X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=3608295eded0c99135ac9584447aecb182d31631;hb=79456f40b33e73e2fb5420a3287ae80854281ef6;hp=5341874070610b009154cbf296d5d8f2e50e06dc;hpb=03968fce3d428957aced82b7f051527fa66e762f;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 5341874..3608295 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -2,51 +2,52 @@ package jalview.bin; import java.io.File; import java.io.IOException; -import java.util.AbstractMap; +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; import java.util.Locale; import java.util.Map; -import java.util.Map.Entry; import jalview.analysis.AlignmentUtils; 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.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder; import jalview.gui.AlignFrame; import jalview.gui.AlignmentPanel; -import jalview.gui.AssociatePdbFileWithSeq; import jalview.gui.Desktop; import jalview.gui.Preferences; import jalview.gui.StructureChooser; import jalview.gui.StructureViewer; +import jalview.gui.StructureViewer.ViewerType; import jalview.io.AppletFormatAdapter; +import jalview.io.BackupFiles; +import jalview.io.BioJsHTMLOutput; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatException; import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.FileLoader; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; -import jalview.schemes.AnnotationColourGradient; +import jalview.io.NewickFile; import jalview.structure.StructureImportSettings.TFType; import jalview.structure.StructureSelectionManager; import jalview.util.HttpUtils; import jalview.util.MessageManager; import jalview.util.Platform; -import mc_view.PDBChain; public class Commands { @@ -85,21 +86,18 @@ public class Commands headless = h; boolean theseArgsWereParsed = false; - if (argParser != null && argParser.linkedIds() != null) + if (argParser != null && argParser.getLinkedIds() != null) { - for (String id : argParser.linkedIds()) + for (String id : argParser.getLinkedIds()) { - ArgValuesMap avm = argParser.linkedArgs(id); + ArgValuesMap avm = argParser.getLinkedArgs(id); theseArgsWereParsed = true; - if (id == null) - { - theseArgsWereParsed &= processUnlinked(id); - } - else - { - theseArgsWereParsed &= processLinked(id); - } + theseArgsWereParsed &= processLinked(id); + processGroovyScript(id); + boolean processLinkedOkay = theseArgsWereParsed; theseArgsWereParsed &= processImages(id); + if (processLinkedOkay) + theseArgsWereParsed &= processOutput(id); // close ap if (avm.getBoolean(Arg.CLOSE)) @@ -114,7 +112,7 @@ public class Commands } } - if (argParser.getBool(Arg.QUIT)) + if (argParser.getBoolean(Arg.QUIT)) { Jalview.getInstance().quit(); return true; @@ -142,7 +140,7 @@ public class Commands protected boolean processLinked(String id) { boolean theseArgsWereParsed = false; - ArgValuesMap avm = argParser.linkedArgs(id); + ArgValuesMap avm = argParser.getLinkedArgs(id); if (avm == null) return true; @@ -153,7 +151,7 @@ public class Commands * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null; * DataSourceType protocol = null; */ - if (avm.containsArg(Arg.OPEN) || avm.containsArg(Arg.OPENNEW)) + if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN)) { commandArgsProvided = true; long progress = -1; @@ -161,21 +159,17 @@ public class Commands boolean first = true; boolean progressBarSet = false; AlignFrame af; - // Combine the OPEN and OPENNEW files into one list, along with whether it - // was OPEN or OPENNEW - List> openAvList = new ArrayList<>(); - avm.getArgValueList(Arg.OPEN).stream() - .forEachOrdered(av -> openAvList.add( - new AbstractMap.SimpleEntry(Arg.OPEN, - av))); - avm.getArgValueList(Arg.OPENNEW).stream() - .forEachOrdered(av -> openAvList - .add(new AbstractMap.SimpleEntry( - Arg.OPENNEW, av))); - for (Entry aav : openAvList) + // Combine the APPEND and OPEN files into one list, along with whether it + // was APPEND or OPEN + List openAvList = new ArrayList<>(); + openAvList.addAll(avm.getArgValueList(Arg.OPEN)); + openAvList.addAll(avm.getArgValueList(Arg.APPEND)); + // sort avlist based on av.getArgIndex() + Collections.sort(openAvList); + for (ArgValue av : openAvList) { - Arg a = aav.getKey(); - ArgValue av = aav.getValue(); + Arg a = av.getArg(); + SubVals sv = av.getSubVals(); String openFile = av.getValue(); if (openFile == null) continue; @@ -223,24 +217,15 @@ public class Commands } af = afMap.get(id); + // When to open a new AlignFrame if (af == null || "true".equals(av.getSubVal("new")) - || a == Arg.OPENNEW || format == FileFormat.Jalview) + || a == Arg.OPEN || format == FileFormat.Jalview) { - /* - * this approach isn't working yet // get default annotations before opening - * AlignFrame if (m.get(Arg.SSANNOTATION) != null) { - * Console.debug("##### SSANNOTATION=" + m.get(Arg.SSANNOTATION).getBoolean()); - * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" + - * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure = - * (m.get(Arg.SSANNOTATION) != null) ? m.get(Arg.SSANNOTATION).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"); @@ -250,32 +235,90 @@ public class Commands format); // wrap alignment? - if (avm.getBoolean(Arg.WRAP)) + 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.getCurrentView().setWrapAlignment(true); + af.changeColour_actionPerformed(colour); + Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour); } - // colour aligment? - if (avm.containsArg(Arg.COLOUR)) + // Change alignment frame title + String title = ArgParser.getFromSubValArgOrPref(avm, av, + Arg.TITLE, sv, null, null, null); + if (title != null) { - af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR)); + af.setTitle(title); + Jalview.testoutput(argParser, Arg.TITLE, "test title", title); } - // change alignment frame title - if (avm.containsArg(Arg.TITLE)) - af.setTitle(avm.getValue(Arg.TITLE)); + // Add features + String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av, + Arg.FEATURES, sv); + if (featuresfile != null) + { + af.parseFeaturesFile(featuresfile, + AppletFormatAdapter.checkProtocol(featuresfile)); + Jalview.testoutput(argParser, Arg.FEATURES, + "examples/testdata/plantfdx.features", featuresfile); + } - /* hacky approach to hiding the annotations */ - // show secondary structure annotations? - if (avm.getBoolean(Arg.SSANNOTATION)) + // Add annotations from file + String annotationsfile = ArgParser.getValueFromSubValOrArg(avm, + av, Arg.ANNOTATIONS, sv); + if (annotationsfile != null) { - // do this better (annotation types?) - AlignmentUtils.showOrHideSequenceAnnotations( - af.getCurrentView().getAlignment(), - Collections.singleton("Secondary Structure"), null, - false, false); + 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)) { @@ -287,31 +330,6 @@ 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); - } - } - } // store the AlignFrame for this id afMap.put(id, af); @@ -323,17 +341,22 @@ public class Commands .getStructureSelectionManager(Desktop.instance); SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0); ssm.computeMapping(false, new SequenceI[] { seq }, null, - openFile, DataSourceType.FILE, null, null, null); + openFile, DataSourceType.FILE, null, null, null, false); } } else { Console.debug( "Opening '" + openFile + "' in existing alignment frame"); - af.getCurrentView().addFile(new File(openFile), format, false); + DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile) + ? DataSourceType.URL + : DataSourceType.FILE; + FileLoader fileLoader = new FileLoader(!headless); + fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null, + false); } - Console.debug("Command " + Arg.OPEN + " executed successfully!"); + Console.debug("Command " + Arg.APPEND + " executed successfully!"); } if (first) // first=true means nothing opened @@ -363,7 +386,7 @@ 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 @@ -424,9 +447,13 @@ 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; @@ -439,17 +466,14 @@ 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(); @@ -461,7 +485,13 @@ public class Commands } } - // get TEMPFAC type from subvals or Arg.TEMPFAC + // showing annotations from structure file or not + boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm, + 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; @@ -498,13 +528,36 @@ public class Commands } } - // TODO pass PAE label + 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; + } + } + } + + boolean addTempFac = tft != null + || Cache.getDefault("ADD_TEMPFACT_ANN", false); + + // TODO use ssFromStructure StructureChooser.openStructureFileForSequence(null, null, ap, seq, - false, structureFilepath, tft, paeFilepath); + false, structureFilepath, tft, paeFilepath, false, + ssFromStructure, false, viewerType); } } } + /* boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING); if (doShading) { @@ -519,13 +572,38 @@ public class Commands Console.info("Changed colour " + acg.toString()); } } + */ 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.linkedArgs(id); + ArgValuesMap avm = argParser.getLinkedArgs(id); AlignFrame af = afMap.get(id); if (af == null) @@ -540,16 +618,18 @@ public class Commands { String val = av.getValue(); SubVals subVal = av.getSubVals(); - String type = "png"; // default String fileName = subVal.getContent(); File file = new File(fileName); - if (subVal.has("type")) - { - type = subVal.get("type"); - } - else if (fileName != null) + String name = af.getName(); + String renderer = ArgParser.getValueFromSubValOrArg(avm, av, + Arg.TEXTRENDERER, subVal); + if (renderer == null) + renderer = "text"; + String type = "png"; // default + type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal); + if (type == null && fileName != null) { - for (String ext : new String[] { "svg", "png", "html" }) + for (String ext : new String[] { "svg", "png", "html", "eps" }) { if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext)) { @@ -563,19 +643,47 @@ public class Commands switch (type) { + case "svg": Console.debug("Outputting type '" + type + "' to " + fileName); - af.createSVG(file); + 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); + htmlSVG.exportHTML(fileName, renderer); break; + + case "biojs": + try + { + BioJsHTMLOutput.refreshVersionInfo( + BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) + { + e.printStackTrace(); + } + 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"); @@ -586,21 +694,147 @@ public class Commands return true; } - private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId) + protected boolean processOutput(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 false; + } + + if (avm.containsArg(Arg.OUTPUT)) + { + for (ArgValue av : avm.getArgValueList(Arg.OUTPUT)) + { + String val = av.getValue(); + SubVals subVals = av.getSubVals(); + String fileName = subVals.getContent(); + 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)) + { + 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); + FileFormats ffs = FileFormats.getInstance(); + List validFormats = ffs.getWritableFormats(false); + + FileFormatI ff = null; + if (format == null && fileName != null) + { + FORMAT: for (String fname : validFormats) + { + FileFormatI tff = ffs.forName(fname); + String[] extensions = tff.getExtensions().split(","); + for (String ext : extensions) + { + if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext)) + { + ff = tff; + format = ff.getName(); + break FORMAT; + } + } + } + } + if (ff == null && format != null) + { + ff = ffs.forName(format); + } + 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(")"); + } + + 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 + .getDefault(BackupFiles.ENABLED, null); + Console.debug("Setting backups to " + backups); + Cache.applicationProperties.put(BackupFiles.ENABLED, + Boolean.toString(backups)); + af.saveAlignment(fileName, ff); + Console.debug("Returning backups to " + savedBackupsPreference); + if (savedBackupsPreference != null) + Cache.applicationProperties.put(BackupFiles.ENABLED, + savedBackupsPreference); + if (af.isSaveAlignmentSuccessful()) + { + Console.debug("Written alignment '" + name + "' in " + + ff.getName() + " format to " + file); + } + else + { + Console.warn("Error writing file " + file + " in " + ff.getName() + + " format!"); + } + + } + } + return true; + } + + 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 (al == null) + return null; + if (subVals != null) { - return al.findName(subId.get("seqid")); + if (subVals.has(Arg.SEQID.getName())) + { + seq = al.findName(subVals.get(Arg.SEQID.getName())); + } + else if (-1 < subVals.getIndex() + && subVals.getIndex() < al.getSequences().size()) + { + seq = al.getSequenceAt(subVals.getIndex()); + } } - else if (-1 < subId.getIndex() - && subId.getIndex() < al.getSequences().size()) + else if (idAv != null) { - return al.getSequenceAt(subId.getIndex()); + seq = al.findName(idAv.getValue()); } - return null; + return seq; } // returns the first Arg value intended for the structure structFilename @@ -631,9 +865,6 @@ public class Commands else { structfile = likelyStructure.getValue(); - Console.debug( - "##### Comparing closest previous structure argument '" - + structfile + "'"); } } }