4 import java.io.IOException;
5 import java.net.URISyntaxException;
6 import java.util.ArrayList;
7 import java.util.Arrays;
8 import java.util.Collections;
9 import java.util.EnumSet;
10 import java.util.HashMap;
11 import java.util.Iterator;
12 import java.util.List;
13 import java.util.Locale;
16 import jalview.analysis.AlignmentUtils;
17 import jalview.api.structures.JalviewStructureDisplayI;
18 import jalview.bin.argparser.Arg;
19 import jalview.bin.argparser.ArgParser;
20 import jalview.bin.argparser.ArgParser.Position;
21 import jalview.bin.argparser.ArgValue;
22 import jalview.bin.argparser.ArgValuesMap;
23 import jalview.bin.argparser.SubVals;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.SequenceI;
26 import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
27 import jalview.gui.AlignFrame;
28 import jalview.gui.AlignmentPanel;
29 import jalview.gui.AppJmol;
30 import jalview.gui.Desktop;
31 import jalview.gui.Preferences;
32 import jalview.gui.StructureChooser;
33 import jalview.gui.StructureViewer;
34 import jalview.gui.StructureViewer.ViewerType;
35 import jalview.io.AppletFormatAdapter;
36 import jalview.io.BackupFiles;
37 import jalview.io.BioJsHTMLOutput;
38 import jalview.io.DataSourceType;
39 import jalview.io.FileFormat;
40 import jalview.io.FileFormatException;
41 import jalview.io.FileFormatI;
42 import jalview.io.FileFormats;
43 import jalview.io.FileLoader;
44 import jalview.io.HtmlSvgOutput;
45 import jalview.io.IdentifyFile;
46 import jalview.io.NewickFile;
47 import jalview.structure.StructureImportSettings.TFType;
48 import jalview.structure.StructureSelectionManager;
49 import jalview.util.FileUtils;
50 import jalview.util.HttpUtils;
51 import jalview.util.ImageMaker;
52 import jalview.util.ImageMaker.TYPE;
53 import jalview.util.MessageManager;
54 import jalview.util.Platform;
55 import jalview.util.imagemaker.BitmapImageSizing;
61 private boolean headless;
63 private ArgParser argParser;
65 private Map<String, AlignFrame> afMap;
67 private boolean commandArgsProvided = false;
69 private boolean argsWereParsed = false;
71 public Commands(ArgParser argparser, boolean headless)
73 this(Desktop.instance, argparser, headless);
76 public Commands(Desktop d, ArgParser argparser, boolean h)
78 argParser = argparser;
81 afMap = new HashMap<>();
82 if (argparser != null)
84 processArgs(argparser, headless);
88 private boolean processArgs(ArgParser argparser, boolean h)
90 argParser = argparser;
92 boolean theseArgsWereParsed = false;
94 if (argParser != null && argParser.getLinkedIds() != null)
96 for (String id : argParser.getLinkedIds())
98 ArgValuesMap avm = argParser.getLinkedArgs(id);
99 theseArgsWereParsed = true;
100 theseArgsWereParsed &= processLinked(id);
101 processGroovyScript(id);
102 boolean processLinkedOkay = theseArgsWereParsed;
104 // wait around until alignFrame isn't busy
105 AlignFrame af=afMap.get(id);
106 while (af!=null && af.getViewport().isCalcInProgress())
110 } catch (Exception q) {};
113 theseArgsWereParsed &= processImages(id);
114 if (processLinkedOkay)
115 theseArgsWereParsed &= processOutput(id);
118 if (avm.getBoolean(Arg.CLOSE))
123 af.closeMenuItem_actionPerformed(true);
130 if (argParser.getBoolean(Arg.QUIT))
132 Jalview.getInstance().quit();
135 // carry on with jalview.bin.Jalview
136 argsWereParsed = theseArgsWereParsed;
137 return argsWereParsed;
140 public boolean commandArgsProvided()
142 return commandArgsProvided;
145 public boolean argsWereParsed()
147 return argsWereParsed;
150 protected boolean processUnlinked(String id)
152 return processLinked(id);
155 protected boolean processLinked(String id)
157 boolean theseArgsWereParsed = false;
158 ArgValuesMap avm = argParser.getLinkedArgs(id);
163 * // script to execute after all loading is completed one way or another String
164 * groovyscript = m.get(Arg.GROOVY) == null ? null :
165 * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
166 * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
167 * DataSourceType protocol = null;
169 if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
171 commandArgsProvided = true;
174 boolean first = true;
175 boolean progressBarSet = false;
177 // Combine the APPEND and OPEN files into one list, along with whether it
178 // was APPEND or OPEN
179 List<ArgValue> openAvList = new ArrayList<>();
180 openAvList.addAll(avm.getArgValueList(Arg.OPEN));
181 openAvList.addAll(avm.getArgValueList(Arg.APPEND));
182 // sort avlist based on av.getArgIndex()
183 Collections.sort(openAvList);
184 for (ArgValue av : openAvList)
187 SubVals sv = av.getSubVals();
188 String openFile = av.getValue();
189 if (openFile == null)
192 theseArgsWereParsed = true;
196 if (!headless && desktop != null)
198 desktop.setProgressBar(
199 MessageManager.getString(
200 "status.processing_commandline_args"),
201 progress = System.currentTimeMillis());
202 progressBarSet = true;
206 if (!Platform.isJS())
208 * ignore in JavaScript -- can't just file existence - could load it?
213 if (!HttpUtils.startsWithHttpOrHttps(openFile))
215 if (!(new File(openFile)).exists())
217 Console.warn("Can't find file '" + openFile + "'");
222 DataSourceType protocol = AppletFormatAdapter
223 .checkProtocol(openFile);
225 FileFormatI format = null;
228 format = new IdentifyFile().identify(openFile, protocol);
229 } catch (FileFormatException e1)
231 Console.error("Unknown file format for '" + openFile + "'");
235 // When to open a new AlignFrame
236 if (af == null || "true".equals(av.getSubVal("new"))
237 || a == Arg.OPEN || format == FileFormat.Jalview)
241 Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
246 "Opening '" + openFile + "' in new alignment frame");
247 FileLoader fileLoader = new FileLoader(!headless);
249 af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
253 boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
254 null, "WRAP_ALIGNMENT", false);
255 af.getCurrentView().setWrapAlignment(wrap);
258 String colour = ArgParser.getFromSubValArgOrPref(avm, av,
259 Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
262 af.changeColour_actionPerformed(colour);
263 Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
266 // Change alignment frame title
267 String title = ArgParser.getFromSubValArgOrPref(avm, av,
268 Arg.TITLE, sv, null, null, null);
272 Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
276 String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av,
278 if (featuresfile != null)
280 af.parseFeaturesFile(featuresfile,
281 AppletFormatAdapter.checkProtocol(featuresfile));
282 Jalview.testoutput(argParser, Arg.FEATURES,
283 "examples/testdata/plantfdx.features", featuresfile);
286 // Add annotations from file
287 String annotationsfile = ArgParser.getValueFromSubValOrArg(avm,
288 av, Arg.ANNOTATIONS, sv);
289 if (annotationsfile != null)
291 af.loadJalviewDataFile(annotationsfile, null, null, null);
292 Jalview.testoutput(argParser, Arg.ANNOTATIONS,
293 "examples/testdata/plantfdx.annotations",
297 // Set or clear the sortbytree flag
298 boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm,
302 af.getViewport().setSortByTree(true);
303 Jalview.testoutput(argParser, Arg.SORTBYTREE);
306 // Load tree from file
307 String treefile = ArgParser.getValueFromSubValOrArg(avm, av,
309 if (treefile != null)
313 NewickFile nf = new NewickFile(treefile,
314 AppletFormatAdapter.checkProtocol(treefile));
315 af.getViewport().setCurrentTree(
316 af.showNewickTree(nf, treefile).getTree());
317 Jalview.testoutput(argParser, Arg.TREE,
318 "examples/testdata/uniref50_test_tree", treefile);
319 } catch (IOException e)
321 Console.warn("Couldn't add tree " + treefile, e);
325 // Show secondary structure annotations?
326 boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
327 Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
328 "STRUCT_FROM_PDB", true);
329 af.setAnnotationsVisibility(showSSAnnotations, true, false);
331 // Show sequence annotations?
332 boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
333 Arg.SHOWANNOTATIONS, av.getSubVals(), null,
334 "SHOW_ANNOTATIONS", true);
335 af.setAnnotationsVisibility(showAnnotations, false, true);
337 // show temperature factor annotations?
338 if (avm.getBoolean(Arg.NOTEMPFAC))
340 // do this better (annotation types?)
341 List<String> hideThese = new ArrayList<>();
342 hideThese.add("Temperature Factor");
343 hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
344 AlignmentUtils.showOrHideSequenceAnnotations(
345 af.getCurrentView().getAlignment(), hideThese, null,
349 // store the AlignFrame for this id
352 // is it its own structure file?
353 if (format.isStructureFile())
355 StructureSelectionManager ssm = StructureSelectionManager
356 .getStructureSelectionManager(Desktop.instance);
357 SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
358 ssm.computeMapping(false, new SequenceI[] { seq }, null,
359 openFile, DataSourceType.FILE, null, null, null, false);
365 "Opening '" + openFile + "' in existing alignment frame");
366 DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
368 : DataSourceType.FILE;
369 FileLoader fileLoader = new FileLoader(!headless);
370 fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
374 Console.debug("Command " + Arg.APPEND + " executed successfully!");
377 if (first) // first=true means nothing opened
381 Jalview.exit("Could not open any files in headless mode", 1);
385 Console.warn("No more files to open");
388 if (progressBarSet && desktop != null)
389 desktop.setProgressBar(null, progress);
393 // open the structure (from same PDB file or given PDBfile)
394 if (!avm.getBoolean(Arg.NOSTRUCTURE))
396 AlignFrame af = afMap.get(id);
397 if (avm.containsArg(Arg.STRUCTURE))
399 commandArgsProvided = true;
400 for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
402 String val = av.getValue();
403 SubVals subVals = av.getSubVals();
404 SequenceI seq = getSpecifiedSequence(af, avm, av);
407 // Could not find sequence from subId, let's assume the first
408 // sequence in the alignframe
409 AlignmentI al = af.getCurrentView().getAlignment();
410 seq = al.getSequenceAt(0);
415 Console.warn("Could not find sequence for argument "
416 + Arg.STRUCTURE.argString() + "=" + val);
417 // you probably want to continue here, not break
421 File structureFile = null;
422 if (subVals.getContent() != null
423 && subVals.getContent().length() != 0)
425 structureFile = new File(subVals.getContent());
426 Console.debug("Using structure file (from argument) '"
427 + structureFile.getAbsolutePath() + "'");
431 * PDBEntry fileEntry = new AssociatePdbFileWithSeq()
432 * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE,
433 * selectedSequence, true, Desktop.instance);
435 * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new
436 * SequenceI[] { selectedSequence });
439 /* THIS DOESN'T WORK */
440 else if (seq.getAllPDBEntries() != null
441 && seq.getAllPDBEntries().size() > 0)
443 structureFile = new File(
444 seq.getAllPDBEntries().elementAt(0).getFile());
445 Console.debug("Using structure file (from sequence) '"
446 + structureFile.getAbsolutePath() + "'");
449 if (structureFile == null)
451 Console.warn("Not provided structure file with '" + val + "'");
455 if (!structureFile.exists())
457 Console.warn("Structure file '"
458 + structureFile.getAbsoluteFile() + "' not found.");
462 Console.debug("Using structure file "
463 + structureFile.getAbsolutePath());
465 // open structure view
466 AlignmentPanel ap = af.alignPanel;
469 Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
470 StructureViewer.ViewerType.JMOL.toString());
473 String structureFilepath = structureFile.getAbsolutePath();
475 // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
476 String paeFilepath = ArgParser
477 .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
478 Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
480 if (paeFilepath != null)
482 File paeFile = new File(paeFilepath);
486 paeFilepath = paeFile.getCanonicalPath();
487 } catch (IOException e)
489 paeFilepath = paeFile.getAbsolutePath();
490 Console.warn("Problem with the PAE file path: '"
491 + paeFile.getPath() + "'");
495 // showing annotations from structure file or not
496 boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
497 Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
500 // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
501 // reference annotations
502 String tftString = ArgParser
503 .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
504 Arg.TEMPFAC, Position.AFTER, av, subVals, null,
506 boolean notempfac = ArgParser.getFromSubValArgOrPref(avm,
507 Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
509 TFType tft = notempfac ? null : TFType.DEFAULT;
510 if (tftString != null && !notempfac)
512 // get kind of temperature factor annotation
515 tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT));
516 Console.debug("Obtained Temperature Factor type of '" + tft
517 + "' for structure '" + structureFilepath + "'");
518 } catch (IllegalArgumentException e)
520 // Just an error message!
521 StringBuilder sb = new StringBuilder().append("Cannot set ")
522 .append(Arg.TEMPFAC.argString()).append(" to '")
524 .append("', ignoring. Valid values are: ");
525 Iterator<TFType> it = Arrays.stream(TFType.values())
529 sb.append(it.next().toString().toLowerCase(Locale.ROOT));
533 Console.warn(sb.toString());
537 String sViewer = ArgParser.getFromSubValArgOrPref(avm,
538 Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
540 ViewerType viewerType = null;
541 if (!"none".equals(sViewer))
543 for (ViewerType v : EnumSet.allOf(ViewerType.class))
545 String name = v.name().toLowerCase(Locale.ROOT)
546 .replaceAll(" ", "");
547 if (sViewer.equals(name))
555 // TODO use ssFromStructure
556 StructureViewer sv = StructureChooser
557 .openStructureFileForSequence(null, null, ap, seq, false,
558 structureFilepath, tft, paeFilepath, false,
559 ssFromStructure, false, viewerType);
566 String structureImageFilename = ArgParser.getValueFromSubValOrArg(
567 avm, av, Arg.STRUCTUREIMAGE, subVals);
568 if (sv != null && structureImageFilename != null)
570 ArgValue siAv = avm.getClosestNextArgValueOfArg(av,
573 if (structureImageFilename.equals(siAv.getValue()))
575 sisv = siAv.getSubVals();
577 File structureImageFile = new File(structureImageFilename);
578 String width = ArgParser.getValueFromSubValOrArg(avm, av,
579 Arg.STRUCTUREIMAGEWIDTH, sisv);
580 String height = ArgParser.getValueFromSubValOrArg(avm, av,
581 Arg.STRUCTUREIMAGEHEIGHT, sisv);
582 String scale = ArgParser.getValueFromSubValOrArg(avm, av,
583 Arg.STRUCTUREIMAGESCALE, sisv);
584 String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
585 Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
586 String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
587 Arg.STRUCTUREIMAGETYPE, sisv);
588 if (typeS == null || typeS.length() == 0)
590 typeS = FileUtils.getExtension(structureImageFile);
595 imageType = Enum.valueOf(TYPE.class,
596 typeS.toUpperCase(Locale.ROOT));
597 } catch (IllegalArgumentException e)
599 Console.warn("Do not know image format '" + typeS
601 imageType = TYPE.PNG;
603 BitmapImageSizing userBis = ImageMaker
604 .parseScaleWidthHeightStrings(scale, width, height);
605 switch (StructureViewer.getViewerType())
611 } catch (InterruptedException e)
613 // TODO Auto-generated catch block
616 JalviewStructureDisplayI sview = sv
617 .getJalviewStructureDisplay();
618 if (sview instanceof AppJmol)
620 AppJmol jmol = (AppJmol) sview;
621 jmol.makePDBImage(structureImageFile, imageType, renderer,
626 Console.warn("Cannot export image for structure viewer "
627 + sv.getViewerType() + " yet");
636 boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
639 AlignFrame af = afMap.get(id);
640 for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
641 .findAnnotation(PDBChain.class.getName().toString()))
643 AnnotationColourGradient acg = new AnnotationColourGradient(aa,
644 af.alignPanel.av.getGlobalColourScheme(), 0);
645 acg.setSeqAssociated(true);
646 af.changeColour(acg);
647 Console.info("Changed colour " + acg.toString());
652 return theseArgsWereParsed;
655 protected void processGroovyScript(String id)
657 ArgValuesMap avm = argParser.getLinkedArgs(id);
658 AlignFrame af = afMap.get(id);
662 Console.warn("Did not have an alignment window for id=" + id);
666 if (avm.containsArg(Arg.GROOVY))
668 String groovyscript = avm.getValue(Arg.GROOVY);
669 if (groovyscript != null)
671 // Execute the groovy script after we've done all the rendering stuff
672 // and before any images or figures are generated.
673 Console.info("Executing script " + groovyscript);
674 Jalview.getInstance().executeGroovyScript(groovyscript, af);
679 protected boolean processImages(String id)
681 ArgValuesMap avm = argParser.getLinkedArgs(id);
682 AlignFrame af = afMap.get(id);
686 Console.warn("Did not have an alignment window for id=" + id);
690 if (avm.containsArg(Arg.IMAGE))
692 for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
694 String val = av.getValue();
695 SubVals subVal = av.getSubVals();
696 String fileName = subVal.getContent();
697 File file = new File(fileName);
698 String name = af.getName();
699 String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
700 Arg.TEXTRENDERER, subVal);
701 if (renderer == null)
703 String type = "png"; // default
705 String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE,
707 String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH,
709 String height = ArgParser.getValueFromSubValOrArg(avm, av,
711 BitmapImageSizing userBis = ImageMaker
712 .parseScaleWidthHeightStrings(scale, width, height);
714 type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
715 if (type == null && fileName != null)
717 for (String ext : new String[] { "svg", "png", "html", "eps" })
719 if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
725 // for moment we disable JSON export
726 Cache.setPropsAreReadOnly(true);
727 Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
729 Console.info("Writing " + file);
735 Console.debug("Outputting type '" + type + "' to " + fileName);
736 af.createSVG(file, renderer);
740 Console.debug("Outputting type '" + type + "' to " + fileName);
741 af.createPNG(file, null, userBis);
745 Console.debug("Outputting type '" + type + "' to " + fileName);
746 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
747 htmlSVG.exportHTML(fileName, renderer);
751 Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName);
754 BioJsHTMLOutput.refreshVersionInfo(
755 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
756 } catch (URISyntaxException e)
760 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
761 bjs.exportHTML(fileName);
765 Console.debug("Creating EPS file: " + fileName);
766 af.createEPS(file, name);
770 Console.debug("Creating ImageMap file: " + fileName);
771 af.createImageMap(file, name);
775 Console.warn(Arg.IMAGE.argString() + " type '" + type
776 + "' not known. Ignoring");
784 protected boolean processOutput(String id)
786 ArgValuesMap avm = argParser.getLinkedArgs(id);
787 AlignFrame af = afMap.get(id);
791 Console.warn("Did not have an alignment window for id=" + id);
795 if (avm.containsArg(Arg.OUTPUT))
797 for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
799 String val = av.getValue();
800 SubVals subVals = av.getSubVals();
801 String fileName = subVals.getContent();
802 File file = new File(fileName);
803 boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
804 Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
805 // backups. Use the Arg.BACKUPS or subval "backups" setting first,
806 // otherwise if headless assume false, if not headless use the user
807 // preference with default true.
808 boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
810 Platform.isHeadless() ? null : BackupFiles.ENABLED,
811 !Platform.isHeadless());
813 // if backups is not true then --overwrite must be specified
814 if (file.exists() && !(overwrite || backups))
816 Console.error("Won't overwrite file '" + fileName + "' without "
817 + Arg.OVERWRITE.argString() + " or "
818 + Arg.BACKUPS.argString() + " set");
822 String name = af.getName();
823 String format = ArgParser.getValueFromSubValOrArg(avm, av,
824 Arg.FORMAT, subVals);
825 FileFormats ffs = FileFormats.getInstance();
826 List<String> validFormats = ffs.getWritableFormats(false);
828 FileFormatI ff = null;
829 if (format == null && fileName != null)
831 FORMAT: for (String fname : validFormats)
833 FileFormatI tff = ffs.forName(fname);
834 String[] extensions = tff.getExtensions().split(",");
835 for (String ext : extensions)
837 if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
840 format = ff.getName();
846 if (ff == null && format != null)
848 ff = ffs.forName(format);
852 StringBuilder validSB = new StringBuilder();
853 for (String f : validFormats)
855 if (validSB.length() > 0)
856 validSB.append(", ");
858 FileFormatI tff = ffs.forName(f);
859 validSB.append(" (");
860 validSB.append(tff.getExtensions());
864 Jalview.exit("No valid format specified for "
865 + Arg.OUTPUT.argString() + ". Valid formats are "
866 + validSB.toString() + ".", 1);
867 // this return really shouldn't happen
871 String savedBackupsPreference = Cache
872 .getDefault(BackupFiles.ENABLED, null);
873 Console.debug("Setting backups to " + backups);
874 Cache.applicationProperties.put(BackupFiles.ENABLED,
875 Boolean.toString(backups));
877 Console.info("Writing " + fileName);
879 af.saveAlignment(fileName, ff);
880 Console.debug("Returning backups to " + savedBackupsPreference);
881 if (savedBackupsPreference != null)
882 Cache.applicationProperties.put(BackupFiles.ENABLED,
883 savedBackupsPreference);
884 if (af.isSaveAlignmentSuccessful())
886 Console.debug("Written alignment '" + name + "' in "
887 + ff.getName() + " format to " + file);
891 Console.warn("Error writing file " + file + " in " + ff.getName()
900 private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
903 SubVals subVals = av.getSubVals();
904 ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
905 SequenceI seq = null;
906 if (subVals == null && idAv == null)
908 if (af == null || af.getCurrentView() == null)
912 AlignmentI al = af.getCurrentView().getAlignment();
919 if (subVals.has(Arg.SEQID.getName()))
921 seq = al.findName(subVals.get(Arg.SEQID.getName()));
923 else if (-1 < subVals.getIndex()
924 && subVals.getIndex() < al.getSequences().size())
926 seq = al.getSequenceAt(subVals.getIndex());
929 else if (idAv != null)
931 seq = al.findName(idAv.getValue());