src/jalview/gui/Jalview2XML_V1.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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  */
  18 package jalview.gui;
  19
  20 import java.io.*;
  21 import java.util.*;
  22 import java.util.jar.*;
  23
  24 import javax.swing.*;
  25
  26 import org.exolab.castor.xml.*;
  27 import jalview.binding.*;
  28 import jalview.schemes.*;
  29 import jalview.util.MessageManager;
  30 import jalview.util.jarInputStreamProvider;
  31
  32 /**
  33  * DOCUMENT ME!
  34  *
  35  * @author $author$
  36  * @version $Revision$
  37  */
  38 public class Jalview2XML_V1
  39 {
  40   boolean raiseGUI = true;
  41
  42   public Jalview2XML_V1()
  43   {
  44
  45   };
  46
  47   public Jalview2XML_V1(boolean raiseGUI)
  48   {
  49     this.raiseGUI = raiseGUI;
  50   };
  51
  52   jalview.schemes.UserColourScheme GetUserColourScheme(
  53           JalviewModelSequence jms, String id)
  54   {
  55     UserColours[] uc = jms.getUserColours();
  56     UserColours colours = null;
  57
  58     for (int i = 0; i < uc.length; i++)
  59     {
  60       if (uc[i].getId().equals(id))
  61       {
  62         colours = uc[i];
  63
  64         break;
  65       }
  66     }
  67
  68     int csize = colours.getUserColourScheme().getColourCount();
  69     java.awt.Color[] newColours = new java.awt.Color[csize];
  70
  71     for (int i = 0; i < csize; i++)
  72     {
  73       newColours[i] = new java.awt.Color(Integer.parseInt(colours
  74               .getUserColourScheme().getColour(i).getRGB(), 16));
  75     }
  76
  77     return new jalview.schemes.UserColourScheme(newColours);
  78   }
  79
  80   /**
  81    * DOCUMENT ME!
  82    *
  83    * @param file
  84    *          DOCUMENT ME!
  85    */
  86   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
  87   {
  88     final String file = jprovider.getFilename();
  89     jalview.gui.AlignFrame af = null;
  90
  91     try
  92     {
  93       JarInputStream jin = null;
  94       JarEntry jarentry = null;
  95       int entryCount = 1;
  96
  97       do
  98       {
  99         jin = jprovider.getJarInputStream();
 100
 101         for (int i = 0; i < entryCount; i++)
 102         {
 103           jarentry = jin.getNextJarEntry();
 104         }
 105
 106         class NoDescIDResolver implements IDResolver
 107         {
 108           public Object resolve(String idref)
 109           {
 110             System.out.println(idref + " used");
 111             return null;
 112           }
 113         }
 114
 115         if (jarentry != null)
 116         {
 117           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 118           JalviewModel object = new JalviewModel();
 119
 120           object = (JalviewModel) object.unmarshal(in);
 121
 122           af = LoadFromObject(object, file);
 123           entryCount++;
 124         }
 125       } while (jarentry != null);
 126     } catch (final java.net.UnknownHostException ex)
 127     {
 128       ex.printStackTrace();
 129       if (raiseGUI)
 130       {
 131         javax.swing.SwingUtilities.invokeLater(new Runnable()
 132         {
 133           public void run()
 134           {
 135
 136             System.err.println("Couldn't locate Jalview XML file : " + ex
 137                     + "\n");
 138             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 139                         MessageManager.formatMessage("label.couldnt_locate", new String[]{file}),
 140                     MessageManager.getString("label.url_not_found"),
 141                     JOptionPane.WARNING_MESSAGE);
 142           }
 143         });
 144       }
 145       ;
 146     } catch (Exception ex)
 147     {
 148       System.err.println("Exception whilst loading jalview XML file : ");
 149       ex.printStackTrace();
 150       if (raiseGUI)
 151       {
 152         javax.swing.SwingUtilities.invokeLater(new Runnable()
 153         {
 154           public void run()
 155           {
 156
 157             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 158                     "Error loading  " + file, "Error loading Jalview file",
 159                     JOptionPane.WARNING_MESSAGE);
 160           }
 161         });
 162       }
 163     }
 164
 165     return af;
 166   }
 167
 168   AlignFrame LoadFromObject(JalviewModel object, String file)
 169   {
 170     Vector seqids = new Vector();
 171     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 172     Sequence[] vamsasSeq = vamsasSet.getSequence();
 173
 174     JalviewModelSequence jms = object.getJalviewModelSequence();
 175
 176     // ////////////////////////////////
 177     // LOAD SEQUENCES
 178     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 179     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 180     for (int i = 0; i < vamsasSeq.length; i++)
 181     {
 182       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 183               vamsasSeq[i].getSequence());
 184       jseqs[i].setStart(JSEQ[i].getStart());
 185       jseqs[i].setEnd(JSEQ[i].getEnd());
 186       seqids.add(jseqs[i]);
 187     }
 188
 189     // /SequenceFeatures are added to the DatasetSequence,
 190     // so we must create the dataset before loading features
 191     // ///////////////////////////////
 192     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 193     al.setDataset(null);
 194     // ///////////////////////////////
 195
 196     for (int i = 0; i < vamsasSeq.length; i++)
 197     {
 198       if (JSEQ[i].getFeaturesCount() > 0)
 199       {
 200         Features[] features = JSEQ[i].getFeatures();
 201         for (int f = 0; f < features.length; f++)
 202         {
 203           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 204                   features[f].getType(), features[f].getDescription(),
 205                   features[f].getStatus(), features[f].getBegin(),
 206                   features[f].getEnd(), null);
 207
 208           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 209         }
 210       }
 211       if (JSEQ[i].getPdbidsCount() > 0)
 212       {
 213         Pdbids[] ids = JSEQ[i].getPdbids();
 214         for (int p = 0; p < ids.length; p++)
 215         {
 216           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 217           entry.setId(ids[p].getId());
 218           entry.setType(ids[p].getType());
 219           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 220         }
 221
 222       }
 223     }
 224
 225     // ///////////////////////////////
 226     // ////////////////////////////////
 227     // LOAD ANNOTATIONS
 228     if (vamsasSet.getAnnotation() != null)
 229     {
 230       Annotation[] an = vamsasSet.getAnnotation();
 231
 232       for (int i = 0; i < an.length; i++)
 233       {
 234         AnnotationElement[] ae = an[i].getAnnotationElement();
 235         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 236                 .getWidth()];
 237
 238         for (int aa = 0; aa < ae.length; aa++)
 239         {
 240           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 241                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 242                   ae[aa].getSecondaryStructure().charAt(0),
 243                   ae[aa].getValue());
 244         }
 245
 246         jalview.datamodel.AlignmentAnnotation jaa = null;
 247
 248         if (an[i].getGraph())
 249         {
 250           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 251                   an[i].getDescription(), anot, 0, 0,
 252                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 253         }
 254         else
 255         {
 256           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 257                   an[i].getDescription(), anot);
 258         }
 259
 260         al.addAnnotation(jaa);
 261       }
 262     }
 263
 264     // ///////////////////////////////
 265     // LOAD VIEWPORT
 266     Viewport[] views = jms.getViewport();
 267     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 268
 269     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 270
 271     af.setFileName(file, "Jalview");
 272
 273     for (int i = 0; i < JSEQ.length; i++)
 274     {
 275       af.viewport.setSequenceColour(af.viewport.getAlignment()
 276               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 277     }
 278
 279     // af.changeColour() );
 280     // ///////////////////////
 281     // LOAD GROUPS
 282     if (jms.getJGroupCount() > 0)
 283     {
 284       JGroup[] groups = jms.getJGroup();
 285
 286       for (int i = 0; i < groups.length; i++)
 287       {
 288         ColourSchemeI cs = null;
 289
 290         if (groups[i].getColour() != null)
 291         {
 292           if (groups[i].getColour().startsWith("ucs"))
 293           {
 294             cs = GetUserColourScheme(jms, groups[i].getColour());
 295           }
 296           else
 297           {
 298             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 299           }
 300
 301           if (cs != null)
 302           {
 303             cs.setThreshold(groups[i].getPidThreshold(), true);
 304           }
 305
 306         }
 307
 308         Vector seqs = new Vector();
 309         int[] ids = groups[i].getSeq();
 310
 311         for (int s = 0; s < ids.length; s++)
 312         {
 313           seqs.addElement((jalview.datamodel.SequenceI) seqids
 314                   .elementAt(ids[s]));
 315         }
 316
 317         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 318                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 319                 groups[i].getDisplayText(), groups[i].getColourText(),
 320                 groups[i].getStart(), groups[i].getEnd());
 321
 322         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 323
 324         if (groups[i].getConsThreshold() != 0)
 325         {
 326           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 327                   "All", ResidueProperties.propHash, 3,
 328                   sg.getSequences(null), 0, sg.getWidth() - 1);
 329           c.calculate();
 330           c.verdict(false, 25);
 331           sg.cs.setConservation(c);
 332         }
 333
 334         al.addGroup(sg);
 335       }
 336     }
 337
 338     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 339             view.getHeight());
 340     af.viewport.setStartRes(view.getStartRes());
 341     af.viewport.setStartSeq(view.getStartSeq());
 342     af.viewport.setShowAnnotation(view.getShowAnnotation());
 343     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 344     af.viewport.setColourText(view.getShowColourText());
 345     af.viewport.setConservationSelected(view.getConservationSelected());
 346     af.viewport.setShowJVSuffix(view.getShowFullId());
 347     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
 348             .getFontStyle(), view.getFontSize()));
 349     af.alignPanel.fontChanged();
 350
 351     af.viewport.setRenderGaps(view.getRenderGaps());
 352     af.viewport.setWrapAlignment(view.getWrapAlignment());
 353     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
 354     af.viewport.setShowAnnotation(view.getShowAnnotation());
 355     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 356     af.viewport.setShowBoxes(view.getShowBoxes());
 357     af.viewport.setShowText(view.getShowText());
 358
 359     ColourSchemeI cs = null;
 360
 361     if (view.getBgColour() != null)
 362     {
 363       if (view.getBgColour().startsWith("ucs"))
 364       {
 365         cs = GetUserColourScheme(jms, view.getBgColour());
 366       }
 367       else
 368       {
 369         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 370       }
 371
 372       if (cs != null)
 373       {
 374         cs.setThreshold(view.getPidThreshold(), true);
 375         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 376       }
 377     }
 378
 379     af.viewport.setGlobalColourScheme(cs);
 380     af.viewport.setColourAppliesToAllGroups(false);
 381     af.changeColour(cs);
 382     if (view.getConservationSelected() && cs != null)
 383     {
 384       cs.setConservationInc(view.getConsThreshold());
 385     }
 386
 387     af.viewport.setColourAppliesToAllGroups(true);
 388     af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
 389
 390     if (jms.getFeatureSettings() != null)
 391     {
 392       af.viewport.featuresDisplayed = new Hashtable();
 393       String[] renderOrder = new String[jms.getFeatureSettings()
 394               .getSettingCount()];
 395       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 396       {
 397         Setting setting = jms.getFeatureSettings().getSetting(fs);
 398
 399         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
 400                 setting.getType(), new java.awt.Color(setting.getColour()));
 401
 402         renderOrder[fs] = setting.getType();
 403
 404         if (setting.getDisplay())
 405         {
 406           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
 407                   setting.getColour()));
 408         }
 409       }
 410       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
 411     }
 412
 413     af.setMenusFromViewport(af.viewport);
 414
 415     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 416             view.getHeight());
 417
 418     // LOAD TREES
 419     // /////////////////////////////////////
 420     if (jms.getTreeCount() > 0)
 421     {
 422       try
 423       {
 424         for (int t = 0; t < jms.getTreeCount(); t++)
 425         {
 426
 427           Tree tree = jms.getTree(t);
 428
 429           TreePanel tp = af.ShowNewickTree(
 430                   new jalview.io.NewickFile(tree.getNewick()),
 431                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 432                   tree.getXpos(), tree.getYpos());
 433
 434           tp.fitToWindow.setState(tree.getFitToWindow());
 435           tp.fitToWindow_actionPerformed(null);
 436
 437           if (tree.getFontName() != null)
 438           {
 439             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 440                     .getFontStyle(), tree.getFontSize()));
 441           }
 442           else
 443           {
 444             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 445                     .getFontStyle(), tree.getFontSize()));
 446           }
 447
 448           tp.showPlaceholders(tree.getMarkUnlinked());
 449           tp.showBootstrap(tree.getShowBootstrap());
 450           tp.showDistances(tree.getShowDistances());
 451
 452           tp.treeCanvas.threshold = tree.getThreshold();
 453
 454           if (tree.getCurrentTree())
 455           {
 456             af.viewport.setCurrentTree(tp.getTree());
 457           }
 458         }
 459
 460       } catch (Exception ex)
 461       {
 462         ex.printStackTrace();
 463       }
 464
 465     }
 466
 467     return af;
 468   }
 469 }