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.InputStream;
33 import java.util.List;
36 * A low level class for alignment and feature IO with alignment formatting
37 * methods used by both applet and application for generating flat alignment
38 * files. It also holds the lists of magic format names that the applet and
39 * application will allow the user to read or write files with.
44 public class AppletFormatAdapter
46 private AlignmentViewPanel viewpanel;
48 public static String FILE = "File";
50 public static String URL = "URL";
52 public static String PASTE = "Paste";
54 public static String CLASSLOADER = "ClassLoader";
57 * add jalview-derived non-secondary structure annotation from PDB structure
59 boolean annotFromStructure = false;
62 * add secondary structure from PDB data with built-in algorithms
64 boolean localSecondaryStruct = false;
67 * process PDB data with web services
69 boolean serviceSecondaryStruct = false;
71 private AlignFile alignFile = null;
76 * character used to write newlines
78 protected String newline = System.getProperty("line.separator");
80 private AlignExportSettingI exportSettings;
83 * List of valid format strings used in the isValidFormat method
85 public static final String[] READABLE_FORMATS = new String[]
86 { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH",
87 "PDB", "JnetFile", "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File,
91 * List of readable format file extensions by application in order
92 * corresponding to READABLE_FNAMES
94 public static final String[] READABLE_EXTENSIONS = new String[]
95 { "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
96 "sto,stk", "xml,rnaml", PhylipFile.FILE_EXT, JSONFile.FILE_EXT,
98 "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[]
105 { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm",
106 "RNAML", PhylipFile.FILE_DESC, JSONFile.FILE_DESC, IdentifyFile.GFF3File, "Jalview",
107 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[]
114 { "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA",
115 "STH", 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[]
130 { "Fasta", "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();
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,
208 boolean valid = false;
209 String[] format_list = (forwriting) ? WRITEABLE_FORMATS
211 for (String element : format_list)
213 if (element.equalsIgnoreCase(format))
223 * Constructs the correct filetype parser for a characterised datasource
230 * File format of data provided by datasource
232 * @return DOCUMENT ME!
234 public AlignmentI readFile(String inFile, String type, String format)
235 throws java.io.IOException
237 // TODO: generalise mapping between format string and io. class instances
238 // using Constructor.invoke reflection
239 this.inFile = inFile;
242 if (format.equals("FASTA"))
244 alignFile = new FastaFile(inFile, type);
246 else if (format.equals("MSF"))
248 alignFile = new MSFfile(inFile, type);
250 else if (format.equals("PileUp"))
252 alignFile = new PileUpfile(inFile, type);
254 else if (format.equals("CLUSTAL"))
256 alignFile = new ClustalFile(inFile, type);
258 else if (format.equals("BLC"))
260 alignFile = new BLCFile(inFile, type);
262 else if (format.equals("PIR"))
264 alignFile = new PIRFile(inFile, type);
266 else if (format.equals("PFAM"))
268 alignFile = new PfamFile(inFile, type);
270 else if (format.equals("JnetFile"))
272 alignFile = new JPredFile(inFile, type);
273 ((JPredFile) alignFile).removeNonSequences();
275 else if (format.equals("PDB"))
277 alignFile = new MCview.PDBfile(annotFromStructure,
278 localSecondaryStruct, serviceSecondaryStruct, inFile, type);
279 // Uncomment to test Jmol data based PDB processing: JAL-1213
280 // afile = new jalview.ext.jmol.PDBFileWithJmol(inFile, type);
282 else if (format.equals("STH"))
284 alignFile = new StockholmFile(inFile, type);
286 else if (format.equals("SimpleBLAST"))
288 alignFile = new SimpleBlastFile(inFile, type);
290 else if (format.equals(PhylipFile.FILE_DESC))
292 alignFile = new PhylipFile(inFile, type);
294 else if (format.equals(JSONFile.FILE_DESC))
296 alignFile = new JSONFile(inFile, type);
298 else if (format.equals(HtmlFile.FILE_DESC))
300 alignFile = new HtmlFile(inFile, type);
302 else if (format.equals("RNAML"))
304 alignFile = new RnamlFile(inFile, type);
306 else if (format.equals(IdentifyFile.GFF3File))
308 alignFile = new Gff3File(inFile, type);
310 return buildAlignmentFrom(alignFile);
311 } catch (Exception e)
314 System.err.println("Failed to read alignment using the '" + format
315 + "' reader.\n" + e);
317 if (e.getMessage() != null
318 && e.getMessage().startsWith(INVALID_CHARACTERS))
320 throw new java.io.IOException(e.getMessage());
323 // Finally test if the user has pasted just the sequence, no id
324 if (type.equalsIgnoreCase("Paste"))
328 // Possible sequence is just residues with no label
329 alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
330 return buildAlignmentFrom(alignFile);
332 } catch (Exception ex)
334 if (ex.toString().startsWith(INVALID_CHARACTERS))
336 throw new java.io.IOException(e.getMessage());
339 ex.printStackTrace();
343 // If we get to this stage, the format was not supported
344 throw new java.io.IOException(SUPPORTED_FORMATS);
349 * Constructs the correct filetype parser for an already open datasource
352 * an existing datasource
354 * File format of data that will be provided by datasource
356 * @return DOCUMENT ME!
358 public AlignmentI readFromFile(FileParse source, String format)
359 throws java.io.IOException
361 // TODO: generalise mapping between format string and io. class instances
362 // using Constructor.invoke reflection
363 // This is exactly the same as the readFile method except we substitute
364 // 'inFile, type' with 'source'
365 this.inFile = source.getInFile();
366 String type = source.type;
369 if (format.equals("FASTA"))
371 alignFile = new FastaFile(source);
373 else if (format.equals("MSF"))
375 alignFile = new MSFfile(source);
377 else if (format.equals("PileUp"))
379 alignFile = new PileUpfile(source);
381 else if (format.equals("CLUSTAL"))
383 alignFile = new ClustalFile(source);
385 else if (format.equals("BLC"))
387 alignFile = new BLCFile(source);
389 else if (format.equals("PIR"))
391 alignFile = new PIRFile(source);
393 else if (format.equals("PFAM"))
395 alignFile = new PfamFile(source);
397 else if (format.equals("JnetFile"))
399 alignFile = new JPredFile(source);
400 ((JPredFile) alignFile).removeNonSequences();
402 else if (format.equals("PDB"))
404 alignFile = new MCview.PDBfile(annotFromStructure,
405 localSecondaryStruct, serviceSecondaryStruct, source);
407 else if (format.equals("STH"))
409 alignFile = new StockholmFile(source);
411 else if (format.equals("RNAML"))
413 alignFile = new RnamlFile(source);
415 else if (format.equals("SimpleBLAST"))
417 alignFile = new SimpleBlastFile(source);
419 else if (format.equals(PhylipFile.FILE_DESC))
421 alignFile = new PhylipFile(source);
423 else if (format.equals(IdentifyFile.GFF3File))
425 alignFile = new Gff3File(inFile, type);
427 else if (format.equals(JSONFile.FILE_DESC))
429 alignFile = new JSONFile(source);
431 else if (format.equals(HtmlFile.FILE_DESC))
433 alignFile = new HtmlFile(source);
436 return buildAlignmentFrom(alignFile);
438 } catch (Exception e)
441 System.err.println("Failed to read alignment using the '" + format
442 + "' reader.\n" + e);
444 if (e.getMessage() != null
445 && e.getMessage().startsWith(INVALID_CHARACTERS))
447 throw new java.io.IOException(e.getMessage());
450 // Finally test if the user has pasted just the sequence, no id
451 if (type.equalsIgnoreCase("Paste"))
455 // Possible sequence is just residues with no label
456 alignFile = new FastaFile(">UNKNOWN\n" + inFile, "Paste");
457 return buildAlignmentFrom(alignFile);
459 } catch (Exception ex)
461 if (ex.toString().startsWith(INVALID_CHARACTERS))
463 throw new java.io.IOException(e.getMessage());
466 ex.printStackTrace();
470 // If we get to this stage, the format was not supported
471 throw new java.io.IOException(SUPPORTED_FORMATS);
477 * boilerplate method to handle data from an AlignFile and construct a new
478 * alignment or import to an existing alignment
481 * @return AlignmentI instance ready to pass to a UI constructor
483 private AlignmentI buildAlignmentFrom(AlignFile alignFile2)
485 // Standard boilerplate for creating alignment from parser
486 alignFile.configureForView(viewpanel);
488 AlignmentI al = new Alignment(alignFile.getSeqsAsArray());
490 alignFile.addAnnotations(al);
492 alignFile.addGroups(al);
498 * create an alignment flatfile from a Jalview alignment view
502 * @param selectedOnly
503 * @return flatfile in a string
505 public String formatSequences(String format, boolean jvsuffix,
506 AlignmentViewPanel ap, boolean selectedOnly)
509 AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
510 selectedOnly, false);
511 AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
513 List<AlignmentAnnotation> ala = (ap.getAlignViewport()
514 .getVisibleAlignmentAnnotation(selectedOnly));
517 for (AlignmentAnnotation aa : ala)
519 aselview.addAnnotation(aa);
523 return formatSequences(format, aselview, jvsuffix);
527 * Construct an output class for an alignment in a particular filetype TODO:
528 * allow caller to detect errors and warnings encountered when generating
532 * string name of alignment format
534 * the alignment to be written out
536 * passed to AlnFile class controls whether /START-END is added to
539 * @return alignment flat file contents
541 public String formatSequences(String format, AlignmentI alignment,
546 AlignFile afile = null;
547 if (format.equalsIgnoreCase("FASTA"))
549 afile = new FastaFile();
551 else if (format.equalsIgnoreCase("MSF"))
553 afile = new MSFfile();
555 else if (format.equalsIgnoreCase("PileUp"))
557 afile = new PileUpfile();
559 else if (format.equalsIgnoreCase("CLUSTAL"))
561 afile = new ClustalFile();
563 else if (format.equalsIgnoreCase("BLC"))
565 afile = new BLCFile();
567 else if (format.equalsIgnoreCase("PIR"))
569 afile = new PIRFile();
571 else if (format.equalsIgnoreCase("PFAM"))
573 afile = new PfamFile();
575 else if (format.equalsIgnoreCase("STH"))
577 afile = new StockholmFile(alignment);
579 else if (format.equalsIgnoreCase("AMSA"))
581 afile = new AMSAFile(alignment);
583 else if (format.equalsIgnoreCase(PhylipFile.FILE_DESC))
585 afile = new PhylipFile();
587 else if (format.equalsIgnoreCase(JSONFile.FILE_DESC))
589 afile = new JSONFile();
591 else if (format.equalsIgnoreCase("RNAML"))
593 afile = new RnamlFile();
598 throw new Exception(MessageManager.getString("error.implementation_error_unknown_file_format_string"));
600 afile.setNewlineString(newline);
601 afile.addJVSuffix(jvsuffix);
603 afile.setExportSettings(exportSettings);
605 afile.configureForView(viewpanel);
607 // check whether we were given a specific alignment to export, rather than
608 // the one in the viewpanel
609 if (viewpanel == null || viewpanel.getAlignment() == null
610 || viewpanel.getAlignment() != alignment)
612 afile.setSeqs(alignment.getSequencesArray());
616 afile.setSeqs(viewpanel.getAlignment().getSequencesArray());
619 String afileresp = afile.print();
620 if (afile.hasWarningMessage())
622 System.err.println("Warning raised when writing as " + format
623 + " : " + afile.getWarningMessage());
626 } catch (Exception e)
628 System.err.println("Failed to write alignment as a '" + format
636 public static String checkProtocol(String file)
638 String protocol = FILE;
639 String ft = file.toLowerCase().trim();
640 if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
641 || ft.indexOf("file:") == 0)
648 public static void main(String[] args)
651 while (i < args.length)
653 File f = new File(args[i]);
658 System.out.println("Reading file: " + f);
659 AppletFormatAdapter afa = new AppletFormatAdapter();
660 Runtime r = Runtime.getRuntime();
662 long memf = -r.totalMemory() + r.freeMemory();
663 long t1 = -System.currentTimeMillis();
664 AlignmentI al = afa.readFile(args[i], FILE,
665 new IdentifyFile().Identify(args[i], FILE));
666 t1 += System.currentTimeMillis();
668 memf += r.totalMemory() - r.freeMemory();
671 System.out.println("Alignment contains " + al.getHeight()
672 + " sequences and " + al.getWidth() + " columns.");
675 System.out.println(new AppletFormatAdapter().formatSequences(
677 } catch (Exception e)
680 .println("Couln't format the alignment for output as a FASTA file.");
681 e.printStackTrace(System.err);
686 System.out.println("Couldn't read alignment");
688 System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
690 .println("Difference between free memory now and before is "
691 + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
692 } catch (Exception e)
694 System.err.println("Exception when dealing with " + i
695 + "'th argument: " + args[i] + "\n" + e);
700 System.err.println("Ignoring argument '" + args[i] + "' (" + i
701 + "'th)- not a readable file.");
708 * try to discover how to access the given file as a valid datasource that
709 * will be identified as the given type.
713 * @return protocol that yields the data parsable as the given type
715 public static String resolveProtocol(String file, String format)
717 return resolveProtocol(file, format, false);
720 public static String resolveProtocol(String file, String format,
723 // TODO: test thoroughly!
724 String protocol = null;
727 System.out.println("resolving datasource started with:\n>>file\n"
728 + file + ">>endfile");
731 // This might throw a security exception in certain browsers
732 // Netscape Communicator for instance.
736 InputStream is = System.getSecurityManager().getClass()
737 .getResourceAsStream("/" + file);
745 System.err.println("Resource '" + file + "' was "
746 + (rtn ? "" : "not") + " located by classloader.");
751 protocol = AppletFormatAdapter.CLASSLOADER;
754 } catch (Exception ex)
757 .println("Exception checking resources: " + file + " " + ex);
760 if (file.indexOf("://") > -1)
762 protocol = AppletFormatAdapter.URL;
766 // skipping codebase prepend check.
767 protocol = AppletFormatAdapter.FILE;
774 System.out.println("Trying to get contents of resource as "
777 fp = new FileParse(file, protocol);
786 System.out.println("Successful.");
789 } catch (Exception e)
793 System.err.println("Exception when accessing content: " + e);
801 System.out.println("Accessing as paste.");
803 protocol = AppletFormatAdapter.PASTE;
807 fp = new FileParse(file, protocol);
812 } catch (Exception e)
814 System.err.println("Failed to access content as paste!");
823 if (format == null || format.length() == 0)
831 String idformat = new jalview.io.IdentifyFile().Identify(file,
833 if (idformat == null)
837 System.out.println("Format not identified. Inaccessible file.");
843 System.out.println("Format identified as " + idformat
844 + "and expected as " + format);
846 if (idformat.equals(format))
850 System.out.println("Protocol identified as " + protocol);
859 .println("File deemed not accessible via " + protocol);
864 } catch (Exception e)
868 System.err.println("File deemed not accessible via " + protocol);
878 public AlignFile getAlignFile()
883 public void setAlignFile(AlignFile alignFile)
885 this.alignFile = alignFile;