From a65cf4f5da37aba7b52abf2cc3c8a06a469f64ed Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Wed, 23 Aug 2023 16:05:03 +0100 Subject: [PATCH] JAL-4250 Fix one word bug for 'af.createEPS(file, renderer)' (was af.createEPS(file, name)'. Everything else is formatting changes. --- src/jalview/bin/Commands.java | 162 ++++++++++++++++++++++------------------- 1 file changed, 89 insertions(+), 73 deletions(-) diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index d7d1ea3..dbc4953 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -103,16 +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()) + AlignFrame af = afMap.get(id); + while (af != null && af.getViewport().isCalcInProgress()) { - try { + try + { Thread.sleep(25); - } catch (Exception q) {}; + } catch (Exception q) + { + } + ; } - + theseArgsWereParsed &= processImages(id); if (processLinkedOkay) theseArgsWereParsed &= processOutput(id); @@ -263,12 +267,16 @@ public class Commands if ("" != colour) { ColourSchemeI cs = ColourSchemeProperty.getColourScheme( - af.getViewport(), af.getViewport().getAlignment(), colour); - - if (cs==null && !"None".equals(colour)) + af.getViewport(), af.getViewport().getAlignment(), + colour); + + if (cs == null && !"None".equals(colour)) + { + Console.warn( + "Couldn't parse '" + colour + "' as a colourscheme."); + } + else { - Console.warn("Couldn't parse '"+colour+"' as a colourscheme."); - } else { af.changeColour(cs); } Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour); @@ -569,15 +577,15 @@ public class Commands structureFilepath, tft, paeFilepath, false, ssFromStructure, false, viewerType); - if (sv==null) + if (sv == null) { Console.error("Failed to import and open structure view."); continue; } try { - long tries=1000; - while (sv.isBusy() && tries>0) + long tries = 1000; + while (sv.isBusy() && tries > 0) { Thread.sleep(25); if (sv.isBusy()) @@ -587,15 +595,18 @@ public class Commands "Waiting for viewer for " + structureFilepath); } } - if (tries==0 && sv.isBusy()) + if (tries == 0 && sv.isBusy()) { - Console.warn("Gave up waiting for structure viewer to load. Something may have gone wrong."); + 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.warn("Exception whilst waiting for structure viewer " + + structureFilepath, x); } - Console.debug("Successfully opened viewer for "+structureFilepath); + Console.debug( + "Successfully opened viewer for " + structureFilepath); String structureImageFilename = ArgParser.getValueFromSubValOrArg( avm, av, Arg.STRUCTUREIMAGE, subVals); if (sv != null && structureImageFilename != null) @@ -652,16 +663,18 @@ public class Commands if (sview instanceof AppJmol) { AppJmol jmol = (AppJmol) sview; - try { - Console.debug("Rendering image to "+structureImageFile); + try + { + Console.debug("Rendering image to " + structureImageFile); jmol.makePDBImage(structureImageFile, imageType, renderer, - userBis); - Console.debug("Finished Rendering image to "+structureImageFile); + userBis); + Console.debug("Finished Rendering image to " + + structureImageFile); - } - catch (ImageOutputException ioexc) + } catch (ImageOutputException ioexc) { - Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc); + Console.warn("Unexpected error whilst exporting image to " + + structureImageFile, ioexc); } } @@ -771,57 +784,60 @@ public class Commands Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false"); Console.info("Writing " + file); - try { - 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": - Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName); - try - { - BioJsHTMLOutput.refreshVersionInfo( - BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); - } catch (URISyntaxException e) + switch (type) { - 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( + "Outputting 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("Outputting EPS file: " + fileName); + af.createEPS(file, renderer); + break; + + case "imagemap": + Console.debug("Outputting 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); - 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); + } catch (Exception ioex) + { + Console.warn("Unexpected error during export", ioex); } } } -- 1.7.10.2