X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=17a1af23857becde1dd2db1095896f1b3e58ae6b;hb=91bb9b5c473c14f3381fbea3570b4dc1875b68f2;hp=3437bfd23ddae485f32541b5c2281a46ab6b299d;hpb=1d1edb58c9ee8baec12686a512eb18d97b9bdba1;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 3437bfd..17a1af2 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -44,6 +44,9 @@ 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; @@ -100,6 +103,20 @@ public class Commands 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); @@ -107,7 +124,7 @@ public class Commands // close ap if (avm.getBoolean(Arg.CLOSE)) { - AlignFrame af = afMap.get(id); + af = afMap.get(id); if (af != null) { af.closeMenuItem_actionPerformed(true); @@ -249,7 +266,19 @@ public class Commands Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", ""); if ("" != colour) { - af.changeColour_actionPerformed(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); } @@ -452,14 +481,6 @@ public class Commands Console.debug("Using structure file " + structureFile.getAbsolutePath()); - // ##### Does this need to happen? Follow - // openStructureFileForSequence() below - /* - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(structureFile.getAbsolutePath(), - DataSourceType.FILE, seq, true, Desktop.instance); - */ - // open structure view AlignmentPanel ap = af.alignPanel; if (headless) @@ -505,15 +526,6 @@ public class Commands Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false, true); TFType tft = notempfac ? null : TFType.DEFAULT; - /* - String tftString = subVals.get("tempfac"); - ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm, - af, structureFilepath); - if (tftString == null && tftAv != null) - { - tftString = tftAv.getSubVals().getContent(); - } - */ if (tftString != null && !notempfac) { // get kind of temperature factor annotation @@ -565,26 +577,58 @@ public class Commands structureFilepath, tft, paeFilepath, false, ssFromStructure, false, viewerType); - if (headless) + if (sv == null) { - sv.setAsync(false); + Console.error("Failed to import and open structure view."); + continue; } - + try + { + long tries = 1000; + while (sv.isBusy() && tries > 0) + { + Thread.sleep(25); + if (sv.isBusy()) + { + tries--; + Console.debug( + "Waiting for viewer for " + structureFilepath); + } + } + if (tries == 0 && sv.isBusy()) + { + Console.warn( + "Gave up waiting for structure viewer to load. Something may have gone wrong."); + } + } catch (Exception x) + { + Console.warn("Exception whilst waiting for structure viewer " + + structureFilepath, x); + } + Console.debug( + "Successfully opened viewer for " + structureFilepath); 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, subVals); + Arg.STRUCTUREIMAGEWIDTH, sisv); String height = ArgParser.getValueFromSubValOrArg(avm, av, - Arg.STRUCTUREIMAGEHEIGHT, subVals); + Arg.STRUCTUREIMAGEHEIGHT, sisv); String scale = ArgParser.getValueFromSubValOrArg(avm, av, - Arg.STRUCTUREIMAGESCALE, subVals); + Arg.STRUCTUREIMAGESCALE, sisv); String renderer = ArgParser.getValueFromSubValOrArg(avm, av, - Arg.STRUCTUREIMAGETEXTRENDERER, subVals); + Arg.STRUCTUREIMAGETEXTRENDERER, sisv); String typeS = ArgParser.getValueFromSubValOrArg(avm, av, - Arg.STRUCTUREIMAGETYPE, subVals); + Arg.STRUCTUREIMAGETYPE, sisv); if (typeS == null || typeS.length() == 0) { typeS = FileUtils.getExtension(structureImageFile); @@ -602,12 +646,13 @@ public class Commands } BitmapImageSizing userBis = ImageMaker .parseScaleWidthHeightStrings(scale, width, height); + // TODO MAKE THIS VIEWER INDEPENDENT!! switch (StructureViewer.getViewerType()) { case JMOL: try { - Thread.sleep(1000); + Thread.sleep(1000); // WHY ??? } catch (InterruptedException e) { // TODO Auto-generated catch block @@ -618,8 +663,20 @@ public class Commands if (sview instanceof AppJmol) { AppJmol jmol = (AppJmol) sview; - jmol.makePDBImage(structureImageFile, imageType, renderer, - userBis); + try + { + Console.debug("Rendering image to " + structureImageFile); + jmol.makePDBImage(structureImageFile, imageType, renderer, + userBis); + Console.debug("Finished Rendering image to " + + structureImageFile); + + } catch (ImageOutputException ioexc) + { + Console.warn("Unexpected error whilst exporting image to " + + structureImageFile, ioexc); + } + } break; default: @@ -727,54 +784,60 @@ public class Commands Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false"); Console.info("Writing " + file); - - switch (type) + try { - - 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": - try + switch (type) { - BioJsHTMLOutput.refreshVersionInfo( - BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); - } catch (URISyntaxException e) - { - e.printStackTrace(); + + 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; } - BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); - bjs.exportHTML(fileName); - Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName); - break; - - case "eps": - af.createEPS(file, name); - Console.debug("Creating EPS file: " + fileName); - break; - - case "imagemap": - af.createImageMap(file, name); - Console.debug("Creating ImageMap file: " + fileName); - break; - - default: - Console.warn(Arg.IMAGE.argString() + " type '" + type - + "' not known. Ignoring"); - break; + } catch (Exception ioex) + { + Console.warn("Unexpected error during export", ioex); } } } @@ -799,6 +862,7 @@ public class Commands String val = av.getValue(); SubVals subVals = av.getSubVals(); 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); @@ -811,7 +875,7 @@ public class Commands !Platform.isHeadless()); // if backups is not true then --overwrite must be specified - if (file.exists() && !(overwrite || backups)) + if (file.exists() && !(overwrite || backups || stdout)) { Console.error("Won't overwrite file '" + fileName + "' without " + Arg.OVERWRITE.argString() + " or " @@ -849,23 +913,30 @@ public class Commands } 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(")"); + if (stdout) + { + ff = FileFormat.Fasta; } + else + { + 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; + 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 @@ -876,7 +947,7 @@ public class Commands Console.info("Writing " + fileName); - af.saveAlignment(fileName, ff); + af.saveAlignment(fileName, ff, stdout); Console.debug("Returning backups to " + savedBackupsPreference); if (savedBackupsPreference != null) Cache.applicationProperties.put(BackupFiles.ENABLED,