X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=5d3b50d69414d0721327d32ab3c52148929fe109;hb=ca160187a050f6d4e50158cd5b51f75c83a7179e;hp=81641821b1a362d1c7e2e2806e6fb1f3c99c4f74;hpb=4fbf1d10221c2780c3ec9c8f9cc080ffae392c61;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 8164182..5d3b50d 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -1,5 +1,6 @@ package jalview.bin; +import java.awt.Color; import java.io.File; import java.io.IOException; import java.net.URISyntaxException; @@ -14,9 +15,9 @@ import java.util.Map; import jalview.analysis.AlignmentUtils; 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; @@ -46,14 +47,17 @@ import jalview.io.NewickFile; import jalview.io.exceptions.ImageOutputException; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; +import jalview.structure.StructureCommandI; import jalview.structure.StructureImportSettings.TFType; import jalview.structure.StructureSelectionManager; +import jalview.util.ColorUtils; 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.StringUtils; import jalview.util.imagemaker.BitmapImageSizing; public class Commands @@ -72,6 +76,8 @@ public class Commands private boolean argsWereParsed = false; + private List errors = new ArrayList<>(); + public Commands(ArgParser argparser, boolean headless) { this(Desktop.instance, argparser, headless); @@ -138,9 +144,22 @@ public class Commands } } + + // report errors - if any + String errorsRaised = errorsToString(); + if (errorsRaised.trim().length() > 0) + { + Console.warn( + "The following errors and warnings occurred whilst processing files:\n" + + errorsRaised); + } + // gui errors reported in Jalview + if (argParser.getBoolean(Arg.QUIT)) { - Jalview.getInstance().quit(); + Jalview.getInstance().exit( + "Exiting due to " + Arg.QUIT.argString() + " argument.", + ExitCode.OK); return true; } // carry on with jalview.bin.Jalview @@ -163,7 +182,11 @@ public class Commands boolean theseArgsWereParsed = false; ArgValuesMap avm = argParser.getLinkedArgs(id); if (avm == null) + { return true; + } + + Boolean isError = Boolean.valueOf(false); // set wrap scope here so it can be applied after structures are opened boolean wrap = false; @@ -216,7 +239,8 @@ public class Commands { if (!(new File(openFile)).exists()) { - Console.warn("Can't find file '" + openFile + "'"); + addError("Can't find file '" + openFile + "'"); + isError = true; continue; } } @@ -231,7 +255,8 @@ public class Commands format = new IdentifyFile().identify(openFile, protocol); } catch (FileFormatException e1) { - Console.error("Unknown file format for '" + openFile + "'"); + addError("Unknown file format for '" + openFile + "'"); + isError = true; continue; } @@ -249,49 +274,37 @@ public class Commands Console.debug( "Opening '" + openFile + "' in new alignment frame"); FileLoader fileLoader = new FileLoader(!headless); - boolean xception=false; - try { + boolean xception = false; + try + { af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format); } catch (Throwable thr) { - xception=true; - Console.error("Couldn't open '"+openFile+"' as "+format+" "+thr.getLocalizedMessage()+ " (Enable debug for full stack trace)"); - Console.debug("Exception when opening '"+openFile+"'",thr); - } - finally + xception = true; + addError("Couldn't open '" + openFile + "' as " + format + " " + + thr.getLocalizedMessage() + + " (Enable debug for full stack trace)"); + isError = true; + Console.debug("Exception when opening '" + openFile + "'", thr); + } finally { - if (af==null && !xception) + if (af == null && !xception) { - Console.info("Ignoring '"+openFile+"' - no alignment data found."); + addInfo("Ignoring '" + openFile + + "' - no alignment data found."); continue; } } - // 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); - } + // 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); @@ -299,7 +312,7 @@ public class Commands } // Add features - String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av, + String featuresfile = avm.getValueFromSubValOrArg(av, Arg.FEATURES, sv); if (featuresfile != null) { @@ -310,8 +323,8 @@ 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); @@ -321,8 +334,8 @@ 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); @@ -330,8 +343,7 @@ 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 @@ -344,18 +356,19 @@ public class Commands "examples/testdata/uniref50_test_tree", treefile); } catch (IOException e) { - Console.warn("Couldn't add tree " + treefile, e); + addError("Couldn't add tree " + treefile, e); + isError = true; } } // 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); @@ -373,7 +386,7 @@ 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 @@ -410,11 +423,12 @@ public class Commands { if (headless) { - Jalview.exit("Could not open any files in headless mode", 1); + Jalview.exit("Could not open any files in headless mode", + ExitCode.NO_FILES); } else { - Console.warn("No more files to open"); + Console.info("No more files to open"); } } if (progressBarSet && desktop != null) @@ -431,8 +445,10 @@ 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) { @@ -444,56 +460,52 @@ public class Commands if (seq == null) { - Console.warn("Could not find sequence for argument " + addWarn("Could not find sequence for argument " + Arg.STRUCTURE.argString() + "=" + val); - // you probably want to continue here, not break - // break; 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) { - Console.warn("Not provided structure file with '" + val + "'"); + addWarn("Not provided structure file with '" + val + "'"); continue; } if (!structureFile.exists()) { - Console.warn("Structure file '" - + structureFile.getAbsoluteFile() + "' not found."); + addWarn("Structure file '" + structureFile.getAbsoluteFile() + + "' not found."); continue; } Console.debug("Using structure file " + structureFile.getAbsolutePath()); + argParser.setStructureFilename(structureFilename); + // open structure view AlignmentPanel ap = af.alignPanel; if (headless) @@ -505,10 +517,9 @@ 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); @@ -519,25 +530,23 @@ public class Commands } catch (IOException e) { paeFilepath = paeFile.getAbsolutePath(); - Console.warn("Problem with the PAE file path: '" + addWarn("Problem with the PAE file path: '" + paeFile.getPath() + "'"); } } // 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) { @@ -562,48 +571,54 @@ public class Commands if (it.hasNext()) sb.append(", "); } - Console.warn(sb.toString()); + addWarn(sb.toString()); } } - 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) { - Console.error("Failed to import and open structure view."); + 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()) { - Console.warn( - "Gave up waiting for structure viewer to load. Something may have gone wrong."); + addWarn("Gave up waiting for structure viewer to load file '" + + structureFile + + "'. Something may have gone wrong."); } } catch (Exception x) { - Console.warn("Exception whilst waiting for structure viewer " + addError("Exception whilst waiting for structure viewer " + structureFilepath, x); + isError = true; } // add StructureViewer to svMap list @@ -615,80 +630,176 @@ 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())) - { - 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) + for (ArgValue structureImageArgValue : avm + .getArgValueList(Arg.STRUCTUREIMAGE)) { - 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); - // 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 { - Console.debug("Rendering image to " + structureImageFile); + 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); + + ///// + // DON'T TRY TO EXPORT IF VIEWER IS UNSUPPORTED + if (viewerType != ViewerType.JMOL) + { + addWarn("Cannot export image for structure viewer " + + viewerType.name() + " yet"); + continue; + } + + ///// + // Apply the temporary colourscheme to the linked alignment + // TODO: enhance for multiple linked alignments. + + String imageColour = avm.getValueFromSubValOrArg( + structureImageArgValue, Arg.IMAGECOLOUR, + structureImageSubVals); + ColourSchemeI originalColourScheme = this + .getColourScheme(af); + this.colourAlignFrame(af, imageColour); + + ///// + // custom image background colour + + String bgcolourstring = avm.getValueFromSubValOrArg( + structureImageArgValue, Arg.BGCOLOUR, + structureImageSubVals); + Color bgcolour = null; + if (bgcolourstring != null && bgcolourstring.length() > 0) + { + bgcolour = ColorUtils.parseColourString(bgcolourstring); + if (bgcolour == null) + { + Console.warn( + "Background colour string '" + bgcolourstring + + "' not recognised -- using default"); + } + } + + JalviewStructureDisplayI sview = structureViewer + .getJalviewStructureDisplay(); + + File sessionToRestore = null; + + List extraCommands = new ArrayList<>(); + + if (extraCommands.size() > 0 || bgcolour != null) + { + try + { + sessionToRestore = sview.saveSession(); + } catch (Throwable t) + { + Console.warn( + "Unable to save temporary session file before custom structure view export operation."); + } + } + + //// + // Do temporary ops + + if (bgcolour != null) + { + sview.getBinding().setBackgroundColour(bgcolour); + } + + sview.getBinding().executeCommands(extraCommands, false, + "Executing Custom Commands"); + + // and export the view as an image + boolean success = this.checksBeforeWritingToFile(avm, + subVals, false, structureImageFilename, + "structure image", isError); + + if (!success) + { + continue; + } + Console.debug("Rendering image to " + structureImageFile); + // + // TODO - extend StructureViewer / Binding with makePDBImage so + // we can do this with every viewer + // + + try + { + // We don't expect class cast exception + AppJmol jmol = (AppJmol) sview; jmol.makePDBImage(structureImageFile, imageType, renderer, userBis); - Console.debug("Finished Rendering image to " + Console.info("Exported structure image to " + structureImageFile); - } catch (ImageOutputException ioexc) + // RESTORE SESSION AFTER EXPORT IF NEED BE + if (sessionToRestore != null) + { + Console.debug("Restoring session from " + + sessionToRestore); + + sview.getBinding().restoreSession(sessionToRestore.getAbsolutePath()); + + } + } catch (ImageOutputException ioexec) + { + addError( + "Unexpected error when restoring structure viewer session after custom view operations."); + isError = true; + continue; + } finally { - Console.warn("Unexpected error whilst exporting image to " - + structureImageFile, ioexc); + try { + this.colourAlignFrame(af, originalColourScheme); + } catch (Exception t) + { + addError("Unexpected error when restoring colourscheme to alignment after temporary change for export.",t); + } } - } - break; - default: - Console.warn("Cannot export image for structure viewer " - + sv.getViewerType() + " yet"); - break; } } + argParser.setStructureFilename(null); } } } @@ -719,7 +830,7 @@ public class Commands } */ - return theseArgsWereParsed; + return theseArgsWereParsed && !isError; } protected void processGroovyScript(String id) @@ -729,7 +840,7 @@ public class Commands if (af == null) { - Console.warn("Did not have an alignment window for id=" + id); + addWarn("Did not have an alignment window for id=" + id); return; } @@ -753,35 +864,36 @@ public class Commands if (af == null) { - Console.warn("Did not have an alignment window for id=" + id); + addWarn("Did not have an alignment window for id=" + id); return false; } + 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" }) @@ -796,7 +908,20 @@ 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, imageSubVals, + false, fileName, "image", isError); + if (!success) + { + continue; + } + try { switch (type) @@ -844,17 +969,21 @@ public class Commands break; default: - Console.warn(Arg.IMAGE.argString() + " type '" + type + addWarn(Arg.IMAGE.argString() + " type '" + type + "' not known. Ignoring"); break; } } catch (Exception ioex) { - Console.warn("Unexpected error during export", ioex); + addError("Unexpected error during export to '" + fileName + "'", + ioex); + isError = true; } + + this.colourAlignFrame(af, originalColourScheme); } } - return true; + return !isError; } protected boolean processOutput(String id) @@ -864,10 +993,12 @@ public class Commands if (af == null) { - Console.warn("Did not have an alignment window for id=" + id); + addWarn("Did not have an alignment window for id=" + id); return false; } + Boolean isError = Boolean.valueOf(false); + if (avm.containsArg(Arg.OUTPUT)) { for (ArgValue av : avm.getArgValueList(Arg.OUTPUT)) @@ -877,28 +1008,10 @@ public class Commands String fileName = subVals.getContent(); boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName); 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 || stdout)) - { - 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); + String format = avm.getValueFromSubValOrArg(av, Arg.FORMAT, + subVals); FileFormats ffs = FileFormats.getInstance(); List validFormats = ffs.getWritableFormats(false); @@ -944,48 +1057,50 @@ public class Commands validSB.append(")"); } - Jalview.exit("No valid format specified for " + addError("No valid format specified for " + Arg.OUTPUT.argString() + ". Valid formats are " - + validSB.toString() + ".", 1); - // this return really shouldn't happen - return false; + + validSB.toString() + "."); + continue; } } - String savedBackupsPreference = Cache - .getDefault(BackupFiles.ENABLED, null); - Console.debug("Setting backups to " + backups); - Cache.applicationProperties.put(BackupFiles.ENABLED, - Boolean.toString(backups)); + boolean success = checksBeforeWritingToFile(avm, subVals, true, + fileName, ff.getName(), isError); + if (!success) + { + continue; + } + + boolean backups = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVals, + null, Platform.isHeadless() ? null : BackupFiles.ENABLED, + !Platform.isHeadless()); Console.info("Writing " + fileName); - af.saveAlignment(fileName, ff, stdout); - Console.debug("Returning backups to " + savedBackupsPreference); - if (savedBackupsPreference != null) - Cache.applicationProperties.put(BackupFiles.ENABLED, - savedBackupsPreference); + af.saveAlignment(fileName, ff, stdout, backups); if (af.isSaveAlignmentSuccessful()) { Console.debug("Written alignment '" + name + "' in " - + ff.getName() + " format to " + file); + + ff.getName() + " format to '" + file + "'"); } else { - Console.warn("Error writing file " + file + " in " + ff.getName() + addError("Error writing file '" + file + "' in " + ff.getName() + " format!"); + isError = true; + continue; } } } - return true; + return !isError; } private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm, 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; @@ -1044,4 +1159,121 @@ 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); + errors.add(errorMessage); + } + + private void addWarn(String errorMessage) + { + Console.warn(errorMessage); + errors.add(errorMessage); + } + + private void addError(String errorMessage) + { + addError(errorMessage, null); + } + + private void addError(String errorMessage, Exception e) + { + Console.error(errorMessage, e); + errors.add(errorMessage); + } + + private boolean checksBeforeWritingToFile(ArgValuesMap avm, + SubVals subVal, boolean includeBackups, String filename, + String adjective, Boolean isError) + { + File file = new File(filename); + + boolean overwrite = avm.getFromSubValArgOrPref(Arg.OVERWRITE, subVal, + null, "OVERWRITE_OUTPUT", false); + boolean stdout = false; + boolean backups = false; + if (includeBackups) + { + stdout = ArgParser.STDOUTFILENAME.equals(filename); + // 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 = avm.getFromSubValArgOrPref(Arg.BACKUPS, subVal, null, + Platform.isHeadless() ? null : BackupFiles.ENABLED, + !Platform.isHeadless()); + } + + if (file.exists() && !(overwrite || backups || stdout)) + { + addWarn("Won't overwrite file '" + filename + "' without " + + Arg.OVERWRITE.argString() + + (includeBackups ? " or " + Arg.BACKUPS.argString() : "") + + " set"); + return false; + } + + boolean mkdirs = avm.getFromSubValArgOrPref(Arg.MKDIRS, subVal, null, + "MKDIRS_OUTPUT", false); + + if (!FileUtils.checkParentDir(file, mkdirs)) + { + addError("Directory '" + + FileUtils.getParentDir(file).getAbsolutePath() + + "' does not exist for " + adjective + " file '" + filename + + "'." + + (mkdirs ? "" : " Try using " + Arg.MKDIRS.argString())); + isError = true; + return false; + } + + return true; + } + + public List getErrors() + { + return errors; + } + + public String errorsToString() + { + StringBuilder sb = new StringBuilder(); + for (String error : errors) + { + if (sb.length() > 0) + sb.append("\n"); + sb.append("- " + error); + } + return sb.toString(); + } }