X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=63247a7856dbc1215051e9961d397fbbf0a107aa;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=79b6ab691abd0509250478be4910185e8bf80284;hpb=5cfef671be8362cbb0598ea405a10f96e08a4df3;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 79b6ab6..63247a7 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; @@ -14,11 +13,11 @@ import java.util.Locale; import java.util.Map; import jalview.analysis.AlignmentUtils; +import jalview.api.structures.JalviewStructureDisplayI; 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.ArgValues; import jalview.bin.argparser.ArgValuesMap; import jalview.bin.argparser.SubVals; import jalview.datamodel.AlignmentI; @@ -26,6 +25,7 @@ import jalview.datamodel.SequenceI; import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder; import jalview.gui.AlignFrame; import jalview.gui.AlignmentPanel; +import jalview.gui.AppJmol; import jalview.gui.Desktop; import jalview.gui.Preferences; import jalview.gui.StructureChooser; @@ -42,11 +42,19 @@ import jalview.io.FileFormats; 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; import jalview.util.HttpUtils; +import jalview.util.ImageMaker; +import jalview.util.ImageMaker.TYPE; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.util.imagemaker.BitmapImageSizing; public class Commands { @@ -72,7 +80,7 @@ public class Commands argParser = argparser; headless = h; desktop = d; - afMap = new HashMap(); + afMap = new HashMap<>(); if (argparser != null) { processArgs(argparser, headless); @@ -92,7 +100,22 @@ public class Commands ArgValuesMap avm = argParser.getLinkedArgs(id); theseArgsWereParsed = true; 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); @@ -100,7 +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); @@ -110,7 +133,7 @@ public class Commands } } - if (argParser.getBool(Arg.QUIT)) + if (argParser.getBoolean(Arg.QUIT)) { Jalview.getInstance().quit(); return true; @@ -142,13 +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; @@ -219,21 +238,11 @@ public class Commands if (af == null || "true".equals(av.getSubVal("new")) || a == Arg.OPEN || format == FileFormat.Jalview) { - /* - * this approach isn't working yet // get default annotations before opening - * AlignFrame if (m.get(Arg.SSANNOTATIONS) != null) { - * Console.debug("##### SSANNOTATIONS=" + m.get(Arg.SSANNOTATIONS).getBoolean()); - * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" + - * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure = - * (m.get(Arg.SSANNOTATIONS) != null) ? m.get(Arg.SSANNOTATIONS).getBoolean() : - * false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ? - * !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" + - * showTemperatureFactor + ", showSS=" + showSecondaryStructure); - * StructureSelectionManager ssm = StructureSelectionManager - * .getStructureSelectionManager(Desktop.instance); if (ssm != null) { - * ssm.setAddTempFacAnnot(showTemperatureFactor); - * ssm.setProcessSecondaryStructure(showSecondaryStructure); } - */ + if (a == Arg.OPEN) + { + Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa", + openFile); + } Console.debug( "Opening '" + openFile + "' in new alignment frame"); @@ -241,46 +250,99 @@ public class Commands af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format); - boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm, - Arg.ANNOTATIONS, av.getSubVals(), null, - "SHOW_ANNOTATIONS", true); - af.setAnnotationsVisibility(showAnnotations, false, true); - // wrap alignment? - boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, - null, "WRAP_ALIGNMENT", false); - af.getCurrentView().setWrapAlignment(wrap); - - // colour aligment? + // 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); } - // change alignment frame title + // Change alignment frame title String title = ArgParser.getFromSubValArgOrPref(avm, av, Arg.TITLE, sv, null, null, null); if (title != null) + { af.setTitle(title); + Jalview.testoutput(argParser, Arg.TITLE, "test title", title); + } - // show secondary structure annotations? - boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm, - Arg.SSANNOTATIONS, av.getSubVals(), null, - "STRUCT_FROM_PDB", true); - if (avm.getBoolean(Arg.SSANNOTATIONS)) + // Add features + String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av, + Arg.FEATURES, sv); + if (featuresfile != null) { - af.setAnnotationsVisibility(showSSAnnotations, true, false); - /* - AlignmentUtils.showOrHideSequenceAnnotations( - af.getCurrentView().getAlignment(), - Collections.singleton("Secondary Structure"), null, - false, false); - */ + af.parseFeaturesFile(featuresfile, + AppletFormatAdapter.checkProtocol(featuresfile)); + Jalview.testoutput(argParser, Arg.FEATURES, + "examples/testdata/plantfdx.features", featuresfile); + } + + // Add annotations from file + String annotationsfile = ArgParser.getValueFromSubValOrArg(avm, + av, Arg.ANNOTATIONS, sv); + if (annotationsfile != null) + { + af.loadJalviewDataFile(annotationsfile, null, null, null); + Jalview.testoutput(argParser, Arg.ANNOTATIONS, + "examples/testdata/plantfdx.annotations", + annotationsfile); + } + + // Set or clear the sortbytree flag + boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm, + Arg.SORTBYTREE, sv); + if (sortbytree) + { + af.getViewport().setSortByTree(true); + Jalview.testoutput(argParser, Arg.SORTBYTREE); } + // Load tree from file + String treefile = ArgParser.getValueFromSubValOrArg(avm, av, + Arg.TREE, sv); + if (treefile != null) + { + try + { + NewickFile nf = new NewickFile(treefile, + AppletFormatAdapter.checkProtocol(treefile)); + af.getViewport().setCurrentTree( + af.showNewickTree(nf, treefile).getTree()); + Jalview.testoutput(argParser, Arg.TREE, + "examples/testdata/uniref50_test_tree", treefile); + } catch (IOException e) + { + Console.warn("Couldn't add tree " + treefile, e); + } + } + + // Show secondary structure annotations? + boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm, + Arg.SHOWSSANNOTATIONS, av.getSubVals(), null, + "STRUCT_FROM_PDB", true); + af.setAnnotationsVisibility(showSSAnnotations, true, false); + + // Show sequence annotations? + boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm, + Arg.SHOWANNOTATIONS, av.getSubVals(), null, + "SHOW_ANNOTATIONS", true); + af.setAnnotationsVisibility(showAnnotations, false, true); + // show temperature factor annotations? if (avm.getBoolean(Arg.NOTEMPFAC)) { @@ -292,33 +354,12 @@ public class Commands af.getCurrentView().getAlignment(), hideThese, null, false, false); } - else - /* - * comment out hacky approach up to here and add this line: if - * (showTemperatureFactor) - */ - { - /* - if (avm.containsArg(Arg.TEMPFAC_LABEL)) - { - AlignmentAnnotation aa = AlignmentUtils - .getFirstSequenceAnnotationOfType( - af.getCurrentView().getAlignment(), - AlignmentAnnotation.LINE_GRAPH); - String label = avm.getValue(Arg.TEMPFAC_LABEL); - if (aa != null) - { - aa.label = label; - } - else - { - Console.info( - "Could not find annotation to apply tempfac_label '" - + label); - } - } - */ - } + + // 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); @@ -375,7 +416,7 @@ public class Commands { String val = av.getValue(); SubVals subVals = av.getSubVals(); - SequenceI seq = getSpecifiedSequence(af, subVals); + SequenceI seq = getSpecifiedSequence(af, avm, av); if (seq == null) { // Could not find sequence from subId, let's assume the first @@ -436,14 +477,6 @@ 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) @@ -455,17 +488,14 @@ public class Commands String structureFilepath = structureFile.getAbsolutePath(); // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX - String paeFilepath = subVals.getWithSubstitutions(argParser, id, - "paematrix"); - String paeLabel = subVals.get("paelabel"); - ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm, - af, structureFilepath); - if (paeFilepath == null && paeAv != null) + String paeFilepath = ArgParser + .getFromSubValArgOrPrefWithSubstitutions(argParser, avm, + Arg.PAEMATRIX, Position.AFTER, av, subVals, null, + null, null); + if (paeFilepath != null) { - SubVals sv = paeAv.getSubVals(); - File paeFile = new File(sv.getContent()); + File paeFile = new File(paeFilepath); - paeLabel = sv.get("label"); try { paeFilepath = paeFile.getCanonicalPath(); @@ -479,21 +509,20 @@ public class Commands // showing annotations from structure file or not boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm, - Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB", + Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB", true); // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds // reference annotations - String tftString = subVals.get("tempfac"); - TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null - : TFType.DEFAULT; - ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm, - af, structureFilepath); - if (tftString == null && tftAv != null) - { - tftString = tftAv.getSubVals().getContent(); - } - if (tftString != null) + 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); + TFType tft = notempfac ? null : TFType.DEFAULT; + if (tftString != null && !notempfac) { // get kind of temperature factor annotation try @@ -521,34 +550,137 @@ public class Commands } String sViewer = ArgParser.getFromSubValArgOrPref(avm, - Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, - "viewer", null, "jmol"); - ViewerType viewerType = null; - if (!"none".equals(sViewer)) + Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null, + null, "jmol"); + ViewerType viewerType = ViewerType.getFromString(sViewer); + + // TODO use ssFromStructure + StructureViewer sv = StructureChooser + .openStructureFileForSequence(null, null, ap, seq, false, + structureFilepath, tft, paeFilepath, false, + ssFromStructure, false, viewerType); + + if (sv == null) { - for (ViewerType v : EnumSet.allOf(ViewerType.class)) + Console.error("Failed to import and open structure view."); + continue; + } + try + { + long tries = 1000; + while (sv.isBusy() && tries > 0) { - String name = v.name().toLowerCase(Locale.ROOT) - .replaceAll(" ", ""); - if (sViewer.equals(name)) + Thread.sleep(25); + if (sv.isBusy()) { - viewerType = v; - break; + 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, 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) + { + 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: + try + { + Thread.sleep(1000); // WHY ??? + } catch (InterruptedException e) + { + // TODO Auto-generated catch block + e.printStackTrace(); + } + JalviewStructureDisplayI sview = sv + .getJalviewStructureDisplay(); + if (sview instanceof AppJmol) + { + AppJmol jmol = (AppJmol) sview; + 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); + } - boolean addTempFac = tft != null - || Cache.getDefault("ADD_TEMPFACT_ANN", false); - - // TODO use ssFromStructure - StructureChooser.openStructureFileForSequence(null, null, ap, seq, - false, structureFilepath, tft, paeFilepath, false, - ssFromStructure, false, viewerType); + } + break; + default: + Console.warn("Cannot export image for structure viewer " + + sv.getViewerType() + " yet"); + break; + } + } } } } + if (wrap) + { + AlignFrame af = afMap.get(id); + if (af != null) + { + af.setWrapFormat(wrap, true); + } + } + /* boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING); if (doShading) @@ -569,6 +701,30 @@ public class Commands return theseArgsWereParsed; } + protected void processGroovyScript(String id) + { + ArgValuesMap avm = argParser.getLinkedArgs(id); + AlignFrame af = afMap.get(id); + + if (af == null) + { + Console.warn("Did not have an alignment window for id=" + id); + return; + } + + if (avm.containsArg(Arg.GROOVY)) + { + String groovyscript = avm.getValue(Arg.GROOVY); + if (groovyscript != null) + { + // Execute the groovy script after we've done all the rendering stuff + // and before any images or figures are generated. + Console.info("Executing script " + groovyscript); + Jalview.getInstance().executeGroovyScript(groovyscript, af); + } + } + } + protected boolean processImages(String id) { ArgValuesMap avm = argParser.getLinkedArgs(id); @@ -590,10 +746,20 @@ public class Commands File file = new File(fileName); String name = af.getName(); String renderer = ArgParser.getValueFromSubValOrArg(avm, av, - Arg.RENDERER, subVal); + Arg.TEXTRENDERER, subVal); 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); + BitmapImageSizing userBis = ImageMaker + .parseScaleWidthHeightStrings(scale, width, height); + type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal); if (type == null && fileName != null) { @@ -609,53 +775,61 @@ public class Commands Cache.setPropsAreReadOnly(true); Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false"); - switch (type) + Console.info("Writing " + file); + 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); - 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); } } } @@ -680,6 +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); @@ -692,7 +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 " @@ -730,23 +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 @@ -754,7 +936,10 @@ public class Commands Console.debug("Setting backups to " + backups); Cache.applicationProperties.put(BackupFiles.ENABLED, Boolean.toString(backups)); - af.saveAlignment(fileName, ff); + + Console.info("Writing " + fileName); + + af.saveAlignment(fileName, ff, stdout); Console.debug("Returning backups to " + savedBackupsPreference); if (savedBackupsPreference != null) Cache.applicationProperties.put(BackupFiles.ENABLED, @@ -775,70 +960,39 @@ public class Commands return true; } - private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId) + private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm, + ArgValue av) { - if (subId == null) + SubVals subVals = av.getSubVals(); + ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID); + SequenceI seq = null; + if (subVals == null && idAv == null) return null; - AlignmentI al = af.getCurrentView().getAlignment(); - if (subId.has("seqid")) + if (af == null || af.getCurrentView() == null) { - return al.findName(subId.get("seqid")); + return null; } - else if (-1 < subId.getIndex() - && subId.getIndex() < al.getSequences().size()) + AlignmentI al = af.getCurrentView().getAlignment(); + if (al == null) { - return al.getSequenceAt(subId.getIndex()); + return null; } - return null; - } - - // returns the first Arg value intended for the structure structFilename - // (in the given AlignFrame from the ArgValuesMap) - private ArgValue getArgAssociatedWithStructure(Arg arg, ArgValuesMap avm, - AlignFrame af, String structFilename) - { - if (af != null) + if (subVals != null) { - for (ArgValue av : avm.getArgValueList(arg)) + if (subVals.has(Arg.SEQID.getName())) { - SubVals subVals = av.getSubVals(); - String structid = subVals.get("structid"); - String structfile = subVals.get("structfile"); - - // let's find a structure - if (structfile == null && structid == null) - { - ArgValue likelyStructure = avm.getClosestPreviousArgValueOfArg(av, - Arg.STRUCTURE); - if (likelyStructure != null) - { - SubVals sv = likelyStructure.getSubVals(); - if (sv != null && sv.has(ArgValues.ID)) - { - structid = sv.get(ArgValues.ID); - } - else - { - structfile = likelyStructure.getValue(); - } - } - } - - if (structfile == null && structid != null) - { - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); - if (ssm != null) - { - structfile = ssm.findFileForPDBId(structid); - } - } - if (structfile != null && structfile.equals(structFilename)) - { - return av; - } + seq = al.findName(subVals.get(Arg.SEQID.getName())); + } + else if (-1 < subVals.getIndex() + && subVals.getIndex() < al.getSequences().size()) + { + seq = al.getSequenceAt(subVals.getIndex()); } } - return null; + else if (idAv != null) + { + seq = al.findName(idAv.getValue()); + } + return seq; } }