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(
  98               colours.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(
 157                     "Couldn't locate Jalview XML file : " + ex + "\n");
 158             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 159                     MessageManager.formatMessage("label.couldnt_locate",
 160                             new String[]
 161                             { file }),
 162                     MessageManager.getString("label.url_not_found"),
 163                     JvOptionPane.WARNING_MESSAGE);
 164           }
 165         });
 166       }
 167       ;
 168     } catch (Exception ex)
 169     {
 170       System.err.println("Exception whilst loading jalview XML file : ");
 171       ex.printStackTrace();
 172       if (raiseGUI)
 173       {
 174         javax.swing.SwingUtilities.invokeLater(new Runnable()
 175         {
 176           @Override
 177           public void run()
 178           {
 179
 180             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 181                     MessageManager.formatMessage(
 182                             "label.error_loading_file_params", new String[]
 183                             { file }),
 184                     MessageManager
 185                             .getString("label.error_loading_jalview_file"),
 186                     JvOptionPane.WARNING_MESSAGE);
 187           }
 188         });
 189       }
 190     }
 191
 192     return af;
 193   }
 194
 195   AlignFrame LoadFromObject(JalviewModel object, String file)
 196   {
 197     Vector seqids = new Vector();
 198     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 199     Sequence[] vamsasSeq = vamsasSet.getSequence();
 200
 201     JalviewModelSequence jms = object.getJalviewModelSequence();
 202
 203     // ////////////////////////////////
 204     // LOAD SEQUENCES
 205     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 206     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 207     for (int i = 0; i < vamsasSeq.length; i++)
 208     {
 209       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 210               vamsasSeq[i].getSequence());
 211       jseqs[i].setStart(JSEQ[i].getStart());
 212       jseqs[i].setEnd(JSEQ[i].getEnd());
 213       seqids.add(jseqs[i]);
 214     }
 215
 216     // /SequenceFeatures are added to the DatasetSequence,
 217     // so we must create the dataset before loading features
 218     // ///////////////////////////////
 219     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 220     al.setDataset(null);
 221     // ///////////////////////////////
 222
 223     for (int i = 0; i < vamsasSeq.length; i++)
 224     {
 225       if (JSEQ[i].getFeaturesCount() > 0)
 226       {
 227         Features[] features = JSEQ[i].getFeatures();
 228         for (int f = 0; f < features.length; f++)
 229         {
 230           SequenceFeature sf = new SequenceFeature(features[f].getType(),
 231                   features[f].getDescription(), features[f].getBegin(),
 232                   features[f].getEnd(), null);
 233           sf.setStatus(features[f].getStatus());
 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             // TODO: update colourscheme with view reference
 339             cs = ColourSchemeProperty.getColourScheme(null, al,
 340                     groups[i].getColour());
 341           }
 342         }
 343         int pidThreshold = groups[i].getPidThreshold();
 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         sg.getGroupColourScheme().setThreshold(pidThreshold, true);
 358
 359         sg.setOutlineColour(
 360                 new java.awt.Color(groups[i].getOutlineColour()));
 361
 362         if (groups[i].getConsThreshold() != 0)
 363         {
 364           Conservation c = new Conservation("All", sg.getSequences(null), 0,
 365                   sg.getWidth() - 1);
 366           c.calculate();
 367           c.verdict(false, 25);
 368           sg.cs.setConservation(c);
 369         }
 370
 371         al.addGroup(sg);
 372       }
 373     }
 374
 375     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 376             view.getHeight());
 377     af.viewport.getRanges().setStartRes(view.getStartRes());
 378     // startSeq set in af.alignPanel.updateLayout below
 379     af.viewport.setShowAnnotation(view.getShowAnnotation());
 380     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 381     af.viewport.setColourText(view.getShowColourText());
 382     af.viewport.setConservationSelected(view.getConservationSelected());
 383     af.viewport.setShowJVSuffix(view.getShowFullId());
 384     af.viewport.setFont(new java.awt.Font(view.getFontName(),
 385             view.getFontStyle(), view.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.getColourScheme(af.viewport, al,
 405                 view.getBgColour());
 406       }
 407
 408       // if (cs != null)
 409       // {
 410       // cs.setThreshold(view.getPidThreshold(), true);
 411       // cs.setConsensus(af.viewport.getSequenceConsensusHash());
 412       // }
 413     }
 414
 415     af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
 416             true);
 417     af.viewport.getResidueShading()
 418             .setConsensus(af.viewport.getSequenceConsensusHash());
 419     af.viewport.setColourAppliesToAllGroups(false);
 420     af.alignPanel.updateLayout();
 421     af.changeColour(cs);
 422     if (view.getConservationSelected() && cs != null)
 423     {
 424       af.viewport.getResidueShading()
 425               .setConservationInc(view.getConsThreshold());
 426     }
 427
 428     af.viewport.setColourAppliesToAllGroups(true);
 429     af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 430
 431     if (jms.getFeatureSettings() != null)
 432     {
 433       Hashtable featuresDisplayed = new Hashtable();
 434       Hashtable featureColours = new Hashtable();
 435       String[] renderOrder = new String[jms.getFeatureSettings()
 436               .getSettingCount()];
 437       for (int fs = 0; fs < jms.getFeatureSettings()
 438               .getSettingCount(); fs++)
 439       {
 440         Setting setting = jms.getFeatureSettings().getSetting(fs);
 441
 442         featureColours.put(setting.getType(),
 443                 new java.awt.Color(setting.getColour()));
 444
 445         renderOrder[fs] = setting.getType();
 446
 447         if (setting.getDisplay())
 448         {
 449           featuresDisplayed.put(setting.getType(),
 450                   new Integer(setting.getColour()));
 451         }
 452       }
 453       FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
 454               new Hashtable(), featureColours, 1.0f, null);
 455       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 456               .transferSettings(frs);
 457     }
 458
 459     af.setMenusFromViewport(af.viewport);
 460
 461     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 462             view.getHeight());
 463
 464     // LOAD TREES
 465     // /////////////////////////////////////
 466     if (jms.getTreeCount() > 0)
 467     {
 468       try
 469       {
 470         for (int t = 0; t < jms.getTreeCount(); t++)
 471         {
 472
 473           Tree tree = jms.getTree(t);
 474
 475           TreePanel tp = af.showNewickTree(
 476                   new jalview.io.NewickFile(tree.getNewick()),
 477                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 478                   tree.getXpos(), tree.getYpos());
 479
 480           tp.fitToWindow.setState(tree.getFitToWindow());
 481           tp.fitToWindow_actionPerformed(null);
 482
 483           if (tree.getFontName() != null)
 484           {
 485             tp.setTreeFont(new java.awt.Font(tree.getFontName(),
 486                     tree.getFontStyle(), tree.getFontSize()));
 487           }
 488           else
 489           {
 490             tp.setTreeFont(new java.awt.Font(view.getFontName(),
 491                     view.getFontStyle(), tree.getFontSize()));
 492           }
 493
 494           tp.showPlaceholders(tree.getMarkUnlinked());
 495           tp.showBootstrap(tree.getShowBootstrap());
 496           tp.showDistances(tree.getShowDistances());
 497
 498           tp.treeCanvas.threshold = tree.getThreshold();
 499
 500           if (tree.getCurrentTree())
 501           {
 502             af.viewport.setCurrentTree(tp.getTree());
 503           }
 504         }
 505
 506       } catch (Exception ex)
 507       {
 508         ex.printStackTrace();
 509       }
 510
 511     }
 512
 513     return af;
 514   }
 515 }