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 java.util.Locale;
25 import jalview.api.AlignExportSettingsI;
26 import jalview.api.AlignmentViewPanel;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.AlignmentView;
31 import jalview.datamodel.PDBEntry.Type;
32 import jalview.datamodel.SequenceI;
33 import jalview.ext.jmol.JmolParser;
34 import jalview.structure.StructureImportSettings;
35 import jalview.util.Platform;
38 import java.io.IOException;
39 import java.io.InputStream;
40 import java.util.List;
43 * A low level class for alignment and feature IO with alignment formatting
44 * methods used by both applet and application for generating flat alignment
45 * files. It also holds the lists of magic format names that the applet and
46 * application will allow the user to read or write files with.
51 public class AppletFormatAdapter
53 private AlignmentViewPanel viewpanel;
56 * add jalview-derived non-secondary structure annotation from PDB structure
58 boolean annotFromStructure = false;
61 * add secondary structure from PDB data with built-in algorithms
63 boolean localSecondaryStruct = false;
66 * process PDB data with web services
68 boolean serviceSecondaryStruct = false;
70 private AlignmentFileReaderI alignFile = null;
75 * character used to write newlines
77 protected String newline = System.getProperty("line.separator");
79 private AlignExportSettingsI exportSettings;
81 private File selectedFile;
83 public static String INVALID_CHARACTERS = "Contains invalid characters";
86 * Returns an error message with a list of supported readable file formats
90 public static String getSupportedFormats()
92 return "Formats currently supported are\n"
93 + prettyPrint(FileFormats.getInstance().getReadableFormats());
96 public AppletFormatAdapter()
100 public AppletFormatAdapter(AlignmentViewPanel viewpanel)
102 this.viewpanel = viewpanel;
105 public AppletFormatAdapter(AlignmentViewPanel alignPanel,
106 AlignExportSettingsI settings)
108 viewpanel = alignPanel;
109 exportSettings = settings;
113 * Formats a grammatically correct(ish) list consisting of the given objects
118 public static String prettyPrint(List<? extends Object> things)
120 StringBuffer list = new StringBuffer();
121 for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
123 list.append(things.get(i).toString());
126 // could i18n 'and' here
127 list.append(" and " + things.get(things.size() - 1).toString() + ".");
128 return list.toString();
131 public void setNewlineString(String nl)
136 public String getNewlineString()
142 * Constructs the correct filetype parser for a characterised datasource
152 public AlignmentI readFile(String file, DataSourceType sourceType,
153 FileFormatI fileFormat) throws IOException
155 return readFile(null, file, sourceType, fileFormat);
158 public AlignmentI readFile(File selectedFile, String file, DataSourceType sourceType,
159 FileFormatI fileFormat) throws IOException
162 this.selectedFile = selectedFile;
163 inFile = (selectedFile == null ? file : selectedFile.getPath());
166 if (fileFormat.isStructureFile())
168 String structureParser = StructureImportSettings
169 .getDefaultPDBFileParser();
170 boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
171 StructureImportSettings.StructureParser.JMOL_PARSER
173 StructureImportSettings.addSettings(annotFromStructure,
174 localSecondaryStruct, serviceSecondaryStruct);
177 // needs a File option
178 alignFile = new JmolParser(selectedFile == null ? inFile : selectedFile, sourceType);
182 // todo is mc_view parsing obsolete yet? JAL-2120
183 StructureImportSettings.setShowSeqFeatures(true);
184 alignFile = new mc_view.PDBfile(annotFromStructure,
185 localSecondaryStruct, serviceSecondaryStruct, inFile,
188 ((StructureFile) alignFile).setDbRefType(
189 FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
191 else if (selectedFile != null) {
192 alignFile = fileFormat.getReader(new FileParse(selectedFile, sourceType));
195 // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
196 alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
198 return buildAlignmentFromFile();
199 } catch (Exception e)
202 System.err.println("Failed to read alignment using the '" + fileFormat
203 + "' reader.\n" + e);
205 if (e.getMessage() != null
206 && e.getMessage().startsWith(INVALID_CHARACTERS))
208 throw new IOException(e.getMessage());
211 // Finally test if the user has pasted just the sequence, no id
212 if (sourceType == DataSourceType.PASTE)
216 // Possible sequence is just residues with no label
217 alignFile = new FastaFile(">UNKNOWN\n" + inFile,
218 DataSourceType.PASTE);
219 return buildAlignmentFromFile();
221 } catch (Exception ex)
223 if (ex.toString().startsWith(INVALID_CHARACTERS))
225 throw new IOException(e.getMessage());
228 ex.printStackTrace();
231 if (FileFormat.Html.equals(fileFormat))
233 throw new IOException(e.getMessage());
236 throw new FileFormatException(getSupportedFormats());
240 * Constructs the correct filetype parser for an already open datasource
243 * an existing datasource
245 * File format of data that will be provided by datasource
249 public AlignmentI readFromFile(FileParse source, FileFormatI format)
252 this.inFile = source.getInFile();
253 DataSourceType type = source.dataSourceType;
256 if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
258 // TODO obtain config value from preference settings
259 boolean isParseWithJMOL = false;
262 StructureImportSettings.addSettings(annotFromStructure,
263 localSecondaryStruct, serviceSecondaryStruct);
264 alignFile = new JmolParser(source);
268 StructureImportSettings.setShowSeqFeatures(true);
269 alignFile = new mc_view.PDBfile(annotFromStructure,
270 localSecondaryStruct, serviceSecondaryStruct, source);
272 ((StructureFile) alignFile).setDbRefType(Type.PDB);
276 alignFile = format.getReader(source);
279 return buildAlignmentFromFile();
281 } catch (Exception e)
284 System.err.println("Failed to read alignment using the '" + format
285 + "' reader.\n" + e);
287 if (e.getMessage() != null
288 && e.getMessage().startsWith(INVALID_CHARACTERS))
290 throw new FileFormatException(e.getMessage());
293 // Finally test if the user has pasted just the sequence, no id
294 if (type == DataSourceType.PASTE)
298 // Possible sequence is just residues with no label
299 alignFile = new FastaFile(">UNKNOWN\n" + inFile,
300 DataSourceType.PASTE);
301 return buildAlignmentFromFile();
303 } catch (Exception ex)
305 if (ex.toString().startsWith(INVALID_CHARACTERS))
307 throw new IOException(e.getMessage());
310 ex.printStackTrace();
314 // If we get to this stage, the format was not supported
315 throw new FileFormatException(getSupportedFormats());
320 * boilerplate method to handle data from an AlignFile and construct a new
321 * alignment or import to an existing alignment
323 * @return AlignmentI instance ready to pass to a UI constructor
325 private AlignmentI buildAlignmentFromFile()
327 // Standard boilerplate for creating alignment from parser
328 // alignFile.configureForView(viewpanel);
330 AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
332 alignFile.addAnnotations(al);
334 alignFile.addGroups(al);
340 * create an alignment flatfile from a Jalview alignment view
345 * @param selectedOnly
346 * @return flatfile in a string
348 public String formatSequences(FileFormatI format, boolean jvsuffix,
349 AlignmentViewPanel ap, boolean selectedOnly)
352 AlignmentView selvew = ap.getAlignViewport()
353 .getAlignmentView(selectedOnly, false);
354 AlignmentI aselview = selvew
355 .getVisibleAlignment(ap.getAlignViewport().getGapCharacter());
356 List<AlignmentAnnotation> ala = (ap.getAlignViewport()
357 .getVisibleAlignmentAnnotation(selectedOnly));
360 for (AlignmentAnnotation aa : ala)
362 aselview.addAnnotation(aa);
366 return formatSequences(format, aselview, jvsuffix);
370 * Construct an output class for an alignment in a particular filetype TODO:
371 * allow caller to detect errors and warnings encountered when generating
375 * string name of alignment format
377 * the alignment to be written out
379 * passed to AlnFile class controls whether /START-END is added to
382 * @return alignment flat file contents
384 public String formatSequences(FileFormatI format, AlignmentI alignment,
389 AlignmentFileWriterI afile = format.getWriter(alignment);
391 afile.setNewlineString(newline);
392 afile.setExportSettings(exportSettings);
393 afile.configureForView(viewpanel);
395 // check whether we were given a specific alignment to export, rather than
396 // the one in the viewpanel
397 SequenceI[] seqs = null;
398 if (viewpanel == null || viewpanel.getAlignment() == null
399 || viewpanel.getAlignment() != alignment)
401 seqs = alignment.getSequencesArray();
405 seqs = viewpanel.getAlignment().getSequencesArray();
408 String afileresp = afile.print(seqs, jvsuffix);
409 if (afile.hasWarningMessage())
411 System.err.println("Warning raised when writing as " + format
412 + " : " + afile.getWarningMessage());
415 } catch (Exception e)
417 System.err.println("Failed to write alignment as a '"
418 + format.getName() + "' file\n");
427 * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
430 * BH 2018 allows File or String, and can return RELATIVE_URL
432 * @param dataObject File or String
433 * @return the protocol for the input data
435 public static DataSourceType checkProtocol(Object dataObject)
437 if(dataObject instanceof File)
439 return DataSourceType.FILE;
442 String data = dataObject.toString();
443 DataSourceType protocol = DataSourceType.PASTE;
444 String ft = data.toLowerCase(Locale.ROOT).trim();
445 if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
446 || ft.indexOf("file:") == 0)
448 protocol = DataSourceType.URL;
450 else if (Platform.isJS())
452 protocol = DataSourceType.RELATIVE_URL;
454 else if (new File(data).exists())
456 protocol = DataSourceType.FILE;
465 public static void main(String[] args)
468 while (i < args.length)
470 File f = new File(args[i]);
475 System.out.println("Reading file: " + f);
476 AppletFormatAdapter afa = new AppletFormatAdapter();
477 Runtime r = Runtime.getRuntime();
479 long memf = -r.totalMemory() + r.freeMemory();
480 long t1 = -System.currentTimeMillis();
481 AlignmentI al = afa.readFile(args[i], DataSourceType.FILE,
482 new IdentifyFile().identify(args[i],
483 DataSourceType.FILE));
484 t1 += System.currentTimeMillis();
486 memf += r.totalMemory() - r.freeMemory();
489 System.out.println("Alignment contains " + al.getHeight()
490 + " sequences and " + al.getWidth() + " columns.");
493 System.out.println(new AppletFormatAdapter()
494 .formatSequences(FileFormat.Fasta, al, true));
495 } catch (Exception e)
498 "Couln't format the alignment for output as a FASTA file.");
499 e.printStackTrace(System.err);
504 System.out.println("Couldn't read alignment");
506 System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
508 "Difference between free memory now and before is "
509 + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
510 } catch (Exception e)
512 System.err.println("Exception when dealing with " + i
513 + "'th argument: " + args[i] + "\n" + e);
518 System.err.println("Ignoring argument '" + args[i] + "' (" + i
519 + "'th)- not a readable file.");
526 * try to discover how to access the given file as a valid datasource that
527 * will be identified as the given type.
531 * @return protocol that yields the data parsable as the given type
533 public static DataSourceType resolveProtocol(String file,
536 return resolveProtocol(file, format, false);
539 public static DataSourceType resolveProtocol(String file,
540 FileFormatI format, boolean debug)
542 // TODO: test thoroughly!
543 DataSourceType protocol = null;
546 System.out.println("resolving datasource started with:\n>>file\n"
547 + file + ">>endfile");
550 // This might throw a security exception in certain browsers
551 // Netscape Communicator for instance.
555 InputStream is = System.getSecurityManager().getClass()
556 .getResourceAsStream("/" + file);
564 System.err.println("Resource '" + file + "' was "
565 + (rtn ? "" : "not") + " located by classloader.");
569 protocol = DataSourceType.CLASSLOADER;
572 } catch (Exception ex)
575 .println("Exception checking resources: " + file + " " + ex);
578 if (file.indexOf("://") > -1)
580 protocol = DataSourceType.URL;
584 // skipping codebase prepend check.
585 protocol = DataSourceType.FILE;
593 "Trying to get contents of resource as " + protocol + ":");
595 fp = new FileParse(file, protocol);
604 System.out.println("Successful.");
607 } catch (Exception e)
611 System.err.println("Exception when accessing content: " + e);
619 System.out.println("Accessing as paste.");
621 protocol = DataSourceType.PASTE;
625 fp = new FileParse(file, protocol);
630 } catch (Exception e)
632 System.err.println("Failed to access content as paste!");
649 FileFormatI idformat = new IdentifyFile().identify(file, protocol);
650 if (idformat == null)
654 System.out.println("Format not identified. Inaccessible file.");
660 System.out.println("Format identified as " + idformat
661 + "and expected as " + format);
663 if (idformat.equals(format))
667 System.out.println("Protocol identified as " + protocol);
676 .println("File deemed not accessible via " + protocol);
681 } catch (Exception e)
685 System.err.println("File deemed not accessible via " + protocol);
693 public AlignmentFileReaderI getAlignFile()