X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=3608295eded0c99135ac9584447aecb182d31631;hb=79456f40b33e73e2fb5420a3287ae80854281ef6;hp=43dc1fd014772f9b9aa3de1504fe53d1a09486a4;hpb=a16741c87b8246f228af144f52bcff904d66e43a;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 43dc1fd..3608295 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -2,54 +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.api.AlignmentViewPanel; 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.structure.StructureImportSettings; +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 jalview.ws.dbsources.EBIAlfaFold; -import mc_view.PDBChain; public class Commands { @@ -88,21 +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)) @@ -117,7 +112,7 @@ public class Commands } } - if (argParser.getBool(Arg.QUIT)) + if (argParser.getBoolean(Arg.QUIT)) { Jalview.getInstance().quit(); return true; @@ -145,21 +140,18 @@ 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; /* - // 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; - */ - if (avm.containsArg(Arg.OPEN)) + * // 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; + */ + if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN)) { commandArgsProvided = true; long progress = -1; @@ -167,19 +159,17 @@ public class Commands boolean first = true; boolean progressBarSet = false; AlignFrame af; - 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; @@ -227,107 +217,108 @@ 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) + if (a == Arg.OPEN) { - 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); - } - */ - - // get kind of temperature factor annotation - StructureImportSettings.TFType tempfacType = TFType.DEFAULT; - if ((!avm.getBoolean(Arg.NOTEMPFAC)) - && avm.containsArg(Arg.TEMPFAC)) - { - try - { - tempfacType = StructureImportSettings.TFType - .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue() - .toUpperCase(Locale.ROOT)); - Console.debug("Obtained Temperature Factor type of '" - + tempfacType + "'"); - } catch (IllegalArgumentException e) - { - // Just an error message! - StringBuilder sb = new StringBuilder().append("Cannot set --") - .append(Arg.TEMPFAC.getName()).append(" to '") - .append(tempfacType) - .append("', ignoring. Valid values are: "); - Iterator it = Arrays - .stream(StructureImportSettings.TFType.values()) - .iterator(); - while (it.hasNext()) - { - sb.append(it.next().toString().toLowerCase(Locale.ROOT)); - if (it.hasNext()) - sb.append(", "); - } - Console.warn(sb.toString()); - } + Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa", + openFile); } Console.debug( "Opening '" + openFile + "' in new alignment frame"); FileLoader fileLoader = new FileLoader(!headless); - StructureImportSettings.setTemperatureFactorType(tempfacType); - af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, 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.changeColour_actionPerformed(colour); + Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour); + } + + // Change alignment frame title + String title = ArgParser.getFromSubValArgOrPref(avm, av, + Arg.TITLE, sv, null, null, null); + if (title != null) { - af.getCurrentView().setWrapAlignment(true); + af.setTitle(title); + Jalview.testoutput(argParser, Arg.TITLE, "test title", title); } - // colour aligment? - if (avm.containsArg(Arg.COLOUR)) + // Add features + String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av, + Arg.FEATURES, sv); + if (featuresfile != null) { - af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR)); + af.parseFeaturesFile(featuresfile, + AppletFormatAdapter.checkProtocol(featuresfile)); + Jalview.testoutput(argParser, Arg.FEATURES, + "examples/testdata/plantfdx.features", featuresfile); } - // change alignment frame title - if (avm.containsArg(Arg.TITLE)) - af.setTitle(avm.getValue(Arg.TITLE)); + // 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); + } - /* hacky approach to hiding the annotations */ - // show secondary structure annotations? - if (avm.getBoolean(Arg.SSANNOTATION)) + // Set or clear the sortbytree flag + boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm, + Arg.SORTBYTREE, sv); + if (sortbytree) { - // do this better (annotation types?) - AlignmentUtils.showOrHideSequenceAnnotations( - af.getCurrentView().getAlignment(), - Collections.singleton("Secondary Structure"), null, - false, false); + 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)) { @@ -339,30 +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); @@ -374,17 +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 @@ -413,38 +385,42 @@ public class Commands for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE)) { String val = av.getValue(); - SubVals subId = new SubVals(val); - SequenceI seq = getSpecifiedSequence(af, subId); + SubVals subVals = av.getSubVals(); + SequenceI seq = getSpecifiedSequence(af, avm, av); + if (seq == null) + { + // Could not find sequence from subId, let's assume the first + // sequence in the alignframe + AlignmentI al = af.getCurrentView().getAlignment(); + seq = al.getSequenceAt(0); + } + if (seq == null) { - Console.warn("Could not find sequence for argument --" - + Arg.STRUCTURE + "=" + val); + Console.warn("Could not find sequence for argument " + + Arg.STRUCTURE.argString() + "=" + val); // you probably want to continue here, not break // break; continue; } File structureFile = null; - if (subId.getContent() != null - && subId.getContent().length() != 0) + if (subVals.getContent() != null + && subVals.getContent().length() != 0) { - structureFile = new File(subId.getContent()); + structureFile = new File(subVals.getContent()); Console.debug("Using structure file (from argument) '" + structureFile.getAbsolutePath() + "'"); } - // TRY THIS /* - PDBEntry fileEntry = new AssociatePdbFileWithSeq() - .associatePdbWithSeq(selectedPdbFileName, - DataSourceType.FILE, selectedSequence, true, - Desktop.instance); - - sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, - ap, new SequenceI[] - { selectedSequence }); - + * PDBEntry fileEntry = new AssociatePdbFileWithSeq() + * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE, + * selectedSequence, true, Desktop.instance); + * + * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new + * SequenceI[] { selectedSequence }); + * */ - /* THIS DOESN'T WORK */ else if (seq.getAllPDBEntries() != null && seq.getAllPDBEntries().size() > 0) @@ -471,9 +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; @@ -483,102 +463,101 @@ public class Commands StructureViewer.ViewerType.JMOL.toString()); } - // get tft, paeFilename, label? - /* - ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId, - Arg.TEMPFAC); - */ - StructureChooser.openStructureFileForSequence(null, null, ap, seq, - false, structureFile.getAbsolutePath(), null, null); // tft, - // paeFilename); - } - } - } + String structureFilepath = structureFile.getAbsolutePath(); - // load a pAE file if given - if (avm.containsArg(Arg.PAEMATRIX)) - { - AlignFrame af = afMap.get(id); - if (af != null) - { - for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX)) - { - String val = av.getValue(); - SubVals subVals = ArgParser.getSubVals(val); - String paeLabel = subVals.get("label"); - File paeFile = new File(subVals.getContent()); - String paePath = null; - try + // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX + String paeFilepath = ArgParser + .getFromSubValArgOrPrefWithSubstitutions(argParser, avm, + Arg.PAEMATRIX, Position.AFTER, av, subVals, null, + null, null); + if (paeFilepath != null) { - paePath = paeFile.getCanonicalPath(); - } catch (IOException e) + File paeFile = new File(paeFilepath); + + try + { + paeFilepath = paeFile.getCanonicalPath(); + } catch (IOException e) + { + paeFilepath = paeFile.getAbsolutePath(); + Console.warn("Problem with the PAE file path: '" + + paeFile.getPath() + "'"); + } + } + + // 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; + ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm, + af, structureFilepath); + if (tftString == null && tftAv != null) { - paePath = paeFile.getAbsolutePath(); - Console.warn( - "Problem with the PAE file path: '" + paePath + "'"); + tftString = tftAv.getSubVals().getContent(); } - String structid = null; - String structfile = null; - String seqid = null; - if (subVals.notSet()) + if (tftString != null) { - ArgValue likelyStructure = avm - .getClosestPreviousArgValueOfArg(av, Arg.STRUCTURE); - if (likelyStructure != null) + // get kind of temperature factor annotation + try { - SubVals sv = likelyStructure.getSubVals(); - if (sv != null && sv.has(ArgValues.ID)) - { - structid = sv.get(ArgValues.ID); - } - else + tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT)); + Console.debug("Obtained Temperature Factor type of '" + tft + + "' for structure '" + structureFilepath + "'"); + } catch (IllegalArgumentException e) + { + // Just an error message! + StringBuilder sb = new StringBuilder().append("Cannot set ") + .append(Arg.TEMPFAC.argString()).append(" to '") + .append(tft) + .append("', ignoring. Valid values are: "); + Iterator it = Arrays.stream(TFType.values()) + .iterator(); + while (it.hasNext()) { - structfile = likelyStructure.getValue(); + sb.append(it.next().toString().toLowerCase(Locale.ROOT)); + if (it.hasNext()) + sb.append(", "); } + Console.warn(sb.toString()); } } - else if (subVals.has("structfile")) - { - structfile = subVals.get("structfile"); - } - else if (subVals.has("structid")) - { - structid = subVals.get("structid"); - } - if (structfile != null) - { - Console.info("***** Attaching paeFile '" + paePath + "' to " - + "structfile=" + subVals.get("structfile")); - EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), - paeFile, subVals.getIndex(), subVals.get("structfile"), - true, false, paeLabel); - } - else if (structid != null) - { - Console.info("***** Attaching paeFile '" + paePath + "' to " - + "structid=" + subVals.get("structid")); - EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), - paeFile, subVals.getIndex(), subVals.get("structid"), - true, true, paeLabel); - } - else - { - Console.debug("***** Attaching paeFile '" + paePath - + "' to sequence index " + subVals.getIndex()); - EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), - paeFile, subVals.getIndex(), null, false, false, - paeLabel); - // required to readjust the height and position of the pAE - // annotation - } - for (AlignmentViewPanel ap : af.getAlignPanels()) + + String sViewer = ArgParser.getFromSubValArgOrPref(avm, + Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null, + null, "jmol"); + ViewerType viewerType = null; + if (!"none".equals(sViewer)) { - ap.adjustAnnotationHeight(); + 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, + ssFromStructure, false, viewerType); } } } + /* boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING); if (doShading) { @@ -593,13 +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) @@ -613,17 +617,19 @@ public class Commands for (ArgValue av : avm.getArgValueList(Arg.IMAGE)) { String val = av.getValue(); - SubVals subVal = new SubVals(val); - String type = "png"; // default + SubVals subVal = av.getSubVals(); 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)) { @@ -637,21 +643,50 @@ 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("--image type '" + type + "' not known. Ignoring"); + Console.warn(Arg.IMAGE.argString() + " type '" + type + + "' not known. Ignoring"); break; } } @@ -659,17 +694,195 @@ 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) { + 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 (-1 < subId.getIndex() - && subId.getIndex() < al.getSequences().size()) + if (al == null) + return null; + if (subVals != null) + { + 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 (idAv != null) { - return al.getSequenceAt(subId.getIndex()); + seq = al.findName(idAv.getValue()); } - else if (subId.has("seqid")) + return seq; + } + + // 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) { - return al.findName(subId.get("seqid")); + for (ArgValue av : avm.getArgValueList(arg)) + { + 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; + } + } } return null; }