action.save_project = Save Project
action.save_project_as = Save Project as...
action.quit = Quit
- label.quit_jalview = Quit Jalview?
+ action.force_quit = Force quit
+ label.quit_jalview = Are you sure you want to quit Jalview?
+ label.wait_for_save = Wait for save
+ label.unsaved_changes = There are unsaved changes.
+ label.unsaved_alignments = There are unsaved alignments.
+ label.save_in_progress = Some files are still saving:
+ label.confirm_quit_viewer = An external viewer is still open. Close the external window as well?
+ label.confirm_quit_viewers = External viewers are still open. Close these external windows as well?
+ label.unknown = Unknown
+ label.quit_after_saving = Jalview will quit after saving.
+ label.all_saved = All files saved.
+ label.quitting_bye = Quitting, bye!
+ action.wait = Wait
+ action.cancel_quit = Cancel quit
action.expand_views = Expand Views
action.gather_views = Gather Views
action.page_setup = Page Setup...
label.colourScheme_buriedindex = Buried Index
label.colourScheme_purine/pyrimidine = Purine/Pyrimidine
label.colourScheme_nucleotide = Nucleotide
+ label.colourScheme_nucleotideambiguity = Nucleotide Ambiguity
label.colourScheme_t-coffeescores = T-Coffee Scores
label.colourScheme_rnahelices = By RNA Helices
label.colourScheme_sequenceid = Sequence ID Colour
label.sequence_details = Sequence Details
label.viewer_help = {0} Help
label.close_viewer = Close Viewer
+ label.close_viewers = Close Viewers
label.confirm_close_viewer = This will close Jalview''s connection to {0}.<br>Do you want to close the {1} window as well?
label.all = All
label.sort_by = Sort alignment by
label.memory_example_tooltip = The memory allocated to Jalview is the smaller of the percentage of physical memory (default 90%) and the maximum absolute memory (default 32GB). If your computer's memory cannot be ascertained then the maximum absolute memory defaults to 8GB (if not customised).<br>Jalview will always try and reserve 512MB for the OS and at least 512MB for itself.
warning.wrong_jvm_version_title = Wrong Java Version
warning.wrong_jvm_version_message = The Java version being used (Java {0}) may lead to problems.\nThis installation of Jalview should be used with Java {1}.
+label.alphafold_reliability = Alphafold Reliability
action.save_project = Guardar proyecto
action.save_project_as = Guardar proyecto como...
action.quit = Salir
- label.quit_jalview = Salir de Jalview?
+ action.force_quit = Forzar la salida
+ label.quit_jalview = ¿Estás seguro de que quieres salir de Jalview?
+ label.wait_for_save = Esperar a guardar
+ label.unsaved_changes = Hay cambios sin guardar.
+ label.unsaved_alignments = Hay alineamientos sin guardar.
+ label.save_in_progress = Algunos archivos aún se están guardando:
+ label.confirm_quit_viewer = Un visualizador externo todavía está abierto. ¿Cerrar también la ventana externa?
+ label.confirm_quit_viewers = Los visualizadores externos siguen abiertos. ¿Cerrar también estas ventanas externas?
+ label.unknown = desconocido
+ label.quit_after_saving = Jalview se cerrará después de guardar.
+ label.all_saved = Todos los archivos guardados.
+ label.quitting_bye = Saliendo ¡chao!
+ action.wait = Espere
+ action.cancel_quit = Cancelar la salida
action.expand_views = Expandir vistas
action.gather_views = Capturar vistas
action.page_setup = Configuración de la página
label.colourScheme_buriedindex = Índice de encubrimiento
label.colourScheme_purine/pyrimidine = Purina/Pirimidina
label.colourScheme_nucleotide = Nucleótido
+ label.colourScheme_nucleotideambiguity = Ambigüedad de nucleótido
label.colourScheme_t-coffeescores = Puntuación del T-Coffee
label.colourScheme_rnahelices = Por hélices de RNA
label.colourScheme_sequenceid = Color de ID de secuencia
label.show_all_seq_annotations=Mostrar anotaciones relacionadas con las secuencias
label.hide_all_seq_annotations=Ocultar anotaciones relacionadas con las secuencias
label.close_viewer=Cerrar Visualizador
+ label.close_viewers=Cerrar Visualizadores
label.all_views=Todas las Vistas
label.search_result=Resultado de búsqueda
action.fetch_sequences=Recuperar Secuencias...
label.memory_example_tooltip = La memoria asignada a Jalview es el menor entre el porcentaje de memoria física (predeterminado 90%) y la memoria absoluta máxima (predeterminado 32 GB). Si no se puede determinar la memoria de su computadora, la memoria absoluta máxima predeterminada es de 8 GB (si no está personalizada).<br>Jalview siempre intentará reservar 512 MB para el sistema operativo y al menos 512 MB para sí mismo.
warning.wrong_jvm_version_title = Versión incorrecta de Java
warning.wrong_jvm_version_message = La versión de Java que se está utilizando (Java {0}) puede generar problemas.\nEsta instalación de Jalview debe usarse con Java {1}.
-
+label.alphafold_reliability = Fiabilidad Alphafold
private static boolean propsAreReadOnly = Platform.isJS();
+ public static boolean isPropsAreReadOnly()
+ {
+ return propsAreReadOnly;
+ }
+
+ public static void setPropsAreReadOnly(boolean propsAreReadOnly)
+ {
+ Cache.propsAreReadOnly = propsAreReadOnly;
+ }
+
private final static String JS_PROPERTY_PREFIX = "jalview_";
/**
sb.append("Java version: ");
sb.append(System.getProperty("java.version"));
sb.append("\n");
+ sb.append("Java platform: ");
sb.append(System.getProperty("os.arch"));
sb.append(" ");
sb.append(System.getProperty("os.name"));
sb.append(" (");
sb.append(lafClass);
sb.append(")\n");
+ appendIfNotNull(sb, "Channel: ",
+ ChannelProperties.getProperty("channel"), "\n", null);
if (Console.isDebugEnabled()
|| !"release".equals(ChannelProperties.getProperty("channel")))
{
- appendIfNotNull(sb, "Channel: ",
- ChannelProperties.getProperty("channel"), "\n", null);
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdowninstanceappdir"), "\n", null);
appendIfNotNull(sb, "Getdown appbase: ",
System.getProperty("getdowninstanceappbase"), "\n", null);
appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
"\n", "unknown");
+ appendIfNotNull(sb, "Preferences file: ", propertiesFile, "\n",
+ "unknown");
}
return sb.toString();
}
import java.util.logging.Level;
import java.util.logging.Logger;
+ import javax.swing.JDialog;
+ import javax.swing.JFrame;
import javax.swing.JOptionPane;
import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.UIManager.LookAndFeelInfo;
+ import javax.swing.UnsupportedLookAndFeelException;
import com.formdev.flatlaf.FlatLightLaf;
+ import com.formdev.flatlaf.themes.FlatMacLightLaf;
import com.formdev.flatlaf.util.SystemInfo;
import com.threerings.getdown.util.LaunchUtil;
//import edu.stanford.ejalbert.launching.IBrowserLaunching;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
+import jalview.bin.ArgParser.Arg;
import jalview.ext.so.SequenceOntology;
import jalview.gui.AlignFrame;
import jalview.gui.Desktop;
import jalview.gui.PromptUserConfig;
+ import jalview.gui.QuitHandler;
+ import jalview.gui.QuitHandler.QResponse;
import jalview.io.AppletFormatAdapter;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
if (!Platform.isJS())
{
System.setSecurityManager(null);
+
+ Runtime.getRuntime().addShutdownHook(new Thread()
+ {
+ public void run()
+ {
+ Console.debug("Running shutdown hook");
+ if (QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT)
+ {
+ // Got to here by a SIGTERM signal.
+ // Note we will not actually cancel the quit from here -- it's too
+ // late -- but we can wait for saving files.
+ Console.debug("Checking for saving files");
+ QuitHandler.getQuitResponse(false);
+ }
+ else
+ {
+ Console.debug("Nothing more to do");
+ }
+ Console.debug("Exiting, bye!");
+ // shutdownHook cannot be cancelled, JVM will now halt
+ }
+ });
}
System.out
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+
String val = System.getProperty("sys.install4jVersion");
if (val != null)
{
System.out.println("Launcher version: " + val);
}
+ if (Platform.isLinux() && LaunchUtils.getJavaVersion() < 11)
+ {
+ System.setProperty("flatlaf.uiScale", "1");
+ }
+
// report Jalview version
Cache.loadBuildProperties(true);
+ // old ArgsParser
ArgsParser aparser = new ArgsParser(args);
+
boolean headless = false;
+ try
+ {
+ Console.initLogger();
+ } catch (NoClassDefFoundError error)
+ {
+ error.printStackTrace();
+ System.out.println("\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
+ System.exit(0);
+ }
+
String usrPropsFile = aparser.getValue("props");
- Cache.loadProperties(usrPropsFile); // must do this before
+ Cache.loadProperties(usrPropsFile); // must do this
+ // before
if (usrPropsFile != null)
{
System.out.println(
"CMD [-props " + usrPropsFile + "] executed successfully!");
}
+ // set log level from cache properties
+ Console.setLogLevel(Cache.getDefault(Cache.JALVIEWLOGLEVEL, "INFO"));
+
+ // new ArgParser
+ ArgParser argparser = new ArgParser(args); // do this after
+ // Console.initLogger, but TODO
+ // want --props before then
+ // CATCH22
+
+ if (argparser.isSet(Arg.HEADLESS))
+ headless = argparser.getBool(Arg.HEADLESS);
+ boolean commandsSuccess = Commands.processArgs(argparser, headless);
+ if (commandsSuccess)
+ {
+ Console.info("Successfully completed commands");
+ if (headless)
+ System.exit(0);
+ }
+ else
+ {
+ Console.warn("Error when running commands");
+ if (headless)
+ System.exit(1);
+ }
+
if (!Platform.isJS())
/**
* Java only
* @j2sIgnore
*/
{
+ if (argparser.isSet(Arg.HEADLESS))
+ {
+ headless = argparser.getBool(Arg.HEADLESS);
+ }
+
if (aparser.contains("help") || aparser.contains("h"))
{
showUsage();
System.exit(0);
}
- if (aparser.contains("nodisplay") || aparser.contains("nogui")
- || aparser.contains("headless"))
+ if (headless || aparser.contains("nodisplay")
+ || aparser.contains("nogui") || aparser.contains("headless"))
{
System.setProperty("java.awt.headless", "true");
headless = true;
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+ try
+ {
+ Console.initLogger();
+ } catch (
+
+ NoClassDefFoundError error)
+ {
+ error.printStackTrace();
+ System.out.println("\nEssential logging libraries not found."
+ + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
+ System.exit(0);
+ }
+
desktop = null;
setLookAndFeel();
}
String file = null, data = null;
+
FileFormatI format = null;
+
DataSourceType protocol = null;
+
FileLoader fileLoader = new FileLoader(!headless);
String groovyscript = null; // script to execute after all loading is
System.out.println("No files to open!");
System.exit(1);
}
+
long progress = -1;
// Finally, deal with the remaining input data.
if (file != null)
}
}
}
+
AlignFrame startUpAlframe = null;
// We'll only open the default file if the desktop is visible.
// And the user
startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
format);
+ // don't ask to save when quitting if only the startup file has been
+ // opened
+ Console.debug("Resetting up-to-date flag for startup file");
+ startUpAlframe.getViewport().setSavedUpToDate(true);
// extract groovy arguments before anything else.
}
Console.error("Could not set requested laf=" + laf);
}
break;
- case "quaqua":
- lafSet = setQuaquaLookAndFeel();
- if (!lafSet)
- {
- Console.error("Could not set requested laf=" + laf);
- }
- break;
- case "vaqua":
- lafSet = setVaquaLookAndFeel();
- if (!lafSet)
- {
- Console.error("Could not set requested laf=" + laf);
- }
- break;
case "mac":
lafSet = setMacLookAndFeel();
if (!lafSet)
setSystemLookAndFeel();
if (Platform.isLinux())
{
- setMetalLookAndFeel();
+ setLinuxLookAndFeel();
}
if (Platform.isMac())
{
private static boolean setFlatLookAndFeel()
{
- boolean set = setSpecificLookAndFeel("flatlaf light",
- "com.formdev.flatlaf.FlatLightLaf", false);
- if (set)
+ boolean set = false;
+ if (SystemInfo.isMacOS)
{
- if (Platform.isMac())
+ try
{
- System.setProperty("apple.laf.useScreenMenuBar", "true");
- System.setProperty("apple.awt.application.name",
- ChannelProperties.getProperty("app_name"));
- System.setProperty("apple.awt.application.appearance", "system");
- if (SystemInfo.isMacFullWindowContentSupported
- && Desktop.desktop != null)
- {
- Desktop.desktop.getRootPane()
- .putClientProperty("apple.awt.fullWindowContent", true);
- Desktop.desktop.getRootPane()
- .putClientProperty("apple.awt.transparentTitleBar", true);
- }
+ UIManager.setLookAndFeel(
+ "com.formdev.flatlaf.themes.FlatMacLightLaf");
+ set = true;
+ Console.debug("Using FlatMacLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ System.setProperty("apple.awt.application.name",
+ ChannelProperties.getProperty("app_name"));
+ System.setProperty("apple.awt.application.appearance", "system");
+ if (SystemInfo.isMacFullWindowContentSupported
+ && Desktop.desktop != null)
+ {
+ Console.debug("Setting transparent title bar");
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.fullWindowContent", true);
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.transparentTitleBar", true);
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.fullscreenable", true);
+ }
+ SwingUtilities.invokeLater(() -> {
+ FlatMacLightLaf.setup();
+ });
+ Console.debug("Using FlatMacLightLaf");
+ set = true;
+ }
+ if (!set)
+ {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ Console.debug("Using FlatLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ // Windows specific properties here
+ SwingUtilities.invokeLater(() -> {
+ FlatLightLaf.setup();
+ });
+ Console.debug("Using FlatLightLaf");
+ set = true;
+ }
+ else if (SystemInfo.isLinux)
+ {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ Console.debug("Using FlatLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ // enable custom window decorations
+ JFrame.setDefaultLookAndFeelDecorated(true);
+ JDialog.setDefaultLookAndFeelDecorated(true);
+ SwingUtilities.invokeLater(() -> {
+ FlatLightLaf.setup();
+ });
+ Console.debug("Using FlatLightLaf");
+ set = true;
+ }
- SwingUtilities.invokeLater(() -> {
- FlatLightLaf.setup();
- });
+ if (!set)
+ {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ Console.debug("Using FlatLightLaf");
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
}
+ }
+ if (set)
+ {
+ UIManager.put("TabbedPane.tabType", "card");
UIManager.put("TabbedPane.showTabSeparators", true);
+ UIManager.put("TabbedPane.showContentSeparator", true);
UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
UIManager.put("TabbedPane.tabsOverlapBorder", true);
- // UIManager.put("TabbedPane.hasFullBorder", true);
+ UIManager.put("TabbedPane.hasFullBorder", true);
UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
UIManager.put("TabbedPane.smoothScrolling", true);
UIManager.put("TabbedPane.tabWidthMode", "compact");
UIManager.put("TabbedPane.selectedBackground", Color.white);
}
- return set;
- }
- private static boolean setQuaquaLookAndFeel()
- {
- return setSpecificLookAndFeel("quaqua",
- ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
- .getName(),
- false);
- }
-
- private static boolean setVaquaLookAndFeel()
- {
- return setSpecificLookAndFeel("vaqua",
- "org.violetlib.aqua.AquaLookAndFeel", false);
+ Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
+ return set;
}
private static boolean setMacLookAndFeel()
return set;
}
+ private static boolean setLinuxLookAndFeel()
+ {
+ boolean set = false;
+ set = setFlatLookAndFeel();
+ if (!set)
+ set = setMetalLookAndFeel();
+ // avoid GtkLookAndFeel -- not good results especially on HiDPI
+ if (!set)
+ set = setNimbusLookAndFeel();
+ return set;
+ }
+
private static void showUsage()
{
System.out.println(
}
/**
- * Quit method delegates to Desktop.quit - unless running in headless mode
- * when it just ends the JVM
+ * jalview.bin.Jalview.quit() will just run the non-GUI shutdownHook and exit
*/
public void quit()
{
- if (desktop != null)
- {
- desktop.quit();
- }
- else
- {
- System.exit(0);
- }
+ // System.exit will run the shutdownHook first
+ System.exit(0);
}
public static AlignFrame getCurrentAlignFrame()
import java.util.List;
import java.util.Locale;
import java.util.Vector;
+ import java.util.concurrent.Callable;
import javax.swing.ButtonGroup;
import javax.swing.JCheckBoxMenuItem;
*/
void init()
{
+ setFrameIcon(null);
+
// setBackground(Color.white); // BH 2019
if (!Jalview.isHeadlessMode())
@Override
public void setProgressBar(String message, long id)
{
- progressBar.setProgressBar(message, id);
+ if (!Platform.isHeadless())
+ progressBar.setProgressBar(message, id);
}
@Override
lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
shortName);
+ Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
+ if (lastSaveSuccessful)
+ {
+ this.getViewport().setSavedUpToDate(true);
+ }
+
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
{ file, format }));
}
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- Runnable cancelAction = new Runnable()
- {
- @Override
- public void run()
+ Callable<Void> cancelAction = () -> {
+ lastSaveSuccessful = false;
+ return null;
+ };
+ Callable<Void> outputAction = () -> {
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport.getAlignExportData(options);
+ String output = new FormatAdapter(alignPanel, options)
+ .formatSequences(format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns());
+ if (output == null)
{
lastSaveSuccessful = false;
}
- };
- Runnable outputAction = new Runnable()
- {
- @Override
- public void run()
+ else
{
- // todo defer this to inside formatSequences (or later)
- AlignmentExportData exportData = viewport
- .getAlignExportData(options);
- String output = new FormatAdapter(alignPanel, options)
- .formatSequences(format, exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getAlignment().getHiddenColumns());
- if (output == null)
+ // create backupfiles object and get new temp filename destination
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = null;
+ if (doBackup)
{
- lastSaveSuccessful = false;
+ Console.trace("ALIGNFRAME making backupfiles object for " + file);
+ backupfiles = new BackupFiles(file);
}
- else
+ try
{
- // create backupfiles object and get new temp filename destination
- boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = null;
- if (doBackup)
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath()
+ : file;
+ Console.trace("ALIGNFRAME setting PrintWriter");
+ PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+
+ if (backupfiles != null)
{
- Console.trace(
- "ALIGNFRAME making backupfiles object for " + file);
- backupfiles = new BackupFiles(file);
+ Console.trace("ALIGNFRAME about to write to temp file "
+ + backupfiles.getTempFilePath());
}
- try
- {
- String tempFilePath = doBackup ? backupfiles.getTempFilePath()
- : file;
- Console.trace("ALIGNFRAME setting PrintWriter");
- PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
- if (backupfiles != null)
- {
- Console.trace("ALIGNFRAME about to write to temp file "
- + backupfiles.getTempFilePath());
- }
+ out.print(output);
+ 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() }));
+ lastSaveSuccessful = true;
+ } catch (IOException e)
+ {
+ lastSaveSuccessful = false;
+ Console.error(
+ "ALIGNFRAME Something happened writing the temp file");
+ Console.error(e.getMessage());
+ Console.debug(Cache.getStackTraceString(e));
+ } catch (Exception ex)
+ {
+ lastSaveSuccessful = false;
+ Console.error(
+ "ALIGNFRAME Something unexpected happened writing the temp file");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
+ }
- out.print(output);
- 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() }));
- lastSaveSuccessful = true;
- } catch (IOException e)
- {
- lastSaveSuccessful = false;
- Console.error(
- "ALIGNFRAME Something happened writing the temp file");
- Console.error(e.getMessage());
- Console.debug(Cache.getStackTraceString(e));
- } catch (Exception ex)
- {
- lastSaveSuccessful = false;
- Console.error(
- "ALIGNFRAME Something unexpected happened writing the temp file");
- Console.error(ex.getMessage());
- Console.debug(Cache.getStackTraceString(ex));
- }
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(lastSaveSuccessful);
+ Console.debug("ALIGNFRAME writing temp file was "
+ + (lastSaveSuccessful ? "" : "NOT ") + "successful");
+ // do the backup file roll and rename the temp file to actual file
+ Console.trace("ALIGNFRAME about to rollBackupsAndRenameTempFile");
+ lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ Console.debug("ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ + (lastSaveSuccessful ? "" : "un") + "successfully");
+ }
- if (doBackup)
- {
- backupfiles.setWriteSuccess(lastSaveSuccessful);
- Console.debug("ALIGNFRAME writing temp file was "
- + (lastSaveSuccessful ? "" : "NOT ") + "successful");
- // do the backup file roll and rename the temp file to actual file
- Console.trace(
- "ALIGNFRAME about to rollBackupsAndRenameTempFile");
- lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
- Console.debug(
- "ALIGNFRAME performed rollBackupsAndRenameTempFile "
- + (lastSaveSuccessful ? "" : "un")
- + "successfully");
- }
+ Console.debug("lastSaveSuccessful=" + lastSaveSuccessful);
+ if (lastSaveSuccessful)
+ {
+ AlignFrame.this.getViewport().setSavedUpToDate(true);
}
}
+ return null;
};
/*
}
else
{
- outputAction.run();
+ try
+ {
+ outputAction.call();
+ } catch (Exception e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
}
}
FileFormatI fileFormat = FileFormats.getInstance()
.forName(fileFormatName);
AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
- Runnable outputAction = new Runnable()
- {
- @Override
- public void run()
+ Callable<Void> outputAction = () -> {
+ // todo defer this to inside formatSequences (or later)
+ AlignmentExportData exportData = viewport.getAlignExportData(options);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
+ cap.setForInput(null);
+ try
{
- // todo defer this to inside formatSequences (or later)
- AlignmentExportData exportData = viewport
- .getAlignExportData(options);
- CutAndPasteTransfer cap = new CutAndPasteTransfer();
- cap.setForInput(null);
- try
- {
- FileFormatI format = fileFormat;
- cap.setText(new FormatAdapter(alignPanel, options)
- .formatSequences(format, exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- viewport.getAlignment().getHiddenColumns()));
- Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.alignment_output_command", new Object[]
- { fileFormat.getName() }), 600, 500);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Outputting alignment as " + fileFormat.getName(),
- oom);
- cap.dispose();
- }
+ FileFormatI format = fileFormat;
+ cap.setText(new FormatAdapter(alignPanel, options).formatSequences(
+ format, exportData.getAlignment(),
+ exportData.getOmitHidden(),
+ exportData.getStartEndPostions(),
+ viewport.getAlignment().getHiddenColumns()));
+ Desktop.addInternalFrame(cap, MessageManager.formatMessage(
+ "label.alignment_output_command", new Object[]
+ { fileFormat.getName() }), 600, 500);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Outputting alignment as " + fileFormat.getName(),
+ oom);
+ cap.dispose();
}
+ return null;
};
/*
}
else
{
- outputAction.run();
+ try
+ {
+ outputAction.call();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
}
}
.getString("label.load_jalview_annotations");
chooser.setDialogTitle(tooltip);
chooser.setToolTipText(tooltip);
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
- }
+ chooser.setResponseHandler(0, () -> {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
+ return null;
});
chooser.showOpenDialog(this);
return;
}
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
+ Callable okAction = () -> {
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(),
- sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
{
- try
- {
- AlignFrame.this.setClosed(true);
- } catch (Exception ex)
- {
- }
}
}
+ return null;
};
/*
}
else
{
- okAction.run();
+ try
+ {
+ okAction.call();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
}
}
viewport.setGatherViewsHere(true);
}
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
return newap;
}
}
/**
- * DOCUMENT ME!
+ * Opens an Overview panel for the alignment, unless one is open already
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
+ boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+ false);
+ openOverviewPanel(showHiddenRegions);
+ }
+
+ public OverviewPanel openOverviewPanel(boolean showHidden)
+ {
if (alignPanel.overviewPanel != null)
{
- return;
+ return alignPanel.overviewPanel;
}
-
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel);
+ final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, MessageManager
- .formatMessage("label.overview_params", new Object[]
- { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
+ Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(),
true, true);
+ frame.setFrameIcon(null);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ final AlignmentPanel thePanel = this.alignPanel;
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
javax.swing.event.InternalFrameEvent evt)
{
overview.dispose();
- alignPanel.setOverviewPanel(null);
+ thePanel.setOverviewPanel(null);
}
});
if (getKeyListeners().length > 0)
}
alignPanel.setOverviewPanel(overview);
+ alignPanel.setOverviewTitle(this);
+
+ return overview;
}
@Override
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
+ chooser.setResponseHandler(0, () -> {
+ String filePath = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", filePath);
+ NewickFile fin = null;
+ try
{
- String filePath = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", filePath);
- NewickFile fin = null;
- try
- {
- fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
- DataSourceType.FILE));
- viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
- } catch (Exception ex)
- {
- JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
- MessageManager
- .getString("label.problem_reading_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- ex.printStackTrace();
- }
- if (fin != null && fin.hasWarningMessage())
- {
- JvOptionPane.showMessageDialog(Desktop.desktop,
- fin.getWarningMessage(),
- MessageManager.getString(
- "label.possible_problem_with_tree_file"),
- JvOptionPane.WARNING_MESSAGE);
- }
+ fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
+ DataSourceType.FILE));
+ viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
+ } catch (Exception ex)
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
+ MessageManager.getString("label.problem_reading_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ ex.printStackTrace();
+ }
+ if (fin != null && fin.hasWarningMessage())
+ {
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ fin.getWarningMessage(),
+ MessageManager
+ .getString("label.possible_problem_with_tree_file"),
+ JvOptionPane.WARNING_MESSAGE);
}
+ return null;
});
chooser.showOpenDialog(this);
}
{
if (index > -1)
{
+ /*
+ * update current Overview window title (if there is one)
+ * to add view name "Original" if necessary
+ */
+ alignPanel.setOverviewTitle(this);
+
+ /*
+ * switch panels and set Overview title (if there is one
+ * because it was opened automatically)
+ */
alignPanel = alignPanels.get(index);
+ alignPanel.setOverviewTitle(this);
+
viewport = alignPanel.av;
avc.setViewportAndAlignmentPanel(viewport, alignPanel);
setMenusFromViewport(viewport);
chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
final AlignFrame us = this;
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- String choice = chooser.getSelectedFile().getPath();
- Cache.setProperty("LAST_DIRECTORY", choice);
- SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
- new VCFLoader(choice).loadVCF(seqs, us);
- }
+ chooser.setResponseHandler(0, () -> {
+ String choice = chooser.getSelectedFile().getPath();
+ Cache.setProperty("LAST_DIRECTORY", choice);
+ SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
+ new VCFLoader(choice).loadVCF(seqs, us);
+ return null;
});
chooser.showOpenDialog(null);
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.Rectangle;
+import java.io.File;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.IdentifyFile;
import jalview.renderer.ResidueShader;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
}
/**
+ * Load a File into this AlignViewport attempting to detect format if not
+ * given or given as null.
+ *
+ * @param file
+ * @param format
+ */
+ public void addFile(File file, FileFormatI format)
+ {
+ DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
+
+ if (format == null)
+ {
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e1)
+ {
+ jalview.bin.Console.error("Unknown file format for '" + file + "'");
+ }
+ }
+ else if (FileFormats.getInstance().isIdentifiable(format))
+ {
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ jalview.bin.Console.error("Unknown file format for '" + file + "'",
+ e);
+ }
+ }
+
+ new FileLoader().LoadFile(this, file, DataSourceType.FILE, format);
+ }
+
+ public void addFile(File file)
+ {
+ addFile(file, null);
+ }
+
+ /**
* Show a dialog with the option to open and link (cDNA <-> protein) as a new
* alignment, either as a standalone alignment or in a split frame. Returns
* true if the new alignment was opened, false if not, because the user
* in reverse order)
*/
JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
- .setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- addDataToAlignment(al);
- }
- }).setResponseHandler(1, new Runnable()
- {
- @Override
- public void run()
- {
- us.openLinkedAlignmentAs(al, title, true);
- }
- }).setResponseHandler(2, new Runnable()
- {
- @Override
- public void run()
- {
- us.openLinkedAlignmentAs(al, title, false);
- }
+ .setResponseHandler(0, () -> {
+ addDataToAlignment(al);
+ return null;
+ }).setResponseHandler(1, () -> {
+ us.openLinkedAlignmentAs(al, title, true);
+ return null;
+ }).setResponseHandler(2, () -> {
+ us.openLinkedAlignmentAs(al, title, false);
+ return null;
});
dialog.showDialog(question,
MessageManager.getString("label.open_split_window"),
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
+import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Locale;
+ import java.util.concurrent.Callable;
import java.util.concurrent.Executors;
import javax.swing.JCheckBox;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.seqfetcher.DbSourceProxy;
List<SequenceI> seqsWithoutSourceDBRef = null;
+ private boolean noChooserGUI = false;
+
private static StructureViewer lastTargetedView = null;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
+ this(selectedSeqs, selectedSeq, ap, false);
+ }
+
+ public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
+ AlignmentPanel ap, boolean noChooserGUI)
+ {
// which FTS engine to use
data = StructureChooserQuerySource.getQuerySourceFor(selectedSeqs);
initDialog();
this.selectedSequence = selectedSeq;
this.selectedSequences = selectedSeqs;
this.progressIndicator = (ap == null) ? null : ap.alignFrame;
+ this.noChooserGUI = noChooserGUI;
init();
}
populateFilterComboBox(isStructuresDiscovered(), cachedPDBExists);
discoverStructureViews();
updateProgressIndicator(null, startTime);
- mainFrame.setVisible(true);
+ mainFrame.setVisible(noChooserGUI);
updateCurrentView();
}
};
// fetch db refs if OK pressed
- final Runnable discoverCanonicalDBrefs = new Runnable()
- {
- @Override
- public void run()
- {
- btn_queryTDB.setEnabled(false);
- populateSeqsWithoutSourceDBRef();
+ final Callable discoverCanonicalDBrefs = () -> {
+ btn_queryTDB.setEnabled(false);
+ populateSeqsWithoutSourceDBRef();
- final int y = seqsWithoutSourceDBRef.size();
- if (y > 0)
- {
- final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
- .toArray(new SequenceI[y]);
- DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
- progressBar, new DbSourceProxy[]
- { new jalview.ws.dbsources.Uniprot() }, null, false);
- dbRefFetcher.addListener(afterDbRefFetch);
- // ideally this would also gracefully run with callbacks
-
- dbRefFetcher.fetchDBRefs(true);
- }
- else
- {
- // call finished action directly
- afterDbRefFetch.finished();
- }
+ final int y = seqsWithoutSourceDBRef.size();
+ if (y > 0)
+ {
+ final SequenceI[] seqWithoutSrcDBRef = seqsWithoutSourceDBRef
+ .toArray(new SequenceI[y]);
+ DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef,
+ progressBar, new DbSourceProxy[]
+ { new jalview.ws.dbsources.Uniprot() }, null, false);
+ dbRefFetcher.addListener(afterDbRefFetch);
+ // ideally this would also gracefully run with callbacks
+
+ dbRefFetcher.fetchDBRefs(true);
}
-
+ else
+ {
+ // call finished action directly
+ afterDbRefFetch.finished();
+ }
+ return null;
};
- final Runnable revertview = new Runnable()
- {
- @Override
- public void run()
+ final Callable revertview = () -> {
+ if (lastSelected != null)
{
- if (lastSelected != null)
- {
- cmb_filterOption.setSelectedItem(lastSelected);
- }
- };
+ cmb_filterOption.setSelectedItem(lastSelected);
+ }
+ return null;
};
int threshold = Cache.getDefault("UNIPROT_AUTOFETCH_THRESHOLD",
THRESHOLD_WARN_UNIPROT_FETCH_NEEDED);
Console.debug("Using Uniprot fetch threshold of " + threshold);
if (ignoreGui || seqsWithoutSourceDBRef.size() < threshold)
{
- Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
- .start();
+ Executors.newSingleThreadExecutor().submit(discoverCanonicalDBrefs);
return;
}
// need cancel and no to result in the discoverPDB action - mocked is
@Override
public void setProgressBar(String message, long id)
{
- progressBar.setProgressBar(message, id);
+ if (!Platform.isHeadless())
+ progressBar.setProgressBar(message, id);
}
@Override
{
return notQueriedTDBYet;
}
+
+ /**
+ * Open a single structure file for a given sequence
+ */
+ public static void openStructureFileForSequence(AlignmentPanel ap,
+ SequenceI seq, File sFile)
+ {
+ StructureChooser sc = new StructureChooser(new SequenceI[] { seq }, seq,
+ ap, true);
+ StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ PDBEntry fileEntry = null;
+ try
+ {
+ fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+ sFile.getAbsolutePath(), DataSourceType.FILE, seq, true,
+ Desktop.instance);
+ } catch (Exception e)
+ {
+ Console.error("Could not open structure file '"
+ + sFile.getAbsolutePath() + "'");
+ return;
+ }
+
+ StructureViewer sViewer = sc.launchStructureViewer(ssm,
+ new PDBEntry[]
+ { fileEntry }, ap, new SequenceI[] { seq });
+
+ sc.mainFrame.dispose();
+ sc.noChooserGUI = false;
+ }
}
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
+ import jalview.gui.QuitHandler;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
+
try
{
if (Desktop.instance != null)
MessageManager.getString("label.couldnt_read_data"),
JvOptionPane.WARNING_MESSAGE);
}
+ this.setShouldBeSaved();
return;
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
{
if (selectedFile == null)
{
- al = fa.readFile(file, protocol, format);
+ al = fa.readFile(null, file, protocol, format);
}
else
{
- al = fa.readFile(selectedFile, protocol, format);
+ al = fa.readFile(selectedFile, null, protocol, format);
}
source = fa.getAlignFile(); // keep reference for later if
// that perform queries to find the 'current working alignment'
Desktop.addInternalFrame(alignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+ /*
+ * for an Overview automatically opened with alignment,
+ * set its title now alignFrame title has been set
+ */
+ alignFrame.alignPanel.setOverviewTitle(alignFrame);
}
try
Desktop.instance.stopLoading();
}
+ this.setShouldBeSaved();
}
/**
return tempStructFile.toString();
}
+ /*
+ * set whether quit should ask to save when just loaded this source
+ */
+ private void setShouldBeSaved()
+ {
+ if (protocol == null)
+ return;
+ AlignFrame af = this.alignFrame;
+ if (af == null)
+ return;
+ AlignViewport avp = af.getViewport();
+ if (avp == null)
+ return;
+ avp.setSavedUpToDate(!protocol.isDynamic(),
+ QuitHandler.Message.UNSAVED_ALIGNMENTS);
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff