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.
24 import java.io.IOException;
25 import java.io.InputStream;
26 import java.util.List;
27 import java.util.Locale;
29 import jalview.api.AlignExportSettingsI;
30 import jalview.api.AlignmentViewPanel;
31 import jalview.datamodel.Alignment;
32 import jalview.datamodel.AlignmentAnnotation;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.AlignmentView;
35 import jalview.datamodel.PDBEntry.Type;
36 import jalview.datamodel.SequenceI;
37 import jalview.ext.jmol.JmolParser;
38 import jalview.structure.StructureImportSettings;
39 import jalview.util.Platform;
42 * A low level class for alignment and feature IO with alignment formatting
43 * methods used by both applet and application for generating flat alignment
44 * files. It also holds the lists of magic format names that the applet and
45 * application will allow the user to read or write files with.
50 public class AppletFormatAdapter
52 private AlignmentViewPanel viewpanel;
55 * add jalview-derived non-secondary structure annotation from PDB structure
57 boolean annotFromStructure = false;
60 * add secondary structure from PDB data with built-in algorithms
62 boolean localSecondaryStruct = false;
65 * process PDB data with web services
67 boolean serviceSecondaryStruct = false;
69 private AlignmentFileReaderI alignFile = null;
74 * character used to write newlines
76 protected String newline = System.getProperty("line.separator");
78 private AlignExportSettingsI exportSettings;
80 private File selectedFile;
82 public static String INVALID_CHARACTERS = "Contains invalid characters";
85 * Returns an error message with a list of supported readable file formats
89 public static String getSupportedFormats()
91 return "Formats currently supported are\n"
92 + prettyPrint(FileFormats.getInstance().getReadableFormats());
95 public AppletFormatAdapter()
99 public AppletFormatAdapter(AlignmentViewPanel viewpanel)
101 this.viewpanel = viewpanel;
104 public AppletFormatAdapter(AlignmentViewPanel alignPanel,
105 AlignExportSettingsI settings)
107 viewpanel = alignPanel;
108 exportSettings = settings;
112 * Formats a grammatically correct(ish) list consisting of the given objects
117 public static String prettyPrint(List<? extends Object> things)
119 StringBuffer list = new StringBuffer();
120 for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
122 list.append(things.get(i).toString());
125 // could i18n 'and' here
126 list.append(" and " + things.get(things.size() - 1).toString() + ".");
127 return list.toString();
130 public void setNewlineString(String nl)
135 public String getNewlineString()
141 * Constructs the correct filetype parser for a characterised datasource
151 public AlignmentI readFile(String file, DataSourceType sourceType,
152 FileFormatI fileFormat) throws IOException
154 return readFile(null, file, sourceType, fileFormat);
157 public AlignmentI readFile(File selectedFile, String file,
158 DataSourceType sourceType, FileFormatI fileFormat)
161 return readFile(selectedFile, file, sourceType, fileFormat, null);
164 public AlignmentI readFile(File selectedFile, String file,
165 DataSourceType sourceType, FileFormatI fileFormat,
166 StructureImportSettings.TFType tempfacType) throws IOException
169 this.selectedFile = selectedFile;
170 if (selectedFile != null)
172 this.inFile = selectedFile.getPath();
177 if (fileFormat.isStructureFile())
179 String structureParser = StructureImportSettings
180 .getDefaultPDBFileParser();
181 boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
182 StructureImportSettings.StructureParser.JMOL_PARSER
184 StructureImportSettings.addSettings(annotFromStructure,
185 localSecondaryStruct, serviceSecondaryStruct);
186 if (tempfacType != null)
188 StructureImportSettings.setTemperatureFactorType(tempfacType);
192 // needs a File option
193 alignFile = new JmolParser(
194 selectedFile == null ? inFile : selectedFile, sourceType,
195 StructureImportSettings.getTemperatureFactorType());
199 // todo is mc_view parsing obsolete yet? JAL-2120
200 StructureImportSettings.setShowSeqFeatures(true);
201 alignFile = new mc_view.PDBfile(annotFromStructure,
202 localSecondaryStruct, serviceSecondaryStruct, inFile,
205 ((StructureFile) alignFile).setDbRefType(
206 FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
208 else if (selectedFile != null)
210 alignFile = fileFormat
211 .getReader(new FileParse(selectedFile, sourceType));
215 // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
216 alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
218 return buildAlignmentFromFile();
219 } catch (Exception e)
222 System.err.println("Failed to read alignment using the '" + fileFormat
223 + "' reader.\n" + e);
225 if (e.getMessage() != null
226 && e.getMessage().startsWith(INVALID_CHARACTERS))
228 throw new IOException(e.getMessage());
231 // Finally test if the user has pasted just the sequence, no id
232 if (sourceType == DataSourceType.PASTE)
236 // Possible sequence is just residues with no label
237 alignFile = new FastaFile(">UNKNOWN\n" + inFile,
238 DataSourceType.PASTE);
239 return buildAlignmentFromFile();
241 } catch (Exception ex)
243 if (ex.toString().startsWith(INVALID_CHARACTERS))
245 throw new IOException(e.getMessage());
248 ex.printStackTrace();
251 if (FileFormat.Html.equals(fileFormat))
253 throw new IOException(e.getMessage());
256 throw new FileFormatException(getSupportedFormats());
260 * Constructs the correct filetype parser for an already open datasource
263 * an existing datasource
265 * File format of data that will be provided by datasource
269 public AlignmentI readFromFile(FileParse source, FileFormatI format)
272 this.inFile = source.getInFile();
273 DataSourceType type = source.dataSourceType;
276 if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
278 // TODO obtain config value from preference settings
279 boolean isParseWithJMOL = false;
282 StructureImportSettings.addSettings(annotFromStructure,
283 localSecondaryStruct, serviceSecondaryStruct);
284 alignFile = new JmolParser(source);
288 StructureImportSettings.setShowSeqFeatures(true);
289 alignFile = new mc_view.PDBfile(annotFromStructure,
290 localSecondaryStruct, serviceSecondaryStruct, source);
292 ((StructureFile) alignFile).setDbRefType(Type.PDB);
296 alignFile = format.getReader(source);
299 return buildAlignmentFromFile();
301 } catch (Exception e)
304 System.err.println("Failed to read alignment using the '" + format
305 + "' reader.\n" + e);
307 if (e.getMessage() != null
308 && e.getMessage().startsWith(INVALID_CHARACTERS))
310 throw new FileFormatException(e.getMessage());
313 // Finally test if the user has pasted just the sequence, no id
314 if (type == DataSourceType.PASTE)
318 // Possible sequence is just residues with no label
319 alignFile = new FastaFile(">UNKNOWN\n" + inFile,
320 DataSourceType.PASTE);
321 return buildAlignmentFromFile();
323 } catch (Exception ex)
325 if (ex.toString().startsWith(INVALID_CHARACTERS))
327 throw new IOException(e.getMessage());
330 ex.printStackTrace();
334 // If we get to this stage, the format was not supported
335 throw new FileFormatException(getSupportedFormats());
340 * boilerplate method to handle data from an AlignFile and construct a new
341 * alignment or import to an existing alignment
343 * @return AlignmentI instance ready to pass to a UI constructor
345 private AlignmentI buildAlignmentFromFile()
347 // Standard boilerplate for creating alignment from parser
348 // alignFile.configureForView(viewpanel);
350 AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
352 alignFile.addAnnotations(al);
354 alignFile.addGroups(al);
360 * create an alignment flatfile from a Jalview alignment view
365 * @param selectedOnly
366 * @return flatfile in a string
368 public String formatSequences(FileFormatI format, boolean jvsuffix,
369 AlignmentViewPanel ap, boolean selectedOnly)
372 AlignmentView selvew = ap.getAlignViewport()
373 .getAlignmentView(selectedOnly, false);
374 AlignmentI aselview = selvew
375 .getVisibleAlignment(ap.getAlignViewport().getGapCharacter());
376 List<AlignmentAnnotation> ala = (ap.getAlignViewport()
377 .getVisibleAlignmentAnnotation(selectedOnly));
380 for (AlignmentAnnotation aa : ala)
382 aselview.addAnnotation(aa);
386 return formatSequences(format, aselview, jvsuffix);
390 * Construct an output class for an alignment in a particular filetype TODO:
391 * allow caller to detect errors and warnings encountered when generating
395 * string name of alignment format
397 * the alignment to be written out
399 * passed to AlnFile class controls whether /START-END is added to
402 * @return alignment flat file contents
404 public String formatSequences(FileFormatI format, AlignmentI alignment,
409 AlignmentFileWriterI afile = format.getWriter(alignment);
411 afile.setNewlineString(newline);
412 afile.setExportSettings(exportSettings);
413 afile.configureForView(viewpanel);
415 // check whether we were given a specific alignment to export, rather than
416 // the one in the viewpanel
417 SequenceI[] seqs = null;
418 if (viewpanel == null || viewpanel.getAlignment() == null
419 || viewpanel.getAlignment() != alignment)
421 seqs = alignment.getSequencesArray();
425 seqs = viewpanel.getAlignment().getSequencesArray();
428 String afileresp = afile.print(seqs, jvsuffix);
429 if (afile.hasWarningMessage())
431 System.err.println("Warning raised when writing as " + format
432 + " : " + afile.getWarningMessage());
435 } catch (Exception e)
437 System.err.println("Failed to write alignment as a '"
438 + format.getName() + "' file\n");
446 * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
449 * BH 2018 allows File or String, and can return RELATIVE_URL
453 * @return the protocol for the input data
455 public static DataSourceType checkProtocol(Object dataObject)
457 if (dataObject instanceof File)
459 return DataSourceType.FILE;
462 String data = dataObject.toString();
463 DataSourceType protocol = DataSourceType.PASTE;
464 String ft = data.toLowerCase(Locale.ROOT).trim();
465 if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
466 || ft.indexOf("file:") == 0)
468 protocol = DataSourceType.URL;
470 else if (Platform.isJS())
472 protocol = DataSourceType.RELATIVE_URL;
474 else if (new File(data).exists())
476 protocol = DataSourceType.FILE;
485 public static void main(String[] args)
488 while (i < args.length)
490 File f = new File(args[i]);
495 System.out.println("Reading file: " + f);
496 AppletFormatAdapter afa = new AppletFormatAdapter();
497 Runtime r = Runtime.getRuntime();
499 long memf = -r.totalMemory() + r.freeMemory();
500 long t1 = -System.currentTimeMillis();
501 AlignmentI al = afa.readFile(args[i], DataSourceType.FILE,
502 new IdentifyFile().identify(args[i],
503 DataSourceType.FILE));
504 t1 += System.currentTimeMillis();
506 memf += r.totalMemory() - r.freeMemory();
509 System.out.println("Alignment contains " + al.getHeight()
510 + " sequences and " + al.getWidth() + " columns.");
513 System.out.println(new AppletFormatAdapter()
514 .formatSequences(FileFormat.Fasta, al, true));
515 } catch (Exception e)
518 "Couln't format the alignment for output as a FASTA file.");
519 e.printStackTrace(System.err);
524 System.out.println("Couldn't read alignment");
526 System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
528 "Difference between free memory now and before is "
529 + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
530 } catch (Exception e)
532 System.err.println("Exception when dealing with " + i
533 + "'th argument: " + args[i] + "\n" + e);
538 System.err.println("Ignoring argument '" + args[i] + "' (" + i
539 + "'th)- not a readable file.");
546 * try to discover how to access the given file as a valid datasource that
547 * will be identified as the given type.
551 * @return protocol that yields the data parsable as the given type
553 public static DataSourceType resolveProtocol(String file,
556 return resolveProtocol(file, format, false);
559 public static DataSourceType resolveProtocol(String file,
560 FileFormatI format, boolean debug)
562 // TODO: test thoroughly!
563 DataSourceType protocol = null;
566 System.out.println("resolving datasource started with:\n>>file\n"
567 + file + ">>endfile");
570 // This might throw a security exception in certain browsers
571 // Netscape Communicator for instance.
575 InputStream is = System.getSecurityManager().getClass()
576 .getResourceAsStream("/" + file);
584 System.err.println("Resource '" + file + "' was "
585 + (rtn ? "" : "not") + " located by classloader.");
589 protocol = DataSourceType.CLASSLOADER;
592 } catch (Exception ex)
595 .println("Exception checking resources: " + file + " " + ex);
598 if (file.indexOf("://") > -1)
600 protocol = DataSourceType.URL;
604 // skipping codebase prepend check.
605 protocol = DataSourceType.FILE;
613 "Trying to get contents of resource as " + protocol + ":");
615 fp = new FileParse(file, protocol);
624 System.out.println("Successful.");
627 } catch (Exception e)
631 System.err.println("Exception when accessing content: " + e);
639 System.out.println("Accessing as paste.");
641 protocol = DataSourceType.PASTE;
645 fp = new FileParse(file, protocol);
650 } catch (Exception e)
652 System.err.println("Failed to access content as paste!");
669 FileFormatI idformat = new IdentifyFile().identify(file, protocol);
670 if (idformat == null)
674 System.out.println("Format not identified. Inaccessible file.");
680 System.out.println("Format identified as " + idformat
681 + "and expected as " + format);
683 if (idformat.equals(format))
687 System.out.println("Protocol identified as " + protocol);
696 .println("File deemed not accessible via " + protocol);
701 } catch (Exception e)
705 System.err.println("File deemed not accessible via " + protocol);
713 public AlignmentFileReaderI getAlignFile()