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.io.FileFormat;
  40 import jalview.schemes.ColourSchemeI;
  41 import jalview.schemes.ColourSchemeProperty;
  42 import jalview.structure.StructureSelectionManager;
  43 import jalview.util.MessageManager;
  44 import jalview.util.jarInputStreamProvider;
  45 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
  46
  47 import java.io.InputStreamReader;
  48 import java.io.Reader;
  49 import java.net.UnknownHostException;
  50 import java.util.Hashtable;
  51 import java.util.Vector;
  52 import java.util.jar.JarEntry;
  53 import java.util.jar.JarInputStream;
  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(
  97               colours.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         if (jarentry != null)
 130         {
 131           entryCount++;
 132           if (jarentry.getName().endsWith(".xml"))
 133           {
 134             Reader in = new InputStreamReader(jin, "UTF-8");
 135             JalviewModel object = new JalviewModel();
 136
 137             object = object.unmarshal(in);
 138
 139             af = LoadFromObject(object, file);
 140           }
 141         }
 142         jin.close();
 143       } while (jarentry != null);
 144     } catch (final UnknownHostException ex)
 145     {
 146       ex.printStackTrace();
 147       if (raiseGUI)
 148       {
 149         javax.swing.SwingUtilities.invokeLater(new Runnable()
 150         {
 151           @Override
 152           public void run()
 153           {
 154
 155             System.err.println(
 156                     "Couldn't locate Jalview XML file : " + ex + "\n");
 157             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 158                     MessageManager.formatMessage("label.couldnt_locate",
 159                             new String[]
 160                             { file }),
 161                     MessageManager.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 }),
 183                     MessageManager
 184                             .getString("label.error_loading_jalview_file"),
 185                     JvOptionPane.WARNING_MESSAGE);
 186           }
 187         });
 188       }
 189     }
 190
 191     return af;
 192   }
 193
 194   AlignFrame LoadFromObject(JalviewModel object, String file)
 195   {
 196     Vector seqids = new Vector();
 197     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 198     Sequence[] vamsasSeq = vamsasSet.getSequence();
 199
 200     JalviewModelSequence jms = object.getJalviewModelSequence();
 201
 202     // ////////////////////////////////
 203     // LOAD SEQUENCES
 204     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 205     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 206     for (int i = 0; i < vamsasSeq.length; i++)
 207     {
 208       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 209               vamsasSeq[i].getSequence());
 210       jseqs[i].setStart(JSEQ[i].getStart());
 211       jseqs[i].setEnd(JSEQ[i].getEnd());
 212       seqids.add(jseqs[i]);
 213     }
 214
 215     // /SequenceFeatures are added to the DatasetSequence,
 216     // so we must create the dataset before loading features
 217     // ///////////////////////////////
 218     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 219     al.setDataset(null);
 220     // ///////////////////////////////
 221
 222     for (int i = 0; i < vamsasSeq.length; i++)
 223     {
 224       if (JSEQ[i].getFeaturesCount() > 0)
 225       {
 226         Features[] features = JSEQ[i].getFeatures();
 227         for (int f = 0; f < features.length; f++)
 228         {
 229           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 230                   features[f].getType(), features[f].getDescription(),
 231                   features[f].getStatus(), features[f].getBegin(),
 232                   features[f].getEnd(), null);
 233
 234           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 235         }
 236       }
 237       if (JSEQ[i].getPdbidsCount() > 0)
 238       {
 239         Pdbids[] ids = JSEQ[i].getPdbids();
 240         for (int p = 0; p < ids.length; p++)
 241         {
 242           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 243           entry.setId(ids[p].getId());
 244           if (ids[p].getType() != null)
 245           {
 246             if (ids[p].getType().equalsIgnoreCase("PDB"))
 247             {
 248               entry.setType(PDBEntry.Type.PDB);
 249             }
 250             else
 251             {
 252               entry.setType(PDBEntry.Type.FILE);
 253             }
 254           }
 255           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 256           StructureSelectionManager
 257                   .getStructureSelectionManager(Desktop.instance)
 258                   .registerPDBEntry(entry);
 259         }
 260
 261       }
 262     }
 263
 264     // ///////////////////////////////
 265     // ////////////////////////////////
 266     // LOAD ANNOTATIONS
 267     if (vamsasSet.getAnnotation() != null)
 268     {
 269       Annotation[] an = vamsasSet.getAnnotation();
 270
 271       for (int i = 0; i < an.length; i++)
 272       {
 273         AnnotationElement[] ae = an[i].getAnnotationElement();
 274         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 275                 .getWidth()];
 276
 277         for (int aa = 0; aa < ae.length; aa++)
 278         {
 279           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 280                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 281                   ae[aa].getSecondaryStructure().charAt(0),
 282                   ae[aa].getValue());
 283         }
 284
 285         jalview.datamodel.AlignmentAnnotation jaa = null;
 286
 287         if (an[i].getGraph())
 288         {
 289           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 290                   an[i].getDescription(), anot, 0, 0,
 291                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 292         }
 293         else
 294         {
 295           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 296                   an[i].getDescription(), anot);
 297         }
 298
 299         al.addAnnotation(jaa);
 300       }
 301     }
 302
 303     // ///////////////////////////////
 304     // LOAD VIEWPORT
 305     Viewport[] views = jms.getViewport();
 306     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 307
 308     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 309
 310     af.setFileName(file, FileFormat.Jalview);
 311
 312     for (int i = 0; i < JSEQ.length; i++)
 313     {
 314       af.viewport.setSequenceColour(
 315               af.viewport.getAlignment().getSequenceAt(i),
 316               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.getColourScheme(al,
 339                     groups[i].getColour());
 340           }
 341         }
 342         int pidThreshold = groups[i].getPidThreshold();
 343
 344         Vector seqs = new Vector();
 345         int[] ids = groups[i].getSeq();
 346
 347         for (int s = 0; s < ids.length; s++)
 348         {
 349           seqs.addElement(seqids.elementAt(ids[s]));
 350         }
 351
 352         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 353                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 354                 groups[i].getDisplayText(), groups[i].getColourText(),
 355                 groups[i].getStart(), groups[i].getEnd());
 356         sg.getGroupColourScheme().setThreshold(pidThreshold, true);
 357
 358         sg.setOutlineColour(
 359                 new java.awt.Color(groups[i].getOutlineColour()));
 360
 361         if (groups[i].getConsThreshold() != 0)
 362         {
 363           Conservation c = new Conservation("All", sg.getSequences(null), 0,
 364                   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.getRanges().setStartRes(view.getStartRes());
 377     // startSeq set in af.alignPanel.updateLayout below
 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(new java.awt.Font(view.getFontName(),
 384             view.getFontStyle(), view.getFontSize()), true);
 385
 386     af.viewport.setRenderGaps(view.getRenderGaps());
 387     af.viewport.setWrapAlignment(view.getWrapAlignment());
 388
 389     af.viewport.setShowAnnotation(view.isShowAnnotation());
 390     af.viewport.setShowBoxes(view.getShowBoxes());
 391     af.viewport.setShowText(view.getShowText());
 392
 393     ColourSchemeI cs = null;
 394
 395     if (view.getBgColour() != null)
 396     {
 397       if (view.getBgColour().startsWith("ucs"))
 398       {
 399         cs = GetUserColourScheme(jms, view.getBgColour());
 400       }
 401       else
 402       {
 403         cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
 404       }
 405
 406       // if (cs != null)
 407       // {
 408       // cs.setThreshold(view.getPidThreshold(), true);
 409       // cs.setConsensus(af.viewport.getSequenceConsensusHash());
 410       // }
 411     }
 412
 413     af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
 414             true);
 415     af.viewport.getResidueShading()
 416             .setConsensus(af.viewport.getSequenceConsensusHash());
 417     af.viewport.setColourAppliesToAllGroups(false);
 418     af.alignPanel.updateLayout();
 419     af.changeColour(cs);
 420     if (view.getConservationSelected() && cs != null)
 421     {
 422       af.viewport.getResidueShading()
 423               .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()
 436               .getSettingCount(); fs++)
 437       {
 438         Setting setting = jms.getFeatureSettings().getSetting(fs);
 439
 440         featureColours.put(setting.getType(),
 441                 new java.awt.Color(setting.getColour()));
 442
 443         renderOrder[fs] = setting.getType();
 444
 445         if (setting.getDisplay())
 446         {
 447           featuresDisplayed.put(setting.getType(),
 448                   new Integer(setting.getColour()));
 449         }
 450       }
 451       FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
 452               new Hashtable(), featureColours, 1.0f, null);
 453       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 454               .transferSettings(frs);
 455     }
 456
 457     af.setMenusFromViewport(af.viewport);
 458
 459     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 460             view.getHeight());
 461
 462     // LOAD TREES
 463     // /////////////////////////////////////
 464     if (jms.getTreeCount() > 0)
 465     {
 466       try
 467       {
 468         for (int t = 0; t < jms.getTreeCount(); t++)
 469         {
 470
 471           Tree tree = jms.getTree(t);
 472
 473           TreePanel tp = af.showNewickTree(
 474                   new jalview.io.NewickFile(tree.getNewick()),
 475                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 476                   tree.getXpos(), tree.getYpos());
 477
 478           tp.fitToWindow.setState(tree.getFitToWindow());
 479           tp.fitToWindow_actionPerformed(null);
 480
 481           if (tree.getFontName() != null)
 482           {
 483             tp.setTreeFont(new java.awt.Font(tree.getFontName(),
 484                     tree.getFontStyle(), tree.getFontSize()));
 485           }
 486           else
 487           {
 488             tp.setTreeFont(new java.awt.Font(view.getFontName(),
 489                     view.getFontStyle(), tree.getFontSize()));
 490           }
 491
 492           tp.showPlaceholders(tree.getMarkUnlinked());
 493           tp.showBootstrap(tree.getShowBootstrap());
 494           tp.showDistances(tree.getShowDistances());
 495
 496           tp.treeCanvas.threshold = tree.getThreshold();
 497
 498           if (tree.getCurrentTree())
 499           {
 500             af.viewport.setCurrentTree(tp.getTree());
 501           }
 502         }
 503
 504       } catch (Exception ex)
 505       {
 506         ex.printStackTrace();
 507       }
 508
 509     }
 510
 511     return af;
 512   }
 513 }