From 147c5664cb8ca080623e9c7c786b8dbfb567bae8 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Wed, 9 Aug 2023 17:16:18 +0100 Subject: [PATCH] JAL-629 Enable output to STDOUT when specifying output filename as '-'. Must check other output is suppressed. --- resources/lang/Messages.properties | 1 + resources/lang/Messages_es.properties | 1 + src/jalview/bin/Commands.java | 167 ++++++++++++++++++--------------- src/jalview/gui/AlignFrame.java | 114 ++++++++++++++-------- 4 files changed, 171 insertions(+), 112 deletions(-) diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 924b9cb..45ed727 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -363,6 +363,7 @@ label.sequences_from = Sequences from {0} label.successfully_loaded_file = Successfully loaded file {0} label.successfully_loaded_matrix = Successfully loaded score matrix {0} label.successfully_saved_to_file_in_format = Successfully saved to file: {0} in {1} format. +label.successfully_printed_to_stdout_in_format = Successfully printed to STDOUT in {0} format. label.copied_sequences_to_clipboard = Copied {0} sequences to clipboard. label.check_file_matches_sequence_ids_alignment = Check that the file matches sequence IDs in the alignment. label.problem_reading_tcoffee_score_file = Problem reading T-COFFEE score file diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index 150a407..5dd8b3d 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -326,6 +326,7 @@ label.sequences_from = Secuencias de {0} label.successfully_loaded_file = Fichero cargado exitosamente {0} label.successfully_loaded_matrix = Matriz cargada exitosamente {0} label.successfully_saved_to_file_in_format = Guardado exitosamente en el fichero: {0} en formato {1}. +label.successfully_printed_to_stdout_in_format = Impresso exitosamente al STDOUT en formato {0}. label.copied_sequences_to_clipboard = Copiadas {0} secuencias en el portapapeles. label.check_file_matches_sequence_ids_alignment = Comprobar que el fichero coincide con el ID de la secuencia en el alineamiento. label.problem_reading_tcoffee_score_file = Problema de lectura del fichero de puntuaciones T-COFFEE diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java index d7d1ea3..a3d87f7 100644 --- a/src/jalview/bin/Commands.java +++ b/src/jalview/bin/Commands.java @@ -103,16 +103,20 @@ public class Commands theseArgsWereParsed &= processLinked(id); processGroovyScript(id); boolean processLinkedOkay = theseArgsWereParsed; - + // wait around until alignFrame isn't busy - AlignFrame af=afMap.get(id); - while (af!=null && af.getViewport().isCalcInProgress()) + AlignFrame af = afMap.get(id); + while (af != null && af.getViewport().isCalcInProgress()) { - try { + try + { Thread.sleep(25); - } catch (Exception q) {}; + } catch (Exception q) + { + } + ; } - + theseArgsWereParsed &= processImages(id); if (processLinkedOkay) theseArgsWereParsed &= processOutput(id); @@ -263,12 +267,16 @@ public class Commands if ("" != colour) { ColourSchemeI cs = ColourSchemeProperty.getColourScheme( - af.getViewport(), af.getViewport().getAlignment(), colour); - - if (cs==null && !"None".equals(colour)) + af.getViewport(), af.getViewport().getAlignment(), + colour); + + if (cs == null && !"None".equals(colour)) + { + Console.warn( + "Couldn't parse '" + colour + "' as a colourscheme."); + } + else { - Console.warn("Couldn't parse '"+colour+"' as a colourscheme."); - } else { af.changeColour(cs); } Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour); @@ -569,15 +577,15 @@ public class Commands structureFilepath, tft, paeFilepath, false, ssFromStructure, false, viewerType); - if (sv==null) + if (sv == null) { Console.error("Failed to import and open structure view."); continue; } try { - long tries=1000; - while (sv.isBusy() && tries>0) + long tries = 1000; + while (sv.isBusy() && tries > 0) { Thread.sleep(25); if (sv.isBusy()) @@ -587,15 +595,18 @@ public class Commands "Waiting for viewer for " + structureFilepath); } } - if (tries==0 && sv.isBusy()) + if (tries == 0 && sv.isBusy()) { - Console.warn("Gave up waiting for structure viewer to load. Something may have gone wrong."); + Console.warn( + "Gave up waiting for structure viewer to load. Something may have gone wrong."); } } catch (Exception x) { - Console.warn("Exception whilst waiting for structure viewer "+structureFilepath,x); + Console.warn("Exception whilst waiting for structure viewer " + + structureFilepath, x); } - Console.debug("Successfully opened viewer for "+structureFilepath); + Console.debug( + "Successfully opened viewer for " + structureFilepath); String structureImageFilename = ArgParser.getValueFromSubValOrArg( avm, av, Arg.STRUCTUREIMAGE, subVals); if (sv != null && structureImageFilename != null) @@ -652,16 +663,18 @@ public class Commands if (sview instanceof AppJmol) { AppJmol jmol = (AppJmol) sview; - try { - Console.debug("Rendering image to "+structureImageFile); + try + { + Console.debug("Rendering image to " + structureImageFile); jmol.makePDBImage(structureImageFile, imageType, renderer, - userBis); - Console.debug("Finished Rendering image to "+structureImageFile); + userBis); + Console.debug("Finished Rendering image to " + + structureImageFile); - } - catch (ImageOutputException ioexc) + } catch (ImageOutputException ioexc) { - Console.warn("Unexpected error whilst exporting image to "+structureImageFile,ioexc); + Console.warn("Unexpected error whilst exporting image to " + + structureImageFile, ioexc); } } @@ -771,57 +784,60 @@ public class Commands Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false"); Console.info("Writing " + file); - try { - switch (type) + try { - - case "svg": - Console.debug("Outputting type '" + type + "' to " + fileName); - af.createSVG(file, renderer); - break; - - case "png": - Console.debug("Outputting type '" + type + "' to " + fileName); - af.createPNG(file, null, userBis); - break; - - case "html": - Console.debug("Outputting type '" + type + "' to " + fileName); - HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); - htmlSVG.exportHTML(fileName, renderer); - break; - - case "biojs": - Console.debug("Creating BioJS MSA Viwer HTML file: " + fileName); - try - { - BioJsHTMLOutput.refreshVersionInfo( - BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); - } catch (URISyntaxException e) + switch (type) { - e.printStackTrace(); + + case "svg": + Console.debug("Outputting type '" + type + "' to " + fileName); + af.createSVG(file, renderer); + break; + + case "png": + Console.debug("Outputting type '" + type + "' to " + fileName); + af.createPNG(file, null, userBis); + break; + + case "html": + Console.debug("Outputting type '" + type + "' to " + fileName); + HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel); + htmlSVG.exportHTML(fileName, renderer); + break; + + case "biojs": + Console.debug( + "Creating BioJS MSA Viwer HTML file: " + fileName); + try + { + BioJsHTMLOutput.refreshVersionInfo( + BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY); + } catch (URISyntaxException e) + { + e.printStackTrace(); + } + BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); + bjs.exportHTML(fileName); + break; + + case "eps": + Console.debug("Creating EPS file: " + fileName); + af.createEPS(file, name); + break; + + case "imagemap": + Console.debug("Creating ImageMap file: " + fileName); + af.createImageMap(file, name); + break; + + default: + Console.warn(Arg.IMAGE.argString() + " type '" + type + + "' not known. Ignoring"); + break; } - BioJsHTMLOutput bjs = new BioJsHTMLOutput(af.alignPanel); - bjs.exportHTML(fileName); - break; - - case "eps": - Console.debug("Creating EPS file: " + fileName); - af.createEPS(file, name); - break; - - case "imagemap": - Console.debug("Creating ImageMap file: " + fileName); - af.createImageMap(file, name); - break; - - default: - Console.warn(Arg.IMAGE.argString() + " type '" + type - + "' not known. Ignoring"); - break; - } - } catch (Exception ioex) { - Console.warn("Unexpected error during export",ioex); + } catch (Exception ioex) + { + Console.warn("Unexpected error during export", ioex); } } } @@ -846,6 +862,7 @@ public class Commands String val = av.getValue(); SubVals subVals = av.getSubVals(); String fileName = subVals.getContent(); + boolean stdout = fileName.equals("-"); File file = new File(fileName); boolean overwrite = ArgParser.getFromSubValArgOrPref(avm, Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false); @@ -858,7 +875,7 @@ public class Commands !Platform.isHeadless()); // if backups is not true then --overwrite must be specified - if (file.exists() && !(overwrite || backups)) + if (file.exists() && !(overwrite || backups || stdout)) { Console.error("Won't overwrite file '" + fileName + "' without " + Arg.OVERWRITE.argString() + " or " @@ -923,7 +940,7 @@ public class Commands Console.info("Writing " + fileName); - af.saveAlignment(fileName, ff); + af.saveAlignment(fileName, ff, stdout); Console.debug("Returning backups to " + savedBackupsPreference); if (savedBackupsPreference != null) Cache.applicationProperties.put(BackupFiles.ENABLED, diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 49bd4e9..711d224 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -49,6 +49,7 @@ import java.beans.PropertyChangeEvent; import java.io.File; import java.io.FileWriter; import java.io.IOException; +import java.io.OutputStreamWriter; import java.io.PrintWriter; import java.net.URL; import java.util.ArrayList; @@ -157,7 +158,6 @@ import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.ViewportRanges; import jalview.ws.DBRefFetcher; import jalview.ws.DBRefFetcher.FetchFinishedListenerI; -import jalview.ws.datamodel.alphafold.PAEContactMatrix; import jalview.ws.jws1.Discoverer; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -1251,8 +1251,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ public void saveAlignment(String file, FileFormatI format) { + saveAlignment(file, format, false); + } + + public void saveAlignment(String file, FileFormatI format, boolean stdout) + { lastSaveSuccessful = true; - lastFilenameSaved = file; + if (!stdout) + { + lastFilenameSaved = file; + } lastFormatSaved = format; if (FileFormat.Jalview.equals(format)) @@ -1263,6 +1271,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, shortName = shortName .substring(shortName.lastIndexOf(File.separatorChar) + 1); } + // TODO deal with stdout=true lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName); @@ -1298,7 +1307,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { // create backupfiles object and get new temp filename destination - boolean doBackup = BackupFiles.getEnabled(); + boolean doBackup = BackupFiles.getEnabled() && !stdout; BackupFiles backupfiles = null; if (doBackup) { @@ -1310,7 +1319,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file; Console.trace("ALIGNFRAME setting PrintWriter"); - PrintWriter out = new PrintWriter(new FileWriter(tempFilePath)); + PrintWriter out = stdout + ? new PrintWriter(new OutputStreamWriter(System.out)) + : new PrintWriter(new FileWriter(tempFilePath)); if (backupfiles != null) { @@ -1319,13 +1330,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } out.print(output); + out.flush(); Console.trace("ALIGNFRAME about to close file"); out.close(); Console.trace("ALIGNFRAME closed file"); - AlignFrame.this.setTitle(file); - statusBar.setText(MessageManager.formatMessage( - "label.successfully_saved_to_file_in_format", new Object[] - { fileName, format.getName() })); + AlignFrame.this.setTitle(stdout ? "STDOUT" : file); + if (stdout) + { + statusBar.setText(MessageManager.formatMessage( + "label.successfully_printed_to_stdout_in_format", + new Object[] + { format.getName() })); + } + else + { + statusBar.setText(MessageManager.formatMessage( + "label.successfully_saved_to_file_in_format", + new Object[] + { fileName, format.getName() })); + } lastSaveSuccessful = true; } catch (IOException e) { @@ -1456,9 +1479,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void htmlMenuItem_actionPerformed(ActionEvent e) { HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel); - try { + try + { htmlSVG.exportHTML(null); - } catch (ImageOutputException x) { + } catch (ImageOutputException x) + { // report problem to console and raise dialog } } @@ -1467,51 +1492,64 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void bioJSMenuItem_actionPerformed(ActionEvent e) { BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel); - try { - bjs.exportHTML(null); - } catch (ImageOutputException x) { - // report problem to console and raise dialog - } + try + { + bjs.exportHTML(null); + } catch (ImageOutputException x) + { + // report problem to console and raise dialog + } } public void createImageMap(File file, String image) { - try { - alignPanel.makePNGImageMap(file, image); - } catch (ImageOutputException x) { + try + { + alignPanel.makePNGImageMap(file, image); + } catch (ImageOutputException x) + { // report problem to console and raise dialog } } @Override - public void createPNG_actionPerformed(ActionEvent e) { - try{ + public void createPNG_actionPerformed(ActionEvent e) + { + try + { createPNG(null); } catch (ImageOutputException ioex) { // raise dialog, and report via console } } + @Override - public void createEPS_actionPerformed(ActionEvent e) { - try{ + public void createEPS_actionPerformed(ActionEvent e) + { + try + { createEPS(null); } catch (ImageOutputException ioex) { // raise dialog, and report via console } - + } + @Override - public void createSVG_actionPerformed(ActionEvent e) { - try{ + public void createSVG_actionPerformed(ActionEvent e) + { + try + { createSVG(null); } catch (ImageOutputException ioex) { // raise dialog, and report via console } - + } + /** * Creates a PNG image of the alignment and writes it to the given file. If * the file is null, the user is prompted to choose a file. @@ -1523,7 +1561,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, createPNG(f, null, BitmapImageSizing.nullBitmapImageSizing()); } - public void createPNG(File f, String renderer, BitmapImageSizing userBis) throws ImageOutputException + public void createPNG(File f, String renderer, BitmapImageSizing userBis) + throws ImageOutputException { alignPanel.makeAlignmentImage(TYPE.PNG, f, renderer, userBis); } @@ -1534,7 +1573,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ - public void createEPS(File f) throws ImageOutputException + public void createEPS(File f) throws ImageOutputException { createEPS(f, null); } @@ -1550,7 +1589,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param f */ - public void createSVG(File f) throws ImageOutputException + public void createSVG(File f) throws ImageOutputException { createSVG(f, null); } @@ -2341,12 +2380,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // annotation was duplicated earlier alignment.addAnnotation(sequences[i].getAnnotation()[a]); // take care of contact matrix too - ContactMatrixI cm=sequences[i].getContactMatrixFor(sequences[i].getAnnotation()[a]); - if (cm!=null) + ContactMatrixI cm = sequences[i] + .getContactMatrixFor(sequences[i].getAnnotation()[a]); + if (cm != null) { - alignment.addContactListFor(sequences[i].getAnnotation()[a], cm); + alignment.addContactListFor(sequences[i].getAnnotation()[a], + cm); } - + alignment.setAnnotationIndex(sequences[i].getAnnotation()[a], a); } @@ -4239,8 +4280,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } - public void showContactMapTree(AlignmentAnnotation aa, - ContactMatrixI cm) + public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm) { int x = 4, y = 5; int w = 400, h = 500; @@ -4249,8 +4289,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { NewickFile fin = new NewickFile( new FileParse(cm.getNewick(), DataSourceType.PASTE)); - String title = aa.label + " " - + cm.getTreeMethod() + " tree" + (aa.sequenceRef != null + String title = aa.label + " " + cm.getTreeMethod() + " tree" + + (aa.sequenceRef != null ? (" for " + aa.sequenceRef.getDisplayId(false)) : ""); -- 1.7.10.2