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.AlignExportSettingI;
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.structure.StructureViewSettings;
30 import jalview.util.MessageManager;
33 import java.io.IOException;
34 import java.io.InputStream;
35 import java.util.List;
38 * A low level class for alignment and feature IO with alignment formatting
39 * methods used by both applet and application for generating flat alignment
40 * files. It also holds the lists of magic format names that the applet and
41 * application will allow the user to read or write files with.
46 public class AppletFormatAdapter
48 private AlignmentViewPanel viewpanel;
50 public static String FILE = "File";
52 public static String URL = "URL";
54 public static String PASTE = "Paste";
56 public static String CLASSLOADER = "ClassLoader";
59 * add jalview-derived non-secondary structure annotation from PDB structure
61 boolean annotFromStructure = false;
64 * add secondary structure from PDB data with built-in algorithms
66 boolean localSecondaryStruct = false;
69 * process PDB data with web services
71 boolean serviceSecondaryStruct = false;
73 private AlignFile alignFile = null;
78 * character used to write newlines
80 protected String newline = System.getProperty("line.separator");
82 private AlignExportSettingI exportSettings;
85 * List of valid format strings used in the isValidFormat method
87 public static final String[] READABLE_FORMATS = new String[] { "BLC",
88 "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
89 "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
90 IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
93 * List of readable format file extensions by application in order
94 * corresponding to READABLE_FNAMES
96 public static final String[] READABLE_EXTENSIONS = new String[] {
97 "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
98 "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
99 ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT, "cif" };
102 * List of readable formats by application in order corresponding to
103 * READABLE_EXTENSIONS
105 public static final String[] READABLE_FNAMES = new String[] { "Fasta",
106 "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
107 PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.FeaturesFile,
108 "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
111 * List of valid format strings for use by callers of the formatSequences
114 public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
115 "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
116 PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
119 * List of extensions corresponding to file format types in WRITABLE_FNAMES
120 * that are writable by the application.
122 public static final String[] WRITABLE_EXTENSIONS = new String[] {
123 "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
124 "sto,stk", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
127 * List of writable formats by the application. Order must correspond with the
128 * WRITABLE_EXTENSIONS list of formats.
130 public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
131 "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
132 PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
134 public static String INVALID_CHARACTERS = "Contains invalid characters";
136 // TODO: make these messages dynamic
137 public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
138 + prettyPrint(READABLE_FORMATS);
140 public AppletFormatAdapter()
144 public AppletFormatAdapter(AlignmentViewPanel viewpanel)
146 this.viewpanel = viewpanel;
149 public AppletFormatAdapter(AlignmentViewPanel alignPanel,
150 AlignExportSettingI settings)
152 viewpanel = alignPanel;
153 exportSettings = settings;
159 * @return grammatically correct(ish) list consisting of els elements.
161 public static String prettyPrint(String[] els)
163 StringBuffer list = new StringBuffer();
164 for (int i = 0, iSize = els.length - 1; i < iSize; i++)
169 list.append(" and " + els[els.length - 1] + ".");
170 return list.toString();
173 public void setNewlineString(String nl)
178 public String getNewlineString()
184 * check that this format is valid for reading
187 * a format string to be compared with READABLE_FORMATS
188 * @return true if format is readable
190 public static final boolean isValidFormat(String format)
192 return isValidFormat(format, false);
196 * validate format is valid for IO
199 * a format string to be compared with either READABLE_FORMATS or
202 * when true, format is checked for containment in WRITEABLE_FORMATS
203 * @return true if format is valid
205 public static final boolean isValidFormat(String format,
212 boolean valid = false;
213 String[] format_list = (forwriting) ? WRITEABLE_FORMATS
215 for (String element : format_list)
217 if (element.equalsIgnoreCase(format))
227 * Constructs the correct filetype parser for a characterised datasource
234 * File format of data provided by datasource
236 * @return DOCUMENT ME!
238 public AlignmentI readFile(String inFile, String type, String format)
239 throws java.io.IOException
241 // TODO: generalise mapping between format string and io. class instances
242 // using Constructor.invoke reflection
243 this.inFile = inFile;
246 if (format.equals("FASTA"))
248 alignFile = new FastaFile(inFile, type);
250 else if (format.equals("MSF"))
252 alignFile = new MSFfile(inFile, type);
254 else if (format.equals("PileUp"))
256 alignFile = new PileUpfile(inFile, type);
258 else if (format.equals("CLUSTAL"))
260 alignFile = new ClustalFile(inFile, type);
262 else if (format.equals("BLC"))
264 alignFile = new BLCFile(inFile, type);
266 else if (format.equals("PIR"))
268 alignFile = new PIRFile(inFile, type);
270 else if (format.equals("PFAM"))
272 alignFile = new PfamFile(inFile, type);
274 else if (format.equals("JnetFile"))
276 alignFile = new JPredFile(inFile, type);
277 ((JPredFile) alignFile).removeNonSequences();
279 else if (format.equals("PDB"))
281 // TODO obtain config value from preference settings.
282 // Set value to 'true' to test PDB processing with Jmol: JAL-1213
283 boolean isParseWithJMOL = !StructureViewSettings
284 .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
287 StructureViewSettings.addSettings(annotFromStructure,
288 localSecondaryStruct, serviceSecondaryStruct);
289 alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
290 localSecondaryStruct, serviceSecondaryStruct, inFile,
295 StructureViewSettings.addSettings(annotFromStructure,
296 localSecondaryStruct, serviceSecondaryStruct);
297 StructureViewSettings.setShowSeqFeatures(true);
298 alignFile = new MCview.PDBfile(annotFromStructure,
299 localSecondaryStruct, serviceSecondaryStruct, inFile,
303 else if (format.equals("mmCIF"))
305 StructureViewSettings.addSettings(annotFromStructure,
306 localSecondaryStruct, serviceSecondaryStruct);
307 alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
308 localSecondaryStruct, serviceSecondaryStruct, inFile, type);
310 else if (format.equals("STH"))
312 alignFile = new StockholmFile(inFile, type);
314 else if (format.equals("SimpleBLAST"))
316 alignFile = new SimpleBlastFile(inFile, type);
318 else if (format.equals(PhylipFile.FILE_DESC))
320 alignFile = new PhylipFile(inFile, type);
322 else if (format.equals(JSONFile.FILE_DESC))
324 alignFile = new JSONFile(inFile, type);
326 else if (format.equals(HtmlFile.FILE_DESC))
328 alignFile = new HtmlFile(inFile, type);
330 else if (format.equals("RNAML"))
332 alignFile = new RnamlFile(inFile, type);
334 else if (format.equals(IdentifyFile.FeaturesFile))
336 alignFile = new FeaturesFile(true, inFile, type);
338 return buildAlignmentFrom(alignFile);
339 } catch (Exception e)
342 System.err.println("Failed to read alignment using the '" + format
343 + "' reader.\n" + e);
345 if (e.getMessage() != null
346 && e.getMessage().startsWith(INVALID_CHARACTERS))
348 throw new java.io.IOException(e.getMessage());
351 // Finally test if the user has pasted just the sequence, no id
352 if (type.equalsIgnoreCase("Paste"))
356 // Possible sequence is just residues with no label
357 alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
358 return buildAlignmentFrom(alignFile);
360 } catch (Exception ex)
362 if (ex.toString().startsWith(INVALID_CHARACTERS))
364 throw new java.io.IOException(e.getMessage());
367 ex.printStackTrace();
370 if (format.equalsIgnoreCase("HTML"))
372 throw new IOException(e.getMessage());
374 // If we get to this stage, the format was not supported
375 throw new java.io.IOException(SUPPORTED_FORMATS);
380 * Constructs the correct filetype parser for an already open datasource
383 * an existing datasource
385 * File format of data that will be provided by datasource
387 * @return DOCUMENT ME!
389 public AlignmentI readFromFile(FileParse source, String format)
390 throws java.io.IOException
392 // TODO: generalise mapping between format string and io. class instances
393 // using Constructor.invoke reflection
394 // This is exactly the same as the readFile method except we substitute
395 // 'inFile, type' with 'source'
396 this.inFile = source.getInFile();
397 String type = source.type;
400 if (format.equals("FASTA"))
402 alignFile = new FastaFile(source);
404 else if (format.equals("MSF"))
406 alignFile = new MSFfile(source);
408 else if (format.equals("PileUp"))
410 alignFile = new PileUpfile(source);
412 else if (format.equals("CLUSTAL"))
414 alignFile = new ClustalFile(source);
416 else if (format.equals("BLC"))
418 alignFile = new BLCFile(source);
420 else if (format.equals("PIR"))
422 alignFile = new PIRFile(source);
424 else if (format.equals("PFAM"))
426 alignFile = new PfamFile(source);
428 else if (format.equals("JnetFile"))
430 alignFile = new JPredFile(source);
431 ((JPredFile) alignFile).removeNonSequences();
433 else if (format.equals("PDB"))
435 // TODO obtain config value from preference settings
436 boolean isParseWithJMOL = false;
439 StructureViewSettings.addSettings(annotFromStructure,
440 localSecondaryStruct, serviceSecondaryStruct);
441 alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
442 localSecondaryStruct, serviceSecondaryStruct, source);
446 StructureViewSettings.setShowSeqFeatures(true);
447 alignFile = new MCview.PDBfile(annotFromStructure,
448 localSecondaryStruct, serviceSecondaryStruct, source);
451 else if (format.equals("mmCIF"))
453 StructureViewSettings.addSettings(annotFromStructure,
454 localSecondaryStruct, serviceSecondaryStruct);
455 alignFile = new jalview.ext.jmol.JmolParser(annotFromStructure,
456 localSecondaryStruct, serviceSecondaryStruct, source);
458 else if (format.equals("STH"))
460 alignFile = new StockholmFile(source);
462 else if (format.equals("RNAML"))
464 alignFile = new RnamlFile(source);
466 else if (format.equals("SimpleBLAST"))
468 alignFile = new SimpleBlastFile(source);
470 else if (format.equals(PhylipFile.FILE_DESC))
472 alignFile = new PhylipFile(source);
474 else if (format.equals(IdentifyFile.FeaturesFile))
476 alignFile = new FeaturesFile(inFile, type);
478 else if (format.equals(JSONFile.FILE_DESC))
480 alignFile = new JSONFile(source);
482 else if (format.equals(HtmlFile.FILE_DESC))
484 alignFile = new HtmlFile(source);
487 return buildAlignmentFrom(alignFile);
489 } catch (Exception e)
492 System.err.println("Failed to read alignment using the '" + format
493 + "' reader.\n" + e);
495 if (e.getMessage() != null
496 && e.getMessage().startsWith(INVALID_CHARACTERS))
498 throw new java.io.IOException(e.getMessage());
501 // Finally test if the user has pasted just the sequence, no id
502 if (type.equalsIgnoreCase("Paste"))
506 // Possible sequence is just residues with no label
507 alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
508 return buildAlignmentFrom(alignFile);
510 } catch (Exception ex)
512 if (ex.toString().startsWith(INVALID_CHARACTERS))
514 throw new java.io.IOException(e.getMessage());
517 ex.printStackTrace();
521 // If we get to this stage, the format was not supported
522 throw new java.io.IOException(SUPPORTED_FORMATS);
527 * boilerplate method to handle data from an AlignFile and construct a new
528 * alignment or import to an existing alignment
531 * @return AlignmentI instance ready to pass to a UI constructor
533 private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
535 // Standard boilerplate for creating alignment from parser
536 // alignFile.configureForView(viewpanel);
538 AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
540 alignFile.addAnnotations(al);
542 alignFile.addGroups(al);
548 * create an alignment flatfile from a Jalview alignment view
553 * @param selectedOnly
554 * @return flatfile in a string
556 public String formatSequences(String format, boolean jvsuffix,
557 AlignmentViewPanel ap, boolean selectedOnly)
560 AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
561 selectedOnly, false);
562 AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
564 List<AlignmentAnnotation> ala = (ap.getAlignViewport()
565 .getVisibleAlignmentAnnotation(selectedOnly));
568 for (AlignmentAnnotation aa : ala)
570 aselview.addAnnotation(aa);
574 return formatSequences(format, aselview, jvsuffix);
578 * Construct an output class for an alignment in a particular filetype TODO:
579 * allow caller to detect errors and warnings encountered when generating
583 * string name of alignment format
585 * the alignment to be written out
587 * passed to AlnFile class controls whether /START-END is added to
590 * @return alignment flat file contents
592 public String formatSequences(String format, AlignmentI alignment,
597 AlignFile afile = null;
598 if (format.equalsIgnoreCase("FASTA"))
600 afile = new FastaFile();
602 else if (format.equalsIgnoreCase("MSF"))
604 afile = new MSFfile();
606 else if (format.equalsIgnoreCase("PileUp"))
608 afile = new PileUpfile();
610 else if (format.equalsIgnoreCase("CLUSTAL"))
612 afile = new ClustalFile();
614 else if (format.equalsIgnoreCase("BLC"))
616 afile = new BLCFile();
618 else if (format.equalsIgnoreCase("PIR"))
620 afile = new PIRFile();
622 else if (format.equalsIgnoreCase("PFAM"))
624 afile = new PfamFile();
626 else if (format.equalsIgnoreCase("STH"))
628 afile = new StockholmFile(alignment);
630 else if (format.equalsIgnoreCase("AMSA"))
632 afile = new AMSAFile(alignment);
634 else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
636 afile = new PhylipFile();
638 else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
640 afile = new JSONFile();
642 else if (format.equalsIgnoreCase("RNAML"))
644 afile = new RnamlFile();
651 .getString("error.implementation_error_unknown_file_format_string"));
654 afile.setNewlineString(newline);
655 afile.addJVSuffix(jvsuffix);
656 afile.setExportSettings(exportSettings);
657 afile.configureForView(viewpanel);
659 // check whether we were given a specific alignment to export, rather than
660 // the one in the viewpanel
661 if (viewpanel == null || viewpanel.getAlignment() == null
662 || viewpanel.getAlignment() != alignment)
664 afile.setSeqs(alignment.getSequencesArray());
668 afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
671 String afileresp = afile.print();
672 if (afile.hasWarningMessage())
674 System.err.println("Warning raised when writing as " + format
675 + " : " + afile.getWarningMessage());
678 } catch (Exception e)
680 System.err.println("Failed to write alignment as a '" + format
688 public static String checkProtocol(String file)
690 String protocol = FILE;
691 String ft = file.toLowerCase().trim();
692 if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
693 || ft.indexOf("file:") == 0)
700 public static void main(String[] args)
703 while (i < args.length)
705 File f = new File(args[i]);
710 System.out.println("Reading file: " + f);
711 AppletFormatAdapter afa = new AppletFormatAdapter();
712 Runtime r = Runtime.getRuntime();
714 long memf = -r.totalMemory() + r.freeMemory();
715 long t1 = -System.currentTimeMillis();
716 AlignmentI al = afa.readFile(args[i], FILE,
717 new IdentifyFile().identify(args[i], FILE));
718 t1 += System.currentTimeMillis();
720 memf += r.totalMemory() - r.freeMemory();
723 System.out.println("Alignment contains " + al.getHeight()
724 + " sequences and " + al.getWidth() + " columns.");
727 System.out.println(new AppletFormatAdapter().formatSequences(
729 } catch (Exception e)
732 .println("Couln't format the alignment for output as a FASTA file.");
733 e.printStackTrace(System.err);
738 System.out.println("Couldn't read alignment");
740 System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
742 .println("Difference between free memory now and before is "
743 + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
744 } catch (Exception e)
746 System.err.println("Exception when dealing with " + i
747 + "'th argument: " + args[i] + "\n" + e);
752 System.err.println("Ignoring argument '" + args[i] + "' (" + i
753 + "'th)- not a readable file.");
760 * try to discover how to access the given file as a valid datasource that
761 * will be identified as the given type.
765 * @return protocol that yields the data parsable as the given type
767 public static String resolveProtocol(String file, String format)
769 return resolveProtocol(file, format, false);
772 public static String resolveProtocol(String file, String format,
775 // TODO: test thoroughly!
776 String protocol = null;
779 System.out.println("resolving datasource started with:\n>>file\n"
780 + file + ">>endfile");
783 // This might throw a security exception in certain browsers
784 // Netscape Communicator for instance.
788 InputStream is = System.getSecurityManager().getClass()
789 .getResourceAsStream("/" + file);
797 System.err.println("Resource '" + file + "' was "
798 + (rtn ? "" : "not") + " located by classloader.");
803 protocol = AppletFormatAdapter.CLASSLOADER;
806 } catch (Exception ex)
809 .println("Exception checking resources: " + file + " " + ex);
812 if (file.indexOf("://") > -1)
814 protocol = AppletFormatAdapter.URL;
818 // skipping codebase prepend check.
819 protocol = AppletFormatAdapter.FILE;
826 System.out.println("Trying to get contents of resource as "
829 fp = new FileParse(file, protocol);
838 System.out.println("Successful.");
841 } catch (Exception e)
845 System.err.println("Exception when accessing content: " + e);
853 System.out.println("Accessing as paste.");
855 protocol = AppletFormatAdapter.PASTE;
859 fp = new FileParse(file, protocol);
864 } catch (Exception e)
866 System.err.println("Failed to access content as paste!");
875 if (format == null || format.length() == 0)
883 String idformat = new jalview.io.IdentifyFile().identify(file,
885 if (idformat == null)
889 System.out.println("Format not identified. Inaccessible file.");
895 System.out.println("Format identified as " + idformat
896 + "and expected as " + format);
898 if (idformat.equals(format))
902 System.out.println("Protocol identified as " + protocol);
911 .println("File deemed not accessible via " + protocol);
916 } catch (Exception e)
920 System.err.println("File deemed not accessible via " + protocol);
930 public AlignFile getAlignFile()
935 public void setAlignFile(AlignFile alignFile)
937 this.alignFile = alignFile;