X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=592ac85cc6679990cb785b0dead5c16e5417330d;hb=82fb94d50a9add200efe5e89214051ce59b42f6c;hp=ba72831c4f402de84217a42bdad948a8cfd59c5d;hpb=fd86db8856109e69c21a5f4102bc8dd94664ae1f;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index ba72831..592ac85 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -1,7 +1,9 @@ package jalview.bin; +import java.awt.Color; import java.io.File; import java.io.IOException; +import java.lang.reflect.Field; import java.net.URISyntaxException; import java.util.ArrayList; import java.util.Arrays; @@ -17,13 +19,14 @@ import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Jalview.ExitCode; 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.ext.jmol.JalviewJmolBinding; +import jalview.ext.jmol.JmolCommands; import jalview.gui.AlignFrame; import jalview.gui.AlignmentPanel; import jalview.gui.AppJmol; @@ -47,6 +50,8 @@ import jalview.io.NewickFile; import jalview.io.exceptions.ImageOutputException; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsI; import jalview.structure.StructureImportSettings.TFType; import jalview.structure.StructureSelectionManager; import jalview.util.FileUtils; @@ -55,6 +60,7 @@ import jalview.util.ImageMaker; import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.util.StringUtils; import jalview.util.imagemaker.BitmapImageSizing; public class Commands @@ -290,29 +296,14 @@ public class Commands } } - // 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)) - { - addWarn("Couldn't parse '" + colour + "' as a colourscheme."); - } - else - { - af.changeColour(cs); - } - Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour); - } + // colour alignment + String colour = avm.getFromSubValArgOrPref(av, Arg.COLOUR, sv, + null, "DEFAULT_COLOUR_PROT", ""); + this.colourAlignFrame(af, colour); // Change alignment frame title - String title = ArgParser.getFromSubValArgOrPref(avm, av, - Arg.TITLE, sv, null, null, null); + String title = avm.getFromSubValArgOrPref(av, Arg.TITLE, sv, null, + null, null); if (title != null) { af.setTitle(title); @@ -320,7 +311,7 @@ public class Commands } // Add features - String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av, + String featuresfile = avm.getValueFromSubValOrArg(av, Arg.FEATURES, sv); if (featuresfile != null) { @@ -331,8 +322,8 @@ public class Commands } // Add annotations from file - String annotationsfile = ArgParser.getValueFromSubValOrArg(avm, - av, Arg.ANNOTATIONS, sv); + String annotationsfile = avm.getValueFromSubValOrArg(av, + Arg.ANNOTATIONS, sv); if (annotationsfile != null) { af.loadJalviewDataFile(annotationsfile, null, null, null); @@ -342,8 +333,8 @@ public class Commands } // Set or clear the sortbytree flag - boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm, - Arg.SORTBYTREE, sv); + boolean sortbytree = avm.getBoolFromSubValOrArg(Arg.SORTBYTREE, + sv); if (sortbytree) { af.getViewport().setSortByTree(true); @@ -351,8 +342,7 @@ public class Commands } // Load tree from file - String treefile = ArgParser.getValueFromSubValOrArg(avm, av, - Arg.TREE, sv); + String treefile = avm.getValueFromSubValOrArg(av, Arg.TREE, sv); if (treefile != null) { try @@ -371,13 +361,13 @@ public class Commands } // Show secondary structure annotations? - boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm, + boolean showSSAnnotations = avm.getFromSubValArgOrPref( Arg.SHOWSSANNOTATIONS, av.getSubVals(), null, "STRUCT_FROM_PDB", true); af.setAnnotationsVisibility(showSSAnnotations, true, false); // Show sequence annotations? - boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm, + boolean showAnnotations = avm.getFromSubValArgOrPref( Arg.SHOWANNOTATIONS, av.getSubVals(), null, "SHOW_ANNOTATIONS", true); af.setAnnotationsVisibility(showAnnotations, false, true); @@ -395,7 +385,7 @@ public class Commands } // wrap alignment? do this last for formatting reasons - wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null, + wrap = avm.getFromSubValArgOrPref(Arg.WRAP, sv, null, "WRAP_ALIGNMENT", false); // af.setWrapFormat(wrap) is applied after structures are opened for // annotation reasons @@ -454,8 +444,10 @@ public class Commands commandArgsProvided = true; for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE)) { + argParser.setStructureFilename(null); String val = av.getValue(); SubVals subVals = av.getSubVals(); + int argIndex = av.getArgIndex(); SequenceI seq = getSpecifiedSequence(af, avm, av); if (seq == null) { @@ -471,35 +463,31 @@ public class Commands + Arg.STRUCTURE.argString() + "=" + val); continue; } + String structureFilename = null; File structureFile = null; if (subVals.getContent() != null && subVals.getContent().length() != 0) { - structureFile = new File(subVals.getContent()); + structureFilename = subVals.getContent(); Console.debug("Using structure file (from argument) '" - + structureFile.getAbsolutePath() + "'"); + + structureFilename + "'"); + structureFile = new File(structureFilename); } - // 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.debug("Using structure file (from sequence) '" + + structureFile.getAbsolutePath() + "'"); + } + structureFilename = structureFile.getAbsolutePath(); } - if (structureFile == null) + if (structureFilename == null || structureFile == null) { addWarn("Not provided structure file with '" + val + "'"); continue; @@ -515,6 +503,8 @@ public class Commands Console.debug("Using structure file " + structureFile.getAbsolutePath()); + argParser.setStructureFilename(structureFilename); + // open structure view AlignmentPanel ap = af.alignPanel; if (headless) @@ -526,10 +516,9 @@ public class Commands 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); + String paeFilepath = avm.getFromSubValArgOrPrefWithSubstitutions( + argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER, av, + subVals, null, null, null); if (paeFilepath != null) { File paeFile = new File(paeFilepath); @@ -546,19 +535,17 @@ public class Commands } // showing annotations from structure file or not - boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm, + boolean ssFromStructure = avm.getFromSubValArgOrPref( 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); + String tftString = avm.getFromSubValArgOrPrefWithSubstitutions( + argParser, Arg.TEMPFAC, ArgValuesMap.Position.AFTER, av, + subVals, null, null, null); + boolean notempfac = avm.getFromSubValArgOrPref(Arg.NOTEMPFAC, + subVals, null, "ADD_TEMPFACT_ANN", false, true); TFType tft = notempfac ? null : TFType.DEFAULT; if (tftString != null && !notempfac) { @@ -587,37 +574,40 @@ public class Commands } } - String sViewer = ArgParser.getFromSubValArgOrPref(avm, - Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null, - null, "jmol"); - ViewerType viewerType = ViewerType.getFromString(sViewer); + String sViewerName = avm.getFromSubValArgOrPref( + Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER, av, + subVals, null, null, "jmol"); + ViewerType viewerType = ViewerType.getFromString(sViewerName); // TODO use ssFromStructure - StructureViewer sv = StructureChooser + StructureViewer structureViewer = StructureChooser .openStructureFileForSequence(null, null, ap, seq, false, structureFilepath, tft, paeFilepath, false, ssFromStructure, false, viewerType); - if (sv == null) + if (structureViewer == null) { - addError("Failed to import and open structure view for file '" - + structureFile + "'."); + if (!StringUtils.equalsIgnoreCase(sViewerName, "none")) + { + addError("Failed to import and open structure view for file '" + + structureFile + "'."); + } continue; } try { long tries = 1000; - while (sv.isBusy() && tries > 0) + while (structureViewer.isBusy() && tries > 0) { Thread.sleep(25); - if (sv.isBusy()) + if (structureViewer.isBusy()) { tries--; Console.debug( "Waiting for viewer for " + structureFilepath); } } - if (tries == 0 && sv.isBusy()) + if (tries == 0 && structureViewer.isBusy()) { addWarn("Gave up waiting for structure viewer to load file '" + structureFile @@ -639,90 +629,165 @@ public class Commands { svMap.put(id, new ArrayList<>()); } - svMap.get(id).add(sv); + svMap.get(id).add(structureViewer); Console.debug( "Successfully opened viewer for " + structureFilepath); - String structureImageFilename = ArgParser.getValueFromSubValOrArg( - avm, av, Arg.STRUCTUREIMAGE, subVals); - if (sv != null && structureImageFilename != null) + + if (avm.containsArg(Arg.STRUCTUREIMAGE)) { - ArgValue siAv = avm.getClosestNextArgValueOfArg(av, - Arg.STRUCTUREIMAGE); - SubVals sisv = null; - if (structureImageFilename.equals(siAv.getValue())) + for (ArgValue structureImageArgValue : avm + .getArgValueList(Arg.STRUCTUREIMAGE)) { - 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) - { - addWarn("Do not know image format '" + typeS - + "', using PNG"); - imageType = TYPE.PNG; - } - BitmapImageSizing userBis = ImageMaker - .parseScaleWidthHeightStrings(scale, width, height); - // TODO MAKE THIS VIEWER INDEPENDENT!! - switch (StructureViewer.getViewerType()) - { - case JMOL: - JalviewStructureDisplayI sview = sv - .getJalviewStructureDisplay(); - if (sview instanceof AppJmol) + String structureImageFilename = argParser.makeSubstitutions( + structureImageArgValue.getValue(), id, true); + if (structureViewer != null && structureImageFilename != null) { - AppJmol jmol = (AppJmol) sview; + SubVals structureImageSubVals = null; + structureImageSubVals = structureImageArgValue.getSubVals(); + File structureImageFile = new File(structureImageFilename); + String width = avm.getValueFromSubValOrArg( + structureImageArgValue, Arg.WIDTH, + structureImageSubVals); + String height = avm.getValueFromSubValOrArg( + structureImageArgValue, Arg.HEIGHT, + structureImageSubVals); + String scale = avm.getValueFromSubValOrArg( + structureImageArgValue, Arg.SCALE, + structureImageSubVals); + String renderer = avm.getValueFromSubValOrArg( + structureImageArgValue, Arg.TEXTRENDERER, + structureImageSubVals); + String typeS = avm.getValueFromSubValOrArg( + structureImageArgValue, Arg.TYPE, + structureImageSubVals); + if (typeS == null || typeS.length() == 0) + { + typeS = FileUtils.getExtension(structureImageFile); + } + TYPE imageType; try { - boolean success = this.checksBeforeWritingToFile(avm, - subVals, false, structureImageFilename, - "structure image", isError); - if (!success) + imageType = Enum.valueOf(TYPE.class, + typeS.toUpperCase(Locale.ROOT)); + } catch (IllegalArgumentException e) + { + addWarn("Do not know image format '" + typeS + + "', using PNG"); + imageType = TYPE.PNG; + } + BitmapImageSizing userBis = ImageMaker + .parseScaleWidthHeightStrings(scale, width, height); + + String imageColour = avm.getValueFromSubValOrArg( + structureImageArgValue, Arg.IMAGECOLOUR, + structureImageSubVals); + ColourSchemeI originalColourScheme = this + .getColourScheme(af); + this.colourAlignFrame(af, imageColour); + + List extraCommands = new ArrayList<>(); + StructureCommandsI sc; + switch (viewerType) + { + case JMOL: + sc = new JmolCommands(); + break; + default: + addWarn("Cannot export image for structure viewer " + + viewerType.name() + " yet"); + continue; + } + + String bgcolourstring = avm.getValueFromSubValOrArg( + structureImageArgValue, Arg.BGCOLOUR, + structureImageSubVals); + Color bgcolour = null; + if (bgcolourstring != null && bgcolourstring.length() > 0) + { + try + { + if (bgcolourstring.charAt(0) == '#') + { + bgcolour = Color.decode(bgcolourstring); + } + else + { + Field field = Color.class.getField(bgcolourstring); + bgcolour = (Color) field.get(null); + } + } catch (IllegalArgumentException | NoSuchFieldException + | SecurityException | IllegalAccessException nfe) { - continue; + Console.warn( + "Background colour string '" + bgcolourstring + + "' not recognised -- using black."); + bgcolour = Color.black; } + extraCommands.add(sc.setBackgroundColour(bgcolour)); + } - Console.debug("Rendering image to " + structureImageFile); - jmol.makePDBImage(structureImageFile, imageType, renderer, - userBis); - Console.debug("Finished Rendering image to " - + structureImageFile); - - } catch (ImageOutputException ioexc) + // TODO MAKE THIS VIEWER INDEPENDENT!! + switch (viewerType) { - addError("Unexpected error whilst exporting image to " - + structureImageFile, ioexc); - isError = true; + case JMOL: + JalviewStructureDisplayI sview = structureViewer + .getJalviewStructureDisplay(); + JmolCommands jc = (JmolCommands) sc; + if (sview instanceof AppJmol) + { + AppJmol jmol = (AppJmol) sview; + JalviewJmolBinding jmb = (JalviewJmolBinding) jmol + .getBinding(); + String state = new StringBuilder() + .append("JalviewCommandsStructureState_") + .append(viewerType.name()).toString(); + jmb.executeCommand(jc.saveState(state), false); + for (StructureCommandI scmd : extraCommands) + { + jmb.executeCommand(scmd, false); + } + try + { + boolean success = this.checksBeforeWritingToFile(avm, + subVals, false, structureImageFilename, + "structure image", isError); + if (!success) + { + continue; + } + + Console.debug( + "Rendering image to " + structureImageFile); + jmol.makePDBImage(structureImageFile, imageType, + renderer, userBis); + Console.debug("Finished Rendering image to " + + structureImageFile); + + } catch (ImageOutputException ioexc) + { + addError("Unexpected error whilst exporting image to " + + structureImageFile, ioexc); + isError = true; + continue; + } finally + { + jmb.executeCommand(jc.restoreState(state), false); + } + + } + break; + default: + // this shouldn't happen! + addWarn("Cannot export image for structure viewer " + + viewerType.name() + " yet"); continue; } - + this.colourAlignFrame(af, originalColourScheme); } - break; - default: - addWarn("Cannot export image for structure viewer " - + sv.getViewerType() + " yet"); - continue; } } + argParser.setStructureFilename(null); } } } @@ -794,29 +859,29 @@ public class Commands Boolean isError = Boolean.valueOf(false); if (avm.containsArg(Arg.IMAGE)) { - for (ArgValue av : avm.getArgValueList(Arg.IMAGE)) + for (ArgValue imageAv : avm.getArgValueList(Arg.IMAGE)) { - String val = av.getValue(); - SubVals subVal = av.getSubVals(); - String fileName = subVal.getContent(); + String val = imageAv.getValue(); + SubVals imageSubVals = imageAv.getSubVals(); + String fileName = imageSubVals.getContent(); File file = new File(fileName); String name = af.getName(); - String renderer = ArgParser.getValueFromSubValOrArg(avm, av, - Arg.TEXTRENDERER, subVal); + String renderer = avm.getValueFromSubValOrArg(imageAv, + Arg.TEXTRENDERER, imageSubVals); 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); + String scale = avm.getValueFromSubValOrArg(imageAv, Arg.SCALE, + imageSubVals); + String width = avm.getValueFromSubValOrArg(imageAv, Arg.WIDTH, + imageSubVals); + String height = avm.getValueFromSubValOrArg(imageAv, Arg.HEIGHT, + imageSubVals); BitmapImageSizing userBis = ImageMaker .parseScaleWidthHeightStrings(scale, width, height); - type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal); + type = avm.getValueFromSubValOrArg(imageAv, Arg.TYPE, imageSubVals); if (type == null && fileName != null) { for (String ext : new String[] { "svg", "png", "html", "eps" }) @@ -831,10 +896,15 @@ public class Commands Cache.setPropsAreReadOnly(true); Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false"); + String imageColour = avm.getValueFromSubValOrArg(imageAv, + Arg.IMAGECOLOUR, imageSubVals); + ColourSchemeI originalColourScheme = this.getColourScheme(af); + this.colourAlignFrame(af, imageColour); + Console.info("Writing " + file); - boolean success = checksBeforeWritingToFile(avm, subVal, false, - fileName, "image", isError); + boolean success = checksBeforeWritingToFile(avm, imageSubVals, + false, fileName, "image", isError); if (!success) { continue; @@ -897,6 +967,8 @@ public class Commands ioex); isError = true; } + + this.colourAlignFrame(af, originalColourScheme); } } return !isError; @@ -926,8 +998,8 @@ public class Commands File file = new File(fileName); String name = af.getName(); - String format = ArgParser.getValueFromSubValOrArg(avm, av, - Arg.FORMAT, subVals); + String format = avm.getValueFromSubValOrArg(av, Arg.FORMAT, + subVals); FileFormats ffs = FileFormats.getInstance(); List validFormats = ffs.getWritableFormats(false); @@ -987,9 +1059,8 @@ public class Commands continue; } - boolean backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, - subVals, null, - Platform.isHeadless() ? null : BackupFiles.ENABLED, + boolean backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVals, + null, Platform.isHeadless() ? null : BackupFiles.ENABLED, !Platform.isHeadless()); Console.info("Writing " + fileName); @@ -1017,7 +1088,7 @@ public class Commands ArgValue av) { SubVals subVals = av.getSubVals(); - ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID); + ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID, true); SequenceI seq = null; if (subVals == null && idAv == null) return null; @@ -1077,6 +1148,36 @@ public class Commands return svs; } + private void colourAlignFrame(AlignFrame af, String colour) + { + // use string "none" to remove colour scheme + if (colour != null && "" != colour) + { + ColourSchemeI cs = ColourSchemeProperty.getColourScheme( + af.getViewport(), af.getViewport().getAlignment(), colour); + if (cs == null && !StringUtils.equalsIgnoreCase(colour, "none")) + { + addWarn("Couldn't parse '" + colour + "' as a colourscheme."); + } + else + { + Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour); + colourAlignFrame(af, cs); + } + } + } + + private void colourAlignFrame(AlignFrame af, ColourSchemeI cs) + { + // Note that cs == null removes colour scheme from af + af.changeColour(cs); + } + + private ColourSchemeI getColourScheme(AlignFrame af) + { + return af.getViewport().getGlobalColourScheme(); + } + private void addInfo(String errorMessage) { Console.info(errorMessage); @@ -1106,8 +1207,8 @@ public class Commands { File file = new File(filename); - boolean overwrite = ArgParser.getFromSubValArgOrPref(avm, Arg.OVERWRITE, - subVal, null, "OVERWRITE_OUTPUT", false); + boolean overwrite = avm.getFromSubValArgOrPref(Arg.OVERWRITE, subVal, + null, "OVERWRITE_OUTPUT", false); boolean stdout = false; boolean backups = false; if (includeBackups) @@ -1116,8 +1217,8 @@ public class Commands // 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. - backups = ArgParser.getFromSubValArgOrPref(avm, Arg.BACKUPS, subVal, - null, Platform.isHeadless() ? null : BackupFiles.ENABLED, + backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVal, null, + Platform.isHeadless() ? null : BackupFiles.ENABLED, !Platform.isHeadless()); } @@ -1130,8 +1231,8 @@ public class Commands return false; } - boolean mkdirs = ArgParser.getFromSubValArgOrPref(avm, Arg.MKDIRS, - subVal, null, "MKDIRS_OUTPUT", false); + boolean mkdirs = avm.getFromSubValArgOrPref(Arg.MKDIRS, subVal, null, + "MKDIRS_OUTPUT", false); if (!FileUtils.checkParentDir(file, mkdirs)) {