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