5 import java.io.IOException;
6 import java.net.URISyntaxException;
7 import java.util.ArrayList;
8 import java.util.Arrays;
9 import java.util.Collections;
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.Jalview.ExitCode;
19 import jalview.bin.argparser.Arg;
20 import jalview.bin.argparser.ArgParser;
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.io.exceptions.ImageOutputException;
48 import jalview.schemes.ColourSchemeI;
49 import jalview.schemes.ColourSchemeProperty;
50 import jalview.structure.StructureCommandI;
51 import jalview.structure.StructureImportSettings.TFType;
52 import jalview.structure.StructureSelectionManager;
53 import jalview.util.ColorUtils;
54 import jalview.util.FileUtils;
55 import jalview.util.HttpUtils;
56 import jalview.util.ImageMaker;
57 import jalview.util.ImageMaker.TYPE;
58 import jalview.util.MessageManager;
59 import jalview.util.Platform;
60 import jalview.util.StringUtils;
61 import jalview.util.imagemaker.BitmapImageSizing;
67 private boolean headless;
69 private ArgParser argParser;
71 private Map<String, AlignFrame> afMap;
73 private Map<String, List<StructureViewer>> svMap;
75 private boolean commandArgsProvided = false;
77 private boolean argsWereParsed = false;
79 private List<String> errors = new ArrayList<>();
81 public Commands(ArgParser argparser, boolean headless)
83 this(Desktop.instance, argparser, headless);
86 public Commands(Desktop d, ArgParser argparser, boolean h)
88 argParser = argparser;
91 afMap = new HashMap<>();
94 protected boolean processArgs()
96 if (argParser == null)
101 boolean theseArgsWereParsed = false;
103 if (argParser != null && argParser.getLinkedIds() != null)
105 for (String id : argParser.getLinkedIds())
107 ArgValuesMap avm = argParser.getLinkedArgs(id);
108 theseArgsWereParsed = true;
109 boolean processLinkedOkay = processLinked(id);
110 theseArgsWereParsed &= processLinkedOkay;
112 processGroovyScript(id);
114 // wait around until alignFrame isn't busy
115 AlignFrame af = afMap.get(id);
116 while (af != null && af.getViewport().isCalcInProgress())
121 } catch (Exception q)
127 theseArgsWereParsed &= processImages(id);
129 if (processLinkedOkay)
131 theseArgsWereParsed &= processOutput(id);
135 if (avm.getBoolean(Arg.CLOSE))
140 af.closeMenuItem_actionPerformed(true);
148 // report errors - if any
149 String errorsRaised = errorsToString();
150 if (errorsRaised.trim().length() > 0)
153 "The following errors and warnings occurred whilst processing files:\n"
156 // gui errors reported in Jalview
158 if (argParser.getBoolean(Arg.QUIT))
160 Jalview.getInstance().exit(
161 "Exiting due to " + Arg.QUIT.argString() + " argument.",
165 // carry on with jalview.bin.Jalview
166 argsWereParsed = theseArgsWereParsed;
167 return argsWereParsed;
170 public boolean commandArgsProvided()
172 return commandArgsProvided;
175 public boolean argsWereParsed()
177 return argsWereParsed;
180 protected boolean processLinked(String id)
182 boolean theseArgsWereParsed = false;
183 ArgValuesMap avm = argParser.getLinkedArgs(id);
189 Boolean isError = Boolean.valueOf(false);
191 // set wrap scope here so it can be applied after structures are opened
192 boolean wrap = false;
194 if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
196 commandArgsProvided = true;
199 boolean first = true;
200 boolean progressBarSet = false;
202 // Combine the APPEND and OPEN files into one list, along with whether it
203 // was APPEND or OPEN
204 List<ArgValue> openAvList = new ArrayList<>();
205 openAvList.addAll(avm.getArgValueList(Arg.OPEN));
206 openAvList.addAll(avm.getArgValueList(Arg.APPEND));
207 // sort avlist based on av.getArgIndex()
208 Collections.sort(openAvList);
209 for (ArgValue av : openAvList)
212 SubVals sv = av.getSubVals();
213 String openFile = av.getValue();
214 if (openFile == null)
217 theseArgsWereParsed = true;
221 if (!headless && desktop != null)
223 desktop.setProgressBar(
224 MessageManager.getString(
225 "status.processing_commandline_args"),
226 progress = System.currentTimeMillis());
227 progressBarSet = true;
231 if (!Platform.isJS())
233 * ignore in JavaScript -- can't just file existence - could load it?
238 if (!HttpUtils.startsWithHttpOrHttps(openFile))
240 if (!(new File(openFile)).exists())
242 addError("Can't find file '" + openFile + "'");
249 DataSourceType protocol = AppletFormatAdapter
250 .checkProtocol(openFile);
252 FileFormatI format = null;
255 format = new IdentifyFile().identify(openFile, protocol);
256 } catch (FileFormatException e1)
258 addError("Unknown file format for '" + openFile + "'");
264 // When to open a new AlignFrame
265 if (af == null || "true".equals(av.getSubVal("new"))
266 || a == Arg.OPEN || format == FileFormat.Jalview)
270 Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
275 "Opening '" + openFile + "' in new alignment frame");
276 FileLoader fileLoader = new FileLoader(!headless);
277 boolean xception = false;
280 af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
282 } catch (Throwable thr)
285 addError("Couldn't open '" + openFile + "' as " + format + " "
286 + thr.getLocalizedMessage()
287 + " (Enable debug for full stack trace)");
289 Console.debug("Exception when opening '" + openFile + "'", thr);
292 if (af == null && !xception)
294 addInfo("Ignoring '" + openFile
295 + "' - no alignment data found.");
301 String colour = avm.getFromSubValArgOrPref(av, Arg.COLOUR, sv,
302 null, "DEFAULT_COLOUR_PROT", "");
303 this.colourAlignFrame(af, colour);
305 // Change alignment frame title
306 String title = avm.getFromSubValArgOrPref(av, Arg.TITLE, sv, null,
311 Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
315 String featuresfile = avm.getValueFromSubValOrArg(av,
317 if (featuresfile != null)
319 af.parseFeaturesFile(featuresfile,
320 AppletFormatAdapter.checkProtocol(featuresfile));
321 Jalview.testoutput(argParser, Arg.FEATURES,
322 "examples/testdata/plantfdx.features", featuresfile);
325 // Add annotations from file
326 String annotationsfile = avm.getValueFromSubValOrArg(av,
327 Arg.ANNOTATIONS, sv);
328 if (annotationsfile != null)
330 af.loadJalviewDataFile(annotationsfile, null, null, null);
331 Jalview.testoutput(argParser, Arg.ANNOTATIONS,
332 "examples/testdata/plantfdx.annotations",
336 // Set or clear the sortbytree flag
337 boolean sortbytree = avm.getBoolFromSubValOrArg(Arg.SORTBYTREE,
341 af.getViewport().setSortByTree(true);
342 Jalview.testoutput(argParser, Arg.SORTBYTREE);
345 // Load tree from file
346 String treefile = avm.getValueFromSubValOrArg(av, Arg.TREE, sv);
347 if (treefile != null)
351 NewickFile nf = new NewickFile(treefile,
352 AppletFormatAdapter.checkProtocol(treefile));
353 af.getViewport().setCurrentTree(
354 af.showNewickTree(nf, treefile).getTree());
355 Jalview.testoutput(argParser, Arg.TREE,
356 "examples/testdata/uniref50_test_tree", treefile);
357 } catch (IOException e)
359 addError("Couldn't add tree " + treefile, e);
364 // Show secondary structure annotations?
365 boolean showSSAnnotations = avm.getFromSubValArgOrPref(
366 Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
367 "STRUCT_FROM_PDB", true);
368 af.setAnnotationsVisibility(showSSAnnotations, true, false);
370 // Show sequence annotations?
371 boolean showAnnotations = avm.getFromSubValArgOrPref(
372 Arg.SHOWANNOTATIONS, av.getSubVals(), null,
373 "SHOW_ANNOTATIONS", true);
374 af.setAnnotationsVisibility(showAnnotations, false, true);
376 // show temperature factor annotations?
377 if (avm.getBoolean(Arg.NOTEMPFAC))
379 // do this better (annotation types?)
380 List<String> hideThese = new ArrayList<>();
381 hideThese.add("Temperature Factor");
382 hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
383 AlignmentUtils.showOrHideSequenceAnnotations(
384 af.getCurrentView().getAlignment(), hideThese, null,
388 // wrap alignment? do this last for formatting reasons
389 wrap = avm.getFromSubValArgOrPref(Arg.WRAP, sv, null,
390 "WRAP_ALIGNMENT", false);
391 // af.setWrapFormat(wrap) is applied after structures are opened for
392 // annotation reasons
394 // store the AlignFrame for this id
397 // is it its own structure file?
398 if (format.isStructureFile())
400 StructureSelectionManager ssm = StructureSelectionManager
401 .getStructureSelectionManager(Desktop.instance);
402 SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
403 ssm.computeMapping(false, new SequenceI[] { seq }, null,
404 openFile, DataSourceType.FILE, null, null, null, false);
410 "Opening '" + openFile + "' in existing alignment frame");
411 DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
413 : DataSourceType.FILE;
414 FileLoader fileLoader = new FileLoader(!headless);
415 fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
419 Console.debug("Command " + Arg.APPEND + " executed successfully!");
422 if (first) // first=true means nothing opened
426 Jalview.exit("Could not open any files in headless mode",
431 Console.info("No more files to open");
434 if (progressBarSet && desktop != null)
435 desktop.setProgressBar(null, progress);
439 // open the structure (from same PDB file or given PDBfile)
440 if (!avm.getBoolean(Arg.NOSTRUCTURE))
442 AlignFrame af = afMap.get(id);
443 if (avm.containsArg(Arg.STRUCTURE))
445 commandArgsProvided = true;
446 for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
448 argParser.setStructureFilename(null);
449 String val = av.getValue();
450 SubVals subVals = av.getSubVals();
451 int argIndex = av.getArgIndex();
452 SequenceI seq = getSpecifiedSequence(af, avm, av);
455 // Could not find sequence from subId, let's assume the first
456 // sequence in the alignframe
457 AlignmentI al = af.getCurrentView().getAlignment();
458 seq = al.getSequenceAt(0);
463 addWarn("Could not find sequence for argument "
464 + Arg.STRUCTURE.argString() + "=" + val);
467 String structureFilename = null;
468 File structureFile = null;
469 if (subVals.getContent() != null
470 && subVals.getContent().length() != 0)
472 structureFilename = subVals.getContent();
473 Console.debug("Using structure file (from argument) '"
474 + structureFilename + "'");
475 structureFile = new File(structureFilename);
477 /* THIS DOESN'T WORK */
478 else if (seq.getAllPDBEntries() != null
479 && seq.getAllPDBEntries().size() > 0)
481 structureFile = new File(
482 seq.getAllPDBEntries().elementAt(0).getFile());
483 if (structureFile != null)
485 Console.debug("Using structure file (from sequence) '"
486 + structureFile.getAbsolutePath() + "'");
488 structureFilename = structureFile.getAbsolutePath();
491 if (structureFilename == null || structureFile == null)
493 addWarn("Not provided structure file with '" + val + "'");
497 if (!structureFile.exists())
499 addWarn("Structure file '" + structureFile.getAbsoluteFile()
504 Console.debug("Using structure file "
505 + structureFile.getAbsolutePath());
507 argParser.setStructureFilename(structureFilename);
509 // open structure view
510 AlignmentPanel ap = af.alignPanel;
513 Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
514 StructureViewer.ViewerType.JMOL.toString());
517 String structureFilepath = structureFile.getAbsolutePath();
519 // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
520 String paeFilepath = avm.getFromSubValArgOrPrefWithSubstitutions(
521 argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER, av,
522 subVals, null, null, null);
523 if (paeFilepath != null)
525 File paeFile = new File(paeFilepath);
529 paeFilepath = paeFile.getCanonicalPath();
530 } catch (IOException e)
532 paeFilepath = paeFile.getAbsolutePath();
533 addWarn("Problem with the PAE file path: '"
534 + paeFile.getPath() + "'");
538 // showing annotations from structure file or not
539 boolean ssFromStructure = avm.getFromSubValArgOrPref(
540 Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
543 // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
544 // reference annotations
545 String tftString = avm.getFromSubValArgOrPrefWithSubstitutions(
546 argParser, Arg.TEMPFAC, ArgValuesMap.Position.AFTER, av,
547 subVals, null, null, null);
548 boolean notempfac = avm.getFromSubValArgOrPref(Arg.NOTEMPFAC,
549 subVals, null, "ADD_TEMPFACT_ANN", false, true);
550 TFType tft = notempfac ? null : TFType.DEFAULT;
551 if (tftString != null && !notempfac)
553 // get kind of temperature factor annotation
556 tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT));
557 Console.debug("Obtained Temperature Factor type of '" + tft
558 + "' for structure '" + structureFilepath + "'");
559 } catch (IllegalArgumentException e)
561 // Just an error message!
562 StringBuilder sb = new StringBuilder().append("Cannot set ")
563 .append(Arg.TEMPFAC.argString()).append(" to '")
565 .append("', ignoring. Valid values are: ");
566 Iterator<TFType> it = Arrays.stream(TFType.values())
570 sb.append(it.next().toString().toLowerCase(Locale.ROOT));
574 addWarn(sb.toString());
578 String sViewerName = avm.getFromSubValArgOrPref(
579 Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER, av,
580 subVals, null, null, "jmol");
581 ViewerType viewerType = ViewerType.getFromString(sViewerName);
583 // TODO use ssFromStructure
584 StructureViewer structureViewer = StructureChooser
585 .openStructureFileForSequence(null, null, ap, seq, false,
586 structureFilepath, tft, paeFilepath, false,
587 ssFromStructure, false, viewerType);
589 if (structureViewer == null)
591 if (!StringUtils.equalsIgnoreCase(sViewerName, "none"))
593 addError("Failed to import and open structure view for file '"
594 + structureFile + "'.");
601 while (structureViewer.isBusy() && tries > 0)
604 if (structureViewer.isBusy())
608 "Waiting for viewer for " + structureFilepath);
611 if (tries == 0 && structureViewer.isBusy())
613 addWarn("Gave up waiting for structure viewer to load file '"
615 + "'. Something may have gone wrong.");
617 } catch (Exception x)
619 addError("Exception whilst waiting for structure viewer "
620 + structureFilepath, x);
624 // add StructureViewer to svMap list
627 svMap = new HashMap<>();
629 if (svMap.get(id) == null)
631 svMap.put(id, new ArrayList<>());
633 svMap.get(id).add(structureViewer);
636 "Successfully opened viewer for " + structureFilepath);
638 if (avm.containsArg(Arg.STRUCTUREIMAGE))
640 for (ArgValue structureImageArgValue : avm
641 .getArgValueList(Arg.STRUCTUREIMAGE))
643 String structureImageFilename = argParser.makeSubstitutions(
644 structureImageArgValue.getValue(), id, true);
645 if (structureViewer != null && structureImageFilename != null)
647 SubVals structureImageSubVals = null;
648 structureImageSubVals = structureImageArgValue.getSubVals();
649 File structureImageFile = new File(structureImageFilename);
650 String width = avm.getValueFromSubValOrArg(
651 structureImageArgValue, Arg.WIDTH,
652 structureImageSubVals);
653 String height = avm.getValueFromSubValOrArg(
654 structureImageArgValue, Arg.HEIGHT,
655 structureImageSubVals);
656 String scale = avm.getValueFromSubValOrArg(
657 structureImageArgValue, Arg.SCALE,
658 structureImageSubVals);
659 String renderer = avm.getValueFromSubValOrArg(
660 structureImageArgValue, Arg.TEXTRENDERER,
661 structureImageSubVals);
662 String typeS = avm.getValueFromSubValOrArg(
663 structureImageArgValue, Arg.TYPE,
664 structureImageSubVals);
665 if (typeS == null || typeS.length() == 0)
667 typeS = FileUtils.getExtension(structureImageFile);
672 imageType = Enum.valueOf(TYPE.class,
673 typeS.toUpperCase(Locale.ROOT));
674 } catch (IllegalArgumentException e)
676 addWarn("Do not know image format '" + typeS
678 imageType = TYPE.PNG;
680 BitmapImageSizing userBis = ImageMaker
681 .parseScaleWidthHeightStrings(scale, width, height);
684 // DON'T TRY TO EXPORT IF VIEWER IS UNSUPPORTED
685 if (viewerType != ViewerType.JMOL)
687 addWarn("Cannot export image for structure viewer "
688 + viewerType.name() + " yet");
693 // Apply the temporary colourscheme to the linked alignment
694 // TODO: enhance for multiple linked alignments.
696 String imageColour = avm.getValueFromSubValOrArg(
697 structureImageArgValue, Arg.IMAGECOLOUR,
698 structureImageSubVals);
699 ColourSchemeI originalColourScheme = this
700 .getColourScheme(af);
701 this.colourAlignFrame(af, imageColour);
704 // custom image background colour
706 String bgcolourstring = avm.getValueFromSubValOrArg(
707 structureImageArgValue, Arg.BGCOLOUR,
708 structureImageSubVals);
709 Color bgcolour = null;
710 if (bgcolourstring != null && bgcolourstring.length() > 0)
712 bgcolour = ColorUtils.parseColourString(bgcolourstring);
713 if (bgcolour == null)
716 "Background colour string '" + bgcolourstring
717 + "' not recognised -- using default");
721 JalviewStructureDisplayI sview = structureViewer
722 .getJalviewStructureDisplay();
724 File sessionToRestore = null;
726 List<StructureCommandI> extraCommands = new ArrayList<>();
728 if (extraCommands.size() > 0 || bgcolour != null)
732 sessionToRestore = sview.saveSession();
733 } catch (Throwable t)
736 "Unable to save temporary session file before custom structure view export operation.");
743 if (bgcolour != null)
745 sview.getBinding().setBackgroundColour(bgcolour);
748 sview.getBinding().executeCommands(extraCommands, false,
749 "Executing Custom Commands");
751 // and export the view as an image
752 boolean success = this.checksBeforeWritingToFile(avm,
753 subVals, false, structureImageFilename,
754 "structure image", isError);
760 Console.debug("Rendering image to " + structureImageFile);
762 // TODO - extend StructureViewer / Binding with makePDBImage so
763 // we can do this with every viewer
768 // We don't expect class cast exception
769 AppJmol jmol = (AppJmol) sview;
770 jmol.makePDBImage(structureImageFile, imageType, renderer,
772 Console.info("Exported structure image to "
773 + structureImageFile);
775 // RESTORE SESSION AFTER EXPORT IF NEED BE
776 if (sessionToRestore != null)
778 Console.debug("Restoring session from "
781 sview.getBinding().restoreSession(sessionToRestore.getAbsolutePath());
784 } catch (ImageOutputException ioexec)
787 "Unexpected error when restoring structure viewer session after custom view operations.");
793 this.colourAlignFrame(af, originalColourScheme);
794 } catch (Exception t)
796 addError("Unexpected error when restoring colourscheme to alignment after temporary change for export.",t);
802 argParser.setStructureFilename(null);
809 AlignFrame af = afMap.get(id);
812 af.setWrapFormat(wrap, true);
817 boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
820 AlignFrame af = afMap.get(id);
821 for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
822 .findAnnotation(PDBChain.class.getName().toString()))
824 AnnotationColourGradient acg = new AnnotationColourGradient(aa,
825 af.alignPanel.av.getGlobalColourScheme(), 0);
826 acg.setSeqAssociated(true);
827 af.changeColour(acg);
828 Console.info("Changed colour " + acg.toString());
833 return theseArgsWereParsed && !isError;
836 protected void processGroovyScript(String id)
838 ArgValuesMap avm = argParser.getLinkedArgs(id);
839 AlignFrame af = afMap.get(id);
843 addWarn("Did not have an alignment window for id=" + id);
847 if (avm.containsArg(Arg.GROOVY))
849 String groovyscript = avm.getValue(Arg.GROOVY);
850 if (groovyscript != null)
852 // Execute the groovy script after we've done all the rendering stuff
853 // and before any images or figures are generated.
854 Console.info("Executing script " + groovyscript);
855 Jalview.getInstance().executeGroovyScript(groovyscript, af);
860 protected boolean processImages(String id)
862 ArgValuesMap avm = argParser.getLinkedArgs(id);
863 AlignFrame af = afMap.get(id);
867 addWarn("Did not have an alignment window for id=" + id);
871 Boolean isError = Boolean.valueOf(false);
872 if (avm.containsArg(Arg.IMAGE))
874 for (ArgValue imageAv : avm.getArgValueList(Arg.IMAGE))
876 String val = imageAv.getValue();
877 SubVals imageSubVals = imageAv.getSubVals();
878 String fileName = imageSubVals.getContent();
879 File file = new File(fileName);
880 String name = af.getName();
881 String renderer = avm.getValueFromSubValOrArg(imageAv,
882 Arg.TEXTRENDERER, imageSubVals);
883 if (renderer == null)
885 String type = "png"; // default
887 String scale = avm.getValueFromSubValOrArg(imageAv, Arg.SCALE,
889 String width = avm.getValueFromSubValOrArg(imageAv, Arg.WIDTH,
891 String height = avm.getValueFromSubValOrArg(imageAv, Arg.HEIGHT,
893 BitmapImageSizing userBis = ImageMaker
894 .parseScaleWidthHeightStrings(scale, width, height);
896 type = avm.getValueFromSubValOrArg(imageAv, Arg.TYPE, imageSubVals);
897 if (type == null && fileName != null)
899 for (String ext : new String[] { "svg", "png", "html", "eps" })
901 if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
907 // for moment we disable JSON export
908 Cache.setPropsAreReadOnly(true);
909 Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
911 String imageColour = avm.getValueFromSubValOrArg(imageAv,
912 Arg.IMAGECOLOUR, imageSubVals);
913 ColourSchemeI originalColourScheme = this.getColourScheme(af);
914 this.colourAlignFrame(af, imageColour);
916 Console.info("Writing " + file);
918 boolean success = checksBeforeWritingToFile(avm, imageSubVals,
919 false, fileName, "image", isError);
931 Console.debug("Outputting type '" + type + "' to " + fileName);
932 af.createSVG(file, renderer);
936 Console.debug("Outputting type '" + type + "' to " + fileName);
937 af.createPNG(file, null, userBis);
941 Console.debug("Outputting type '" + type + "' to " + fileName);
942 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
943 htmlSVG.exportHTML(fileName, renderer);
948 "Outputting BioJS MSA Viwer HTML file: " + fileName);
951 BioJsHTMLOutput.refreshVersionInfo(
952 BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
953 } catch (URISyntaxException e)
957 BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel);
958 bjs.exportHTML(fileName);
962 Console.debug("Outputting EPS file: " + fileName);
963 af.createEPS(file, renderer);
967 Console.debug("Outputting ImageMap file: " + fileName);
968 af.createImageMap(file, name);
972 addWarn(Arg.IMAGE.argString() + " type '" + type
973 + "' not known. Ignoring");
976 } catch (Exception ioex)
978 addError("Unexpected error during export to '" + fileName + "'",
983 this.colourAlignFrame(af, originalColourScheme);
989 protected boolean processOutput(String id)
991 ArgValuesMap avm = argParser.getLinkedArgs(id);
992 AlignFrame af = afMap.get(id);
996 addWarn("Did not have an alignment window for id=" + id);
1000 Boolean isError = Boolean.valueOf(false);
1002 if (avm.containsArg(Arg.OUTPUT))
1004 for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
1006 String val = av.getValue();
1007 SubVals subVals = av.getSubVals();
1008 String fileName = subVals.getContent();
1009 boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
1010 File file = new File(fileName);
1012 String name = af.getName();
1013 String format = avm.getValueFromSubValOrArg(av, Arg.FORMAT,
1015 FileFormats ffs = FileFormats.getInstance();
1016 List<String> validFormats = ffs.getWritableFormats(false);
1018 FileFormatI ff = null;
1019 if (format == null && fileName != null)
1021 FORMAT: for (String fname : validFormats)
1023 FileFormatI tff = ffs.forName(fname);
1024 String[] extensions = tff.getExtensions().split(",");
1025 for (String ext : extensions)
1027 if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
1030 format = ff.getName();
1036 if (ff == null && format != null)
1038 ff = ffs.forName(format);
1044 ff = FileFormat.Fasta;
1048 StringBuilder validSB = new StringBuilder();
1049 for (String f : validFormats)
1051 if (validSB.length() > 0)
1052 validSB.append(", ");
1054 FileFormatI tff = ffs.forName(f);
1055 validSB.append(" (");
1056 validSB.append(tff.getExtensions());
1057 validSB.append(")");
1060 addError("No valid format specified for "
1061 + Arg.OUTPUT.argString() + ". Valid formats are "
1062 + validSB.toString() + ".");
1067 boolean success = checksBeforeWritingToFile(avm, subVals, true,
1068 fileName, ff.getName(), isError);
1074 boolean backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVals,
1075 null, Platform.isHeadless() ? null : BackupFiles.ENABLED,
1076 !Platform.isHeadless());
1078 Console.info("Writing " + fileName);
1080 af.saveAlignment(fileName, ff, stdout, backups);
1081 if (af.isSaveAlignmentSuccessful())
1083 Console.debug("Written alignment '" + name + "' in "
1084 + ff.getName() + " format to '" + file + "'");
1088 addError("Error writing file '" + file + "' in " + ff.getName()
1099 private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
1102 SubVals subVals = av.getSubVals();
1103 ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID, true);
1104 SequenceI seq = null;
1105 if (subVals == null && idAv == null)
1107 if (af == null || af.getCurrentView() == null)
1111 AlignmentI al = af.getCurrentView().getAlignment();
1116 if (subVals != null)
1118 if (subVals.has(Arg.SEQID.getName()))
1120 seq = al.findName(subVals.get(Arg.SEQID.getName()));
1122 else if (-1 < subVals.getIndex()
1123 && subVals.getIndex() < al.getSequences().size())
1125 seq = al.getSequenceAt(subVals.getIndex());
1128 if (seq == null && idAv != null)
1130 seq = al.findName(idAv.getValue());
1135 public AlignFrame[] getAlignFrames()
1137 AlignFrame[] afs = null;
1140 afs = (AlignFrame[]) afMap.values().toArray();
1146 public List<StructureViewer> getStructureViewers()
1148 List<StructureViewer> svs = null;
1151 for (List<StructureViewer> svList : svMap.values())
1155 svs = new ArrayList<>();
1163 private void colourAlignFrame(AlignFrame af, String colour)
1165 // use string "none" to remove colour scheme
1166 if (colour != null && "" != colour)
1168 ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
1169 af.getViewport(), af.getViewport().getAlignment(), colour);
1170 if (cs == null && !StringUtils.equalsIgnoreCase(colour, "none"))
1172 addWarn("Couldn't parse '" + colour + "' as a colourscheme.");
1176 Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
1177 colourAlignFrame(af, cs);
1182 private void colourAlignFrame(AlignFrame af, ColourSchemeI cs)
1184 // Note that cs == null removes colour scheme from af
1185 af.changeColour(cs);
1188 private ColourSchemeI getColourScheme(AlignFrame af)
1190 return af.getViewport().getGlobalColourScheme();
1193 private void addInfo(String errorMessage)
1195 Console.info(errorMessage);
1196 errors.add(errorMessage);
1199 private void addWarn(String errorMessage)
1201 Console.warn(errorMessage);
1202 errors.add(errorMessage);
1205 private void addError(String errorMessage)
1207 addError(errorMessage, null);
1210 private void addError(String errorMessage, Exception e)
1212 Console.error(errorMessage, e);
1213 errors.add(errorMessage);
1216 private boolean checksBeforeWritingToFile(ArgValuesMap avm,
1217 SubVals subVal, boolean includeBackups, String filename,
1218 String adjective, Boolean isError)
1220 File file = new File(filename);
1222 boolean overwrite = avm.getFromSubValArgOrPref(Arg.OVERWRITE, subVal,
1223 null, "OVERWRITE_OUTPUT", false);
1224 boolean stdout = false;
1225 boolean backups = false;
1228 stdout = ArgParser.STDOUTFILENAME.equals(filename);
1229 // backups. Use the Arg.BACKUPS or subval "backups" setting first,
1230 // otherwise if headless assume false, if not headless use the user
1231 // preference with default true.
1232 backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVal, null,
1233 Platform.isHeadless() ? null : BackupFiles.ENABLED,
1234 !Platform.isHeadless());
1237 if (file.exists() && !(overwrite || backups || stdout))
1239 addWarn("Won't overwrite file '" + filename + "' without "
1240 + Arg.OVERWRITE.argString()
1241 + (includeBackups ? " or " + Arg.BACKUPS.argString() : "")
1246 boolean mkdirs = avm.getFromSubValArgOrPref(Arg.MKDIRS, subVal, null,
1247 "MKDIRS_OUTPUT", false);
1249 if (!FileUtils.checkParentDir(file, mkdirs))
1251 addError("Directory '"
1252 + FileUtils.getParentDir(file).getAbsolutePath()
1253 + "' does not exist for " + adjective + " file '" + filename
1255 + (mkdirs ? "" : " Try using " + Arg.MKDIRS.argString()));
1263 public List<String> getErrors()
1268 public String errorsToString()
1270 StringBuilder sb = new StringBuilder();
1271 for (String error : errors)
1273 if (sb.length() > 0)
1275 sb.append("- " + error);
1277 return sb.toString();