X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=26ce8c32c1709ebfa7d81a923b8d4271947392a0;hb=a5928e2c1b9e2cea8d9c43f3d03f9cce2604f3b2;hp=4239ec7d8ec5c7ff2736995393373ef6c0a31951;hpb=4d4e95690af1676f81cc520ba7618c3e69ba99ba;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 4239ec7..26ce8c3 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -1,6 +1,7 @@ package jalview.bin; import java.io.File; +import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; @@ -13,68 +14,135 @@ 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.ArgValue; +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.io.AppletFormatAdapter; import jalview.io.DataSourceType; import jalview.io.FileFormatException; import jalview.io.FileFormatI; 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 void processArgs(ArgParser ap, boolean h) + private boolean commandArgsProvided = false; + + private boolean argsWereParsed = false; + + public Commands(ArgParser argparser, boolean headless) + { + this(Desktop.instance, argparser, headless); + } + + public Commands(Desktop d, ArgParser argparser, boolean h) { - argParser = ap; + argParser = argparser; headless = h; - for (String id : argParser.linkedIds()) + desktop = d; + afMap = new HashMap(); + if (argparser != null) { - Commands cmds = new Commands(); - if (id == null) - { - cmds.processUnlinked(id); - } - else + processArgs(argparser, headless); + } + } + + private boolean processArgs(ArgParser argparser, boolean h) + { + argParser = argparser; + headless = h; + boolean theseArgsWereParsed = false; + + if (argParser != null && argParser.linkedIds() != null) + { + for (String id : argParser.linkedIds()) { - cmds.processLinked(id); + ArgValuesMap avm = argParser.linkedArgs(id); + theseArgsWereParsed = true; + if (id == null) + { + theseArgsWereParsed &= processUnlinked(id); + } + else + { + theseArgsWereParsed &= processLinked(id); + } + theseArgsWereParsed &= processImages(id); + + // close ap + if (avm.getBoolean(Arg.CLOSE)) + { + AlignFrame af = afMap.get(id); + if (af != null) + { + af.closeMenuItem_actionPerformed(true); + } + } + } + } + if (argParser.getBool(Arg.QUIT)) + { + Jalview.getInstance().quit(); + return true; + } + // carry on with jalview.bin.Jalview + argsWereParsed = theseArgsWereParsed; + return argsWereParsed; } - public Commands() + public boolean commandArgsProvided() { - this(Desktop.instance); + return commandArgsProvided; } - public Commands(Desktop d) + public boolean argsWereParsed() { - this.desktop = d; - afMap = new HashMap(); + return argsWereParsed; } - protected void processUnlinked(String id) + protected boolean processUnlinked(String 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.linkedArgs(id); + if (avm == null) + return true; /* // script to execute after all loading is completed one way or another @@ -86,27 +154,31 @@ public class Commands FileFormatI format = null; DataSourceType protocol = null; */ - - if (m.get(Arg.OPEN) != null) + if (avm.containsArg(Arg.OPEN)) { + commandArgsProvided = true; long progress = -1; boolean first = true; + boolean progressBarSet = false; AlignFrame af; - OPEN: for (String openFile : m.get(Arg.OPEN).getValues()) + for (ArgValue av : avm.getArgValueList(Arg.OPEN)) { + String openFile = av.getValue(); if (openFile == null) - continue OPEN; + continue; + 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; } } @@ -122,7 +194,6 @@ public class Commands if (!(new File(openFile)).exists()) { Console.warn("Can't find file '" + openFile + "'"); - continue OPEN; } } } @@ -142,27 +213,57 @@ public class Commands af = afMap.get(id); if (af == null) { + /* + * 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); + } + */ + // get kind of temperature factor annotation - AlignmentAnnotation.TFType tempfacType = null; - if ((m.get(Arg.NOTEMPFAC) == null - || !m.get(Arg.NOTEMPFAC).getBoolean()) - && m.get(Arg.TEMPFAC) != null) + StructureImportSettings.TFType tempfacType = TFType.DEFAULT; + if ((!avm.getBoolean(Arg.NOTEMPFAC)) + && avm.containsArg(Arg.TEMPFAC)) { try { - tempfacType = AlignmentAnnotation.TFType - .valueOf(m.get(Arg.TEMPFAC).getValue() + 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(AlignmentAnnotation.TFType.values()) + Iterator it = Arrays + .stream(StructureImportSettings.TFType.values()) .iterator(); while (it.hasNext()) { @@ -177,22 +278,31 @@ public class Commands Console.debug( "Opening '" + openFile + "' in new alignment frame"); FileLoader fileLoader = new FileLoader(!headless); - af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format, - tempfacType); + + StructureImportSettings.setTemperatureFactorType(tempfacType); + + af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, + format); // wrap alignment? - if (m.get(Arg.WRAP) != null && m.get(Arg.WRAP).getBoolean()) + if (avm.getBoolean(Arg.WRAP)) { af.getCurrentView().setWrapAlignment(true); } + // colour aligment? + if (avm.containsArg(Arg.COLOUR)) + { + af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR)); + } + // change alignment frame title - if (m.get(Arg.TITLE) != null) - af.setTitle(m.get(Arg.TITLE).getValue()); + if (avm.containsArg(Arg.TITLE)) + af.setTitle(avm.getValue(Arg.TITLE)); + /* hacky approach to hiding the annotations */ // show secondary structure annotations? - if (m.get(Arg.SSANNOTATION) != null - && !m.get(Arg.SSANNOTATION).getBoolean()) + if (avm.getBoolean(Arg.SSANNOTATION)) { // do this better (annotation types?) AlignmentUtils.showOrHideSequenceAnnotations( @@ -202,45 +312,62 @@ public class Commands } // show temperature factor annotations? - if (m.get(Arg.NOTEMPFAC) != null - && m.get(Arg.NOTEMPFAC).getBoolean()) + if (avm.getBoolean(Arg.NOTEMPFAC)) { // do this better (annotation types?) List hideThese = new ArrayList<>(); hideThese.add("Temperature Factor"); - hideThese.add(MessageManager - .getString("label.alphafold_reliability")); + hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL); AlignmentUtils.showOrHideSequenceAnnotations( af.getCurrentView().getAlignment(), hideThese, null, false, false); } else + /* comment out hacky approach up to here and add this line: + if (showTemperatureFactor) + */ { - if (m.get(Arg.TEMPFAC_LABEL) != null) + 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 = m.get(Arg.TEMPFAC_LABEL).getValue(); + 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); + + // is it its own structure file? + if (format.isStructureFile()) + { + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0); + ssm.computeMapping(false, new SequenceI[] { seq }, null, + openFile, DataSourceType.FILE, null, null, null); + } } else { Console.debug( "Opening '" + openFile + "' in existing alignment frame"); - af.getCurrentView().addFile(new File(openFile), format); + af.getCurrentView().addFile(new File(openFile), format, false); } - System.out - .println("Command " + Arg.OPEN + " executed successfully!"); + Console.debug("Command " + Arg.OPEN + " executed successfully!"); } if (first) // first=true means nothing opened @@ -250,31 +377,159 @@ public class Commands Console.error("Could not open any files in headless mode"); System.exit(1); } + else + { + Console.warn("No more files to open"); + } } - else + if (progressBarSet && desktop != null) + desktop.setProgressBar(null, progress); + + } + + // open the structure (from same PDB file or given PDBfile) + if (!avm.getBoolean(Arg.NOSTRUCTURE)) + { + AlignFrame af = afMap.get(id); + if (avm.containsArg(Arg.STRUCTURE)) { - Console.warn("No more files to open"); - if (desktop != null) - desktop.setProgressBar(null, progress); - } + commandArgsProvided = true; + for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE)) + { + String val = av.getValue(); + SubVals subId = new SubVals(val); + SequenceI seq = getSpecifiedSequence(af, subId); + if (seq == null) + { + Console.warn("Could not find sequence for argument --" + + Arg.STRUCTURE + "=" + val); + // you probably want to continue here, not break + // break; + continue; + } + File structureFile = null; + if (subId.getContent() != null + && subId.getContent().length() != 0) + { + structureFile = new File(subId.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) + { + structureFile = new File( + seq.getAllPDBEntries().elementAt(0).getFile()); + Console.debug("Using structure file (from sequence) '" + + structureFile.getAbsolutePath() + "'"); + } + + if (structureFile == null) + { + Console.warn("Not provided structure file with '" + val + "'"); + continue; + } + + if (!structureFile.exists()) + { + Console.warn("Structure file '" + + structureFile.getAbsoluteFile() + "' not found."); + continue; + } + + Console.debug("Using structure file " + + structureFile.getAbsolutePath()); + + PDBEntry fileEntry = new AssociatePdbFileWithSeq() + .associatePdbWithSeq(structureFile.getAbsolutePath(), + DataSourceType.FILE, seq, true, Desktop.instance); + + // open structure view + AlignmentPanel ap = af.alignPanel; + if (headless) + { + Cache.setProperty(Preferences.STRUCTURE_DISPLAY, + 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); + } + } } // load a pAE file if given - if (m.get(Arg.PAEMATRIX) != null) + if (avm.containsArg(Arg.PAEMATRIX)) { AlignFrame af = afMap.get(id); if (af != null) { - for (String val : m.get(Arg.PAEMATRIX).getValues()) + for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX)) { - SubId subId = new SubId(val); - File paeFile = new File(subId.content); - EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), - paeFile, subId.index, - "id".equals(subId.keyName) ? subId.keyValue : null); - // required to readjust the height and position of the pAE - // annotation + String val = av.getValue(); + SubVals subVals = ArgParser.getSubVals(val); + File paeFile = new File(subVals.getContent()); + String paePath = null; + try + { + paePath = paeFile.getCanonicalPath(); + } catch (IOException e) + { + paePath = paeFile.getAbsolutePath(); + Console.warn( + "Problem with the PAE file path: '" + paePath + "'"); + } + String structId = subVals.get("structid"); + if (subVals.notSet()) + { + // take structid from pdbfilename + } + if (subVals.has("structfile")) + { + Console.info("***** Attaching paeFile '" + paePath + "' to " + + "structfile=" + subVals.get("structfile")); + EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), + paeFile, subVals.getIndex(), subVals.get("structfile"), + true, false); + } + else if (subVals.has("structid")) + { + Console.info("***** Attaching paeFile '" + paePath + "' to " + + "structid=" + subVals.get("structid")); + EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), + paeFile, subVals.getIndex(), subVals.get("structid"), + true, true); + } + else + { + Console.debug("***** Attaching paeFile '" + paePath + + "' to sequence index " + subVals.getIndex()); + EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(), + paeFile, subVals.getIndex(), null, false, false); + // required to readjust the height and position of the pAE + // annotation + } for (AlignmentViewPanel ap : af.getAlignPanels()) { ap.adjustAnnotationHeight(); @@ -282,56 +537,99 @@ public class Commands } } } - } - /** - * A helper class to parse a string of the possible forms "content" - * "[index]content", "[keyName=keyValue]content" and return the integer index, - * the strings keyName and keyValue, and the content after the square brackets - * (if present). Values not set will be -1 or null. - */ - protected class SubId - { - protected int index = 0; + boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING); + if (doShading) + { + AlignFrame af = afMap.get(id); + for (AlignmentAnnotation aa : af.alignPanel.getAlignment() + .findAnnotation(PDBChain.class.getName().toString())) + { + AnnotationColourGradient acg = new AnnotationColourGradient(aa, + af.alignPanel.av.getGlobalColourScheme(), 0); + acg.setSeqAssociated(true); + af.changeColour(acg); + Console.info("Changed colour " + acg.toString()); + } + } - protected String keyName = null; + return theseArgsWereParsed; + } - protected String keyValue = null; + protected boolean processImages(String id) + { + ArgValuesMap avm = argParser.linkedArgs(id); + AlignFrame af = afMap.get(id); - protected String content = null; + if (af == null) + { + Console.warn("Did not have an alignment window for id=" + id); + return false; + } - protected SubId(String item) + if (avm.containsArg(Arg.IMAGE)) { - if (item.indexOf('[') == 0 && item.indexOf(']') > 1) + for (ArgValue av : avm.getArgValueList(Arg.IMAGE)) { - int openBracket = item.indexOf('['); - int closeBracket = item.indexOf(']'); - String indexString = item.substring(openBracket + 1, closeBracket); - this.content = item.substring(closeBracket + 1); - int equals = indexString.indexOf('='); - if (equals > -1) + String val = av.getValue(); + SubVals subVal = new SubVals(val); + String type = "png"; // default + String fileName = subVal.getContent(); + File file = new File(fileName); + if (subVal.has("type")) { - this.keyName = indexString.substring(0, equals); - this.keyValue = indexString.substring(equals + 1); - this.index = -1; + type = subVal.get("type"); } - else + else if (fileName != null) { - try - { - this.index = Integer.parseInt(indexString); - } catch (NumberFormatException e) + for (String ext : new String[] { "svg", "png", "html" }) { - Console.warn("Failed to obtain sequenced id or index from '" - + item + "'. Setting index=0 and using content='" - + content + "'."); + if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext)) + { + type = ext; + } } } + // for moment we disable JSON export + Cache.setPropsAreReadOnly(true); + Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false"); + + switch (type) + { + case "svg": + Console.debug("Outputting type '" + type + "' to " + fileName); + af.createSVG(file); + 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); + break; + default: + Console.warn("--image type '" + type + "' not known. Ignoring"); + break; + } } - else - { - this.content = item; - } } + return true; + } + + private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId) + { + AlignmentI al = af.getCurrentView().getAlignment(); + if (-1 < subId.getIndex() + && subId.getIndex() < al.getSequences().size()) + { + return al.getSequenceAt(subId.getIndex()); + } + else if (subId.has("seqid")) + { + return al.findName(subId.get("seqid")); + } + return null; } }