.getResidueShading().setConservationInc(
 418               view.getConsThreshold());
 419     }
 420
 421     af.viewport.setColourAppliesToAllGroups(true);
 422     af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 423
 424     if (jms.getFeatureSettings() != null)
 425     {
 426       Hashtable featuresDisplayed = new Hashtable();
 427       Hashtable featureColours = new Hashtable();
 428       String[] renderOrder = new String[jms.getFeatureSettings()
 429               .getSettingCount()];
 430       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 431       {
 432         Setting setting = jms.getFeatureSettings().getSetting(fs);
 433
 434         featureColours.put(setting.getType(),
 435                 new java.awt.Color(setting.getColour()));
 436
 437         renderOrder[fs] = setting.getType();
 438
 439         if (setting.getDisplay())
 440         {
 441           featuresDisplayed.put(setting.getType(),
 442                   new Integer(setting.getColour()));
 443         }
 444       }
 445       FeatureRendererSettings frs = new FeatureRendererSettings(
 446               renderOrder, new Hashtable(), featureColours, 1.0f, null);
 447       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 448               .transferSettings(frs);
 449     }
 450
 451     af.setMenusFromViewport(af.viewport);
 452
 453     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 454             view.getHeight());
 455
 456     // LOAD TREES
 457     // /////////////////////////////////////
 458     if (jms.getTreeCount() > 0)
 459     {
 460       try
 461       {
 462         for (int t = 0; t < jms.getTreeCount(); t++)
 463         {
 464
 465           Tree tree = jms.getTree(t);
 466
 467           TreePanel tp = af.showNewickTree(
 468                   new jalview.io.NewickFile(tree.getNewick()),
 469                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 470                   tree.getXpos(), tree.getYpos());
 471
 472           tp.fitToWindow.setState(tree.getFitToWindow());
 473           tp.fitToWindow_actionPerformed(null);
 474
 475           if (tree.getFontName() != null)
 476           {
 477             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 478                     .getFontStyle(), tree.getFontSize()));
 479           }
 480           else
 481           {
 482             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 483                     .getFontStyle(), tree.getFontSize()));
 484           }
 485
 486           tp.showPlaceholders(tree.getMarkUnlinked());
 487           tp.showBootstrap(tree.getShowBootstrap());
 488           tp.showDistances(tree.getShowDistances());
 489
 490           tp.treeCanvas.threshold = tree.getThreshold();
 491
 492           if (tree.getCurrentTree())
 493           {
 494             af.viewport.setCurrentTree(tp.getTree());
 495           }
 496         }
 497
 498       } catch (Exception ex)
 499       {
 500         ex.printStackTrace();
 501       }
 502
 503     }
 504
 505     return af;
 506   }
 507 }