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.HashMap;
10 import java.util.Iterator;
11 import java.util.List;
12 import java.util.Locale;
15 import jalview.analysis.AlignmentUtils;
16 import jalview.api.structures.JalviewStructureDisplayI;
17 import jalview.bin.argparser.Arg;
18 import jalview.bin.argparser.ArgParser;
19 import jalview.bin.argparser.ArgParser.Position;
20 import jalview.bin.argparser.ArgValue;
21 import jalview.bin.argparser.ArgValuesMap;
22 import jalview.bin.argparser.SubVals;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.SequenceI;
25 import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
26 import jalview.gui.AlignFrame;
27 import jalview.gui.AlignmentPanel;
28 import jalview.gui.AppJmol;
29 import jalview.gui.Desktop;
30 import jalview.gui.Preferences;
31 import jalview.gui.StructureChooser;
32 import jalview.gui.StructureViewer;
33 import jalview.gui.StructureViewer.ViewerType;
34 import jalview.io.AppletFormatAdapter;
35 import jalview.io.BackupFiles;
36 import jalview.io.BioJsHTMLOutput;
37 import jalview.io.DataSourceType;
38 import jalview.io.FileFormat;
39 import jalview.io.FileFormatException;
40 import jalview.io.FileFormatI;
41 import jalview.io.FileFormats;
42 import jalview.io.FileLoader;
43 import jalview.io.HtmlSvgOutput;
44 import jalview.io.IdentifyFile;
45 import jalview.io.NewickFile;
46 import jalview.io.exceptions.ImageOutputException;
47 import jalview.schemes.ColourSchemeI;
48 import jalview.schemes.ColourSchemeProperty;
49 import jalview.structure.StructureImportSettings.TFType;
50 import jalview.structure.StructureSelectionManager;
51 import jalview.util.FileUtils;
52 import jalview.util.HttpUtils;
53 import jalview.util.ImageMaker;
54 import jalview.util.ImageMaker.TYPE;
55 import jalview.util.MessageManager;
56 import jalview.util.Platform;
57 import jalview.util.imagemaker.BitmapImageSizing;
63 private boolean headless;
65 private ArgParser argParser;
67 private Map<String, AlignFrame> afMap;
69 private Map<String, List<StructureViewer>> svMap;
71 private boolean commandArgsProvided = false;
73 private boolean argsWereParsed = false;
75 public Commands(ArgParser argparser, boolean headless)
77 this(Desktop.instance, argparser, headless);
80 public Commands(Desktop d, ArgParser argparser, boolean h)
82 argParser = argparser;
85 afMap = new HashMap<>();
88 protected boolean processArgs()
90 if (argParser == null)
95 boolean theseArgsWereParsed = false;
97 if (argParser != null && argParser.getLinkedIds() != null)
99 for (String id : argParser.getLinkedIds())
101 ArgValuesMap avm = argParser.getLinkedArgs(id);
102 theseArgsWereParsed = true;
103 boolean processLinkedOkay = processLinked(id);
104 theseArgsWereParsed &= processLinkedOkay;
106 processGroovyScript(id);
108 // wait around until alignFrame isn't busy
109 AlignFrame af = afMap.get(id);
110 while (af != null && af.getViewport().isCalcInProgress())
115 } catch (Exception q)
121 theseArgsWereParsed &= processImages(id);
123 if (processLinkedOkay)
125 theseArgsWereParsed &= processOutput(id);
129 if (avm.getBoolean(Arg.CLOSE))
134 af.closeMenuItem_actionPerformed(true);
141 if (argParser.getBoolean(Arg.QUIT))
143 Jalview.getInstance().quit();
146 // carry on with jalview.bin.Jalview
147 argsWereParsed = theseArgsWereParsed;
148 return argsWereParsed;
151 public boolean commandArgsProvided()
153 return commandArgsProvided;
156 public boolean argsWereParsed()
158 return argsWereParsed;
161 protected boolean processLinked(String id)
163 boolean theseArgsWereParsed = false;
164 ArgValuesMap avm = argParser.getLinkedArgs(id);
168 // set wrap scope here so it can be applied after structures are opened
169 boolean wrap = false;
171 if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
173 commandArgsProvided = true;
176 boolean first = true;
177 boolean progressBarSet = false;
179 // Combine the APPEND and OPEN files into one list, along with whether it
180 // was APPEND or OPEN
181 List<ArgValue> openAvList = new ArrayList<>();
182 openAvList.addAll(avm.getArgValueList(Arg.OPEN));
183 openAvList.addAll(avm.getArgValueList(Arg.APPEND));
184 // sort avlist based on av.getArgIndex()
185 Collections.sort(openAvList);
186 for (ArgValue av : openAvList)
189 SubVals sv = av.getSubVals();
190 String openFile = av.getValue();
191 if (openFile == null)
194 theseArgsWereParsed = true;
198 if (!headless && desktop != null)
200 desktop.setProgressBar(
201 MessageManager.getString(
202 "status.processing_commandline_args"),
203 progress = System.currentTimeMillis());
204 progressBarSet = true;
208 if (!Platform.isJS())
210 * ignore in JavaScript -- can't just file existence - could load it?
215 if (!HttpUtils.startsWithHttpOrHttps(openFile))
217 if (!(new File(openFile)).exists())
219 Console.warn("Can't find file '" + openFile + "'");
224 DataSourceType protocol = AppletFormatAdapter
225 .checkProtocol(openFile);
227 FileFormatI format = null;
230 format = new IdentifyFile().identify(openFile, protocol);
231 } catch (FileFormatException e1)
233 Console.error("Unknown file format for '" + openFile + "'");
237 // When to open a new AlignFrame
238 if (af == null || "true".equals(av.getSubVal("new"))
239 || a == Arg.OPEN || format == FileFormat.Jalview)
243 Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
248 "Opening '" + openFile + "' in new alignment frame");
249 FileLoader fileLoader = new FileLoader(!headless);
250 boolean xception=false;
252 af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
254 } catch (Throwable thr)
257 Console.error("Couldn't open '"+openFile+"' as "+format+" "+thr.getLocalizedMessage()+ " (Enable debug for full stack trace)");
258 Console.debug("Exception when opening '"+openFile+"'",thr);
262 if (af==null && !xception)
264 Console.info("Ignoring '"+openFile+"' - no alignment data found.");
270 String colour = ArgParser.getFromSubValArgOrPref(avm, av,
271 Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
274 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
275 af.getViewport(), af.getViewport().getAlignment(),
278 if (cs == null && !"None".equals(colour))
281 "Couldn't parse '" + colour + "' as a colourscheme.");
287 Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
290 // Change alignment frame title
291 String title = ArgParser.getFromSubValArgOrPref(avm, av,
292 Arg.TITLE, sv, null, null, null);
296 Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
300 String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av,
302 if (featuresfile != null)
304 af.parseFeaturesFile(featuresfile,
305 AppletFormatAdapter.checkProtocol(featuresfile));
306 Jalview.testoutput(argParser, Arg.FEATURES,
307 "examples/testdata/plantfdx.features", featuresfile);
310 // Add annotations from file
311 String annotationsfile = ArgParser.getValueFromSubValOrArg(avm,
312 av, Arg.ANNOTATIONS, sv);
313 if (annotationsfile != null)
315 af.loadJalviewDataFile(annotationsfile, null, null, null);
316 Jalview.testoutput(argParser, Arg.ANNOTATIONS,
317 "examples/testdata/plantfdx.annotations",
321 // Set or clear the sortbytree flag
322 boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm,
326 af.getViewport().setSortByTree(true);
327 Jalview.testoutput(argParser, Arg.SORTBYTREE);
330 // Load tree from file
331 String treefile = ArgParser.getValueFromSubValOrArg(avm, av,
333 if (treefile != null)
337 NewickFile nf = new NewickFile(treefile,
338 AppletFormatAdapter.checkProtocol(treefile));
339 af.getViewport().setCurrentTree(
340 af.showNewickTree(nf, treefile).getTree());
341 Jalview.testoutput(argParser, Arg.TREE,
342 "examples/testdata/uniref50_test_tree", treefile);
343 } catch (IOException e)
345 Console.warn("Couldn't add tree " + treefile, e);
349 // Show secondary structure annotations?
350 boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
351 Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
352 "STRUCT_FROM_PDB", true);
353 af.setAnnotationsVisibility(showSSAnnotations, true, false);
355 // Show sequence annotations?
356 boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
357 Arg.SHOWANNOTATIONS, av.getSubVals(), null,
358 "SHOW_ANNOTATIONS", true);
359 af.setAnnotationsVisibility(showAnnotations, false, true);
361 // show temperature factor annotations?
362 if (avm.getBoolean(Arg.NOTEMPFAC))
364 // do this better (annotation types?)
365 List<String> hideThese = new ArrayList<>();
366 hideThese.add("Temperature Factor");
367 hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
368 AlignmentUtils.showOrHideSequenceAnnotations(
369 af.getCurrentView().getAlignment(), hideThese, null,
373 // wrap alignment? do this last for formatting reasons
374 wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null,
375 "WRAP_ALIGNMENT", false);
376 // af.setWrapFormat(wrap) is applied after structures are opened for
377 // annotation reasons
379 // store the AlignFrame for this id
382 // is it its own structure file?
383 if (format.isStructureFile())
385 StructureSelectionManager ssm = StructureSelectionManager
386 .getStructureSelectionManager(Desktop.instance);
387 SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
388 ssm.computeMapping(false, new SequenceI[] { seq }, null,
389 openFile, DataSourceType.FILE, null, null, null, false);
395 "Opening '" + openFile + "' in existing alignment frame");
396 DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
398 : DataSourceType.FILE;
399 FileLoader fileLoader = new FileLoader(!headless);
400 fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
404 Console.debug("Command " + Arg.APPEND + " executed successfully!");
407 if (first) // first=true means nothing opened
411 Jalview.exit("Could not open any files in headless mode", 1);
415 Console.warn("No more files to open");
418 if (progressBarSet && desktop != null)
419 desktop.setProgressBar(null, progress);
423 // open the structure (from same PDB file or given PDBfile)
424 if (!avm.getBoolean(Arg.NOSTRUCTURE))
426 AlignFrame af = afMap.get(id);
427 if (avm.containsArg(Arg.STRUCTURE))
429 commandArgsProvided = true;
430 for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
432 String val = av.getValue();
433 SubVals subVals = av.getSubVals();
434 SequenceI seq = getSpecifiedSequence(af, avm, av);
437 // Could not find sequence from subId, let's assume the first
438 // sequence in the alignframe
439 AlignmentI al = af.getCurrentView().getAlignment();
440 seq = al.getSequenceAt(0);
445 Console.warn("Could not find sequence for argument "
446 + Arg.STRUCTURE.argString() + "=" + val);
447 // you probably want to continue here, not break
451 File structureFile = null;
452 if (subVals.getContent() != null
453 && subVals.getContent().length() != 0)
455 structureFile = new File(subVals.getContent());
456 Console.debug("Using structure file (from argument) '"
457 + structureFile.getAbsolutePath() + "'");
461 * PDBEntry fileEntry = new AssociatePdbFileWithSeq()
462 * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE,
463 * selectedSequence, true, Desktop.instance);
465 * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new
466 * SequenceI[] { selectedSequence });
469 /* THIS DOESN'T WORK */
470 else if (seq.getAllPDBEntries() != null
471 && seq.getAllPDBEntries().size() > 0)
473 structureFile = new File(
474 seq.getAllPDBEntries().elementAt(0).getFile());
475 Console.debug("Using structure file (from sequence) '"
476 + structureFile.getAbsolutePath() + "'");
479 if (structureFile == null)
481 Console.warn("Not provided structure file with '" + val + "'");
485 if (!structureFile.exists())
487 Console.warn("Structure file '"
488 + structureFile.getAbsoluteFile() + "' not found.");
492 Console.debug("Using structure file "
493 + structureFile.getAbsolutePath());
495 // open structure view
496 AlignmentPanel ap = af.alignPanel;
499 Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
500 StructureViewer.ViewerType.JMOL.toString());
503 String structureFilepath = structureFile.getAbsolutePath();
505 // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
506 String paeFilepath = ArgParser
507 .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
508 Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
510 if (paeFilepath != null)
512 File paeFile = new File(paeFilepath);
516 paeFilepath = paeFile.getCanonicalPath();
517 } catch (IOException e)
519 paeFilepath = paeFile.getAbsolutePath();
520 Console.warn("Problem with the PAE file path: '"
521 + paeFile.getPath() + "'");
525 // showing annotations from structure file or not
526 boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
527 Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
530 // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
531 // reference annotations
532 String tftString = ArgParser
533 .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
534 Arg.TEMPFAC, Position.AFTER, av, subVals, null,
536 boolean notempfac = ArgParser.getFromSubValArgOrPref(avm,
537 Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
539 TFType tft = notempfac ? null : TFType.DEFAULT;
540 if (tftString != null && !notempfac)
542 // get kind of temperature factor annotation
545 tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT));
546 Console.debug("Obtained Temperature Factor type of '" + tft
547 + "' for structure '" + structureFilepath + "'");
548 } catch (IllegalArgumentException e)
550 // Just an error message!
551 StringBuilder sb = new StringBuilder().append("Cannot set ")
552 .append(Arg.TEMPFAC.argString()).append(" to '")
554 .append("', ignoring. Valid values are: ");
555 Iterator<TFType> it = Arrays.stream(TFType.values())
559 sb.append(it.next().toString().toLowerCase(Locale.ROOT));
563 Console.warn(sb.toString());
567 String sViewer = ArgParser.getFromSubValArgOrPref(avm,
568 Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
570 ViewerType viewerType = ViewerType.getFromString(sViewer);
572 // TODO use ssFromStructure
573 StructureViewer sv = StructureChooser
574 .openStructureFileForSequence(null, null, ap, seq, false,
575 structureFilepath, tft, paeFilepath, false,
576 ssFromStructure, false, viewerType);
580 Console.error("Failed to import and open structure view.");
586 while (sv.isBusy() && tries > 0)
593 "Waiting for viewer for " + structureFilepath);
596 if (tries == 0 && sv.isBusy())
599 "Gave up waiting for structure viewer to load. Something may have gone wrong.");
601 } catch (Exception x)
603 Console.warn("Exception whilst waiting for structure viewer "
604 + structureFilepath, x);
607 // add StructureViewer to svMap list
610 svMap = new HashMap<>();
612 if (svMap.get(id) == null)
614 svMap.put(id, new ArrayList<>());
616 svMap.get(id).add(sv);
619 "Successfully opened viewer for " + structureFilepath);
620 String structureImageFilename = ArgParser.getValueFromSubValOrArg(
621 avm, av, Arg.STRUCTUREIMAGE, subVals);
622 if (sv != null && structureImageFilename != null)
624 ArgValue siAv = avm.getClosestNextArgValueOfArg(av,
627 if (structureImageFilename.equals(siAv.getValue()))
629 sisv = siAv.getSubVals();
631 File structureImageFile = new File(structureImageFilename);
632 String width = ArgParser.getValueFromSubValOrArg(avm, av,
633 Arg.STRUCTUREIMAGEWIDTH, sisv);
634 String height = ArgParser.getValueFromSubValOrArg(avm, av,
635 Arg.STRUCTUREIMAGEHEIGHT, sisv);
636 String scale = ArgParser.getValueFromSubValOrArg(avm, av,
637 Arg.STRUCTUREIMAGESCALE, sisv);
638 String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
639 Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
640 String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
641 Arg.STRUCTUREIMAGETYPE, sisv);
642 if (typeS == null || typeS.length() == 0)
644 typeS = FileUtils.getExtension(structureImageFile);
649 imageType = Enum.valueOf(TYPE.class,
650 typeS.toUpperCase(Locale.ROOT));
651 } catch (IllegalArgumentException e)
653 Console.warn("Do not know image format '" + typeS
655 imageType = TYPE.PNG;
657 BitmapImageSizing userBis = ImageMaker
658 .parseScaleWidthHeightStrings(scale, width, height);
659 // TODO MAKE THIS VIEWER INDEPENDENT!!
660 switch (StructureViewer.getViewerType())
663 JalviewStructureDisplayI sview = sv
664 .getJalviewStructureDisplay();
665 if (sview instanceof AppJmol)
667 AppJmol jmol = (AppJmol) sview;
670 Console.debug("Rendering image to " + structureImageFile);
671 jmol.makePDBImage(structureImageFile, imageType, renderer,
673 Console.debug("Finished Rendering image to "
674 + structureImageFile);
676 } catch (ImageOutputException ioexc)
678 Console.warn("Unexpected error whilst exporting image to "
679 + structureImageFile, ioexc);
685 Console.warn("Cannot export image for structure viewer "
686 + sv.getViewerType() + " yet");
696 AlignFrame af = afMap.get(id);
699 af.setWrapFormat(wrap, true);
704 boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
707 AlignFrame af = afMap.get(id);
708 for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
709 .findAnnotation(PDBChain.class.getName().toString()))
711 AnnotationColourGradient acg = new AnnotationColourGradient(aa,
712 af.alignPanel.av.getGlobalColourScheme(), 0);
713 acg.setSeqAssociated(true);
714 af.changeColour(acg);
715 Console.info("Changed colour " + acg.toString());
720 return theseArgsWereParsed;
723 protected void processGroovyScript(String id)
725 ArgValuesMap avm = argParser.getLinkedArgs(id);
726 AlignFrame af = afMap.get(id);
730 Console.warn("Did not have an alignment window for id=" + id);
734 if (avm.containsArg(Arg.GROOVY))
736 String groovyscript = avm.getValue(Arg.GROOVY);
737 if (groovyscript != null)
739 // Execute the groovy script after we've done all the rendering stuff
740 // and before any images or figures are generated.
741 Console.info("Executing script " + groovyscript);
742 Jalview.getInstance().executeGroovyScript(groovyscript, af);
747 protected boolean processImages(String id)
749 ArgValuesMap avm = argParser.getLinkedArgs(id);
750 AlignFrame af = afMap.get(id);
754 Console.warn("Did not have an alignment window for id=" + id);
758 if (avm.containsArg(Arg.IMAGE))
760 for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
762 String val = av.getValue();
763 SubVals subVal = av.getSubVals();
764 String fileName = subVal.getContent();
765 File file = new File(fileName);
766 String name = af.getName();
767 String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
768 Arg.TEXTRENDERER, subVal);
769 if (renderer == null)
771 String type = "png"; // default
773 String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE,
775 String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH,
777 String height = ArgParser.getValueFromSubValOrArg(avm, av,
779 BitmapImageSizing userBis = ImageMaker
780 .parseScaleWidthHeightStrings(scale, width, height);
782 type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
783 if (type == null && fileName != null)
785 for (String ext : new String[] { "svg", "png", "html", "eps" })
787 if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
793 // for moment we disable JSON export
794 Cache.setPropsAreReadOnly(true);
795 Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
797 Console.info("Writing " + file);
804 Console.debug("Outputting type '" + type + "' to " + fileName);
805 af.createSVG(file, renderer);
809 Console.debug("Outputting type '" + type + "' to " + fileName);
810 af.createPNG(file, null, userBis);
814 Console.debug("Outputting type '" + type + "' to " + fileName);
815 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
816 htmlSVG.exportHTML(fileName, renderer);
821 "Outputting BioJS MSA Viwer HTML file: " + fileName);
824 BioJsHTMLOutput.refreshVersionInfo(
825 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
826 } catch (URISyntaxException e)
830 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
831 bjs.exportHTML(fileName);
835 Console.debug("Outputting EPS file: " + fileName);
836 af.createEPS(file, renderer);
840 Console.debug("Outputting ImageMap file: " + fileName);
841 af.createImageMap(file, name);
845 Console.warn(Arg.IMAGE.argString() + " type '" + type
846 + "' not known. Ignoring");
849 } catch (Exception ioex)
851 Console.warn("Unexpected error during export", ioex);
858 protected boolean processOutput(String id)
860 ArgValuesMap avm = argParser.getLinkedArgs(id);
861 AlignFrame af = afMap.get(id);
865 Console.warn("Did not have an alignment window for id=" + id);
869 if (avm.containsArg(Arg.OUTPUT))
871 for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
873 String val = av.getValue();
874 SubVals subVals = av.getSubVals();
875 String fileName = subVals.getContent();
876 boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
877 File file = new File(fileName);
878 boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
879 Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
880 // backups. Use the Arg.BACKUPS or subval "backups" setting first,
881 // otherwise if headless assume false, if not headless use the user
882 // preference with default true.
883 boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS,
885 Platform.isHeadless() ? null : BackupFiles.ENABLED,
886 !Platform.isHeadless());
888 // if backups is not true then --overwrite must be specified
889 if (file.exists() && !(overwrite || backups || stdout))
891 Console.error("Won't overwrite file '" + fileName + "' without "
892 + Arg.OVERWRITE.argString() + " or "
893 + Arg.BACKUPS.argString() + " set");
897 String name = af.getName();
898 String format = ArgParser.getValueFromSubValOrArg(avm, av,
899 Arg.FORMAT, subVals);
900 FileFormats ffs = FileFormats.getInstance();
901 List<String> validFormats = ffs.getWritableFormats(false);
903 FileFormatI ff = null;
904 if (format == null && fileName != null)
906 FORMAT: for (String fname : validFormats)
908 FileFormatI tff = ffs.forName(fname);
909 String[] extensions = tff.getExtensions().split(",");
910 for (String ext : extensions)
912 if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
915 format = ff.getName();
921 if (ff == null && format != null)
923 ff = ffs.forName(format);
929 ff = FileFormat.Fasta;
933 StringBuilder validSB = new StringBuilder();
934 for (String f : validFormats)
936 if (validSB.length() > 0)
937 validSB.append(", ");
939 FileFormatI tff = ffs.forName(f);
940 validSB.append(" (");
941 validSB.append(tff.getExtensions());
945 Jalview.exit("No valid format specified for "
946 + Arg.OUTPUT.argString() + ". Valid formats are "
947 + validSB.toString() + ".", 1);
948 // this return really shouldn't happen
953 String savedBackupsPreference = Cache
954 .getDefault(BackupFiles.ENABLED, null);
955 Console.debug("Setting backups to " + backups);
956 Cache.applicationProperties.put(BackupFiles.ENABLED,
957 Boolean.toString(backups));
959 Console.info("Writing " + fileName);
961 af.saveAlignment(fileName, ff, stdout);
962 Console.debug("Returning backups to " + savedBackupsPreference);
963 if (savedBackupsPreference != null)
964 Cache.applicationProperties.put(BackupFiles.ENABLED,
965 savedBackupsPreference);
966 if (af.isSaveAlignmentSuccessful())
968 Console.debug("Written alignment '" + name + "' in "
969 + ff.getName() + " format to " + file);
973 Console.warn("Error writing file " + file + " in " + ff.getName()
982 private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
985 SubVals subVals = av.getSubVals();
986 ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
987 SequenceI seq = null;
988 if (subVals == null && idAv == null)
990 if (af == null || af.getCurrentView() == null)
994 AlignmentI al = af.getCurrentView().getAlignment();
1001 if (subVals.has(Arg.SEQID.getName()))
1003 seq = al.findName(subVals.get(Arg.SEQID.getName()));
1005 else if (-1 < subVals.getIndex()
1006 && subVals.getIndex() < al.getSequences().size())
1008 seq = al.getSequenceAt(subVals.getIndex());
1011 if (seq == null && idAv != null)
1013 seq = al.findName(idAv.getValue());
1018 public AlignFrame[] getAlignFrames()
1020 AlignFrame[] afs = null;
1023 afs = (AlignFrame[]) afMap.values().toArray();
1029 public List<StructureViewer> getStructureViewers()
1031 List<StructureViewer> svs = null;
1034 for (List<StructureViewer> svList : svMap.values())
1038 svs = new ArrayList<>();