src/jalview/gui/Jalview2XML_V1.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.gui;
  20
  21 import java.io.*;
  22 import java.util.*;
  23 import java.util.jar.*;
  24
  25 import javax.swing.*;
  26
  27 import org.exolab.castor.xml.*;
  28 import jalview.binding.*;
  29 import jalview.schemes.*;
  30 import jalview.util.MessageManager;
  31 import jalview.util.jarInputStreamProvider;
  32
  33 /**
  34  * DOCUMENT ME!
  35  *
  36  * @author $author$
  37  * @version $Revision$
  38  */
  39 public class Jalview2XML_V1
  40 {
  41   boolean raiseGUI = true;
  42
  43   public Jalview2XML_V1()
  44   {
  45
  46   };
  47
  48   public Jalview2XML_V1(boolean raiseGUI)
  49   {
  50     this.raiseGUI = raiseGUI;
  51   };
  52
  53   jalview.schemes.UserColourScheme GetUserColourScheme(
  54           JalviewModelSequence jms, String id)
  55   {
  56     UserColours[] uc = jms.getUserColours();
  57     UserColours colours = null;
  58
  59     for (int i = 0; i < uc.length; i++)
  60     {
  61       if (uc[i].getId().equals(id))
  62       {
  63         colours = uc[i];
  64
  65         break;
  66       }
  67     }
  68
  69     int csize = colours.getUserColourScheme().getColourCount();
  70     java.awt.Color[] newColours = new java.awt.Color[csize];
  71
  72     for (int i = 0; i < csize; i++)
  73     {
  74       newColours[i] = new java.awt.Color(Integer.parseInt(colours
  75               .getUserColourScheme().getColour(i).getRGB(), 16));
  76     }
  77
  78     return new jalview.schemes.UserColourScheme(newColours);
  79   }
  80
  81   /**
  82    * DOCUMENT ME!
  83    *
  84    * @param file
  85    *          DOCUMENT ME!
  86    */
  87   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
  88   {
  89     final String file = jprovider.getFilename();
  90     jalview.gui.AlignFrame af = null;
  91
  92     try
  93     {
  94       JarInputStream jin = null;
  95       JarEntry jarentry = null;
  96       int entryCount = 1;
  97
  98       do
  99       {
 100         jin = jprovider.getJarInputStream();
 101
 102         for (int i = 0; i < entryCount; i++)
 103         {
 104           jarentry = jin.getNextJarEntry();
 105         }
 106
 107         class NoDescIDResolver implements IDResolver
 108         {
 109           public Object resolve(String idref)
 110           {
 111             System.out.println(idref + " used");
 112             return null;
 113           }
 114         }
 115
 116         if (jarentry != null)
 117         {
 118           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 119           JalviewModel object = new JalviewModel();
 120
 121           object = (JalviewModel) object.unmarshal(in);
 122
 123           af = LoadFromObject(object, file);
 124           entryCount++;
 125         }
 126       } while (jarentry != null);
 127     } catch (final java.net.UnknownHostException ex)
 128     {
 129       ex.printStackTrace();
 130       if (raiseGUI)
 131       {
 132         javax.swing.SwingUtilities.invokeLater(new Runnable()
 133         {
 134           public void run()
 135           {
 136
 137             System.err.println("Couldn't locate Jalview XML file : " + ex
 138                     + "\n");
 139             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 140                         MessageManager.formatMessage("label.couldnt_locate", new String[]{file}),
 141                     MessageManager.getString("label.url_not_found"),
 142                     JOptionPane.WARNING_MESSAGE);
 143           }
 144         });
 145       }
 146       ;
 147     } catch (Exception ex)
 148     {
 149       System.err.println("Exception whilst loading jalview XML file : ");
 150       ex.printStackTrace();
 151       if (raiseGUI)
 152       {
 153         javax.swing.SwingUtilities.invokeLater(new Runnable()
 154         {
 155           public void run()
 156           {
 157
 158             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 159                     "Error loading  " + file, "Error loading Jalview file",
 160                     JOptionPane.WARNING_MESSAGE);
 161           }
 162         });
 163       }
 164     }
 165
 166     return af;
 167   }
 168
 169   AlignFrame LoadFromObject(JalviewModel object, String file)
 170   {
 171     Vector seqids = new Vector();
 172     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 173     Sequence[] vamsasSeq = vamsasSet.getSequence();
 174
 175     JalviewModelSequence jms = object.getJalviewModelSequence();
 176
 177     // ////////////////////////////////
 178     // LOAD SEQUENCES
 179     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 180     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 181     for (int i = 0; i < vamsasSeq.length; i++)
 182     {
 183       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 184               vamsasSeq[i].getSequence());
 185       jseqs[i].setStart(JSEQ[i].getStart());
 186       jseqs[i].setEnd(JSEQ[i].getEnd());
 187       seqids.add(jseqs[i]);
 188     }
 189
 190     // /SequenceFeatures are added to the DatasetSequence,
 191     // so we must create the dataset before loading features
 192     // ///////////////////////////////
 193     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 194     al.setDataset(null);
 195     // ///////////////////////////////
 196
 197     for (int i = 0; i < vamsasSeq.length; i++)
 198     {
 199       if (JSEQ[i].getFeaturesCount() > 0)
 200       {
 201         Features[] features = JSEQ[i].getFeatures();
 202         for (int f = 0; f < features.length; f++)
 203         {
 204           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 205                   features[f].getType(), features[f].getDescription(),
 206                   features[f].getStatus(), features[f].getBegin(),
 207                   features[f].getEnd(), null);
 208
 209           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 210         }
 211       }
 212       if (JSEQ[i].getPdbidsCount() > 0)
 213       {
 214         Pdbids[] ids = JSEQ[i].getPdbids();
 215         for (int p = 0; p < ids.length; p++)
 216         {
 217           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 218           entry.setId(ids[p].getId());
 219           entry.setType(ids[p].getType());
 220           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 221         }
 222
 223       }
 224     }
 225
 226     // ///////////////////////////////
 227     // ////////////////////////////////
 228     // LOAD ANNOTATIONS
 229     if (vamsasSet.getAnnotation() != null)
 230     {
 231       Annotation[] an = vamsasSet.getAnnotation();
 232
 233       for (int i = 0; i < an.length; i++)
 234       {
 235         AnnotationElement[] ae = an[i].getAnnotationElement();
 236         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 237                 .getWidth()];
 238
 239         for (int aa = 0; aa < ae.length; aa++)
 240         {
 241           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 242                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 243                   ae[aa].getSecondaryStructure().charAt(0),
 244                   ae[aa].getValue());
 245         }
 246
 247         jalview.datamodel.AlignmentAnnotation jaa = null;
 248
 249         if (an[i].getGraph())
 250         {
 251           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 252                   an[i].getDescription(), anot, 0, 0,
 253                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 254         }
 255         else
 256         {
 257           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 258                   an[i].getDescription(), anot);
 259         }
 260
 261         al.addAnnotation(jaa);
 262       }
 263     }
 264
 265     // ///////////////////////////////
 266     // LOAD VIEWPORT
 267     Viewport[] views = jms.getViewport();
 268     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 269
 270     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 271
 272     af.setFileName(file, "Jalview");
 273
 274     for (int i = 0; i < JSEQ.length; i++)
 275     {
 276       af.viewport.setSequenceColour(af.viewport.getAlignment()
 277               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 278     }
 279
 280     // af.changeColour() );
 281     // ///////////////////////
 282     // LOAD GROUPS
 283     if (jms.getJGroupCount() > 0)
 284     {
 285       JGroup[] groups = jms.getJGroup();
 286
 287       for (int i = 0; i < groups.length; i++)
 288       {
 289         ColourSchemeI cs = null;
 290
 291         if (groups[i].getColour() != null)
 292         {
 293           if (groups[i].getColour().startsWith("ucs"))
 294           {
 295             cs = GetUserColourScheme(jms, groups[i].getColour());
 296           }
 297           else
 298           {
 299             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 300           }
 301
 302           if (cs != null)
 303           {
 304             cs.setThreshold(groups[i].getPidThreshold(), true);
 305           }
 306
 307         }
 308
 309         Vector seqs = new Vector();
 310         int[] ids = groups[i].getSeq();
 311
 312         for (int s = 0; s < ids.length; s++)
 313         {
 314           seqs.addElement((jalview.datamodel.SequenceI) seqids
 315                   .elementAt(ids[s]));
 316         }
 317
 318         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 319                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 320                 groups[i].getDisplayText(), groups[i].getColourText(),
 321                 groups[i].getStart(), groups[i].getEnd());
 322
 323         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 324
 325         if (groups[i].getConsThreshold() != 0)
 326         {
 327           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 328                   "All", ResidueProperties.propHash, 3,
 329                   sg.getSequences(null), 0, sg.getWidth() - 1);
 330           c.calculate();
 331           c.verdict(false, 25);
 332           sg.cs.setConservation(c);
 333         }
 334
 335         al.addGroup(sg);
 336       }
 337     }
 338
 339     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 340             view.getHeight());
 341     af.viewport.setStartRes(view.getStartRes());
 342     af.viewport.setStartSeq(view.getStartSeq());
 343     af.viewport.setShowAnnotation(view.getShowAnnotation());
 344     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 345     af.viewport.setColourText(view.getShowColourText());
 346     af.viewport.setConservationSelected(view.getConservationSelected());
 347     af.viewport.setShowJVSuffix(view.getShowFullId());
 348     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
 349             .getFontStyle(), view.getFontSize()));
 350     af.alignPanel.fontChanged();
 351
 352     af.viewport.setRenderGaps(view.getRenderGaps());
 353     af.viewport.setWrapAlignment(view.getWrapAlignment());
 354     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
 355     af.viewport.setShowAnnotation(view.getShowAnnotation());
 356     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 357     af.viewport.setShowBoxes(view.getShowBoxes());
 358     af.viewport.setShowText(view.getShowText());
 359
 360     ColourSchemeI cs = null;
 361
 362     if (view.getBgColour() != null)
 363     {
 364       if (view.getBgColour().startsWith("ucs"))
 365       {
 366         cs = GetUserColourScheme(jms, view.getBgColour());
 367       }
 368       else
 369       {
 370         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 371       }
 372
 373       if (cs != null)
 374       {
 375         cs.setThreshold(view.getPidThreshold(), true);
 376         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 377       }
 378     }
 379
 380     af.viewport.setGlobalColourScheme(cs);
 381     af.viewport.setColourAppliesToAllGroups(false);
 382     af.changeColour(cs);
 383     if (view.getConservationSelected() && cs != null)
 384     {
 385       cs.setConservationInc(view.getConsThreshold());
 386     }
 387
 388     af.viewport.setColourAppliesToAllGroups(true);
 389     af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
 390
 391     if (jms.getFeatureSettings() != null)
 392     {
 393       af.viewport.featuresDisplayed = new Hashtable();
 394       String[] renderOrder = new String[jms.getFeatureSettings()
 395               .getSettingCount()];
 396       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 397       {
 398         Setting setting = jms.getFeatureSettings().getSetting(fs);
 399
 400         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
 401                 setting.getType(), new java.awt.Color(setting.getColour()));
 402
 403         renderOrder[fs] = setting.getType();
 404
 405         if (setting.getDisplay())
 406         {
 407           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
 408                   setting.getColour()));
 409         }
 410       }
 411       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
 412     }
 413
 414     af.setMenusFromViewport(af.viewport);
 415
 416     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 417             view.getHeight());
 418
 419     // LOAD TREES
 420     // /////////////////////////////////////
 421     if (jms.getTreeCount() > 0)
 422     {
 423       try
 424       {
 425         for (int t = 0; t < jms.getTreeCount(); t++)
 426         {
 427
 428           Tree tree = jms.getTree(t);
 429
 430           TreePanel tp = af.ShowNewickTree(
 431                   new jalview.io.NewickFile(tree.getNewick()),
 432                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 433                   tree.getXpos(), tree.getYpos());
 434
 435           tp.fitToWindow.setState(tree.getFitToWindow());
 436           tp.fitToWindow_actionPerformed(null);
 437
 438           if (tree.getFontName() != null)
 439           {
 440             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 441                     .getFontStyle(), tree.getFontSize()));
 442           }
 443           else
 444           {
 445             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 446                     .getFontStyle(), tree.getFontSize()));
 447           }
 448
 449           tp.showPlaceholders(tree.getMarkUnlinked());
 450           tp.showBootstrap(tree.getShowBootstrap());
 451           tp.showDistances(tree.getShowDistances());
 452
 453           tp.treeCanvas.threshold = tree.getThreshold();
 454
 455           if (tree.getCurrentTree())
 456           {
 457             af.viewport.setCurrentTree(tp.getTree());
 458           }
 459         }
 460
 461       } catch (Exception ex)
 462       {
 463         ex.printStackTrace();
 464       }
 465
 466     }
 467
 468     return af;
 469   }
 470 }