package jalview.bin; import java.io.File; import java.io.IOException; import java.net.URISyntaxException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.EnumSet; import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Locale; import java.util.Map; import jalview.analysis.AlignmentUtils; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.argparser.Arg; import jalview.bin.argparser.ArgParser; import jalview.bin.argparser.ArgParser.Position; import jalview.bin.argparser.ArgValue; import jalview.bin.argparser.ArgValuesMap; import jalview.bin.argparser.SubVals; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder; import jalview.gui.AlignFrame; import jalview.gui.AlignmentPanel; import jalview.gui.AppJmol; import jalview.gui.Desktop; import jalview.gui.Preferences; import jalview.gui.StructureChooser; import jalview.gui.StructureViewer; import jalview.gui.StructureViewer.ViewerType; import jalview.io.AppletFormatAdapter; import jalview.io.BackupFiles; import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatException; import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; import jalview.io.NewickFile; import jalview.io.exceptions.ImageOutputException; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.structure.StructureImportSettings.TFType; import jalview.structure.StructureSelectionManager; import jalview.util.FileUtils; import jalview.util.HttpUtils; import jalview.util.ImageMaker; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.imagemaker.BitmapImageSizing; public class Commands { Desktop desktop; private boolean headless; private ArgParser argParser; private Map afMap; private boolean commandArgsProvided = false; private boolean argsWereParsed = false; public Commands(ArgParser argparser, boolean headless) { this(Desktop.instance, argparser, headless); } public Commands(Desktop d, ArgParser argparser, boolean h) { argParser = argparser; headless = h; desktop = d; afMap = new HashMap<>(); if (argparser != null) { processArgs(argparser, headless); } } private boolean processArgs(ArgParser argparser, boolean h) { argParser = argparser; headless = h; boolean theseArgsWereParsed = false; if (argParser != null && argParser.getLinkedIds() != null) { for (String id : argParser.getLinkedIds()) { ArgValuesMap avm = argParser.getLinkedArgs(id); theseArgsWereParsed = true; theseArgsWereParsed &= processLinked(id); processGroovyScript(id); boolean processLinkedOkay = theseArgsWereParsed; // wait around until alignFrame isn't busy AlignFrame af=afMap.get(id); while (af!=null && af.getViewport().isCalcInProgress()) { try { Thread.sleep(25); } catch (Exception q) {}; } theseArgsWereParsed &= processImages(id); if (processLinkedOkay) theseArgsWereParsed &= processOutput(id); // close ap if (avm.getBoolean(Arg.CLOSE)) { af = afMap.get(id); if (af != null) { af.closeMenuItem_actionPerformed(true); } } } } if (argParser.getBoolean(Arg.QUIT)) { Jalview.getInstance().quit(); return true; } // carry on with jalview.bin.Jalview argsWereParsed = theseArgsWereParsed; return argsWereParsed; } public boolean commandArgsProvided() { return commandArgsProvided; } public boolean argsWereParsed() { return argsWereParsed; } protected boolean processUnlinked(String id) { return processLinked(id); } protected boolean processLinked(String id) { boolean theseArgsWereParsed = false; ArgValuesMap avm = argParser.getLinkedArgs(id); if (avm == null) return true; /* * // script to execute after all loading is completed one way or another String * groovyscript = m.get(Arg.GROOVY) == null ? null : * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null : * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null; * DataSourceType protocol = null; */ if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN)) { commandArgsProvided = true; long progress = -1; boolean first = true; boolean progressBarSet = false; AlignFrame af; // Combine the APPEND and OPEN files into one list, along with whether it // was APPEND or OPEN List openAvList = new ArrayList<>(); openAvList.addAll(avm.getArgValueList(Arg.OPEN)); openAvList.addAll(avm.getArgValueList(Arg.APPEND)); // sort avlist based on av.getArgIndex() Collections.sort(openAvList); for (ArgValue av : openAvList) { Arg a = av.getArg(); SubVals sv = av.getSubVals(); String openFile = av.getValue(); if (openFile == null) continue; theseArgsWereParsed = true; if (first) { first = false; if (!headless && desktop != null) { desktop.setProgressBar( MessageManager.getString( "status.processing_commandline_args"), progress = System.currentTimeMillis()); progressBarSet = true; } } if (!Platform.isJS()) /** * ignore in JavaScript -- can't just file existence - could load it? * * @j2sIgnore */ { if (!HttpUtils.startsWithHttpOrHttps(openFile)) { if (!(new File(openFile)).exists()) { Console.warn("Can't find file '" + openFile + "'"); } } } DataSourceType protocol = AppletFormatAdapter .checkProtocol(openFile); FileFormatI format = null; try { format = new IdentifyFile().identify(openFile, protocol); } catch (FileFormatException e1) { Console.error("Unknown file format for '" + openFile + "'"); } af = afMap.get(id); // When to open a new AlignFrame if (af == null || "true".equals(av.getSubVal("new")) || a == Arg.OPEN || format == FileFormat.Jalview) { if (a == Arg.OPEN) { Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa", openFile); } Console.debug( "Opening '" + openFile + "' in new alignment frame"); FileLoader fileLoader = new FileLoader(!headless); af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format); // wrap alignment? boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null, "WRAP_ALIGNMENT", false); af.getCurrentView().setWrapAlignment(wrap); // colour alignment? String colour = ArgParser.getFromSubValArgOrPref(avm, av, Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", ""); if ("" != colour) { ColourSchemeI cs = ColourSchemeProperty.getColourScheme( af.getViewport(), af.getViewport().getAlignment(), colour); if (cs==null && !"None".equals(colour)) { Console.warn("Couldn't parse '"+colour+"' as a colourscheme."); } else { af.changeColour(cs); } Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour); } // Change alignment frame title String title = ArgParser.getFromSubValArgOrPref(avm, av, Arg.TITLE, sv, null, null, null); if (title != null) { af.setTitle(title); Jalview.testoutput(argParser, Arg.TITLE, "test title", title); } // Add features String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av, Arg.FEATURES, sv); if (featuresfile != null) { af.parseFeaturesFile(featuresfile, AppletFormatAdapter.checkProtocol(featuresfile)); Jalview.testoutput(argParser, Arg.FEATURES, "examples/testdata/plantfdx.features", featuresfile); } // Add annotations from file String annotationsfile = ArgParser.getValueFromSubValOrArg(avm, av, Arg.ANNOTATIONS, sv); if (annotationsfile != null) { af.loadJalviewDataFile(annotationsfile, null, null, null); Jalview.testoutput(argParser, Arg.ANNOTATIONS, "examples/testdata/plantfdx.annotations", annotationsfile); } // Set or clear the sortbytree flag boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm, Arg.SORTBYTREE, sv); if (sortbytree) { af.getViewport().setSortByTree(true); Jalview.testoutput(argParser, Arg.SORTBYTREE); } // Load tree from file String treefile = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TREE, sv); if (treefile != null) { try { NewickFile nf = new NewickFile(treefile, AppletFormatAdapter.checkProtocol(treefile)); af.getViewport().setCurrentTree( af.showNewickTree(nf, treefile).getTree()); Jalview.testoutput(argParser, Arg.TREE, "examples/testdata/uniref50_test_tree", treefile); } catch (IOException e) { Console.warn("Couldn't add tree " + treefile, e); } } // Show secondary structure annotations? boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm, Arg.SHOWSSANNOTATIONS, av.getSubVals(), null, "STRUCT_FROM_PDB", true); af.setAnnotationsVisibility(showSSAnnotations, true, false); // Show sequence annotations? boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm, Arg.SHOWANNOTATIONS, av.getSubVals(), null, "SHOW_ANNOTATIONS", true); af.setAnnotationsVisibility(showAnnotations, false, true); // show temperature factor annotations? if (avm.getBoolean(Arg.NOTEMPFAC)) { // do this better (annotation types?) List hideThese = new ArrayList<>(); hideThese.add("Temperature Factor"); hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL); AlignmentUtils.showOrHideSequenceAnnotations( af.getCurrentView().getAlignment(), hideThese, null, false, false); } // store the AlignFrame for this id afMap.put(id, af); // is it its own structure file? if (format.isStructureFile()) { StructureSelectionManager ssm = StructureSelectionManager .getStructureSelectionManager(Desktop.instance); SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0); ssm.computeMapping(false, new SequenceI[] { seq }, null, openFile, DataSourceType.FILE, null, null, null, false); } } else { Console.debug( "Opening '" + openFile + "' in existing alignment frame"); DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile) ? DataSourceType.URL : DataSourceType.FILE; FileLoader fileLoader = new FileLoader(!headless); fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null, false); } Console.debug("Command " + Arg.APPEND + " executed successfully!"); } if (first) // first=true means nothing opened { if (headless) { Jalview.exit("Could not open any files in headless mode", 1); } else { Console.warn("No more files to open"); } } if (progressBarSet && desktop != null) desktop.setProgressBar(null, progress); } // open the structure (from same PDB file or given PDBfile) if (!avm.getBoolean(Arg.NOSTRUCTURE)) { AlignFrame af = afMap.get(id); if (avm.containsArg(Arg.STRUCTURE)) { commandArgsProvided = true; for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE)) { String val = av.getValue(); SubVals subVals = av.getSubVals(); SequenceI seq = getSpecifiedSequence(af, avm, av); if (seq == null) { // Could not find sequence from subId, let's assume the first // sequence in the alignframe AlignmentI al = af.getCurrentView().getAlignment(); seq = al.getSequenceAt(0); } if (seq == null) { Console.warn("Could not find sequence for argument " + Arg.STRUCTURE.argString() + "=" + val); // you probably want to continue here, not break // break; continue; } File structureFile = null; if (subVals.getContent() != null && subVals.getContent().length() != 0) { structureFile = new File(subVals.getContent()); Console.debug("Using structure file (from argument) '" + structureFile.getAbsolutePath() + "'"); } // TRY THIS /* * PDBEntry fileEntry = new AssociatePdbFileWithSeq() * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE, * selectedSequence, true, Desktop.instance); * * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new * SequenceI[] { selectedSequence }); * */ /* THIS DOESN'T WORK */ else if (seq.getAllPDBEntries() != null && seq.getAllPDBEntries().size() > 0) { structureFile = new File( seq.getAllPDBEntries().elementAt(0).getFile()); Console.debug("Using structure file (from sequence) '" + structureFile.getAbsolutePath() + "'"); } if (structureFile == null) { Console.warn("Not provided structure file with '" + val + "'"); continue; } if (!structureFile.exists()) { Console.warn("Structure file '" + structureFile.getAbsoluteFile() + "' not found."); continue; } Console.debug("Using structure file " + structureFile.getAbsolutePath()); // open structure view AlignmentPanel ap = af.alignPanel; if (headless) { Cache.setProperty(Preferences.STRUCTURE_DISPLAY, StructureViewer.ViewerType.JMOL.toString()); } String structureFilepath = structureFile.getAbsolutePath(); // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX String paeFilepath = ArgParser .getFromSubValArgOrPrefWithSubstitutions(argParser, avm, Arg.PAEMATRIX, Position.AFTER, av, subVals, null, null, null); if (paeFilepath != null) { File paeFile = new File(paeFilepath); try { paeFilepath = paeFile.getCanonicalPath(); } catch (IOException e) { paeFilepath = paeFile.getAbsolutePath(); Console.warn("Problem with the PAE file path: '" + paeFile.getPath() + "'"); } } // showing annotations from structure file or not boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm, Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB", true); // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds // reference annotations String tftString = ArgParser .getFromSubValArgOrPrefWithSubstitutions(argParser, avm, Arg.TEMPFAC, Position.AFTER, av, subVals, null, null, null); boolean notempfac = ArgParser.getFromSubValArgOrPref(avm, Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false, true); TFType tft = notempfac ? null : TFType.DEFAULT; if (tftString != null && !notempfac) { // get kind of temperature factor annotation try { tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT)); Console.debug("Obtained Temperature Factor type of '" + tft + "' for structure '" + structureFilepath + "'"); } catch (IllegalArgumentException e) { // Just an error message! StringBuilder sb = new StringBuilder().append("Cannot set ") .append(Arg.TEMPFAC.argString()).append(" to '") .append(tft) .append("', ignoring. Valid values are: "); Iterator it = Arrays.stream(TFType.values()) .iterator(); while (it.hasNext()) { sb.append(it.next().toString().toLowerCase(Locale.ROOT)); if (it.hasNext()) sb.append(", "); } Console.warn(sb.toString()); } } String sViewer = ArgParser.getFromSubValArgOrPref(avm, Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null, null, "jmol"); ViewerType viewerType = null; if (!"none".equals(sViewer)) { for (ViewerType v : EnumSet.allOf(ViewerType.class)) { String name = v.name().toLowerCase(Locale.ROOT) .replaceAll(" ", ""); if (sViewer.equals(name)) { viewerType = v; break; } } } // TODO use ssFromStructure StructureViewer sv = StructureChooser .openStructureFileForSequence(null, null, ap, seq, false, structureFilepath, tft, paeFilepath, false, ssFromStructure, false, viewerType); if (headless) { sv.setAsync(false); } String structureImageFilename = ArgParser.getValueFromSubValOrArg( avm, av, Arg.STRUCTUREIMAGE, subVals); if (sv != null && structureImageFilename != null) { ArgValue siAv = avm.getClosestNextArgValueOfArg(av, Arg.STRUCTUREIMAGE); SubVals sisv = null; if (structureImageFilename.equals(siAv.getValue())) { sisv = siAv.getSubVals(); } File structureImageFile = new File(structureImageFilename); String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.STRUCTUREIMAGEWIDTH, sisv); String height = ArgParser.getValueFromSubValOrArg(avm, av, Arg.STRUCTUREIMAGEHEIGHT, sisv); String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.STRUCTUREIMAGESCALE, sisv); String renderer = ArgParser.getValueFromSubValOrArg(avm, av, Arg.STRUCTUREIMAGETEXTRENDERER, sisv); String typeS = ArgParser.getValueFromSubValOrArg(avm, av, Arg.STRUCTUREIMAGETYPE, sisv); if (typeS == null || typeS.length() == 0) { typeS = FileUtils.getExtension(structureImageFile); } TYPE imageType; try { imageType = Enum.valueOf(TYPE.class, typeS.toUpperCase(Locale.ROOT)); } catch (IllegalArgumentException e) { Console.warn("Do not know image format '" + typeS + "', using PNG"); imageType = TYPE.PNG; } BitmapImageSizing userBis = ImageMaker .parseScaleWidthHeightStrings(scale, width, height); switch (StructureViewer.getViewerType()) { case JMOL: try { Thread.sleep(1000); } catch (InterruptedException e) { // TODO Auto-generated catch block e.printStackTrace(); } JalviewStructureDisplayI sview = sv .getJalviewStructureDisplay(); if (sview instanceof AppJmol) { AppJmol jmol = (AppJmol) sview; try { jmol.makePDBImage(structureImageFile, imageType, renderer, userBis); } catch (ImageOutputException ioexc) { Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc); } } break; default: Console.warn("Cannot export image for structure viewer " + sv.getViewerType() + " yet"); break; } } } } } /* boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING); if (doShading) { AlignFrame af = afMap.get(id); for (AlignmentAnnotation aa : af.alignPanel.getAlignment() .findAnnotation(PDBChain.class.getName().toString())) { AnnotationColourGradient acg = new AnnotationColourGradient(aa, af.alignPanel.av.getGlobalColourScheme(), 0); acg.setSeqAssociated(true); af.changeColour(acg); Console.info("Changed colour " + acg.toString()); } } */ return theseArgsWereParsed; } protected void processGroovyScript(String id) { ArgValuesMap avm = argParser.getLinkedArgs(id); AlignFrame af = afMap.get(id); if (af == null) { Console.warn("Did not have an alignment window for id=" + id); return; } if (avm.containsArg(Arg.GROOVY)) { String groovyscript = avm.getValue(Arg.GROOVY); if (groovyscript != null) { // Execute the groovy script after we've done all the rendering stuff // and before any images or figures are generated. Console.info("Executing script " + groovyscript); Jalview.getInstance().executeGroovyScript(groovyscript, af); } } } protected boolean processImages(String id) { ArgValuesMap avm = argParser.getLinkedArgs(id); AlignFrame af = afMap.get(id); if (af == null) { Console.warn("Did not have an alignment window for id=" + id); return false; } if (avm.containsArg(Arg.IMAGE)) { for (ArgValue av : avm.getArgValueList(Arg.IMAGE)) { String val = av.getValue(); SubVals subVal = av.getSubVals(); String fileName = subVal.getContent(); File file = new File(fileName); String name = af.getName(); String renderer = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TEXTRENDERER, subVal); if (renderer == null) renderer = "text"; String type = "png"; // default String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE, subVal); String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH, subVal); String height = ArgParser.getValueFromSubValOrArg(avm, av, Arg.HEIGHT, subVal); BitmapImageSizing userBis = ImageMaker .parseScaleWidthHeightStrings(scale, width, height); type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal); if (type == null && fileName != null) { for (String ext : new String[] { "svg", "png", "html", "eps" }) { if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext)) { type = ext; } } } // for moment we disable JSON export Cache.setPropsAreReadOnly(true); Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false"); Console.info("Writing " + file); try { switch (type) { case "svg": Console.debug("Outputting type '" + type + "' to " + fileName); af.createSVG(file, renderer); break; case "png": Console.debug("Outputting type '" + type + "' to " + fileName); af.createPNG(file, null, userBis); break; case "html": Console.debug("Outputting type '" + type + "' to " + fileName); HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); htmlSVG.exportHTML(fileName, renderer); break; case "biojs": Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName); try { BioJsHTMLOutput.refreshVersionInfo( BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); } catch (URISyntaxException e) { e.printStackTrace(); } BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); bjs.exportHTML(fileName); break; case "eps": Console.debug("Creating EPS file: " + fileName); af.createEPS(file, name); break; case "imagemap": Console.debug("Creating ImageMap file: " + fileName); af.createImageMap(file, name); break; default: Console.warn(Arg.IMAGE.argString() + " type '" + type + "' not known. Ignoring"); break; } } catch (Exception ioex) { Console.warn("Unexpected error during export",ioex); } } } return true; } protected boolean processOutput(String id) { ArgValuesMap avm = argParser.getLinkedArgs(id); AlignFrame af = afMap.get(id); if (af == null) { Console.warn("Did not have an alignment window for id=" + id); return false; } if (avm.containsArg(Arg.OUTPUT)) { for (ArgValue av : avm.getArgValueList(Arg.OUTPUT)) { String val = av.getValue(); SubVals subVals = av.getSubVals(); String fileName = subVals.getContent(); File file = new File(fileName); boolean overwrite = ArgParser.getFromSubValArgOrPref(avm, Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false); // backups. Use the Arg.BACKUPS or subval "backups" setting first, // otherwise if headless assume false, if not headless use the user // preference with default true. boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, subVals, null, Platform.isHeadless() ? null : BackupFiles.ENABLED, !Platform.isHeadless()); // if backups is not true then --overwrite must be specified if (file.exists() && !(overwrite || backups)) { Console.error("Won't overwrite file '" + fileName + "' without " + Arg.OVERWRITE.argString() + " or " + Arg.BACKUPS.argString() + " set"); return false; } String name = af.getName(); String format = ArgParser.getValueFromSubValOrArg(avm, av, Arg.FORMAT, subVals); FileFormats ffs = FileFormats.getInstance(); List validFormats = ffs.getWritableFormats(false); FileFormatI ff = null; if (format == null && fileName != null) { FORMAT: for (String fname : validFormats) { FileFormatI tff = ffs.forName(fname); String[] extensions = tff.getExtensions().split(","); for (String ext : extensions) { if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext)) { ff = tff; format = ff.getName(); break FORMAT; } } } } if (ff == null && format != null) { ff = ffs.forName(format); } if (ff == null) { StringBuilder validSB = new StringBuilder(); for (String f : validFormats) { if (validSB.length() > 0) validSB.append(", "); validSB.append(f); FileFormatI tff = ffs.forName(f); validSB.append(" ("); validSB.append(tff.getExtensions()); validSB.append(")"); } Jalview.exit("No valid format specified for " + Arg.OUTPUT.argString() + ". Valid formats are " + validSB.toString() + ".", 1); // this return really shouldn't happen return false; } String savedBackupsPreference = Cache .getDefault(BackupFiles.ENABLED, null); Console.debug("Setting backups to " + backups); Cache.applicationProperties.put(BackupFiles.ENABLED, Boolean.toString(backups)); Console.info("Writing " + fileName); af.saveAlignment(fileName, ff); Console.debug("Returning backups to " + savedBackupsPreference); if (savedBackupsPreference != null) Cache.applicationProperties.put(BackupFiles.ENABLED, savedBackupsPreference); if (af.isSaveAlignmentSuccessful()) { Console.debug("Written alignment '" + name + "' in " + ff.getName() + " format to " + file); } else { Console.warn("Error writing file " + file + " in " + ff.getName() + " format!"); } } } return true; } private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm, ArgValue av) { SubVals subVals = av.getSubVals(); ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID); SequenceI seq = null; if (subVals == null && idAv == null) return null; if (af == null || af.getCurrentView() == null) { return null; } AlignmentI al = af.getCurrentView().getAlignment(); if (al == null) { return null; } if (subVals != null) { if (subVals.has(Arg.SEQID.getName())) { seq = al.findName(subVals.get(Arg.SEQID.getName())); } else if (-1 < subVals.getIndex() && subVals.getIndex() < al.getSequences().size()) { seq = al.getSequenceAt(subVals.getIndex()); } } else if (idAv != null) { seq = al.findName(idAv.getValue()); } return seq; } }