src/jalview/gui/Jalview2XML_V1.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   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 java.io.*;
  24 import java.util.*;
  25 import java.util.jar.*;
  26
  27 import javax.swing.*;
  28
  29 import org.exolab.castor.xml.*;
  30 import jalview.binding.*;
  31 import jalview.schemes.*;
  32 import jalview.util.MessageManager;
  33 import jalview.util.jarInputStreamProvider;
  34
  35 /**
  36  * DOCUMENT ME!
  37  *
  38  * @author $author$
  39  * @version $Revision$
  40  */
  41 public class Jalview2XML_V1
  42 {
  43   boolean raiseGUI = true;
  44
  45   public Jalview2XML_V1()
  46   {
  47
  48   };
  49
  50   public Jalview2XML_V1(boolean raiseGUI)
  51   {
  52     this.raiseGUI = raiseGUI;
  53   };
  54
  55   jalview.schemes.UserColourScheme GetUserColourScheme(
  56           JalviewModelSequence jms, String id)
  57   {
  58     UserColours[] uc = jms.getUserColours();
  59     UserColours colours = null;
  60
  61     for (int i = 0; i < uc.length; i++)
  62     {
  63       if (uc[i].getId().equals(id))
  64       {
  65         colours = uc[i];
  66
  67         break;
  68       }
  69     }
  70
  71     int csize = colours.getUserColourScheme().getColourCount();
  72     java.awt.Color[] newColours = new java.awt.Color[csize];
  73
  74     for (int i = 0; i < csize; i++)
  75     {
  76       newColours[i] = new java.awt.Color(Integer.parseInt(colours
  77               .getUserColourScheme().getColour(i).getRGB(), 16));
  78     }
  79
  80     return new jalview.schemes.UserColourScheme(newColours);
  81   }
  82
  83   /**
  84    * DOCUMENT ME!
  85    *
  86    * @param file
  87    *          DOCUMENT ME!
  88    */
  89   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
  90   {
  91     final String file = jprovider.getFilename();
  92     jalview.gui.AlignFrame af = null;
  93
  94     try
  95     {
  96       JarInputStream jin = null;
  97       JarEntry jarentry = null;
  98       int entryCount = 1;
  99
 100       do
 101       {
 102         jin = jprovider.getJarInputStream();
 103
 104         for (int i = 0; i < entryCount; i++)
 105         {
 106           jarentry = jin.getNextJarEntry();
 107         }
 108
 109         class NoDescIDResolver implements IDResolver
 110         {
 111           public Object resolve(String idref)
 112           {
 113             System.out.println(idref + " used");
 114             return null;
 115           }
 116         }
 117
 118         if (jarentry != null)
 119         {
 120           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 121           JalviewModel object = new JalviewModel();
 122
 123           object = (JalviewModel) object.unmarshal(in);
 124
 125           af = LoadFromObject(object, file);
 126           entryCount++;
 127         }
 128       } while (jarentry != null);
 129     } catch (final java.net.UnknownHostException ex)
 130     {
 131       ex.printStackTrace();
 132       if (raiseGUI)
 133       {
 134         javax.swing.SwingUtilities.invokeLater(new Runnable()
 135         {
 136           public void run()
 137           {
 138
 139             System.err.println("Couldn't locate Jalview XML file : " + ex
 140                     + "\n");
 141             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 142                         MessageManager.formatMessage("label.couldnt_locate", new String[]{file}),
 143                     MessageManager.getString("label.url_not_found"),
 144                     JOptionPane.WARNING_MESSAGE);
 145           }
 146         });
 147       }
 148       ;
 149     } catch (Exception ex)
 150     {
 151       System.err.println("Exception whilst loading jalview XML file : ");
 152       ex.printStackTrace();
 153       if (raiseGUI)
 154       {
 155         javax.swing.SwingUtilities.invokeLater(new Runnable()
 156         {
 157           public void run()
 158           {
 159
 160             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 161                     "Error loading  " + file, "Error loading Jalview file",
 162                     JOptionPane.WARNING_MESSAGE);
 163           }
 164         });
 165       }
 166     }
 167
 168     return af;
 169   }
 170
 171   AlignFrame LoadFromObject(JalviewModel object, String file)
 172   {
 173     Vector seqids = new Vector();
 174     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 175     Sequence[] vamsasSeq = vamsasSet.getSequence();
 176
 177     JalviewModelSequence jms = object.getJalviewModelSequence();
 178
 179     // ////////////////////////////////
 180     // LOAD SEQUENCES
 181     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 182     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 183     for (int i = 0; i < vamsasSeq.length; i++)
 184     {
 185       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 186               vamsasSeq[i].getSequence());
 187       jseqs[i].setStart(JSEQ[i].getStart());
 188       jseqs[i].setEnd(JSEQ[i].getEnd());
 189       seqids.add(jseqs[i]);
 190     }
 191
 192     // /SequenceFeatures are added to the DatasetSequence,
 193     // so we must create the dataset before loading features
 194     // ///////////////////////////////
 195     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 196     al.setDataset(null);
 197     // ///////////////////////////////
 198
 199     for (int i = 0; i < vamsasSeq.length; i++)
 200     {
 201       if (JSEQ[i].getFeaturesCount() > 0)
 202       {
 203         Features[] features = JSEQ[i].getFeatures();
 204         for (int f = 0; f < features.length; f++)
 205         {
 206           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 207                   features[f].getType(), features[f].getDescription(),
 208                   features[f].getStatus(), features[f].getBegin(),
 209                   features[f].getEnd(), null);
 210
 211           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 212         }
 213       }
 214       if (JSEQ[i].getPdbidsCount() > 0)
 215       {
 216         Pdbids[] ids = JSEQ[i].getPdbids();
 217         for (int p = 0; p < ids.length; p++)
 218         {
 219           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 220           entry.setId(ids[p].getId());
 221           entry.setType(ids[p].getType());
 222           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 223         }
 224
 225       }
 226     }
 227
 228     // ///////////////////////////////
 229     // ////////////////////////////////
 230     // LOAD ANNOTATIONS
 231     if (vamsasSet.getAnnotation() != null)
 232     {
 233       Annotation[] an = vamsasSet.getAnnotation();
 234
 235       for (int i = 0; i < an.length; i++)
 236       {
 237         AnnotationElement[] ae = an[i].getAnnotationElement();
 238         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 239                 .getWidth()];
 240
 241         for (int aa = 0; aa < ae.length; aa++)
 242         {
 243           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 244                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 245                   ae[aa].getSecondaryStructure().charAt(0),
 246                   ae[aa].getValue());
 247         }
 248
 249         jalview.datamodel.AlignmentAnnotation jaa = null;
 250
 251         if (an[i].getGraph())
 252         {
 253           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 254                   an[i].getDescription(), anot, 0, 0,
 255                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 256         }
 257         else
 258         {
 259           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 260                   an[i].getDescription(), anot);
 261         }
 262
 263         al.addAnnotation(jaa);
 264       }
 265     }
 266
 267     // ///////////////////////////////
 268     // LOAD VIEWPORT
 269     Viewport[] views = jms.getViewport();
 270     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 271
 272     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 273
 274     af.setFileName(file, "Jalview");
 275
 276     for (int i = 0; i < JSEQ.length; i++)
 277     {
 278       af.viewport.setSequenceColour(af.viewport.getAlignment()
 279               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 280     }
 281
 282     // af.changeColour() );
 283     // ///////////////////////
 284     // LOAD GROUPS
 285     if (jms.getJGroupCount() > 0)
 286     {
 287       JGroup[] groups = jms.getJGroup();
 288
 289       for (int i = 0; i < groups.length; i++)
 290       {
 291         ColourSchemeI cs = null;
 292
 293         if (groups[i].getColour() != null)
 294         {
 295           if (groups[i].getColour().startsWith("ucs"))
 296           {
 297             cs = GetUserColourScheme(jms, groups[i].getColour());
 298           }
 299           else
 300           {
 301             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 302           }
 303
 304           if (cs != null)
 305           {
 306             cs.setThreshold(groups[i].getPidThreshold(), true);
 307           }
 308
 309         }
 310
 311         Vector seqs = new Vector();
 312         int[] ids = groups[i].getSeq();
 313
 314         for (int s = 0; s < ids.length; s++)
 315         {
 316           seqs.addElement((jalview.datamodel.SequenceI) seqids
 317                   .elementAt(ids[s]));
 318         }
 319
 320         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 321                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 322                 groups[i].getDisplayText(), groups[i].getColourText(),
 323                 groups[i].getStart(), groups[i].getEnd());
 324
 325         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 326
 327         if (groups[i].getConsThreshold() != 0)
 328         {
 329           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 330                   "All", ResidueProperties.propHash, 3,
 331                   sg.getSequences(null), 0, sg.getWidth() - 1);
 332           c.calculate();
 333           c.verdict(false, 25);
 334           sg.cs.setConservation(c);
 335         }
 336
 337         al.addGroup(sg);
 338       }
 339     }
 340
 341     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 342             view.getHeight());
 343     af.viewport.setStartRes(view.getStartRes());
 344     af.viewport.setStartSeq(view.getStartSeq());
 345     af.viewport.setShowAnnotation(view.getShowAnnotation());
 346     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 347     af.viewport.setColourText(view.getShowColourText());
 348     af.viewport.setConservationSelected(view.getConservationSelected());
 349     af.viewport.setShowJVSuffix(view.getShowFullId());
 350     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
 351             .getFontStyle(), view.getFontSize()));
 352     af.alignPanel.fontChanged();
 353
 354     af.viewport.setRenderGaps(view.getRenderGaps());
 355     af.viewport.setWrapAlignment(view.getWrapAlignment());
 356     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
 357     af.viewport.setShowAnnotation(view.getShowAnnotation());
 358     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 359     af.viewport.setShowBoxes(view.getShowBoxes());
 360     af.viewport.setShowText(view.getShowText());
 361
 362     ColourSchemeI cs = null;
 363
 364     if (view.getBgColour() != null)
 365     {
 366       if (view.getBgColour().startsWith("ucs"))
 367       {
 368         cs = GetUserColourScheme(jms, view.getBgColour());
 369       }
 370       else
 371       {
 372         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 373       }
 374
 375       if (cs != null)
 376       {
 377         cs.setThreshold(view.getPidThreshold(), true);
 378         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 379       }
 380     }
 381
 382     af.viewport.setGlobalColourScheme(cs);
 383     af.viewport.setColourAppliesToAllGroups(false);
 384     af.changeColour(cs);
 385     if (view.getConservationSelected() && cs != null)
 386     {
 387       cs.setConservationInc(view.getConsThreshold());
 388     }
 389
 390     af.viewport.setColourAppliesToAllGroups(true);
 391     af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
 392
 393     if (jms.getFeatureSettings() != null)
 394     {
 395       af.viewport.featuresDisplayed = new Hashtable();
 396       String[] renderOrder = new String[jms.getFeatureSettings()
 397               .getSettingCount()];
 398       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 399       {
 400         Setting setting = jms.getFeatureSettings().getSetting(fs);
 401
 402         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
 403                 setting.getType(), new java.awt.Color(setting.getColour()));
 404
 405         renderOrder[fs] = setting.getType();
 406
 407         if (setting.getDisplay())
 408         {
 409           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
 410                   setting.getColour()));
 411         }
 412       }
 413       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
 414     }
 415
 416     af.setMenusFromViewport(af.viewport);
 417
 418     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 419             view.getHeight());
 420
 421     // LOAD TREES
 422     // /////////////////////////////////////
 423     if (jms.getTreeCount() > 0)
 424     {
 425       try
 426       {
 427         for (int t = 0; t < jms.getTreeCount(); t++)
 428         {
 429
 430           Tree tree = jms.getTree(t);
 431
 432           TreePanel tp = af.ShowNewickTree(
 433                   new jalview.io.NewickFile(tree.getNewick()),
 434                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 435                   tree.getXpos(), tree.getYpos());
 436
 437           tp.fitToWindow.setState(tree.getFitToWindow());
 438           tp.fitToWindow_actionPerformed(null);
 439
 440           if (tree.getFontName() != null)
 441           {
 442             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 443                     .getFontStyle(), tree.getFontSize()));
 444           }
 445           else
 446           {
 447             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 448                     .getFontStyle(), tree.getFontSize()));
 449           }
 450
 451           tp.showPlaceholders(tree.getMarkUnlinked());
 452           tp.showBootstrap(tree.getShowBootstrap());
 453           tp.showDistances(tree.getShowDistances());
 454
 455           tp.treeCanvas.threshold = tree.getThreshold();
 456
 457           if (tree.getCurrentTree())
 458           {
 459             af.viewport.setCurrentTree(tp.getTree());
 460           }
 461         }
 462
 463       } catch (Exception ex)
 464       {
 465         ex.printStackTrace();
 466       }
 467
 468     }
 469
 470     return af;
 471   }
 472 }