X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=61ee1be035007f54965f49da9fae084c9348f45a;hb=09eebd8c6997a33049084e307078717cc1a693a6;hp=420e1d1809ca866aa018c03216356fe9fb531a73;hpb=c91960b43b7acd33dc76b9789bb61bafa05d3d09;p=jalview.git diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index 420e1d1..61ee1be 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -1,24 +1,42 @@ package jalview.bin; import java.io.File; +import java.util.ArrayList; +import java.util.Arrays; import java.util.Collections; import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +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.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.StructureChooser; 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.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; public class Commands { @@ -30,22 +48,49 @@ public class Commands private Map afMap; - public static void processArgs(ArgParser ap, boolean h) + public static boolean processArgs(ArgParser ap, boolean h) { argParser = ap; headless = h; - for (String id : argParser.linkedIds()) + boolean argsWereParsed = false; + if (headless) { - Commands cmds = new Commands(); - if (id == null) - { - cmds.processUnlinked(id); - } - else + System.setProperty("java.awt.headless", "true"); + } + + if (argParser != null && argParser.linkedIds() != null) + { + for (String id : argParser.linkedIds()) { - cmds.processLinked(id); + Console.debug("##### id=" + id); + Commands cmds = new Commands(); + if (id == null) + { + cmds.processUnlinked(id); + } + else + { + cmds.processLinked(id); + } + cmds.processImages(id); + argsWereParsed |= cmds.wereParsed(); } + } + if (argParser.getBool(Arg.QUIT)) + { + Jalview.getInstance().quit(); + return true; + } + // carry on with jalview.bin.Jalview + return argsWereParsed; + } + + boolean argsWereParsed = false; + + private boolean wereParsed() + { + return argsWereParsed; } public Commands() @@ -61,13 +106,14 @@ public class Commands protected void processUnlinked(String id) { + Map m = argParser.linkedArgs(id); + processLinked(id); } protected void processLinked(String id) { Map m = argParser.linkedArgs(id); - FileLoader fileLoader = new FileLoader(!headless); /* // script to execute after all loading is completed one way or another @@ -79,19 +125,18 @@ public class Commands FileFormatI format = null; DataSourceType protocol = null; */ - - if (m.get(Arg.OPEN) != null) + if (ArgParser.getArgValues(m, Arg.OPEN) != null) { long progress = -1; boolean first = true; AlignFrame af; - OPEN: for (String openFile : m.get(Arg.OPEN).getValues()) + for (String openFile : ArgParser.getValues(m, Arg.OPEN)) { if (openFile == null) - continue OPEN; - Console.debug("********** id = " + id + ", openFile = " + openFile); + continue; + argsWereParsed = true; if (first) { first = false; @@ -116,7 +161,6 @@ public class Commands if (!(new File(openFile)).exists()) { Console.warn("Can't find file '" + openFile + "'"); - continue OPEN; } } } @@ -136,14 +180,89 @@ 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 + 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); - if (m.get(Arg.TITLE) != null) - af.setTitle(m.get(Arg.TITLE).getValue()); - if (m.get(Arg.SSANNOTATION) != null - && !m.get(Arg.SSANNOTATION).getBoolean()) + + // wrap alignment? + if (ArgParser.getBoolean(m, Arg.WRAP)) + { + af.getCurrentView().setWrapAlignment(true); + } + + // change alignment frame title + if (ArgParser.getValue(m, Arg.TITLE) != null) + af.setTitle(ArgParser.getValue(m, Arg.TITLE)); + + /* hacky approach to hiding the annotations */ + // show secondary structure annotations? + if (ArgParser.getBoolean(m, Arg.SSANNOTATION)) { // do this better (annotation types?) AlignmentUtils.showOrHideSequenceAnnotations( @@ -151,22 +270,55 @@ public class Commands Collections.singleton("Secondary Structure"), null, false, false); } - if (m.get(Arg.NOTEMPFAC) != null - && m.get(Arg.NOTEMPFAC).getBoolean()) + + // show temperature factor annotations? + if (ArgParser.getBoolean(m, Arg.NOTEMPFAC)) { // do this better (annotation types?) + List hideThese = new ArrayList<>(); + hideThese.add("Temperature Factor"); + hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL); AlignmentUtils.showOrHideSequenceAnnotations( - af.getCurrentView().getAlignment(), - Collections.singleton("Temperature Factor"), null, - false, false); - AlignmentUtils.showOrHideSequenceAnnotations( - af.getCurrentView().getAlignment(), - Collections.singleton("Alphafold Reliability"), null, + af.getCurrentView().getAlignment(), hideThese, null, false, false); } + else + /* comment out hacky approach up to here and add this line: + if (showTemperatureFactor) + */ + { + if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null) + { + AlignmentAnnotation aa = AlignmentUtils + .getFirstSequenceAnnotationOfType( + af.getCurrentView().getAlignment(), + AlignmentAnnotation.LINE_GRAPH); + String label = ArgParser.getValue(m, 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); + + // 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); + } } else { @@ -186,15 +338,195 @@ public class Commands Console.error("Could not open any files in headless mode"); System.exit(1); } + // TOREMOVE COMMENT + // @Ben assumed this was the GUI version of above, rather then the + // first==false state + else + { + Console.warn("No more files to open"); + if (desktop != null) + desktop.setProgressBar(null, progress); + } + } + + } + + // 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 structId = "structid".equals(subVal.keyName) + ? subVal.keyValue + : null; + if (subVal.notSet()) + { + // take structid from pdbfilename + } + if ("structfile".equals(subVal.keyName)) + { + EBIAlfaFold.addAlphaFoldPAEToStructure( + af.getCurrentView().getAlignment(), paeFile, + subVal.index, subVal.keyValue, false); + } + else if ("structid".equals(subVal.keyName)) + { + EBIAlfaFold.addAlphaFoldPAEToStructure( + af.getCurrentView().getAlignment(), paeFile, + subVal.index, subVal.keyValue, true); + } + else + { + EBIAlfaFold.addAlphaFoldPAEToSequence( + af.getCurrentView().getAlignment(), paeFile, + subVal.index, + "seqid".equals(subVal.keyName) ? subVal.keyValue + : null); + // required to readjust the height and position of the pAE + // annotation + } + for (AlignmentViewPanel ap : af.getAlignPanels()) + { + ap.adjustAnnotationHeight(); + } + } } - else + } + + // open the structure (from same PDB file or given PDBfile) + if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE)) + { + AlignFrame af = afMap.get(id); + if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null) { - Console.warn("No more files to open"); - if (desktop != null) - desktop.setProgressBar(null, progress); + for (String val : ArgParser.getValues(m, Arg.STRUCTURE)) + { + SubVal subId = new SubVal(val); + SequenceI seq = getSpecifiedSequence(af, subId); + if (seq == null) + { + Console.warn("Could not find sequence for argument --" + + Arg.STRUCTURE + "=" + val); + break STRUCTURE; + } + File structureFile = null; + if (subId.content != null && subId.content.length() != 0) + { + structureFile = new File(subId.content); + Console.debug("Using structure file (from argument) '" + + structureFile.getAbsolutePath() + "'"); + } + /* 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()); + + // open structure view + AlignmentPanel ap = af.alignPanel; + StructureChooser.openStructureFileForSequence(ap, seq, + structureFile); + } } + } + } + + protected void processImages(String id) + { + Map m = argParser.linkedArgs(id); + AlignFrame af = afMap.get(id); + + if (af == null) + { + Console.warn("Did not have an alignment window for id=" + id); + return; + } + + if (ArgParser.getValues(m, Arg.IMAGE) != null) + { + for (String val : ArgParser.getValues(m, Arg.IMAGE)) + { + SubVal subVal = new SubVal(val); + String type = "png"; // default + String fileName = subVal.content; + File file = new File(fileName); + if ("type".equals(subVal.keyName)) + { + type = subVal.keyValue; + } + else if (fileName != null) + { + for (String ext : new String[] { "svg", "png", "html" }) + { + 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; + } + } } } + private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId) + { + AlignmentI al = af.getCurrentView().getAlignment(); + if (-1 < subId.index && subId.index < al.getSequences().size()) + { + return al.getSequenceAt(subId.index); + } + else if ("id".equals(subId.keyName)) + { + return al.findName(subId.keyValue); + } + return null; + } }