src/jalview/gui/Jalview2XML_V1.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
   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.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                     "Couldn't locate " + file, "URL not found",
 140                     JOptionPane.WARNING_MESSAGE);
 141           }
 142         });
 143       }
 144       ;
 145     } catch (Exception ex)
 146     {
 147       System.err.println("Exception whilst loading jalview XML file : ");
 148       ex.printStackTrace();
 149       if (raiseGUI)
 150       {
 151         javax.swing.SwingUtilities.invokeLater(new Runnable()
 152         {
 153           public void run()
 154           {
 155
 156             JOptionPane.showInternalMessageDialog(Desktop.desktop,
 157                     "Error loading  " + file, "Error loading Jalview file",
 158                     JOptionPane.WARNING_MESSAGE);
 159           }
 160         });
 161       }
 162     }
 163
 164     return af;
 165   }
 166
 167   AlignFrame LoadFromObject(JalviewModel object, String file)
 168   {
 169     Vector seqids = new Vector();
 170     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 171     Sequence[] vamsasSeq = vamsasSet.getSequence();
 172
 173     JalviewModelSequence jms = object.getJalviewModelSequence();
 174
 175     // ////////////////////////////////
 176     // LOAD SEQUENCES
 177     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 178     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 179     for (int i = 0; i < vamsasSeq.length; i++)
 180     {
 181       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 182               vamsasSeq[i].getSequence());
 183       jseqs[i].setStart(JSEQ[i].getStart());
 184       jseqs[i].setEnd(JSEQ[i].getEnd());
 185       seqids.add(jseqs[i]);
 186     }
 187
 188     // /SequenceFeatures are added to the DatasetSequence,
 189     // so we must create the dataset before loading features
 190     // ///////////////////////////////
 191     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 192     al.setDataset(null);
 193     // ///////////////////////////////
 194
 195     for (int i = 0; i < vamsasSeq.length; i++)
 196     {
 197       if (JSEQ[i].getFeaturesCount() > 0)
 198       {
 199         Features[] features = JSEQ[i].getFeatures();
 200         for (int f = 0; f < features.length; f++)
 201         {
 202           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
 203                   features[f].getType(), features[f].getDescription(),
 204                   features[f].getStatus(), features[f].getBegin(),
 205                   features[f].getEnd(), null);
 206
 207           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 208         }
 209       }
 210       if (JSEQ[i].getPdbidsCount() > 0)
 211       {
 212         Pdbids[] ids = JSEQ[i].getPdbids();
 213         for (int p = 0; p < ids.length; p++)
 214         {
 215           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 216           entry.setId(ids[p].getId());
 217           entry.setType(ids[p].getType());
 218           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 219         }
 220
 221       }
 222     }
 223
 224     // ///////////////////////////////
 225     // ////////////////////////////////
 226     // LOAD ANNOTATIONS
 227     if (vamsasSet.getAnnotation() != null)
 228     {
 229       Annotation[] an = vamsasSet.getAnnotation();
 230
 231       for (int i = 0; i < an.length; i++)
 232       {
 233         AnnotationElement[] ae = an[i].getAnnotationElement();
 234         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 235                 .getWidth()];
 236
 237         for (int aa = 0; aa < ae.length; aa++)
 238         {
 239           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 240                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 241                   ae[aa].getSecondaryStructure().charAt(0),
 242                   ae[aa].getValue());
 243         }
 244
 245         jalview.datamodel.AlignmentAnnotation jaa = null;
 246
 247         if (an[i].getGraph())
 248         {
 249           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 250                   an[i].getDescription(), anot, 0, 0,
 251                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 252         }
 253         else
 254         {
 255           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 256                   an[i].getDescription(), anot);
 257         }
 258
 259         al.addAnnotation(jaa);
 260       }
 261     }
 262
 263     // ///////////////////////////////
 264     // LOAD VIEWPORT
 265     Viewport[] views = jms.getViewport();
 266     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 267
 268     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 269
 270     af.setFileName(file, "Jalview");
 271
 272     for (int i = 0; i < JSEQ.length; i++)
 273     {
 274       af.viewport.setSequenceColour(af.viewport.getAlignment()
 275               .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
 276     }
 277
 278     // af.changeColour() );
 279     // ///////////////////////
 280     // LOAD GROUPS
 281     if (jms.getJGroupCount() > 0)
 282     {
 283       JGroup[] groups = jms.getJGroup();
 284
 285       for (int i = 0; i < groups.length; i++)
 286       {
 287         ColourSchemeI cs = null;
 288
 289         if (groups[i].getColour() != null)
 290         {
 291           if (groups[i].getColour().startsWith("ucs"))
 292           {
 293             cs = GetUserColourScheme(jms, groups[i].getColour());
 294           }
 295           else
 296           {
 297             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());
 298           }
 299
 300           if (cs != null)
 301           {
 302             cs.setThreshold(groups[i].getPidThreshold(), true);
 303           }
 304
 305         }
 306
 307         Vector seqs = new Vector();
 308         int[] ids = groups[i].getSeq();
 309
 310         for (int s = 0; s < ids.length; s++)
 311         {
 312           seqs.addElement((jalview.datamodel.SequenceI) seqids
 313                   .elementAt(ids[s]));
 314         }
 315
 316         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 317                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 318                 groups[i].getDisplayText(), groups[i].getColourText(),
 319                 groups[i].getStart(), groups[i].getEnd());
 320
 321         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
 322
 323         if (groups[i].getConsThreshold() != 0)
 324         {
 325           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
 326                   "All", ResidueProperties.propHash, 3,
 327                   sg.getSequences(null), 0, sg.getWidth() - 1);
 328           c.calculate();
 329           c.verdict(false, 25);
 330           sg.cs.setConservation(c);
 331         }
 332
 333         al.addGroup(sg);
 334       }
 335     }
 336
 337     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 338             view.getHeight());
 339     af.viewport.setStartRes(view.getStartRes());
 340     af.viewport.setStartSeq(view.getStartSeq());
 341     af.viewport.setShowAnnotation(view.getShowAnnotation());
 342     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 343     af.viewport.setColourText(view.getShowColourText());
 344     af.viewport.setConservationSelected(view.getConservationSelected());
 345     af.viewport.setShowJVSuffix(view.getShowFullId());
 346     af.viewport.setFont(new java.awt.Font(view.getFontName(), view
 347             .getFontStyle(), view.getFontSize()));
 348     af.alignPanel.fontChanged();
 349
 350     af.viewport.setRenderGaps(view.getRenderGaps());
 351     af.viewport.setWrapAlignment(view.getWrapAlignment());
 352     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
 353     af.viewport.setShowAnnotation(view.getShowAnnotation());
 354     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
 355     af.viewport.setShowBoxes(view.getShowBoxes());
 356     af.viewport.setShowText(view.getShowText());
 357
 358     ColourSchemeI cs = null;
 359
 360     if (view.getBgColour() != null)
 361     {
 362       if (view.getBgColour().startsWith("ucs"))
 363       {
 364         cs = GetUserColourScheme(jms, view.getBgColour());
 365       }
 366       else
 367       {
 368         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
 369       }
 370
 371       if (cs != null)
 372       {
 373         cs.setThreshold(view.getPidThreshold(), true);
 374         cs.setConsensus(af.viewport.getSequenceConsensusHash());
 375       }
 376     }
 377
 378     af.viewport.setGlobalColourScheme(cs);
 379     af.viewport.setColourAppliesToAllGroups(false);
 380     af.changeColour(cs);
 381     if (view.getConservationSelected() && cs != null)
 382     {
 383       cs.setConservationInc(view.getConsThreshold());
 384     }
 385
 386     af.viewport.setColourAppliesToAllGroups(true);
 387     af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
 388
 389     if (jms.getFeatureSettings() != null)
 390     {
 391       af.viewport.featuresDisplayed = new Hashtable();
 392       String[] renderOrder = new String[jms.getFeatureSettings()
 393               .getSettingCount()];
 394       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
 395       {
 396         Setting setting = jms.getFeatureSettings().getSetting(fs);
 397
 398         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
 399                 setting.getType(), new java.awt.Color(setting.getColour()));
 400
 401         renderOrder[fs] = setting.getType();
 402
 403         if (setting.getDisplay())
 404         {
 405           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
 406                   setting.getColour()));
 407         }
 408       }
 409       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
 410     }
 411
 412     af.setMenusFromViewport(af.viewport);
 413
 414     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 415             view.getHeight());
 416
 417     // LOAD TREES
 418     // /////////////////////////////////////
 419     if (jms.getTreeCount() > 0)
 420     {
 421       try
 422       {
 423         for (int t = 0; t < jms.getTreeCount(); t++)
 424         {
 425
 426           Tree tree = jms.getTree(t);
 427
 428           TreePanel tp = af.ShowNewickTree(
 429                   new jalview.io.NewickFile(tree.getNewick()),
 430                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 431                   tree.getXpos(), tree.getYpos());
 432
 433           tp.fitToWindow.setState(tree.getFitToWindow());
 434           tp.fitToWindow_actionPerformed(null);
 435
 436           if (tree.getFontName() != null)
 437           {
 438             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
 439                     .getFontStyle(), tree.getFontSize()));
 440           }
 441           else
 442           {
 443             tp.setTreeFont(new java.awt.Font(view.getFontName(), view
 444                     .getFontStyle(), tree.getFontSize()));
 445           }
 446
 447           tp.showPlaceholders(tree.getMarkUnlinked());
 448           tp.showBootstrap(tree.getShowBootstrap());
 449           tp.showDistances(tree.getShowDistances());
 450
 451           tp.treeCanvas.threshold = tree.getThreshold();
 452
 453           if (tree.getCurrentTree())
 454           {
 455             af.viewport.setCurrentTree(tp.getTree());
 456           }
 457         }
 458
 459       } catch (Exception ex)
 460       {
 461         ex.printStackTrace();
 462       }
 463
 464     }
 465
 466     return af;
 467   }
 468 }