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",
 143                             new String[]
 144                             { file }), MessageManager
 145                             .getString("label.url_not_found"),
 146                     JOptionPane.WARNING_MESSAGE);
 147           }
 148         });
 149       }
 150       ;
 151     } catch (Exception ex)
 152     {
 153       System.err.println("Exception whilst loading jalview XML file : ");
 154       ex.printStackTrace();
 155       if (raiseGUI)
 156       {
 157         javax.swing.SwingUtilities.invokeLater(new Runnable()
 158         {
 159           public void run()
 160           {
 161
 162             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 163                     MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
 164                     JOptionPane.WARNING_MESSAGE);
 165           }
 166         });
 167       }
 168     }
 169
 170     return af;
 171   }
 172
 173   AlignFrame LoadFromObject(JalviewModel object, String file)
 174   {
 175     Vector seqids = new Vector();
 176     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 177     Sequence[] vamsasSeq = vamsasSet.getSequence();
 178
 179     JalviewModelSequence jms = object.getJalviewModelSequence();
 180
 181     // ////////////////////////////////
 182     // LOAD SEQUENCES
 183     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 184     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 185     for (int i = 0; i < vamsasSeq.length; i++)
 186     {
 187       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 188               vamsasSeq[i].getSequence());
 189       jseqs[i].setStart(JSEQ[i].getStart());
 190       jseqs[i].setEnd(JSEQ[i].getEnd());
 191       seqids.add(jseqs[i]);
 192     }
 193
 194     // /SequenceFeatures are added to the DatasetSequence,
 195     // so we must create the dataset before loading features
 196     // ///////////////////////////////
 197     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 198     al.setDataset(null);
 199     // ///////////////////////////////
 200
 201     for (int i = 0; i < vamsasSeq.length; i++)
 202     {
 203       if (JSEQ[i].getFeaturesCount() > 0)
 204       {
 205         Features[] features = JSEQ[i].getFeatures();
 206         for (int f = 0; f < features.length; f++)
 207         {
 208           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 209                   features[f].getType(), features[f].getDescription(),
 210                   features[f].getStatus(), features[f].getBegin(),
 211                   features[f].getEnd(), null);
 212
 213           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 214         }
 215       }
 216       if (JSEQ[i].getPdbidsCount() > 0)
 217       {
 218         Pdbids[] ids = JSEQ[i].getPdbids();
 219         for (int p = 0; p < ids.length; p++)
 220         {
 221           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 222           entry.setId(ids[p].getId());
 223           entry.setType(ids[p].getType());
 224           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 225         }
 226
 227       }
 228     }
 229
 230     // ///////////////////////////////
 231     // ////////////////////////////////
 232     // LOAD ANNOTATIONS
 233     if (vamsasSet.getAnnotation() != null)
 234     {
 235       Annotation[] an = vamsasSet.getAnnotation();
 236
 237       for (int i = 0; i < an.length; i++)
 238       {
 239         AnnotationElement[] ae = an[i].getAnnotationElement();
 240         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 241                 .getWidth()];
 242
 243         for (int aa = 0; aa < ae.length; aa++)
 244         {
 245           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 246                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 247                   ae[aa].getSecondaryStructure().charAt(0),
 248                   ae[aa].getValue());
 249         }
 250
 251         jalview.datamodel.AlignmentAnnotation jaa = null;
 252
 253         if (an[i].getGraph())
 254         {
 255           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 256                   an[i].getDescription(), anot, 0, 0,
 257                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 258         }
 259         else
 260         {
 261           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 262                   an[i].getDescription(), anot);
 263         }
 264
 265         al.addAnnotation(jaa);
 266       }
 267     }
 268
 269     // ///////////////////////////////
 270     // LOAD VIEWPORT
 271     Viewport[] views = jms.getViewport();
 272     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 273
 274     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 275
 276     af.setFileName(file, "Jalview");
 277
 278     for (int i = 0; i < JSEQ.length; i++)
 279     {
 280       af.viewport.setSequenceColour(af.viewport.getAlignment()
 281               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 282     }
 283
 284     // af.changeColour() );
 285     // ///////////////////////
 286     // LOAD GROUPS
 287     if (jms.getJGroupCount() > 0)
 288     {
 289       JGroup[] groups = jms.getJGroup();
 290
 291       for (int i = 0; i < groups.length; i++)
 292       {
 293         ColourSchemeI cs = null;
 294
 295         if (groups[i].getColour() != null)
 296         {
 297           if (groups[i].getColour().startsWith("ucs"))
 298           {
 299             cs = GetUserColourScheme(jms, groups[i].getColour());
 300           }
 301           else
 302           {
 303             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 304           }
 305
 306           if (cs != null)
 307           {
 308             cs.setThreshold(groups[i].getPidThreshold(), true);
 309           }
 310
 311         }
 312
 313         Vector seqs = new Vector();
 314         int[] ids = groups[i].getSeq();
 315
 316         for (int s = 0; s < ids.length; s++)
 317         {
 318           seqs.addElement((jalview.datamodel.SequenceI) seqids
 319                   .elementAt(ids[s]));
 320         }
 321
 322         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 323                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 324                 groups[i].getDisplayText(), groups[i].getColourText(),
 325                 groups[i].getStart(), groups[i].getEnd());
 326
 327         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 328
 329         if (groups[i].getConsThreshold() != 0)
 330         {
 331           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 332                   "All", ResidueProperties.propHash, 3,
 333                   sg.getSequences(null), 0, sg.getWidth() - 1);
 334           c.calculate();
 335           c.verdict(false, 25);
 336           sg.cs.setConservation(c);
 337         }
 338
 339         al.addGroup(sg);
 340       }
 341     }
 342
 343     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 344             view.getHeight());
 345     af.viewport.setStartRes(view.getStartRes());
 346     af.viewport.setStartSeq(view.getStartSeq());
 347     af.viewport.setShowAnnotation(view.getShowAnnotation());
 348     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 349     af.viewport.setColourText(view.getShowColourText());
 350     af.viewport.setConservationSelected(view.getConservationSelected());
 351     af.viewport.setShowJVSuffix(view.getShowFullId());
 352     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
 353             .getFontStyle(), view.getFontSize()));
 354     af.alignPanel.fontChanged();
 355
 356     af.viewport.setRenderGaps(view.getRenderGaps());
 357     af.viewport.setWrapAlignment(view.getWrapAlignment());
 358     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
 359     af.viewport.setShowAnnotation(view.getShowAnnotation());
 360     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 361     af.viewport.setShowBoxes(view.getShowBoxes());
 362     af.viewport.setShowText(view.getShowText());
 363
 364     ColourSchemeI cs = null;
 365
 366     if (view.getBgColour() != null)
 367     {
 368       if (view.getBgColour().startsWith("ucs"))
 369       {
 370         cs = GetUserColourScheme(jms, view.getBgColour());
 371       }
 372       else
 373       {
 374         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 375       }
 376
 377       if (cs != null)
 378       {
 379         cs.setThreshold(view.getPidThreshold(), true);
 380         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 381       }
 382     }
 383
 384     af.viewport.setGlobalColourScheme(cs);
 385     af.viewport.setColourAppliesToAllGroups(false);
 386     af.changeColour(cs);
 387     if (view.getConservationSelected() && cs != null)
 388     {
 389       cs.setConservationInc(view.getConsThreshold());
 390     }
 391
 392     af.viewport.setColourAppliesToAllGroups(true);
 393     af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
 394
 395     if (jms.getFeatureSettings() != null)
 396     {
 397       af.viewport.featuresDisplayed = new Hashtable();
 398       String[] renderOrder = new String[jms.getFeatureSettings()
 399               .getSettingCount()];
 400       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 401       {
 402         Setting setting = jms.getFeatureSettings().getSetting(fs);
 403
 404         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
 405                 setting.getType(), new java.awt.Color(setting.getColour()));
 406
 407         renderOrder[fs] = setting.getType();
 408
 409         if (setting.getDisplay())
 410         {
 411           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
 412                   setting.getColour()));
 413         }
 414       }
 415       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
 416     }
 417
 418     af.setMenusFromViewport(af.viewport);
 419
 420     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 421             view.getHeight());
 422
 423     // LOAD TREES
 424     // /////////////////////////////////////
 425     if (jms.getTreeCount() > 0)
 426     {
 427       try
 428       {
 429         for (int t = 0; t < jms.getTreeCount(); t++)
 430         {
 431
 432           Tree tree = jms.getTree(t);
 433
 434           TreePanel tp = af.ShowNewickTree(
 435                   new jalview.io.NewickFile(tree.getNewick()),
 436                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 437                   tree.getXpos(), tree.getYpos());
 438
 439           tp.fitToWindow.setState(tree.getFitToWindow());
 440           tp.fitToWindow_actionPerformed(null);
 441
 442           if (tree.getFontName() != null)
 443           {
 444             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 445                     .getFontStyle(), tree.getFontSize()));
 446           }
 447           else
 448           {
 449             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 450                     .getFontStyle(), tree.getFontSize()));
 451           }
 452
 453           tp.showPlaceholders(tree.getMarkUnlinked());
 454           tp.showBootstrap(tree.getShowBootstrap());
 455           tp.showDistances(tree.getShowDistances());
 456
 457           tp.treeCanvas.threshold = tree.getThreshold();
 458
 459           if (tree.getCurrentTree())
 460           {
 461             af.viewport.setCurrentTree(tp.getTree());
 462           }
 463         }
 464
 465       } catch (Exception ex)
 466       {
 467         ex.printStackTrace();
 468       }
 469
 470     }
 471
 472     return af;
 473   }
 474 }