X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FCommands.java;h=79b6ab691abd0509250478be4910185e8bf80284;hb=5cfef671be8362cbb0598ea405a10f96e08a4df3;hp=faf2c9c21aa32ed2c55d70b4f5fd752be33296e7;hpb=01f8ff469a507604ed961418f7c80f9b245e60ca;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index faf2c9c..79b6ab6 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -2,9 +2,11 @@ package jalview.bin; import java.io.File; import java.io.IOException; +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; @@ -12,70 +14,99 @@ import java.util.Locale; import java.util.Map; import jalview.analysis.AlignmentUtils; -import jalview.api.AlignmentViewPanel; -import jalview.bin.ArgParser.Arg; -import jalview.bin.ArgParser.ArgValues; -import jalview.bin.ArgParser.SubVal; -import jalview.datamodel.AlignmentAnnotation; +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; import jalview.datamodel.SequenceI; import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder; import jalview.gui.AlignFrame; import jalview.gui.AlignmentPanel; 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.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 { Desktop desktop; - private static boolean headless; + private boolean headless; - private static ArgParser argParser; + private ArgParser argParser; private Map afMap; - public static boolean processArgs(ArgParser ap, boolean h) + private boolean commandArgsProvided = false; + + private boolean argsWereParsed = false; + + public Commands(ArgParser argparser, boolean headless) { - argParser = ap; + this(Desktop.instance, argparser, headless); + } + + public Commands(Desktop d, ArgParser argparser, boolean h) + { + argParser = argparser; headless = h; - boolean argsWereParsed = false; - if (headless) + desktop = d; + afMap = new HashMap(); + if (argparser != null) { - System.setProperty("java.awt.headless", "true"); + processArgs(argparser, headless); } + } - if (argParser != null && argParser.linkedIds() != null) + private boolean processArgs(ArgParser argparser, boolean h) + { + argParser = argparser; + headless = h; + boolean theseArgsWereParsed = false; + + if (argParser != null && argParser.getLinkedIds() != null) { - for (String id : argParser.linkedIds()) + for (String id : argParser.getLinkedIds()) { - Commands cmds = new Commands(); - if (id == null) - { - cmds.processUnlinked(id); - } - else + ArgValuesMap avm = argParser.getLinkedArgs(id); + theseArgsWereParsed = true; + theseArgsWereParsed &= processLinked(id); + boolean processLinkedOkay = theseArgsWereParsed; + theseArgsWereParsed &= processImages(id); + if (processLinkedOkay) + theseArgsWereParsed &= processOutput(id); + + // close ap + if (avm.getBoolean(Arg.CLOSE)) { - cmds.processLinked(id); + AlignFrame af = afMap.get(id); + if (af != null) + { + af.closeMenuItem_actionPerformed(true); + } } - cmds.processImages(id); - argsWereParsed |= cmds.wereParsed(); + } } @@ -85,69 +116,73 @@ public class Commands return true; } // carry on with jalview.bin.Jalview + argsWereParsed = theseArgsWereParsed; return argsWereParsed; } - boolean argsWereParsed = false; - - private boolean wereParsed() + public boolean commandArgsProvided() { - return argsWereParsed; + return commandArgsProvided; } - public Commands() + public boolean argsWereParsed() { - this(Desktop.instance); - } - - public Commands(Desktop d) - { - this.desktop = d; - afMap = new HashMap(); + return argsWereParsed; } - protected void processUnlinked(String id) + protected boolean processUnlinked(String id) { - Map m = argParser.linkedArgs(id); - - processLinked(id); + return processLinked(id); } - protected void processLinked(String id) + protected boolean processLinked(String id) { - Map m = argParser.linkedArgs(id); + boolean theseArgsWereParsed = false; + 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 (ArgParser.getArgValues(m, Arg.OPEN) != null) + * // 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; boolean first = true; + boolean progressBarSet = false; AlignFrame af; - for (String openFile : ArgParser.getValues(m, Arg.OPEN)) + // 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 = av.getArg(); + SubVals sv = av.getSubVals(); + String openFile = av.getValue(); if (openFile == null) continue; - argsWereParsed = true; + theseArgsWereParsed = true; if (first) { first = false; - if (!headless) + if (!headless && desktop != null) { desktop.setProgressBar( MessageManager.getString( "status.processing_commandline_args"), progress = System.currentTimeMillis()); + progressBarSet = true; } } @@ -180,108 +215,74 @@ public class Commands } af = afMap.get(id); - if (af == null) + // When to open a new AlignFrame + 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.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); - } + * 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); } */ - // get kind of temperature factor annotation - StructureImportSettings.TFType tempfacType = TFType.DEFAULT; - if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC)) - && ArgParser.getArgValues(m, Arg.TEMPFAC) != null) - { - try - { - tempfacType = StructureImportSettings.TFType.valueOf(ArgParser - .getValue(m, Arg.TEMPFAC).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()); - } - } - Console.debug( "Opening '" + openFile + "' in new alignment frame"); FileLoader fileLoader = new FileLoader(!headless); - StructureImportSettings.setTemperatureFactorType(tempfacType); - 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? - if (ArgParser.getBoolean(m, Arg.WRAP)) - { - af.getCurrentView().setWrapAlignment(true); - } + boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, + null, "WRAP_ALIGNMENT", false); + af.getCurrentView().setWrapAlignment(wrap); // colour aligment? - if (ArgParser.hasValue(m, Arg.COLOUR)) + String colour = ArgParser.getFromSubValArgOrPref(avm, av, + Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", ""); + + if ("" != colour) { - af.changeColour_actionPerformed( - ArgParser.getValue(m, Arg.COLOUR)); + af.changeColour_actionPerformed(colour); } // change alignment frame title - if (ArgParser.getValue(m, Arg.TITLE) != null) - af.setTitle(ArgParser.getValue(m, Arg.TITLE)); + String title = ArgParser.getFromSubValArgOrPref(avm, av, + Arg.TITLE, sv, null, null, null); + if (title != null) + af.setTitle(title); - /* hacky approach to hiding the annotations */ // show secondary structure annotations? - if (ArgParser.getBoolean(m, Arg.SSANNOTATION)) + boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm, + Arg.SSANNOTATIONS, av.getSubVals(), null, + "STRUCT_FROM_PDB", true); + if (avm.getBoolean(Arg.SSANNOTATIONS)) { - // do this better (annotation types?) + af.setAnnotationsVisibility(showSSAnnotations, true, false); + /* AlignmentUtils.showOrHideSequenceAnnotations( af.getCurrentView().getAlignment(), Collections.singleton("Secondary Structure"), null, false, false); + */ } // show temperature factor annotations? - if (ArgParser.getBoolean(m, Arg.NOTEMPFAC)) + if (avm.getBoolean(Arg.NOTEMPFAC)) { // do this better (annotation types?) List hideThese = new ArrayList<>(); @@ -292,17 +293,19 @@ public class Commands false, false); } else - /* comment out hacky approach up to here and add this line: - if (showTemperatureFactor) - */ + /* + * comment out hacky approach up to here and add this line: if + * (showTemperatureFactor) + */ { - if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null) + /* + if (avm.containsArg(Arg.TEMPFAC_LABEL)) { AlignmentAnnotation aa = AlignmentUtils .getFirstSequenceAnnotationOfType( af.getCurrentView().getAlignment(), AlignmentAnnotation.LINE_GRAPH); - String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL); + String label = avm.getValue(Arg.TEMPFAC_LABEL); if (aa != null) { aa.label = label; @@ -314,6 +317,7 @@ public class Commands + label); } } + */ } // store the AlignFrame for this id @@ -326,61 +330,86 @@ public class Commands .getStructureSelectionManager(Desktop.instance); SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0); ssm.computeMapping(false, new SequenceI[] { seq }, null, - openFile, DataSourceType.FILE, null); + openFile, DataSourceType.FILE, null, null, null, false); } } else { Console.debug( "Opening '" + openFile + "' in existing alignment frame"); - af.getCurrentView().addFile(new File(openFile), format); + 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 { if (headless) { - Console.error("Could not open any files in headless mode"); - System.exit(1); + Jalview.exit("Could not open any files in headless mode", 1); } else { Console.warn("No more files to open"); - if (desktop != null) - desktop.setProgressBar(null, progress); } } + if (progressBarSet && desktop != null) + desktop.setProgressBar(null, progress); } // open the structure (from same PDB file or given PDBfile) - if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE)) + if (!avm.getBoolean(Arg.NOSTRUCTURE)) { AlignFrame af = afMap.get(id); - if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null) + if (avm.containsArg(Arg.STRUCTURE)) { - for (String val : ArgParser.getValues(m, Arg.STRUCTURE)) + commandArgsProvided = true; + for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE)) { - SubVal subId = new SubVal(val); - SequenceI seq = getSpecifiedSequence(af, subId); + String val = av.getValue(); + SubVals subVals = av.getSubVals(); + SequenceI seq = getSpecifiedSequence(af, subVals); + 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.content != null && subId.content.length() != 0) + if (subVals.getContent() != null + && subVals.getContent().length() != 0) { - structureFile = new File(subId.content); + 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 }); + * + */ /* THIS DOESN'T WORK */ else if (seq.getAllPDBEntries() != null && seq.getAllPDBEntries().size() > 0) @@ -407,76 +436,121 @@ 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; - StructureChooser.openStructureFileForSequence(ap, seq, - structureFile); - } - } - } - - // load a pAE file if given - if (ArgParser.getValues(m, Arg.PAEMATRIX) != null) - { - AlignFrame af = afMap.get(id); - if (af != null) - { - for (String val : ArgParser.getValues(m, Arg.PAEMATRIX)) - { - SubVal subVal = ArgParser.getSubVal(val); - File paeFile = new File(subVal.content); - String paePath = null; - try - { - paePath = paeFile.getCanonicalPath(); - } catch (IOException e) + if (headless) { - paePath = paeFile.getAbsolutePath(); - Console.warn( - "Problem with the PAE file path: '" + paePath + "'"); + Cache.setProperty(Preferences.STRUCTURE_DISPLAY, + StructureViewer.ViewerType.JMOL.toString()); } - String structId = "structid".equals(subVal.keyName) - ? subVal.keyValue - : null; - if (subVal.notSet()) - { - // take structid from pdbfilename - } - if ("structfile".equals(subVal.keyName)) + + 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) { - Console.info("***** Attaching paeFile '" + paePath + "' to " - + subVal.keyName + "=" + subVal.keyValue); - EBIAlfaFold.addAlphaFoldPAEToStructure( - af.getCurrentView().getAlignment(), paeFile, - subVal.index, subVal.keyValue, false); + SubVals sv = paeAv.getSubVals(); + File paeFile = new File(sv.getContent()); + + paeLabel = sv.get("label"); + try + { + paeFilepath = paeFile.getCanonicalPath(); + } catch (IOException e) + { + paeFilepath = paeFile.getAbsolutePath(); + Console.warn("Problem with the PAE file path: '" + + paeFile.getPath() + "'"); + } } - else if ("structid".equals(subVal.keyName)) + + // showing annotations from structure file or not + boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm, + Arg.SSANNOTATIONS, 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) { - Console.info("***** Attaching paeFile '" + paePath + "' to " - + subVal.keyName + "=" + subVal.keyValue); - EBIAlfaFold.addAlphaFoldPAEToStructure( - af.getCurrentView().getAlignment(), paeFile, - subVal.index, subVal.keyValue, true); + tftString = tftAv.getSubVals().getContent(); } - else + if (tftString != null) { - Console.debug("***** Attaching paeFile '" + paePath - + "' to sequence index " + subVal.index); - EBIAlfaFold.addAlphaFoldPAEToSequence( - af.getCurrentView().getAlignment(), paeFile, - subVal.index, null); - // required to readjust the height and position of the pAE - // annotation + // get kind of temperature factor annotation + try + { + 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()) + { + sb.append(it.next().toString().toLowerCase(Locale.ROOT)); + if (it.hasNext()) + sb.append(", "); + } + Console.warn(sb.toString()); + } } - for (AlignmentViewPanel ap : af.getAlignPanels()) + + String sViewer = ArgParser.getFromSubValArgOrPref(avm, + Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, + "viewer", 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 = ArgParser.getBoolean(m, Arg.TEMPFAC_SHADING); + /* + boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING); if (doShading) { AlignFrame af = afMap.get(id); @@ -490,34 +564,40 @@ public class Commands Console.info("Changed colour " + acg.toString()); } } + */ + + return theseArgsWereParsed; } - protected void processImages(String id) + protected boolean processImages(String id) { - Map m = argParser.linkedArgs(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; + return false; } - if (ArgParser.getValues(m, Arg.IMAGE) != null) + if (avm.containsArg(Arg.IMAGE)) { - for (String val : ArgParser.getValues(m, Arg.IMAGE)) + for (ArgValue av : avm.getArgValueList(Arg.IMAGE)) { - SubVal subVal = new SubVal(val); - String type = "png"; // default - String fileName = subVal.content; + String val = av.getValue(); + SubVals subVal = av.getSubVals(); + String fileName = subVal.getContent(); File file = new File(fileName); - if ("type".equals(subVal.keyName)) - { - type = subVal.keyValue; - } - else if (fileName != null) + String name = af.getName(); + String renderer = ArgParser.getValueFromSubValOrArg(avm, av, + Arg.RENDERER, 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)) { @@ -531,37 +611,233 @@ 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; } } } + return true; } - private SequenceI getSpecifiedSequence(AlignFrame af, SubVal 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, SubVals subId) + { + if (subId == null) + return null; AlignmentI al = af.getCurrentView().getAlignment(); - if (-1 < subId.index && subId.index < al.getSequences().size()) + if (subId.has("seqid")) + { + return al.findName(subId.get("seqid")); + } + else if (-1 < subId.getIndex() + && subId.getIndex() < al.getSequences().size()) { - return al.getSequenceAt(subId.index); + return al.getSequenceAt(subId.getIndex()); } - else if ("id".equals(subId.keyName)) + 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) { - return al.findName(subId.keyValue); + 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; }