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.AlignExportSettingsI;
24 import jalview.api.AlignmentViewPanel;
25 import jalview.datamodel.Alignment;
26 import jalview.datamodel.AlignmentAnnotation;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.AlignmentView;
29 import jalview.datamodel.PDBEntry.Type;
30 import jalview.datamodel.SequenceI;
31 import jalview.ext.jmol.JmolParser;
32 import jalview.structure.StructureImportSettings;
33 import jalview.util.Platform;
36 import java.io.IOException;
37 import java.io.InputStream;
38 import java.util.List;
41 * A low level class for alignment and feature IO with alignment formatting
42 * methods used by both applet and application for generating flat alignment
43 * files. It also holds the lists of magic format names that the applet and
44 * application will allow the user to read or write files with.
49 public class AppletFormatAdapter
51 private AlignmentViewPanel viewpanel;
54 * add jalview-derived non-secondary structure annotation from PDB structure
56 boolean annotFromStructure = false;
59 * add secondary structure from PDB data with built-in algorithms
61 boolean localSecondaryStruct = false;
64 * process PDB data with web services
66 boolean serviceSecondaryStruct = false;
68 private AlignmentFileReaderI alignFile = null;
73 * character used to write newlines
75 protected String newline = System.getProperty("line.separator");
77 private AlignExportSettingsI exportSettings;
79 private File selectedFile;
81 public static String INVALID_CHARACTERS = "Contains invalid characters";
84 * Returns an error message with a list of supported readable file formats
88 public static String getSupportedFormats()
90 return "Formats currently supported are\n"
91 + prettyPrint(FileFormats.getInstance().getReadableFormats());
94 public AppletFormatAdapter()
98 public AppletFormatAdapter(AlignmentViewPanel viewpanel)
100 this.viewpanel = viewpanel;
103 public AppletFormatAdapter(AlignmentViewPanel alignPanel,
104 AlignExportSettingsI settings)
106 viewpanel = alignPanel;
107 exportSettings = settings;
111 * Formats a grammatically correct(ish) list consisting of the given objects
116 public static String prettyPrint(List<? extends Object> things)
118 StringBuffer list = new StringBuffer();
119 for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
121 list.append(things.get(i).toString());
124 // could i18n 'and' here
125 list.append(" and " + things.get(things.size() - 1).toString() + ".");
126 return list.toString();
129 public void setNewlineString(String nl)
134 public String getNewlineString()
140 * Constructs the correct filetype parser for a characterised datasource
150 public AlignmentI readFile(String file, DataSourceType sourceType,
151 FileFormatI fileFormat) throws IOException
153 return readFile(null, file, sourceType, fileFormat);
156 public AlignmentI readFile(File selectedFile, String file, DataSourceType sourceType,
157 FileFormatI fileFormat) throws IOException
160 this.selectedFile = selectedFile;
161 inFile = (selectedFile == null ? file : selectedFile.getPath());
164 if (fileFormat.isStructureFile())
166 String structureParser = StructureImportSettings
167 .getDefaultPDBFileParser();
168 boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
169 StructureImportSettings.StructureParser.JMOL_PARSER
171 StructureImportSettings.addSettings(annotFromStructure,
172 localSecondaryStruct, serviceSecondaryStruct);
175 // needs a File option
176 alignFile = new JmolParser(selectedFile == null ? inFile : selectedFile, sourceType);
180 // todo is mc_view parsing obsolete yet? JAL-2120
181 StructureImportSettings.setShowSeqFeatures(true);
182 alignFile = new mc_view.PDBfile(annotFromStructure,
183 localSecondaryStruct, serviceSecondaryStruct, inFile,
186 ((StructureFile) alignFile).setDbRefType(
187 FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
189 else if (selectedFile != null) {
190 alignFile = fileFormat.getReader(new FileParse(selectedFile, sourceType));
193 // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
194 alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
196 return buildAlignmentFromFile();
197 } catch (Exception e)
200 System.err.println("Failed to read alignment using the '" + fileFormat
201 + "' reader.\n" + e);
203 if (e.getMessage() != null
204 && e.getMessage().startsWith(INVALID_CHARACTERS))
206 throw new IOException(e.getMessage());
209 // Finally test if the user has pasted just the sequence, no id
210 if (sourceType == DataSourceType.PASTE)
214 // Possible sequence is just residues with no label
215 alignFile = new FastaFile(">UNKNOWN\n" + inFile,
216 DataSourceType.PASTE);
217 return buildAlignmentFromFile();
219 } catch (Exception ex)
221 if (ex.toString().startsWith(INVALID_CHARACTERS))
223 throw new IOException(e.getMessage());
226 ex.printStackTrace();
229 if (FileFormat.Html.equals(fileFormat))
231 throw new IOException(e.getMessage());
234 throw new FileFormatException(getSupportedFormats());
238 * Constructs the correct filetype parser for an already open datasource
241 * an existing datasource
243 * File format of data that will be provided by datasource
247 public AlignmentI readFromFile(FileParse source, FileFormatI format)
250 this.inFile = source.getInFile();
251 DataSourceType type = source.dataSourceType;
254 if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
256 // TODO obtain config value from preference settings
257 boolean isParseWithJMOL = false;
260 StructureImportSettings.addSettings(annotFromStructure,
261 localSecondaryStruct, serviceSecondaryStruct);
262 alignFile = new JmolParser(source);
266 StructureImportSettings.setShowSeqFeatures(true);
267 alignFile = new mc_view.PDBfile(annotFromStructure,
268 localSecondaryStruct, serviceSecondaryStruct, source);
270 ((StructureFile) alignFile).setDbRefType(Type.PDB);
274 alignFile = format.getReader(source);
277 return buildAlignmentFromFile();
279 } catch (Exception e)
282 System.err.println("Failed to read alignment using the '" + format
283 + "' reader.\n" + e);
285 if (e.getMessage() != null
286 && e.getMessage().startsWith(INVALID_CHARACTERS))
288 throw new FileFormatException(e.getMessage());
291 // Finally test if the user has pasted just the sequence, no id
292 if (type == DataSourceType.PASTE)
296 // Possible sequence is just residues with no label
297 alignFile = new FastaFile(">UNKNOWN\n" + inFile,
298 DataSourceType.PASTE);
299 return buildAlignmentFromFile();
301 } catch (Exception ex)
303 if (ex.toString().startsWith(INVALID_CHARACTERS))
305 throw new IOException(e.getMessage());
308 ex.printStackTrace();
312 // If we get to this stage, the format was not supported
313 throw new FileFormatException(getSupportedFormats());
318 * boilerplate method to handle data from an AlignFile and construct a new
319 * alignment or import to an existing alignment
321 * @return AlignmentI instance ready to pass to a UI constructor
323 private AlignmentI buildAlignmentFromFile()
325 // Standard boilerplate for creating alignment from parser
326 // alignFile.configureForView(viewpanel);
328 AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
330 alignFile.addAnnotations(al);
332 alignFile.addGroups(al);
338 * create an alignment flatfile from a Jalview alignment view
343 * @param selectedOnly
344 * @return flatfile in a string
346 public String formatSequences(FileFormatI format, boolean jvsuffix,
347 AlignmentViewPanel ap, boolean selectedOnly)
350 AlignmentView selvew = ap.getAlignViewport()
351 .getAlignmentView(selectedOnly, false);
352 AlignmentI aselview = selvew
353 .getVisibleAlignment(ap.getAlignViewport().getGapCharacter());
354 List<AlignmentAnnotation> ala = (ap.getAlignViewport()
355 .getVisibleAlignmentAnnotation(selectedOnly));
358 for (AlignmentAnnotation aa : ala)
360 aselview.addAnnotation(aa);
364 return formatSequences(format, aselview, jvsuffix);
368 * Construct an output class for an alignment in a particular filetype TODO:
369 * allow caller to detect errors and warnings encountered when generating
373 * string name of alignment format
375 * the alignment to be written out
377 * passed to AlnFile class controls whether /START-END is added to
380 * @return alignment flat file contents
382 public String formatSequences(FileFormatI format, AlignmentI alignment,
387 AlignmentFileWriterI afile = format.getWriter(alignment);
389 afile.setNewlineString(newline);
390 afile.setExportSettings(exportSettings);
391 afile.configureForView(viewpanel);
393 // check whether we were given a specific alignment to export, rather than
394 // the one in the viewpanel
395 SequenceI[] seqs = null;
396 if (viewpanel == null || viewpanel.getAlignment() == null
397 || viewpanel.getAlignment() != alignment)
399 seqs = alignment.getSequencesArray();
403 seqs = viewpanel.getAlignment().getSequencesArray();
406 String afileresp = afile.print(seqs, jvsuffix);
407 if (afile.hasWarningMessage())
409 System.err.println("Warning raised when writing as " + format
410 + " : " + afile.getWarningMessage());
413 } catch (Exception e)
415 System.err.println("Failed to write alignment as a '"
416 + format.getName() + "' file\n");
425 * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
428 * BH 2018 allows File or String, and can return RELATIVE_URL
430 * @param dataObject File or String
431 * @return the protocol for the input data
433 public static DataSourceType checkProtocol(Object dataObject)
435 if(dataObject instanceof File)
437 return DataSourceType.FILE;
440 String data = dataObject.toString();
441 DataSourceType protocol = DataSourceType.PASTE;
442 String ft = data.toLowerCase().trim();
443 if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
444 || ft.indexOf("file:") == 0)
446 protocol = DataSourceType.URL;
448 else if (Platform.isJS())
450 protocol = DataSourceType.RELATIVE_URL;
452 else if (new File(data).exists())
454 protocol = DataSourceType.FILE;
463 public static void main(String[] args)
466 while (i < args.length)
468 File f = new File(args[i]);
473 System.out.println("Reading file: " + f);
474 AppletFormatAdapter afa = new AppletFormatAdapter();
475 Runtime r = Runtime.getRuntime();
477 long memf = -r.totalMemory() + r.freeMemory();
478 long t1 = -System.currentTimeMillis();
479 AlignmentI al = afa.readFile(args[i], DataSourceType.FILE,
480 new IdentifyFile().identify(args[i],
481 DataSourceType.FILE));
482 t1 += System.currentTimeMillis();
484 memf += r.totalMemory() - r.freeMemory();
487 System.out.println("Alignment contains " + al.getHeight()
488 + " sequences and " + al.getWidth() + " columns.");
491 System.out.println(new AppletFormatAdapter()
492 .formatSequences(FileFormat.Fasta, al, true));
493 } catch (Exception e)
496 "Couln't format the alignment for output as a FASTA file.");
497 e.printStackTrace(System.err);
502 System.out.println("Couldn't read alignment");
504 System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
506 "Difference between free memory now and before is "
507 + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
508 } catch (Exception e)
510 System.err.println("Exception when dealing with " + i
511 + "'th argument: " + args[i] + "\n" + e);
516 System.err.println("Ignoring argument '" + args[i] + "' (" + i
517 + "'th)- not a readable file.");
524 * try to discover how to access the given file as a valid datasource that
525 * will be identified as the given type.
529 * @return protocol that yields the data parsable as the given type
531 public static DataSourceType resolveProtocol(String file,
534 return resolveProtocol(file, format, false);
537 public static DataSourceType resolveProtocol(String file,
538 FileFormatI format, boolean debug)
540 // TODO: test thoroughly!
541 DataSourceType protocol = null;
544 System.out.println("resolving datasource started with:\n>>file\n"
545 + file + ">>endfile");
548 // This might throw a security exception in certain browsers
549 // Netscape Communicator for instance.
553 InputStream is = System.getSecurityManager().getClass()
554 .getResourceAsStream("/" + file);
562 System.err.println("Resource '" + file + "' was "
563 + (rtn ? "" : "not") + " located by classloader.");
567 protocol = DataSourceType.CLASSLOADER;
570 } catch (Exception ex)
573 .println("Exception checking resources: " + file + " " + ex);
576 if (file.indexOf("://") > -1)
578 protocol = DataSourceType.URL;
582 // skipping codebase prepend check.
583 protocol = DataSourceType.FILE;
591 "Trying to get contents of resource as " + protocol + ":");
593 fp = new FileParse(file, protocol);
602 System.out.println("Successful.");
605 } catch (Exception e)
609 System.err.println("Exception when accessing content: " + e);
617 System.out.println("Accessing as paste.");
619 protocol = DataSourceType.PASTE;
623 fp = new FileParse(file, protocol);
628 } catch (Exception e)
630 System.err.println("Failed to access content as paste!");
647 FileFormatI idformat = new IdentifyFile().identify(file, protocol);
648 if (idformat == null)
652 System.out.println("Format not identified. Inaccessible file.");
658 System.out.println("Format identified as " + idformat
659 + "and expected as " + format);
661 if (idformat.equals(format))
665 System.out.println("Protocol identified as " + protocol);
674 .println("File deemed not accessible via " + protocol);
679 } catch (Exception e)
683 System.err.println("File deemed not accessible via " + protocol);
691 public AlignmentFileReaderI getAlignFile()