2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import jalview.api.ComplexAlignFile;
24 import jalview.api.FeatureSettingsModelI;
25 import jalview.api.FeaturesDisplayedI;
26 import jalview.api.FeaturesSourceI;
27 import jalview.bin.Cache;
28 import jalview.bin.Jalview;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.HiddenColumns;
31 import jalview.datamodel.PDBEntry;
32 import jalview.datamodel.SequenceI;
33 import jalview.gui.AlignFrame;
34 import jalview.gui.AlignViewport;
35 import jalview.gui.Desktop;
36 import jalview.gui.Jalview2XML;
37 import jalview.gui.JvOptionPane;
38 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
39 import jalview.schemes.ColourSchemeI;
40 import jalview.structure.StructureSelectionManager;
41 import jalview.util.MessageManager;
42 import jalview.ws.utils.UrlDownloadClient;
45 import java.io.IOException;
46 import java.util.StringTokenizer;
47 import java.util.Vector;
49 import javax.swing.SwingUtilities;
51 public class FileLoader implements Runnable
55 DataSourceType protocol;
59 AlignmentFileReaderI source = null; // alternative specification of where data
64 AlignViewport viewport;
66 AlignFrame alignFrame;
72 boolean raiseGUI = true;
75 * default constructor always raised errors in GUI dialog boxes
83 * construct a Fileloader that may raise errors non-interactively
86 * true if errors are to be raised as GUI dialog boxes
88 public FileLoader(boolean raiseGUI)
90 this.raiseGUI = raiseGUI;
93 public void LoadFile(AlignViewport viewport, String file,
94 DataSourceType protocol, FileFormatI format)
96 this.viewport = viewport;
97 LoadFile(file, protocol, format);
100 public void LoadFile(String file, DataSourceType protocol,
104 this.protocol = protocol;
105 this.format = format;
107 final Thread loader = new Thread(this);
109 SwingUtilities.invokeLater(new Runnable()
120 * Load a (file, protocol) source of unknown type
125 public void LoadFile(String file, DataSourceType protocol)
127 LoadFile(file, protocol, null);
131 * Load alignment from (file, protocol) and wait till loaded
135 * @return alignFrame constructed from file contents
137 public AlignFrame LoadFileWaitTillLoaded(String file,
138 DataSourceType sourceType)
140 return LoadFileWaitTillLoaded(file, sourceType, null);
144 * Load alignment from (file, protocol) of type format and wait till loaded
149 * @return alignFrame constructed from file contents
151 public AlignFrame LoadFileWaitTillLoaded(String file,
152 DataSourceType sourceType, FileFormatI format)
155 this.protocol = sourceType;
156 this.format = format;
157 return _LoadFileWaitTillLoaded();
161 * Load alignment from FileParse source of type format and wait till loaded
165 * @return alignFrame constructed from file contents
167 public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
170 this.source = source;
172 file = source.getInFile();
173 protocol = source.getDataSourceType();
174 this.format = format;
175 return _LoadFileWaitTillLoaded();
179 * start thread and wait until finished, then return the alignFrame that's
180 * (hopefully) been read.
184 protected AlignFrame _LoadFileWaitTillLoaded()
186 Thread loader = new Thread(this);
189 while (loader.isAlive())
194 } catch (Exception ex)
202 public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
203 String file, DataSourceType sourceType, FileFormatI format)
205 this.viewport = viewport;
207 this.protocol = sourceType;
208 this.format = format;
209 _LoadAlignmentFileWaitTillLoaded();
212 protected void _LoadAlignmentFileWaitTillLoaded()
214 Thread loader = new Thread(this);
217 while (loader.isAlive())
222 } catch (Exception ex)
228 public void updateRecentlyOpened()
230 Vector recent = new Vector();
231 if (protocol == DataSourceType.PASTE)
233 // do nothing if the file was pasted in as text... there is no filename to
238 && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
240 // ignore files loaded from the system's temporary directory
243 String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
246 String historyItems = jalview.bin.Cache.getProperty(type);
250 if (historyItems != null)
252 st = new StringTokenizer(historyItems, "\t");
254 while (st.hasMoreTokens())
256 recent.addElement(st.nextElement().toString().trim());
260 if (recent.contains(file))
265 StringBuffer newHistory = new StringBuffer(file);
266 for (int i = 0; i < recent.size() && i < 10; i++)
268 newHistory.append("\t");
269 newHistory.append(recent.elementAt(i));
272 Cache.setProperty(type, newHistory.toString());
274 if (protocol == DataSourceType.FILE)
276 Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
283 String title = protocol == DataSourceType.PASTE
284 ? "Copied From Clipboard"
286 Runtime rt = Runtime.getRuntime();
289 if (Desktop.instance != null)
291 Desktop.instance.startLoading(file);
295 // just in case the caller didn't identify the file for us
298 format = new IdentifyFile().identify(source, false);
299 // identify stream and rewind rather than close
303 format = new IdentifyFile().identify(file, protocol);
310 Desktop.instance.stopLoading();
311 System.err.println("The input file \"" + file
312 + "\" has null or unidentifiable data content!");
313 if (!Jalview.isHeadlessMode())
315 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
316 MessageManager.getString("label.couldnt_read_data")
317 + " in " + file + "\n"
318 + AppletFormatAdapter.getSupportedFormats(),
319 MessageManager.getString("label.couldnt_read_data"),
320 JvOptionPane.WARNING_MESSAGE);
324 // TODO: cache any stream datasources as a temporary file (eg. PDBs
325 // retrieved via URL)
326 if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
329 memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
334 loadtime = -System.currentTimeMillis();
335 AlignmentI al = null;
337 if (FileFormat.Jalview.equals(format))
341 // Tell the user (developer?) that this is going to cause a problem
343 "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
344 // We read the data anyway - it might make sense.
346 alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
350 String error = AppletFormatAdapter.getSupportedFormats();
355 // read from the provided source
356 al = new FormatAdapter().readFromFile(source, format);
361 // open a new source and read from it
362 FormatAdapter fa = new FormatAdapter();
363 boolean downloadStructureFile = format.isStructureFile()
364 && protocol.equals(DataSourceType.URL);
365 if (downloadStructureFile)
367 String structExt = format.getExtensions().split(",")[0];
368 String urlLeafName = file.substring(
370 System.getProperty("file.separator")),
371 file.lastIndexOf("."));
372 String tempStructureFileStr = createNamedJvTempFile(
373 urlLeafName, structExt);
374 UrlDownloadClient.download(file, tempStructureFileStr);
375 al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
377 source = fa.getAlignFile();
381 al = fa.readFile(file, protocol, format);
382 source = fa.getAlignFile(); // keep reference for later if
386 } catch (java.io.IOException ex)
388 error = ex.getMessage();
391 if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
393 // construct and register dataset sequences
394 for (SequenceI sq : al.getSequences())
396 while (sq.getDatasetSequence() != null)
398 sq = sq.getDatasetSequence();
400 if (sq.getAllPDBEntries() != null)
402 for (PDBEntry pdbe : sq.getAllPDBEntries())
404 // register PDB entries with desktop's structure selection
406 StructureSelectionManager
407 .getStructureSelectionManager(Desktop.instance)
408 .registerPDBEntry(pdbe);
413 FeatureSettingsModelI proxyColourScheme = source
414 .getFeatureColourScheme();
415 if (viewport != null)
417 if (proxyColourScheme != null)
419 viewport.applyFeaturesStyle(proxyColourScheme);
421 // append to existing alignment
422 viewport.addAlignment(al, title);
423 if (source instanceof HMMFile)
425 AlignmentI alignment = viewport.getAlignment();
426 SequenceI seq = alignment
427 .getSequenceAt(alignment.getAbsoluteHeight() - 1);
428 if (seq.isHMMConsensusSequence())
431 * fudge: move HMM consensus sequence from last to first
433 alignment.deleteSequence(alignment.getAbsoluteHeight() - 1);
434 alignment.insertSequenceAt(0, seq);
435 alignment.setHmmConsensus(seq);
437 viewport.getAlignPanel().adjustAnnotationHeight();
438 viewport.updateSequenceIdColours();
443 // otherwise construct the alignFrame
445 if (source instanceof ComplexAlignFile)
447 HiddenColumns colSel = ((ComplexAlignFile) source)
449 SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
450 .getHiddenSequences();
451 String colourSchemeName = ((ComplexAlignFile) source)
452 .getGlobalColourScheme();
453 FeaturesDisplayedI fd = ((ComplexAlignFile) source)
454 .getDisplayedFeatures();
455 alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
456 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
457 alignFrame.getViewport().setFeaturesDisplayed(fd);
458 alignFrame.getViewport().setShowSequenceFeatures(
459 ((ComplexAlignFile) source).isShowSeqFeatures());
460 ColourSchemeI cs = ColourSchemeMapper
461 .getJalviewColourScheme(colourSchemeName, al);
464 alignFrame.changeColour(cs);
469 alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
470 AlignFrame.DEFAULT_HEIGHT);
471 if (source instanceof FeaturesSourceI)
473 alignFrame.getViewport().setShowSequenceFeatures(true);
476 // add metadata and update ui
477 if (!(protocol == DataSourceType.PASTE))
479 alignFrame.setFileName(file, format);
481 if (proxyColourScheme != null)
483 alignFrame.getViewport()
484 .applyFeaturesStyle(proxyColourScheme);
486 alignFrame.statusBar.setText(MessageManager.formatMessage(
487 "label.successfully_loaded_file", new String[]
492 // add the window to the GUI
493 // note - this actually should happen regardless of raiseGUI
494 // status in Jalview 3
495 // TODO: define 'virtual desktop' for benefit of headless scripts
496 // that perform queries to find the 'current working alignment'
497 Desktop.addInternalFrame(alignFrame, title,
498 AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
503 alignFrame.setMaximum(jalview.bin.Cache
504 .getDefault("SHOW_FULLSCREEN", false));
505 } catch (java.beans.PropertyVetoException ex)
512 if (Desktop.instance != null)
514 Desktop.instance.stopLoading();
517 final String errorMessage = MessageManager.getString(
518 "label.couldnt_load_file") + " " + title + "\n" + error;
519 // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
521 if (raiseGUI && Desktop.desktop != null)
523 javax.swing.SwingUtilities.invokeLater(new Runnable()
528 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
531 .getString("label.error_loading_file"),
532 JvOptionPane.WARNING_MESSAGE);
538 System.err.println(errorMessage);
543 updateRecentlyOpened();
545 } catch (Exception er)
547 System.err.println("Exception whilst opening file '" + file);
548 er.printStackTrace();
551 javax.swing.SwingUtilities.invokeLater(new Runnable()
556 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
557 MessageManager.formatMessage(
558 "label.problems_opening_file", new String[]
560 MessageManager.getString("label.file_open_error"),
561 JvOptionPane.WARNING_MESSAGE);
566 } catch (OutOfMemoryError er)
569 er.printStackTrace();
573 javax.swing.SwingUtilities.invokeLater(new Runnable()
578 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
579 MessageManager.formatMessage(
580 "warn.out_of_memory_loading_file", new String[]
582 MessageManager.getString("label.out_of_memory"),
583 JvOptionPane.WARNING_MESSAGE);
587 System.err.println("Out of memory loading file " + file + "!!");
590 loadtime += System.currentTimeMillis();
591 // TODO: Estimate percentage of memory used by a newly loaded alignment -
592 // warn if more memory will be needed to work with it
595 - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference
600 if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
602 if (alignFrame != null)
604 AlignmentI al = alignFrame.getViewport().getAlignment();
606 System.out.println("Loaded '" + title + "' in "
607 + (loadtime / 1000.0) + "s, took an additional "
608 + (1.0 * memused / (1024.0 * 1024.0)) + " MB ("
609 + al.getHeight() + " seqs by " + al.getWidth() + " cols)");
613 // report that we didn't load anything probably due to an out of memory
615 System.out.println("Failed to load '" + title + "' in "
616 + (loadtime / 1000.0) + "s, took an additional "
617 + (1.0 * memused / (1024.0 * 1024.0))
618 + " MB (alignment is null)");
621 // remove the visual delay indicator
622 if (Desktop.instance != null)
624 Desktop.instance.stopLoading();
630 * This method creates the file -
631 * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied
632 * file name and extension
635 * the name of the temp file to be created
637 * the extension of the temp file to be created
640 private static String createNamedJvTempFile(String fileName,
641 String extension) throws IOException
643 String seprator = System.getProperty("file.separator");
644 String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview"
645 + seprator + System.currentTimeMillis();
646 File tempStructFile = new File(
647 jvTempDir + seprator + fileName + "." + extension);
648 tempStructFile.mkdirs();
649 return tempStructFile.toString();