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.util.MessageManager;
32 import java.io.IOException;
33 import java.io.InputStream;
34 import java.util.List;
37 * A low level class for alignment and feature IO with alignment formatting
38 * methods used by both applet and application for generating flat alignment
39 * files. It also holds the lists of magic format names that the applet and
40 * application will allow the user to read or write files with.
45 public class AppletFormatAdapter
47 private AlignmentViewPanel viewpanel;
49 public static String FILE = "File";
51 public static String URL = "URL";
53 public static String PASTE = "Paste";
55 public static String CLASSLOADER = "ClassLoader";
58 * add jalview-derived non-secondary structure annotation from PDB structure
60 boolean annotFromStructure = false;
63 * add secondary structure from PDB data with built-in algorithms
65 boolean localSecondaryStruct = false;
68 * process PDB data with web services
70 boolean serviceSecondaryStruct = false;
72 private AlignFile alignFile = null;
77 * character used to write newlines
79 protected String newline = System.getProperty("line.separator");
81 private AlignExportSettingI exportSettings;
84 * List of valid format strings used in the isValidFormat method
86 public static final String[] READABLE_FORMATS = new String[] { "BLC",
87 "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
88 "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC,
89 IdentifyFile.FeaturesFile, "HTML" };
92 * List of readable format file extensions by application in order
93 * corresponding to READABLE_FNAMES
95 public static final String[] READABLE_EXTENSIONS = new String[] {
96 "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
97 "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
98 ".gff2,gff3", "jar,jvp", HtmlFile.FILE_EXT };
101 * List of readable formats by application in order corresponding to
102 * READABLE_EXTENSIONS
104 public static final String[] READABLE_FNAMES = new String[] { "Fasta",
105 "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
106 PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.FeaturesFile,
107 "Jalview", HtmlFile.FILE_DESC };
110 * List of valid format strings for use by callers of the formatSequences
113 public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
114 "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
115 PhylipFile.FILE_DESC, JSONFile.FILE_DESC };
118 * List of extensions corresponding to file format types in WRITABLE_FNAMES
119 * that are writable by the application.
121 public static final String[] WRITABLE_EXTENSIONS = new String[] {
122 "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
123 "sto,stk", PhylipFile.FILE_EXT, JSONFile.FILE_EXT, "jvp" };
126 * List of writable formats by the application. Order must correspond with the
127 * WRITABLE_EXTENSIONS list of formats.
129 public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
130 "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
131 PhylipFile.FILE_DESC, JSONFile.FILE_DESC, "Jalview" };
133 public static String INVALID_CHARACTERS = "Contains invalid characters";
135 // TODO: make these messages dynamic
136 public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
137 + prettyPrint(READABLE_FORMATS);
139 public AppletFormatAdapter()
143 public AppletFormatAdapter(AlignmentViewPanel viewpanel)
145 this.viewpanel = viewpanel;
148 public AppletFormatAdapter(AlignmentViewPanel alignPanel,
149 AlignExportSettingI settings)
151 viewpanel = alignPanel;
152 exportSettings = settings;
158 * @return grammatically correct(ish) list consisting of els elements.
160 public static String prettyPrint(String[] els)
162 StringBuffer list = new StringBuffer();
163 for (int i = 0, iSize = els.length - 1; i < iSize; i++)
168 list.append(" and " + els[els.length - 1] + ".");
169 return list.toString();
172 public void setNewlineString(String nl)
177 public String getNewlineString()
183 * check that this format is valid for reading
186 * a format string to be compared with READABLE_FORMATS
187 * @return true if format is readable
189 public static final boolean isValidFormat(String format)
191 return isValidFormat(format, false);
195 * validate format is valid for IO
198 * a format string to be compared with either READABLE_FORMATS or
201 * when true, format is checked for containment in WRITEABLE_FORMATS
202 * @return true if format is valid
204 public static final boolean isValidFormat(String format,
211 boolean valid = false;
212 String[] format_list = (forwriting) ? WRITEABLE_FORMATS
214 for (String element : format_list)
216 if (element.equalsIgnoreCase(format))
226 * Constructs the correct filetype parser for a characterised datasource
233 * File format of data provided by datasource
235 * @return DOCUMENT ME!
237 public AlignmentI readFile(String inFile, String type, String format)
238 throws java.io.IOException
240 // TODO: generalise mapping between format string and io. class instances
241 // using Constructor.invoke reflection
242 this.inFile = inFile;
245 if (format.equals("FASTA"))
247 alignFile = new FastaFile(inFile, type);
249 else if (format.equals("MSF"))
251 alignFile = new MSFfile(inFile, type);
253 else if (format.equals("PileUp"))
255 alignFile = new PileUpfile(inFile, type);
257 else if (format.equals("CLUSTAL"))
259 alignFile = new ClustalFile(inFile, type);
261 else if (format.equals("BLC"))
263 alignFile = new BLCFile(inFile, type);
265 else if (format.equals("PIR"))
267 alignFile = new PIRFile(inFile, type);
269 else if (format.equals("PFAM"))
271 alignFile = new PfamFile(inFile, type);
273 else if (format.equals("JnetFile"))
275 alignFile = new JPredFile(inFile, type);
276 ((JPredFile) alignFile).removeNonSequences();
278 else if (format.equals("PDB"))
280 alignFile = new MCview.PDBfile(annotFromStructure,
281 localSecondaryStruct, serviceSecondaryStruct, inFile, type);
282 // Uncomment to test Jmol data based PDB processing: JAL-1213
283 // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
285 else if (format.equals("STH"))
287 alignFile = new StockholmFile(inFile, type);
289 else if (format.equals("SimpleBLAST"))
291 alignFile = new SimpleBlastFile(inFile, type);
293 else if (format.equals(PhylipFile.FILE_DESC))
295 alignFile = new PhylipFile(inFile, type);
297 else if (format.equals(JSONFile.FILE_DESC))
299 alignFile = new JSONFile(inFile, type);
301 else if (format.equals(HtmlFile.FILE_DESC))
303 alignFile = new HtmlFile(inFile, type);
305 else if (format.equals("RNAML"))
307 alignFile = new RnamlFile(inFile, type);
309 else if (format.equals(IdentifyFile.FeaturesFile))
311 alignFile = new FeaturesFile(true, inFile, type);
313 return buildAlignmentFrom(alignFile);
314 } catch (Exception e)
317 System.err.println("Failed to read alignment using the '" + format
318 + "' reader.\n" + e);
320 if (e.getMessage() != null
321 && e.getMessage().startsWith(INVALID_CHARACTERS))
323 throw new java.io.IOException(e.getMessage());
326 // Finally test if the user has pasted just the sequence, no id
327 if (type.equalsIgnoreCase("Paste"))
331 // Possible sequence is just residues with no label
332 alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
333 return buildAlignmentFrom(alignFile);
335 } catch (Exception ex)
337 if (ex.toString().startsWith(INVALID_CHARACTERS))
339 throw new java.io.IOException(e.getMessage());
342 ex.printStackTrace();
345 if (format.equalsIgnoreCase("HTML"))
347 throw new IOException(e.getMessage());
349 // If we get to this stage, the format was not supported
350 throw new java.io.IOException(SUPPORTED_FORMATS);
355 * Constructs the correct filetype parser for an already open datasource
358 * an existing datasource
360 * File format of data that will be provided by datasource
362 * @return DOCUMENT ME!
364 public AlignmentI readFromFile(FileParse source, String format)
365 throws java.io.IOException
367 // TODO: generalise mapping between format string and io. class instances
368 // using Constructor.invoke reflection
369 // This is exactly the same as the readFile method except we substitute
370 // 'inFile, type' with 'source'
371 this.inFile = source.getInFile();
372 String type = source.type;
375 if (format.equals("FASTA"))
377 alignFile = new FastaFile(source);
379 else if (format.equals("MSF"))
381 alignFile = new MSFfile(source);
383 else if (format.equals("PileUp"))
385 alignFile = new PileUpfile(source);
387 else if (format.equals("CLUSTAL"))
389 alignFile = new ClustalFile(source);
391 else if (format.equals("BLC"))
393 alignFile = new BLCFile(source);
395 else if (format.equals("PIR"))
397 alignFile = new PIRFile(source);
399 else if (format.equals("PFAM"))
401 alignFile = new PfamFile(source);
403 else if (format.equals("JnetFile"))
405 alignFile = new JPredFile(source);
406 ((JPredFile) alignFile).removeNonSequences();
408 else if (format.equals("PDB"))
410 alignFile = new MCview.PDBfile(annotFromStructure,
411 localSecondaryStruct, serviceSecondaryStruct, source);
413 else if (format.equals("STH"))
415 alignFile = new StockholmFile(source);
417 else if (format.equals("RNAML"))
419 alignFile = new RnamlFile(source);
421 else if (format.equals("SimpleBLAST"))
423 alignFile = new SimpleBlastFile(source);
425 else if (format.equals(PhylipFile.FILE_DESC))
427 alignFile = new PhylipFile(source);
429 else if (format.equals(IdentifyFile.FeaturesFile))
431 // enforce 'parseImmediately' here:
432 alignFile = new FeaturesFile(true, inFile, type);
434 else if (format.equals(JSONFile.FILE_DESC))
436 alignFile = new JSONFile(source);
438 else if (format.equals(HtmlFile.FILE_DESC))
440 alignFile = new HtmlFile(source);
443 return buildAlignmentFrom(alignFile);
445 } catch (Exception e)
448 System.err.println("Failed to read alignment using the '" + format
449 + "' reader.\n" + e);
451 if (e.getMessage() != null
452 && e.getMessage().startsWith(INVALID_CHARACTERS))
454 throw new java.io.IOException(e.getMessage());
457 // Finally test if the user has pasted just the sequence, no id
458 if (type.equalsIgnoreCase("Paste"))
462 // Possible sequence is just residues with no label
463 alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
464 return buildAlignmentFrom(alignFile);
466 } catch (Exception ex)
468 if (ex.toString().startsWith(INVALID_CHARACTERS))
470 throw new java.io.IOException(e.getMessage());
473 ex.printStackTrace();
477 // If we get to this stage, the format was not supported
478 throw new java.io.IOException(SUPPORTED_FORMATS);
483 * boilerplate method to handle data from an AlignFile and construct a new
484 * alignment or import to an existing alignment
487 * @return AlignmentI instance ready to pass to a UI constructor
489 private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
491 // Standard boilerplate for creating alignment from parser
492 // alignFile.configureForView(viewpanel);
494 AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
496 alignFile.addAnnotations(al);
498 alignFile.addGroups(al);
504 * create an alignment flatfile from a Jalview alignment view
509 * @param selectedOnly
510 * @return flatfile in a string
512 public String formatSequences(String format, boolean jvsuffix,
513 AlignmentViewPanel ap, boolean selectedOnly)
516 AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
517 selectedOnly, false);
518 AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
520 List<AlignmentAnnotation> ala = (ap.getAlignViewport()
521 .getVisibleAlignmentAnnotation(selectedOnly));
524 for (AlignmentAnnotation aa : ala)
526 aselview.addAnnotation(aa);
530 return formatSequences(format, aselview, jvsuffix);
534 * Construct an output class for an alignment in a particular filetype TODO:
535 * allow caller to detect errors and warnings encountered when generating
539 * string name of alignment format
541 * the alignment to be written out
543 * passed to AlnFile class controls whether /START-END is added to
546 * @return alignment flat file contents
548 public String formatSequences(String format, AlignmentI alignment,
553 AlignFile afile = null;
554 if (format.equalsIgnoreCase("FASTA"))
556 afile = new FastaFile();
558 else if (format.equalsIgnoreCase("MSF"))
560 afile = new MSFfile();
562 else if (format.equalsIgnoreCase("PileUp"))
564 afile = new PileUpfile();
566 else if (format.equalsIgnoreCase("CLUSTAL"))
568 afile = new ClustalFile();
570 else if (format.equalsIgnoreCase("BLC"))
572 afile = new BLCFile();
574 else if (format.equalsIgnoreCase("PIR"))
576 afile = new PIRFile();
578 else if (format.equalsIgnoreCase("PFAM"))
580 afile = new PfamFile();
582 else if (format.equalsIgnoreCase("STH"))
584 afile = new StockholmFile(alignment);
586 else if (format.equalsIgnoreCase("AMSA"))
588 afile = new AMSAFile(alignment);
590 else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
592 afile = new PhylipFile();
594 else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
596 afile = new JSONFile();
598 else if (format.equalsIgnoreCase("RNAML"))
600 afile = new RnamlFile();
607 .getString("error.implementation_error_unknown_file_format_string"));
610 afile.setNewlineString(newline);
611 afile.addJVSuffix(jvsuffix);
612 afile.setExportSettings(exportSettings);
613 afile.configureForView(viewpanel);
615 // check whether we were given a specific alignment to export, rather than
616 // the one in the viewpanel
617 if (viewpanel == null || viewpanel.getAlignment() == null
618 || viewpanel.getAlignment() != alignment)
620 afile.setSeqs(alignment.getSequencesArray());
624 afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
627 String afileresp = afile.print();
628 if (afile.hasWarningMessage())
630 System.err.println("Warning raised when writing as " + format
631 + " : " + afile.getWarningMessage());
634 } catch (Exception e)
636 System.err.println("Failed to write alignment as a '" + format
644 public static String checkProtocol(String file)
646 String protocol = FILE;
647 String ft = file.toLowerCase().trim();
648 if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
649 || ft.indexOf("file:") == 0)
656 public static void main(String[] args)
659 while (i < args.length)
661 File f = new File(args[i]);
666 System.out.println("Reading file: " + f);
667 AppletFormatAdapter afa = new AppletFormatAdapter();
668 Runtime r = Runtime.getRuntime();
670 long memf = -r.totalMemory() + r.freeMemory();
671 long t1 = -System.currentTimeMillis();
672 AlignmentI al = afa.readFile(args[i], FILE,
673 new IdentifyFile().identify(args[i], FILE));
674 t1 += System.currentTimeMillis();
676 memf += r.totalMemory() - r.freeMemory();
679 System.out.println("Alignment contains " + al.getHeight()
680 + " sequences and " + al.getWidth() + " columns.");
683 System.out.println(new AppletFormatAdapter().formatSequences(
685 } catch (Exception e)
688 .println("Couln't format the alignment for output as a FASTA file.");
689 e.printStackTrace(System.err);
694 System.out.println("Couldn't read alignment");
696 System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
698 .println("Difference between free memory now and before is "
699 + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
700 } catch (Exception e)
702 System.err.println("Exception when dealing with " + i
703 + "'th argument: " + args[i] + "\n" + e);
708 System.err.println("Ignoring argument '" + args[i] + "' (" + i
709 + "'th)- not a readable file.");
716 * try to discover how to access the given file as a valid datasource that
717 * will be identified as the given type.
721 * @return protocol that yields the data parsable as the given type
723 public static String resolveProtocol(String file, String format)
725 return resolveProtocol(file, format, false);
728 public static String resolveProtocol(String file, String format,
731 // TODO: test thoroughly!
732 String protocol = null;
735 System.out.println("resolving datasource started with:\n>>file\n"
736 + file + ">>endfile");
739 // This might throw a security exception in certain browsers
740 // Netscape Communicator for instance.
744 InputStream is = System.getSecurityManager().getClass()
745 .getResourceAsStream("/" + file);
753 System.err.println("Resource '" + file + "' was "
754 + (rtn ? "" : "not") + " located by classloader.");
759 protocol = AppletFormatAdapter.CLASSLOADER;
762 } catch (Exception ex)
765 .println("Exception checking resources: " + file + " " + ex);
768 if (file.indexOf("://") > -1)
770 protocol = AppletFormatAdapter.URL;
774 // skipping codebase prepend check.
775 protocol = AppletFormatAdapter.FILE;
782 System.out.println("Trying to get contents of resource as "
785 fp = new FileParse(file, protocol);
794 System.out.println("Successful.");
797 } catch (Exception e)
801 System.err.println("Exception when accessing content: " + e);
809 System.out.println("Accessing as paste.");
811 protocol = AppletFormatAdapter.PASTE;
815 fp = new FileParse(file, protocol);
820 } catch (Exception e)
822 System.err.println("Failed to access content as paste!");
831 if (format == null || format.length() == 0)
839 String idformat = new jalview.io.IdentifyFile().identify(file,
841 if (idformat == null)
845 System.out.println("Format not identified. Inaccessible file.");
851 System.out.println("Format identified as " + idformat
852 + "and expected as " + format);
854 if (idformat.equals(format))
858 System.out.println("Protocol identified as " + protocol);
867 .println("File deemed not accessible via " + protocol);
872 } catch (Exception e)
876 System.err.println("File deemed not accessible via " + protocol);
886 public AlignFile getAlignFile()
891 public void setAlignFile(AlignFile alignFile)
893 this.alignFile = alignFile;