X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=06684e73335d85446a3ff0f813f4e1d45c592890;hb=28273e567a94f7c69c16bd338ab6ee6f594e79af;hp=3d475051b7874b0611456869a9a547b84ee76958;hpb=9fd03d86789221ae4f6cf720cadf3d99cc68ac33;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 3d47505..06684e7 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -6,7 +6,6 @@ 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; @@ -44,6 +43,9 @@ 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 +102,20 @@ 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 +123,7 @@ 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); @@ -149,13 +165,9 @@ public class Commands 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; - */ + // set wrap scope here so it can be applied after structures are opened + boolean wrap = false; + if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN)) { commandArgsProvided = true; @@ -239,17 +251,24 @@ public class Commands 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) { - 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); } @@ -336,6 +355,12 @@ public class Commands false, false); } + // wrap alignment? do this last for formatting reasons + wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null, + "WRAP_ALIGNMENT", false); + // af.setWrapFormat(wrap) is applied after structures are opened for + // annotation reasons + // store the AlignFrame for this id afMap.put(id, af); @@ -527,20 +552,7 @@ public class Commands 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; - } - } - } + ViewerType viewerType = ViewerType.getFromString(sViewer); // TODO use ssFromStructure StructureViewer sv = StructureChooser @@ -548,11 +560,36 @@ 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) @@ -592,12 +629,13 @@ 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 @@ -608,8 +646,20 @@ 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: @@ -622,6 +672,15 @@ public class Commands } } + if (wrap) + { + AlignFrame af = afMap.get(id); + if (af != null) + { + af.setWrapFormat(wrap, true); + } + } + /* boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING); if (doShading) @@ -717,54 +776,60 @@ 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": - 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); } } } @@ -789,6 +854,7 @@ 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); @@ -801,7 +867,7 @@ 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 " @@ -839,23 +905,30 @@ 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 @@ -866,7 +939,7 @@ 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, @@ -916,7 +989,7 @@ public class Commands seq = al.getSequenceAt(subVals.getIndex()); } } - else if (idAv != null) + if (seq == null && idAv != null) { seq = al.findName(idAv.getValue()); }