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
  31 import jalview.binding.*;
  32 import jalview.schemes.*;
  33 import jalview.util.MessageManager;
  34 import jalview.util.jarInputStreamProvider;
  35 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
  36
  37 /**
  38  * DOCUMENT ME!
  39  *
  40  * @author $author$
  41  * @version $Revision$
  42  */
  43 public class Jalview2XML_V1
  44 {
  45   boolean raiseGUI = true;
  46
  47   public Jalview2XML_V1()
  48   {
  49
  50   };
  51
  52   public Jalview2XML_V1(boolean raiseGUI)
  53   {
  54     this.raiseGUI = raiseGUI;
  55   };
  56
  57   jalview.schemes.UserColourScheme GetUserColourScheme(
  58           JalviewModelSequence jms, String id)
  59   {
  60     UserColours[] uc = jms.getUserColours();
  61     UserColours colours = null;
  62
  63     for (int i = 0; i < uc.length; i++)
  64     {
  65       if (uc[i].getId().equals(id))
  66       {
  67         colours = uc[i];
  68
  69         break;
  70       }
  71     }
  72
  73     int csize = colours.getUserColourScheme().getColourCount();
  74     java.awt.Color[] newColours = new java.awt.Color[csize];
  75
  76     for (int i = 0; i < csize; i++)
  77     {
  78       newColours[i] = new java.awt.Color(Integer.parseInt(colours
  79               .getUserColourScheme().getColour(i).getRGB(), 16));
  80     }
  81
  82     return new jalview.schemes.UserColourScheme(newColours);
  83   }
  84
  85   /**
  86    * DOCUMENT ME!
  87    *
  88    * @param file
  89    *          DOCUMENT ME!
  90    */
  91   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
  92   {
  93     final String file = jprovider.getFilename();
  94     jalview.gui.AlignFrame af = null;
  95
  96     try
  97     {
  98       JarInputStream jin = null;
  99       JarEntry jarentry = null;
 100       int entryCount = 1;
 101
 102       do
 103       {
 104         jin = jprovider.getJarInputStream();
 105
 106         for (int i = 0; i < entryCount; i++)
 107         {
 108           jarentry = jin.getNextJarEntry();
 109         }
 110
 111         class NoDescIDResolver implements IDResolver
 112         {
 113           public Object resolve(String idref)
 114           {
 115             System.out.println(idref + " used");
 116             return null;
 117           }
 118         }
 119
 120         if (jarentry != null)
 121         {
 122           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 123           JalviewModel object = new JalviewModel();
 124
 125           object = (JalviewModel) object.unmarshal(in);
 126
 127           af = LoadFromObject(object, file);
 128           entryCount++;
 129         }
 130       } while (jarentry != null);
 131     } catch (final java.net.UnknownHostException ex)
 132     {
 133       ex.printStackTrace();
 134       if (raiseGUI)
 135       {
 136         javax.swing.SwingUtilities.invokeLater(new Runnable()
 137         {
 138           public void run()
 139           {
 140
 141             System.err.println("Couldn't locate Jalview XML file : " + ex
 142                     + "\n");
 143             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 144                     MessageManager.formatMessage("label.couldnt_locate",
 145                             new String[]
 146                             { file }), MessageManager
 147                             .getString("label.url_not_found"),
 148                     JOptionPane.WARNING_MESSAGE);
 149           }
 150         });
 151       }
 152       ;
 153     } catch (Exception ex)
 154     {
 155       System.err.println("Exception whilst loading jalview XML file : ");
 156       ex.printStackTrace();
 157       if (raiseGUI)
 158       {
 159         javax.swing.SwingUtilities.invokeLater(new Runnable()
 160         {
 161           public void run()
 162           {
 163
 164             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 165                     "Error loading  " + file, "Error loading Jalview file",
 166                     JOptionPane.WARNING_MESSAGE);
 167           }
 168         });
 169       }
 170     }
 171
 172     return af;
 173   }
 174
 175   AlignFrame LoadFromObject(JalviewModel object, String file)
 176   {
 177     Vector seqids = new Vector();
 178     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 179     Sequence[] vamsasSeq = vamsasSet.getSequence();
 180
 181     JalviewModelSequence jms = object.getJalviewModelSequence();
 182
 183     // ////////////////////////////////
 184     // LOAD SEQUENCES
 185     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 186     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 187     for (int i = 0; i < vamsasSeq.length; i++)
 188     {
 189       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 190               vamsasSeq[i].getSequence());
 191       jseqs[i].setStart(JSEQ[i].getStart());
 192       jseqs[i].setEnd(JSEQ[i].getEnd());
 193       seqids.add(jseqs[i]);
 194     }
 195
 196     // /SequenceFeatures are added to the DatasetSequence,
 197     // so we must create the dataset before loading features
 198     // ///////////////////////////////
 199     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 200     al.setDataset(null);
 201     // ///////////////////////////////
 202
 203     for (int i = 0; i < vamsasSeq.length; i++)
 204     {
 205       if (JSEQ[i].getFeaturesCount() > 0)
 206       {
 207         Features[] features = JSEQ[i].getFeatures();
 208         for (int f = 0; f < features.length; f++)
 209         {
 210           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 211                   features[f].getType(), features[f].getDescription(),
 212                   features[f].getStatus(), features[f].getBegin(),
 213                   features[f].getEnd(), null);
 214
 215           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 216         }
 217       }
 218       if (JSEQ[i].getPdbidsCount() > 0)
 219       {
 220         Pdbids[] ids = JSEQ[i].getPdbids();
 221         for (int p = 0; p < ids.length; p++)
 222         {
 223           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 224           entry.setId(ids[p].getId());
 225           entry.setType(ids[p].getType());
 226           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 227         }
 228
 229       }
 230     }
 231
 232     // ///////////////////////////////
 233     // ////////////////////////////////
 234     // LOAD ANNOTATIONS
 235     if (vamsasSet.getAnnotation() != null)
 236     {
 237       Annotation[] an = vamsasSet.getAnnotation();
 238
 239       for (int i = 0; i < an.length; i++)
 240       {
 241         AnnotationElement[] ae = an[i].getAnnotationElement();
 242         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 243                 .getWidth()];
 244
 245         for (int aa = 0; aa < ae.length; aa++)
 246         {
 247           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 248                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 249                   ae[aa].getSecondaryStructure().charAt(0),
 250                   ae[aa].getValue());
 251         }
 252
 253         jalview.datamodel.AlignmentAnnotation jaa = null;
 254
 255         if (an[i].getGraph())
 256         {
 257           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 258                   an[i].getDescription(), anot, 0, 0,
 259                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 260         }
 261         else
 262         {
 263           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 264                   an[i].getDescription(), anot);
 265         }
 266
 267         al.addAnnotation(jaa);
 268       }
 269     }
 270
 271     // ///////////////////////////////
 272     // LOAD VIEWPORT
 273     Viewport[] views = jms.getViewport();
 274     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 275
 276     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 277
 278     af.setFileName(file, "Jalview");
 279
 280     for (int i = 0; i < JSEQ.length; i++)
 281     {
 282       af.viewport.setSequenceColour(af.viewport.getAlignment()
 283               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 284     }
 285
 286     // af.changeColour() );
 287     // ///////////////////////
 288     // LOAD GROUPS
 289     if (jms.getJGroupCount() > 0)
 290     {
 291       JGroup[] groups = jms.getJGroup();
 292
 293       for (int i = 0; i < groups.length; i++)
 294       {
 295         ColourSchemeI cs = null;
 296
 297         if (groups[i].getColour() != null)
 298         {
 299           if (groups[i].getColour().startsWith("ucs"))
 300           {
 301             cs = GetUserColourScheme(jms, groups[i].getColour());
 302           }
 303           else
 304           {
 305             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 306           }
 307
 308           if (cs != null)
 309           {
 310             cs.setThreshold(groups[i].getPidThreshold(), true);
 311           }
 312
 313         }
 314
 315         Vector seqs = new Vector();
 316         int[] ids = groups[i].getSeq();
 317
 318         for (int s = 0; s < ids.length; s++)
 319         {
 320           seqs.addElement((jalview.datamodel.SequenceI) seqids
 321                   .elementAt(ids[s]));
 322         }
 323
 324         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 325                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 326                 groups[i].getDisplayText(), groups[i].getColourText(),
 327                 groups[i].getStart(), groups[i].getEnd());
 328
 329         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 330
 331         if (groups[i].getConsThreshold() != 0)
 332         {
 333           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 334                   "All", ResidueProperties.propHash, 3,
 335                   sg.getSequences(null), 0, sg.getWidth() - 1);
 336           c.calculate();
 337           c.verdict(false, 25);
 338           sg.cs.setConservation(c);
 339         }
 340
 341         al.addGroup(sg);
 342       }
 343     }
 344
 345     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 346             view.getHeight());
 347     af.viewport.setStartRes(view.getStartRes());
 348     af.viewport.setStartSeq(view.getStartSeq());
 349     af.viewport.setShowAnnotation(view.getShowAnnotation());
 350     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 351     af.viewport.setColourText(view.getShowColourText());
 352     af.viewport.setConservationSelected(view.getConservationSelected());
 353     af.viewport.setShowJVSuffix(view.getShowFullId());
 354     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
 355             .getFontStyle(), view.getFontSize()));
 356     af.alignPanel.fontChanged();
 357
 358     af.viewport.setRenderGaps(view.getRenderGaps());
 359     af.viewport.setWrapAlignment(view.getWrapAlignment());
 360     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
 361     af.viewport.setShowAnnotation(view.getShowAnnotation());
 362     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 363     af.viewport.setShowBoxes(view.getShowBoxes());
 364     af.viewport.setShowText(view.getShowText());
 365
 366     ColourSchemeI cs = null;
 367
 368     if (view.getBgColour() != null)
 369     {
 370       if (view.getBgColour().startsWith("ucs"))
 371       {
 372         cs = GetUserColourScheme(jms, view.getBgColour());
 373       }
 374       else
 375       {
 376         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 377       }
 378
 379       if (cs != null)
 380       {
 381         cs.setThreshold(view.getPidThreshold(), true);
 382         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 383       }
 384     }
 385
 386     af.viewport.setGlobalColourScheme(cs);
 387     af.viewport.setColourAppliesToAllGroups(false);
 388     af.changeColour(cs);
 389     if (view.getConservationSelected() && cs != null)
 390     {
 391       cs.setConservationInc(view.getConsThreshold());
 392     }
 393
 394     af.viewport.setColourAppliesToAllGroups(true);
 395     af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 396
 397     if (jms.getFeatureSettings() != null)
 398     {
 399       Hashtable featuresDisplayed = new Hashtable();
 400       Hashtable featureColours = new Hashtable();
 401       String[] renderOrder = new String[jms.getFeatureSettings()
 402               .getSettingCount()];
 403       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 404       {
 405         Setting setting = jms.getFeatureSettings().getSetting(fs);
 406
 407         featureColours.put(
 408                 setting.getType(), new java.awt.Color(setting.getColour()));
 409
 410         renderOrder[fs] = setting.getType();
 411
 412         if (setting.getDisplay())
 413         {
 414           featuresDisplayed.put(setting.getType(), new Integer(
 415                   setting.getColour()));
 416         }
 417       }
 418       FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
 419       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().transferSettings(frs);
 420     }
 421
 422     af.setMenusFromViewport(af.viewport);
 423
 424     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 425             view.getHeight());
 426
 427     // LOAD TREES
 428     // /////////////////////////////////////
 429     if (jms.getTreeCount() > 0)
 430     {
 431       try
 432       {
 433         for (int t = 0; t < jms.getTreeCount(); t++)
 434         {
 435
 436           Tree tree = jms.getTree(t);
 437
 438           TreePanel tp = af.ShowNewickTree(
 439                   new jalview.io.NewickFile(tree.getNewick()),
 440                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 441                   tree.getXpos(), tree.getYpos());
 442
 443           tp.fitToWindow.setState(tree.getFitToWindow());
 444           tp.fitToWindow_actionPerformed(null);
 445
 446           if (tree.getFontName() != null)
 447           {
 448             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 449                     .getFontStyle(), tree.getFontSize()));
 450           }
 451           else
 452           {
 453             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 454                     .getFontStyle(), tree.getFontSize()));
 455           }
 456
 457           tp.showPlaceholders(tree.getMarkUnlinked());
 458           tp.showBootstrap(tree.getShowBootstrap());
 459           tp.showDistances(tree.getShowDistances());
 460
 461           tp.treeCanvas.threshold = tree.getThreshold();
 462
 463           if (tree.getCurrentTree())
 464           {
 465             af.viewport.setCurrentTree(tp.getTree());
 466           }
 467         }
 468
 469       } catch (Exception ex)
 470       {
 471         ex.printStackTrace();
 472       }
 473
 474     }
 475
 476     return af;
 477   }
 478 }