src/jalview/gui/Jalview2XML_V1.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ 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 jalview.analysis.Conservation;
  24 import jalview.api.FeatureColourI;
  25 import jalview.binding.Annotation;
  26 import jalview.binding.AnnotationElement;
  27 import jalview.binding.Features;
  28 import jalview.binding.JGroup;
  29 import jalview.binding.JSeq;
  30 import jalview.binding.JalviewModel;
  31 import jalview.binding.JalviewModelSequence;
  32 import jalview.binding.Pdbids;
  33 import jalview.binding.Sequence;
  34 import jalview.binding.SequenceSet;
  35 import jalview.binding.Setting;
  36 import jalview.binding.Tree;
  37 import jalview.binding.UserColours;
  38 import jalview.binding.Viewport;
  39 import jalview.datamodel.PDBEntry;
  40 import jalview.datamodel.SequenceFeature;
  41 import jalview.io.FileFormat;
  42 import jalview.schemes.ColourSchemeI;
  43 import jalview.schemes.ColourSchemeProperty;
  44 import jalview.schemes.FeatureColour;
  45 import jalview.structure.StructureSelectionManager;
  46 import jalview.util.MessageManager;
  47 import jalview.util.jarInputStreamProvider;
  48 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
  49
  50 import java.io.InputStreamReader;
  51 import java.io.Reader;
  52 import java.net.UnknownHostException;
  53 import java.util.Hashtable;
  54 import java.util.Vector;
  55 import java.util.jar.JarEntry;
  56 import java.util.jar.JarInputStream;
  57
  58 /**
  59  * DOCUMENT ME!
  60  *
  61  * @author $author$
  62  * @version $Revision$
  63  */
  64 public class Jalview2XML_V1
  65 {
  66   boolean raiseGUI = true;
  67
  68   public Jalview2XML_V1()
  69   {
  70
  71   };
  72
  73   public Jalview2XML_V1(boolean raiseGUI)
  74   {
  75     this.raiseGUI = raiseGUI;
  76   };
  77
  78   jalview.schemes.UserColourScheme GetUserColourScheme(
  79           JalviewModelSequence jms, String id)
  80   {
  81     UserColours[] uc = jms.getUserColours();
  82     UserColours colours = null;
  83
  84     for (int i = 0; i < uc.length; i++)
  85     {
  86       if (uc[i].getId().equals(id))
  87       {
  88         colours = uc[i];
  89
  90         break;
  91       }
  92     }
  93
  94     int csize = colours.getUserColourScheme().getColourCount();
  95     java.awt.Color[] newColours = new java.awt.Color[csize];
  96
  97     for (int i = 0; i < csize; i++)
  98     {
  99       newColours[i] = new java.awt.Color(Integer.parseInt(
 100               colours.getUserColourScheme().getColour(i).getRGB(), 16));
 101     }
 102
 103     return new jalview.schemes.UserColourScheme(newColours);
 104   }
 105
 106   /**
 107    * DOCUMENT ME!
 108    *
 109    * @param file
 110    *          DOCUMENT ME!
 111    */
 112   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
 113   {
 114     final String file = jprovider.getFilename();
 115     jalview.gui.AlignFrame af = null;
 116
 117     try
 118     {
 119       JarInputStream jin = null;
 120       JarEntry jarentry = null;
 121       int entryCount = 1;
 122
 123       do
 124       {
 125         jin = jprovider.getJarInputStream();
 126
 127         for (int i = 0; i < entryCount; i++)
 128         {
 129           jarentry = jin.getNextJarEntry();
 130         }
 131
 132         if (jarentry != null)
 133         {
 134           entryCount++;
 135           if (jarentry.getName().endsWith(".xml"))
 136           {
 137             Reader in = new InputStreamReader(jin, "UTF-8");
 138             JalviewModel object = new JalviewModel();
 139
 140             object = object.unmarshal(in);
 141
 142             af = LoadFromObject(object, file);
 143           }
 144         }
 145         jin.close();
 146       } while (jarentry != null);
 147     } catch (final UnknownHostException ex)
 148     {
 149       ex.printStackTrace();
 150       if (raiseGUI)
 151       {
 152         javax.swing.SwingUtilities.invokeLater(new Runnable()
 153         {
 154           @Override
 155           public void run()
 156           {
 157
 158             System.err.println(
 159                     "Couldn't locate Jalview XML file : " + ex + "\n");
 160             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 161                     MessageManager.formatMessage("label.couldnt_locate",
 162                             new String[]
 163                             { file }),
 164                     MessageManager.getString("label.url_not_found"),
 165                     JvOptionPane.WARNING_MESSAGE);
 166           }
 167         });
 168       }
 169       ;
 170     } catch (Exception ex)
 171     {
 172       System.err.println("Exception whilst loading jalview XML file : ");
 173       ex.printStackTrace();
 174       if (raiseGUI)
 175       {
 176         javax.swing.SwingUtilities.invokeLater(new Runnable()
 177         {
 178           @Override
 179           public void run()
 180           {
 181
 182             JvOptionPane.showInternalMessageDialog(Desktop.desktop,
 183                     MessageManager.formatMessage(
 184                             "label.error_loading_file_params", new String[]
 185                             { file }),
 186                     MessageManager
 187                             .getString("label.error_loading_jalview_file"),
 188                     JvOptionPane.WARNING_MESSAGE);
 189           }
 190         });
 191       }
 192     }
 193
 194     return af;
 195   }
 196
 197   AlignFrame LoadFromObject(JalviewModel object, String file)
 198   {
 199     Vector seqids = new Vector();
 200     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
 201     Sequence[] vamsasSeq = vamsasSet.getSequence();
 202
 203     JalviewModelSequence jms = object.getJalviewModelSequence();
 204
 205     // ////////////////////////////////
 206     // LOAD SEQUENCES
 207     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
 208     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
 209     for (int i = 0; i < vamsasSeq.length; i++)
 210     {
 211       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
 212               vamsasSeq[i].getSequence());
 213       jseqs[i].setStart(JSEQ[i].getStart());
 214       jseqs[i].setEnd(JSEQ[i].getEnd());
 215       seqids.add(jseqs[i]);
 216     }
 217
 218     // /SequenceFeatures are added to the DatasetSequence,
 219     // so we must create the dataset before loading features
 220     // ///////////////////////////////
 221     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
 222     al.setDataset(null);
 223     // ///////////////////////////////
 224
 225     for (int i = 0; i < vamsasSeq.length; i++)
 226     {
 227       if (JSEQ[i].getFeaturesCount() > 0)
 228       {
 229         Features[] features = JSEQ[i].getFeatures();
 230         for (int f = 0; f < features.length; f++)
 231         {
 232           SequenceFeature sf = new SequenceFeature(features[f].getType(),
 233                   features[f].getDescription(), features[f].getBegin(),
 234                   features[f].getEnd(), null);
 235           sf.setStatus(features[f].getStatus());
 236           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
 237         }
 238       }
 239       if (JSEQ[i].getPdbidsCount() > 0)
 240       {
 241         Pdbids[] ids = JSEQ[i].getPdbids();
 242         for (int p = 0; p < ids.length; p++)
 243         {
 244           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
 245           entry.setId(ids[p].getId());
 246           if (ids[p].getType() != null)
 247           {
 248             if (ids[p].getType().equalsIgnoreCase("PDB"))
 249             {
 250               entry.setType(PDBEntry.Type.PDB);
 251             }
 252             else
 253             {
 254               entry.setType(PDBEntry.Type.FILE);
 255             }
 256           }
 257           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
 258           StructureSelectionManager
 259                   .getStructureSelectionManager(Desktop.instance)
 260                   .registerPDBEntry(entry);
 261         }
 262
 263       }
 264     }
 265
 266     // ///////////////////////////////
 267     // ////////////////////////////////
 268     // LOAD ANNOTATIONS
 269     if (vamsasSet.getAnnotation() != null)
 270     {
 271       Annotation[] an = vamsasSet.getAnnotation();
 272
 273       for (int i = 0; i < an.length; i++)
 274       {
 275         AnnotationElement[] ae = an[i].getAnnotationElement();
 276         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
 277                 .getWidth()];
 278
 279         for (int aa = 0; aa < ae.length; aa++)
 280         {
 281           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
 282                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
 283                   ae[aa].getSecondaryStructure().charAt(0),
 284                   ae[aa].getValue());
 285         }
 286
 287         jalview.datamodel.AlignmentAnnotation jaa = null;
 288
 289         if (an[i].getGraph())
 290         {
 291           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 292                   an[i].getDescription(), anot, 0, 0,
 293                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
 294         }
 295         else
 296         {
 297           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
 298                   an[i].getDescription(), anot);
 299         }
 300
 301         al.addAnnotation(jaa);
 302       }
 303     }
 304
 305     // ///////////////////////////////
 306     // LOAD VIEWPORT
 307     Viewport[] views = jms.getViewport();
 308     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
 309
 310     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
 311
 312     af.setFileName(file, FileFormat.Jalview);
 313
 314     for (int i = 0; i < JSEQ.length; i++)
 315     {
 316       af.viewport.setSequenceColour(
 317               af.viewport.getAlignment().getSequenceAt(i),
 318               new java.awt.Color(JSEQ[i].getColour()));
 319     }
 320
 321     // af.changeColour() );
 322     // ///////////////////////
 323     // LOAD GROUPS
 324     if (jms.getJGroupCount() > 0)
 325     {
 326       JGroup[] groups = jms.getJGroup();
 327
 328       for (int i = 0; i < groups.length; i++)
 329       {
 330         ColourSchemeI cs = null;
 331
 332         if (groups[i].getColour() != null)
 333         {
 334           if (groups[i].getColour().startsWith("ucs"))
 335           {
 336             cs = GetUserColourScheme(jms, groups[i].getColour());
 337           }
 338           else
 339           {
 340             cs = ColourSchemeProperty.getColourScheme(al,
 341                     groups[i].getColour());
 342           }
 343         }
 344         int pidThreshold = groups[i].getPidThreshold();
 345
 346         Vector seqs = new Vector();
 347         int[] ids = groups[i].getSeq();
 348
 349         for (int s = 0; s < ids.length; s++)
 350         {
 351           seqs.addElement(seqids.elementAt(ids[s]));
 352         }
 353
 354         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
 355                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
 356                 groups[i].getDisplayText(), groups[i].getColourText(),
 357                 groups[i].getStart(), groups[i].getEnd());
 358         sg.getGroupColourScheme().setThreshold(pidThreshold, true);
 359
 360         sg.setOutlineColour(
 361                 new java.awt.Color(groups[i].getOutlineColour()));
 362
 363         if (groups[i].getConsThreshold() != 0)
 364         {
 365           Conservation c = new Conservation("All", sg.getSequences(null), 0,
 366                   sg.getWidth() - 1);
 367           c.calculate();
 368           c.verdict(false, 25);
 369           sg.cs.setConservation(c);
 370         }
 371
 372         al.addGroup(sg);
 373       }
 374     }
 375
 376     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
 377             view.getHeight());
 378     af.viewport.getRanges().setStartRes(view.getStartRes());
 379     // startSeq set in af.alignPanel.updateLayout below
 380     af.viewport.setShowAnnotation(view.getShowAnnotation());
 381     af.viewport.setAbovePIDThreshold(view.getPidSelected());
 382     af.viewport.setColourText(view.getShowColourText());
 383     af.viewport.setConservationSelected(view.getConservationSelected());
 384     af.viewport.setShowJVSuffix(view.getShowFullId());
 385     af.viewport.setFont(new java.awt.Font(view.getFontName(),
 386             view.getFontStyle(), view.getFontSize()), true);
 387
 388     af.viewport.setRenderGaps(view.getRenderGaps());
 389     af.viewport.setWrapAlignment(view.getWrapAlignment());
 390
 391     af.viewport.setShowAnnotation(view.isShowAnnotation());
 392     af.viewport.setShowBoxes(view.getShowBoxes());
 393     af.viewport.setShowText(view.getShowText());
 394
 395     ColourSchemeI cs = null;
 396
 397     if (view.getBgColour() != null)
 398     {
 399       if (view.getBgColour().startsWith("ucs"))
 400       {
 401         cs = GetUserColourScheme(jms, view.getBgColour());
 402       }
 403       else
 404       {
 405         cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
 406       }
 407
 408       // if (cs != null)
 409       // {
 410       // cs.setThreshold(view.getPidThreshold(), true);
 411       // cs.setConsensus(af.viewport.getSequenceConsensusHash());
 412       // }
 413     }
 414
 415     af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
 416             true);
 417     af.viewport.getResidueShading()
 418             .setConsensus(af.viewport.getSequenceConsensusHash());
 419     af.viewport.setColourAppliesToAllGroups(false);
 420     af.alignPanel.updateLayout();
 421     af.changeColour(cs);
 422     if (view.getConservationSelected() && cs != null)
 423     {
 424       af.viewport.getResidueShading()
 425               .setConservationInc(view.getConsThreshold());
 426     }
 427
 428     af.viewport.setColourAppliesToAllGroups(true);
 429     af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
 430
 431     if (jms.getFeatureSettings() != null)
 432     {
 433       Hashtable<String, Integer> featuresDisplayed = new Hashtable<>();
 434       Hashtable<String, FeatureColourI> featureColours = new Hashtable<>();
 435       String[] renderOrder = new String[jms.getFeatureSettings()
 436               .getSettingCount()];
 437       for (int fs = 0; fs < jms.getFeatureSettings()
 438               .getSettingCount(); fs++)
 439       {
 440         Setting setting = jms.getFeatureSettings().getSetting(fs);
 441
 442         featureColours.put(setting.getType(),
 443                 new FeatureColour(new java.awt.Color(setting.getColour())));
 444
 445         renderOrder[fs] = setting.getType();
 446
 447         if (setting.getDisplay())
 448         {
 449           featuresDisplayed.put(setting.getType(),
 450                   new Integer(setting.getColour()));
 451         }
 452       }
 453       FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
 454               new Hashtable<String, Boolean>(), featureColours, 1.0f, null,
 455               null);
 456       af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
 457               .transferSettings(frs);
 458     }
 459
 460     af.setMenusFromViewport(af.viewport);
 461
 462     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
 463             view.getHeight());
 464
 465     // LOAD TREES
 466     // /////////////////////////////////////
 467     if (jms.getTreeCount() > 0)
 468     {
 469       try
 470       {
 471         for (int t = 0; t < jms.getTreeCount(); t++)
 472         {
 473
 474           Tree tree = jms.getTree(t);
 475
 476           TreePanel tp = af.showNewickTree(
 477                   new jalview.io.NewickFile(tree.getNewick()),
 478                   tree.getTitle(), tree.getWidth(), tree.getHeight(),
 479                   tree.getXpos(), tree.getYpos());
 480
 481           tp.fitToWindow.setState(tree.getFitToWindow());
 482           tp.fitToWindow_actionPerformed(null);
 483
 484           if (tree.getFontName() != null)
 485           {
 486             tp.setTreeFont(new java.awt.Font(tree.getFontName(),
 487                     tree.getFontStyle(), tree.getFontSize()));
 488           }
 489           else
 490           {
 491             tp.setTreeFont(new java.awt.Font(view.getFontName(),
 492                     view.getFontStyle(), tree.getFontSize()));
 493           }
 494
 495           tp.showPlaceholders(tree.getMarkUnlinked());
 496           tp.showBootstrap(tree.getShowBootstrap());
 497           tp.showDistances(tree.getShowDistances());
 498
 499           tp.treeCanvas.threshold = tree.getThreshold();
 500
 501           if (tree.getCurrentTree())
 502           {
 503             af.viewport.setCurrentTree(tp.getTree());
 504           }
 505         }
 506
 507       } catch (Exception ex)
 508       {
 509         ex.printStackTrace();
 510       }
 511
 512     }
 513
 514     return af;
 515   }
 516 }