jalview.release=releases/Release_2_11_3_Branch
-jalview.version=2.11.3
+jalview.version=2.11.3.0
id 'eclipse'
id "com.diffplug.gradle.spotless" version "3.28.0"
id 'com.github.johnrengelman.shadow' version '4.0.3'
- id 'com.install4j.gradle' version '9.0.6'
+ id 'com.install4j.gradle' version '10.0.3'
id 'com.dorongold.task-tree' version '2.1.0' // only needed to display task dependency tree with gradle task1 [task2 ...] taskTree
id 'com.palantir.git-version' version '0.13.0' apply false
}
// for install4j
JAVA_MIN_VERSION = JAVA_VERSION
JAVA_MAX_VERSION = JAVA_VERSION
- def jreInstallsDir = string(jre_installs_dir)
+ jreInstallsDir = string(jre_installs_dir)
if (jreInstallsDir.startsWith("~/")) {
jreInstallsDir = System.getProperty("user.home") + jreInstallsDir.substring(1)
}
- macosJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-mac-x64/jre")
- windowsJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-windows-x64/jre")
- linuxJavaVMDir = string("${jreInstallsDir}/jre-${JAVA_INTEGER_VERSION}-linux-x64/jre")
- macosJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_mac_x64.tar.gz")
- windowsJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_windows_x64.tar.gz")
- linuxJavaVMTgz = string("${jreInstallsDir}/tgz/jre_${JAVA_INTEGER_VERSION}_linux_x64.tar.gz")
install4jDir = string("${jalviewDir}/${install4j_utils_dir}")
install4jConfFileName = string("jalview-install4j-conf.install4j")
install4jConfFile = file("${install4jDir}/${install4jConfFileName}")
'JAVA_VERSION': JAVA_VERSION,
'JAVA_INTEGER_VERSION': JAVA_INTEGER_VERSION,
'VERSION': JALVIEW_VERSION,
- 'MACOS_JAVA_VM_DIR': macosJavaVMDir,
- 'WINDOWS_JAVA_VM_DIR': windowsJavaVMDir,
- 'LINUX_JAVA_VM_DIR': linuxJavaVMDir,
- 'MACOS_JAVA_VM_TGZ': macosJavaVMTgz,
- 'WINDOWS_JAVA_VM_TGZ': windowsJavaVMTgz,
- 'LINUX_JAVA_VM_TGZ': linuxJavaVMTgz,
'COPYRIGHT_MESSAGE': install4j_copyright_message,
'BUNDLE_ID': install4jBundleId,
'INTERNAL_ID': install4jInternalId,
'WINDOWS_ICONS_FILE': install4jWindowsIconsFile,
'PNG_ICON_FILE': install4jPngIconFile,
'BACKGROUND': install4jBackground,
+ ]
+ def varNameMap = [
+ 'mac': 'MACOS',
+ 'windows': 'WINDOWS',
+ 'linux': 'LINUX'
+ ]
+
+ // these are the bundled OS/architecture VMs needed by install4j
+ def osArch = [
+ [ "mac", "x64" ],
+ [ "mac", "aarch64" ],
+ [ "windows", "x64" ],
+ [ "linux", "x64" ],
+ [ "linux", "aarch64" ]
]
+ osArch.forEach { os, arch ->
+ variables[ sprintf("%s_%s_JAVA_VM_DIR", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/jre-%s-%s-%s/jre", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch)
+ // N.B. For some reason install4j requires the below filename to have underscores and not hyphens
+ // otherwise running `gradle installers` generates a non-useful error:
+ // `install4j: compilation failed. Reason: java.lang.NumberFormatException: For input string: "windows"`
+ variables[ sprintf("%s_%s_JAVA_VM_TGZ", varNameMap[os], arch.toUpperCase(Locale.ROOT)) ] = sprintf("%s/tgz/jre_%s_%s_%s.tar.gz", jreInstallsDir, JAVA_INTEGER_VERSION, os, arch)
+ }
//println("INSTALL4J VARIABLES:")
//variables.each{k,v->println("${k}=${v}")}
inputs.dir(getdownAppBaseDir)
inputs.file(install4jConfFile)
inputs.file("${install4jDir}/${install4j_info_plist_file_associations}")
- inputs.dir(macosJavaVMDir)
- inputs.dir(windowsJavaVMDir)
outputs.dir("${jalviewDir}/${install4j_build_dir}/${JAVA_VERSION}")
}
channel_properties_dir = utils/channels
channel_props = channel.props
-install4j_home_dir = ~/buildtools/install4j9
+install4j_home_dir = ~/buildtools/install4j10
install4j_copyright_message = ...
install4j_bundle_id = org.jalview.jalview-desktop
install4j_utils_dir = utils/install4j
install4j_images_dir = utils/install4j
-install4j_template = install4j9_template.install4j
+install4j_template = install4j10_template.install4j
install4j_info_plist_file_associations = file_associations_auto-Info_plist.xml
-install4j_installer_file_associations = file_associations_auto-install4j8.xml
+install4j_installer_file_associations = file_associations_auto-install4j10.xml
#install4j_DMG_uninstaller_app_files = uninstall_old_jalview_files.xml
install4j_build_dir = build/install4j
install4j_executable_name = jalviewg
<mapID target="colours.turn" url="html/colourSchemes/turn.html" />
<mapID target="colours.buried" url="html/colourSchemes/buried.html" />
<mapID target="colours.nucleotide" url="html/colourSchemes/nucleotide.html" />
+ <mapID target="colours.nucleotideambiguity" url="html/colourSchemes/nucleotideambiguity.html" />
<mapID target="colours.blosum" url="html/colourSchemes/blosum.html" />
<mapID target="colours.pid" url="html/colourSchemes/pid.html" />
<mapID target="colours.user" url="html/colourSchemes/user.html"/>
<tocitem text="Turn propensity" target="colours.turn" />
<tocitem text="Buried index" target="colours.buried" />
<tocitem text="Nucleotide colours" target="colours.nucleotide" />
+ <tocitem text="Nucleotide Ambiguity colours" target="colours.nucleotideambiguity" />
<tocitem text="Purine/Pyrimidine colours" target="colours.purinepyrimidine" />
<tocitem text="Blosum62" target="colours.blosum" />
<tocitem text="by Percentage Identity" target="colours.pid" />
<td>I</td>
<!--Inosine-->
<td>X</td>
- <!--Xanthine-->
+ <!--Unknown (sometimes Xanthine)-->
<td>R</td>
<!--Unknown Purine-->
<td>Y</td>
<!--Unknown Pyrimidine-->
- <td>N</td>
- <!--Unknown-->
<td>W</td>
<!--Weak nucleotide (A or T)-->
<td>S</td>
<td>D</td>
<!--Not C (A or G or T)-->
<td>V</td>
- <!--Not T (A or G or C-->
+ <!--Not T (A or G or C)-->
+ <td>N</td>
+ <!--Unknown-->
</tr>
<tr>
<td height="24">Nucleotide</td>
<td></td>
</tr>
<tr>
+ <td height="24">Nucleotide Ambiguity</td>
+ <td bgcolor="#f0fff0"></td>
+ <td bgcolor="#f0fff0"></td>
+ <td bgcolor="#f0fff0"></td>
+ <td bgcolor="#f0fff0"></td>
+ <td bgcolor="#f0fff0"></td>
+ <td bgcolor="#ffffff"></td>
+ <td bgcolor="#4f6f6f"></td>
+ <td bgcolor="#CD5C5C"></td>
+ <td bgcolor="#008000"></td>
+ <td bgcolor="#4682B4"></td>
+ <td bgcolor="#FF8C00"></td>
+ <td bgcolor="#9ACD32"></td>
+ <td bgcolor="#9932CC"></td>
+ <td bgcolor="#8b4513"></td>
+ <td bgcolor="#808080"></td>
+ <td bgcolor="#483D8B"></td>
+ <td bgcolor="#b8860b"></td>
+ <td bgcolor="#2f4f4f"></td>
+ </tr>
+ <tr>
<td height="24">Purine/Pyrimidine</td>
<td bgcolor="#FF83FA"></td>
<td bgcolor="#40E0D0"></td>
--- /dev/null
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ -->
+<head>
+<title>Nucleotide Colour Scheme</title>
+<style type="text/css">
+<!--
+td {
+ text-align: center;
+}
+-->
+</style>
+</head>
+
+<body>
+ <p>
+ <strong>Nucleotide Ambiguity Colours</strong>
+ </p>
+
+
+ <p>
+ This colour scheme was devised by Suzanne Duce and the Jalview Team to highlight ambiguity codes used in nucleotide sequences.
+ </p>
+ <p>
+ The use of X to represent an unknown base is acknowledged, but this is not recommended as the symbol refers to xanthine (see IUPAC-IUB Commission on Biochemical Nomenclature (CBN). <a href="https://iupac.qmul.ac.uk/misc/naabb.html">Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents.</a>)
+ </p>
+ <div align="center">
+ <table width="200" border="1">
+ <tr>
+ <td bgcolor="#f0fff0">A</td>
+ <td>Adenine</td>
+ </tr>
+ <tr>
+ <td bgcolor="#f0fff0">C</td>
+ <td>Cytosine</td>
+ </tr>
+ <tr>
+ <td bgcolor="#f0fff0">G</td>
+ <td>Guanine</td>
+ </tr>
+ <tr>
+ <td bgcolor="#f0fff0">T</td>
+ <td>Thymine</td>
+ </tr>
+ <tr>
+ <td bgcolor="#f0fff0">U</td>
+ <td>Uracil</td>
+ </tr>
+ <tr>
+ <td bgcolor="#ffffff">I</td>
+ <td>Inosine</td>
+ </tr>
+ <tr>
+ <td bgcolor="#4f6f6f">X</td>
+ <td>Unknown (sometimes Xanthine)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#CD5C5C">R</td>
+ <td>Unknown Purine</td>
+ </tr>
+ <tr>
+ <td bgcolor="#008000">Y</td>
+ <td>Unknown Pyrimidine</td>
+ </tr>
+ <tr>
+ <td bgcolor="#4682B4">W</td>
+ <td>Weak nucleotide (A or T)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#FF8C00">S</td>
+ <td>Strong nucleotide (G or C)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#9ACD32">M</td>
+ <td>Amino (A or C)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#9932CC">K</td>
+ <td>Keto (G or T)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#8b4513">B</td>
+ <td>Not A (G or C or T)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#808080">H</td>
+ <td>Not G (A or C or T)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#483D8B">D</td>
+ <td>Not C (A or G or T)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#b8860b">V</td>
+ <td>Not T (A or G or C)</td>
+ </tr>
+ <tr>
+ <td bgcolor="#2f4f4f">N</td>
+ <td>Unknown</td>
+ </tr>
+ </table>
+ </div>
+</body>
+</html>
Blosum62 Score, Percentage Identity, Zappo, Taylor,
gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
- Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+ Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User
Defined<br>
</strong> <em>See <a href="../colourSchemes/index.html">colours</a>
for a description of all colour schemes.
Blosum62 Score, Percentage Identity, Zappo, Taylor,
gecos:flower, gecos:blossom, gecos:sunset, gecos:ocean,
Hydrophobicity, Helix Propensity, Strand Propensity, Turn
- Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, User
+ Propensity, Buried Index, Nucleotide, Nucleotide Ambiguity, Purine/Pyrimidine, User
Defined<br>
</strong> <em>See <a href="../colourSchemes/index.html">colours</a> for
a description of all colour schemes.
--- /dev/null
+---
+version: 2.11.3.0
+date: 2023-03-07
+channel: "release"
+---
+
+## New Features
+JAL-4064 Native M1 build for macOS using Adoptium JRE 11 macos-aarch64
+JAL-4054 Installers built with install4j10
+JAL-3676 Allow log level configuration via Jalview's Java Console, and a Copy to Clipboard button
+JAL-3416 FlatLAF default look and feel on Linux, OSX and everywhere else ?
+
+## Issues Resolved
+JAL-3776 Cancelling interactive calculation leaves empty progress bar.
+JAL-3772 Unsaved Alignment windows close without prompting to save, individually or at application quit.
+JAL-1988 Can quit Jalview while 'save project' is in progress
+
--- /dev/null
+The 2.11.3 series includes support for in-depth exploration of predicted alignment error matrices from AlphaFold in the context of multiple alignments, along with support for standard colourschemes for shading models according to their pLDDT.
+
+It also introduces new support for native ARM-based OSX architectures, and a few other goodies!
+
+
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.save_in_progress = Some files are still saving:
+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
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.save_in_progress = Algunos archivos aún se están guardando:
+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
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();
}
if (customProxySet &&
// we have a username but no password for the scheme being
// requested
- (protocol.equalsIgnoreCase("http")
- && (httpUser != null && httpUser.length() > 0
- && (httpPassword == null
- || httpPassword.length == 0)))
+ (protocol.equalsIgnoreCase("http")
+ && (httpUser != null
+ && httpUser.length() > 0
+ && (httpPassword == null
+ || httpPassword.length == 0)))
|| (protocol.equalsIgnoreCase("https")
&& (httpsUser != null
&& httpsUser.length() > 0
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.util.SystemInfo;
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)
{
Cache.loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
+
boolean headless = false;
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(
try
{
Console.initLogger();
- } catch (NoClassDefFoundError error)
+ } catch (
+
+ NoClassDefFoundError error)
{
error.printStackTrace();
System.out.println("\nEssential logging libraries not found."
}
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
setSystemLookAndFeel();
if (Platform.isLinux())
{
- setMetalLookAndFeel();
+ setLinuxLookAndFeel();
}
if (Platform.isMac())
{
private static boolean setFlatLookAndFeel()
{
- boolean set = setSpecificLookAndFeel("flatlaf light",
- "com.formdev.flatlaf.FlatLightLaf", false);
+ boolean set = false;
+ if (Platform.isMac()) {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.themes.FlatMacLightLaf");
+ set = true;
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatMacLightLaf", e);
+ }
+ }
+ if (!set) {
+ try
+ {
+ UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
+ set = true;
+ } catch (ClassNotFoundException | InstantiationException
+ | IllegalAccessException | UnsupportedLookAndFeelException e)
+ {
+ Console.debug("Exception loading FlatLightLaf", e);
+ }
+ }
if (set)
{
if (Platform.isMac())
UIManager.put("TabbedPane.tabWidthMode", "compact");
UIManager.put("TabbedPane.selectedBackground", Color.white);
}
+
+ Desktop.setLiveDragMode(Cache.getDefault("FLAT_LIVE_DRAG_MODE", true));
return set;
}
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()
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.jbgui;
-
-import javax.swing.JFrame;
-import javax.swing.JOptionPane;
+package jalview.gui;
import com.formdev.flatlaf.extras.FlatDesktop;
import com.formdev.flatlaf.extras.FlatDesktop.Action;
-import jalview.util.MessageManager;
import jalview.util.Platform;
public class APQHandlers
public static boolean setQuit = false;
- public static boolean setAPQHandlers(GDesktop desktop)
+ public static boolean setAPQHandlers(Desktop desktop)
{
if (Platform.isJS())
{
}
if (FlatDesktop.isSupported(Action.APP_QUIT_HANDLER))
{
- FlatDesktop.setQuitHandler(response -> {
- boolean confirmQuit = jalview.bin.Cache.getDefault(
- jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT, true);
- boolean canQuit = !confirmQuit;
- int n;
- if (confirmQuit)
- {
- // ensure Jalview window is brought to front for Quit confirmation
- // window to be visible
-
- // this method of raising the Jalview window is broken in java
- // jalviewDesktop.setVisible(true);
- // jalviewDesktop.toFront();
-
- // a better hack which works instead
- JFrame dialogParent = new JFrame();
- dialogParent.setAlwaysOnTop(true);
-
- n = JOptionPane.showConfirmDialog(dialogParent,
- MessageManager.getString("label.quit_jalview"),
- MessageManager.getString("action.quit"),
- JOptionPane.OK_CANCEL_OPTION, JOptionPane.PLAIN_MESSAGE,
- null);
-
- dialogParent.setAlwaysOnTop(false);
- dialogParent.dispose();
- }
- else
- {
- n = JOptionPane.OK_OPTION;
- }
- canQuit = (n == JOptionPane.OK_OPTION);
- if (canQuit)
- {
- response.performQuit();
- }
- else
- {
- response.cancelQuit();
- }
- });
+ QuitHandler.setQuitHandler();
setQuit = true;
}
// if we got to here, no exceptions occurred when we set the handlers.
*/
package jalview.gui;
-import jalview.api.AlignExportSettingsI;
-import jalview.api.AlignViewportI;
-import jalview.io.FileFormatI;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
+import java.util.concurrent.Callable;
import javax.swing.JCheckBox;
import javax.swing.JPanel;
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignViewportI;
+import jalview.io.FileFormatI;
+import jalview.util.MessageManager;
+
/**
* A dialog that allows the user to specify whether to include hidden columns or
* sequences in an alignment export, and possibly features, annotations and
*
* @param action
*/
- public void setResponseAction(Object response, Runnable action)
+ public void setResponseAction(Object response, Callable action)
{
dialog.setResponseHandler(response, action);
}
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())
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();
+ }
}
}
.formatMessage("label.overview_params", new Object[]
{ this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
true, true);
+ frame.setFrameIcon(null);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(
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);
}
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);
* 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"),
*/
package jalview.gui;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceGroup;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Checkbox;
import java.awt.CheckboxGroup;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
/**
* A panel that allows the user to select which sequence-associated annotation
* rows to show or hide.
private void showFrame()
{
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceGroup;
-import jalview.gui.JalviewColourChooser.ColourChooserListener;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
import net.miginfocom.swing.MigLayout;
@SuppressWarnings("serial")
}
}
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
{
super(av, ap);
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
*/
package jalview.gui;
-import java.util.Locale;
-
-import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.SequenceI;
-import jalview.io.AnnotationFile;
-import jalview.io.FeaturesFile;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.util.MessageManager;
-
import java.awt.Color;
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.FileWriter;
import java.io.PrintWriter;
+import java.util.Locale;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
import javax.swing.JRadioButton;
import javax.swing.SwingConstants;
+import jalview.api.FeatureRenderer;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceI;
+import jalview.io.AnnotationFile;
+import jalview.io.FeaturesFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.util.MessageManager;
+
/**
*
* GUI dialog for exporting features or alignment annotations depending upon
}
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Dimension preferredSize = frame.getPreferredSize();
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, name, description);
- dialog.showDialog(ap.alignFrame, title, new Runnable()
- {
- @Override
- public void run()
+ dialog.showDialog(ap.alignFrame, title, () -> {
+ annotation.label = dialog.getName();
+ String text = dialog.getDescription();
+ if (text != null && text.length() == 0)
{
- annotation.label = dialog.getName();
- String text = dialog.getDescription();
- if (text != null && text.length() == 0)
- {
- text = null;
- }
- annotation.description = text;
- if (addNew)
- {
- ap.av.getAlignment().addAnnotation(annotation);
- ap.av.getAlignment().setAnnotationIndex(annotation, 0);
- }
- ap.refresh(true);
+ text = null;
+ }
+ annotation.description = text;
+ if (addNew)
+ {
+ ap.av.getAlignment().addAnnotation(annotation);
+ ap.av.getAlignment().setAnnotationIndex(annotation, 0);
}
+ ap.refresh(true);
+ return null;
});
}
*/
package jalview.gui;
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.RnaViewerModel;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.ext.varna.RnaModel;
-import jalview.structure.SecondaryStructureListener;
-import jalview.structure.SelectionListener;
-import jalview.structure.SelectionSource;
-import jalview.structure.StructureSelectionManager;
-import jalview.structure.VamsasSource;
-import jalview.util.Comparison;
-import jalview.util.MessageManager;
-import jalview.util.ShiftList;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.util.Collection;
import fr.orsay.lri.varna.models.annotations.HighlightRegionAnnotation;
import fr.orsay.lri.varna.models.rna.ModeleBase;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.RnaViewerModel;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.ext.varna.RnaModel;
+import jalview.structure.SecondaryStructureListener;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.ShiftList;
public class AppVarna extends JInternalFrame
implements SelectionListener, SecondaryStructureListener,
*/
protected AppVarna(AlignmentPanel ap)
{
+ this.setFrameIcon(null);
this.ap = ap;
this.viewId = System.currentTimeMillis() + "." + this.hashCode();
vab = new AppVarnaBinding();
*/
package jalview.gui;
-import jalview.analysis.TreeBuilder;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.analysis.scoremodels.SimilarityParams;
-import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.SimilarityParamsI;
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceGroup;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
/**
* A dialog where a user can choose and action Tree or PCA calculation options
*/
{
setLayout(new BorderLayout());
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
this.setBackground(Color.white);
frame.addFocusListener(new FocusListener()
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
frame = initFrame("Java Console", screenSize.width / 2,
screenSize.height / 2, -1, -1);
+ frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
initConsole(true);
}
{
}
}
+ /*
if (!frame.isVisible())
{
frame.dispose();
}
+ */
// System.exit(0);
}
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GCutAndPasteHtmlTransfer;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-
import java.awt.Toolkit;
import java.awt.datatransfer.Clipboard;
import java.awt.datatransfer.StringSelection;
import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.HyperlinkListener;
+import jalview.bin.Cache;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GCutAndPasteHtmlTransfer;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
/**
* Cut'n'paste files into the desktop See JAL-1105
*
public CutAndPasteHtmlTransfer()
{
super();
+ this.setFrameIcon(null);
displaySource.setSelected(false);
textarea.addKeyListener(new KeyListener()
{
*/
package jalview.gui;
-import jalview.bin.Cache;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+
+import javax.swing.JMenuItem;
+import javax.swing.JPopupMenu;
+import javax.swing.SwingUtilities;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
import jalview.api.FeaturesSourceI;
+import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.PrintWriter;
-
-import javax.swing.JMenuItem;
-import javax.swing.JPopupMenu;
-import javax.swing.SwingUtilities;
-
/**
* Cut'n'paste files into the desktop See JAL-1105
*
public CutAndPasteTransfer()
{
+ this.setFrameIcon(null);
SwingUtilities.invokeLater(new Runnable()
{
@Override
import java.util.ListIterator;
import java.util.Locale;
import java.util.Vector;
+import java.util.concurrent.Callable;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Semaphore;
import javax.swing.JComboBox;
import javax.swing.JComponent;
import javax.swing.JDesktopPane;
+import javax.swing.JFrame;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JMenuItem;
import javax.swing.JTextField;
import javax.swing.KeyStroke;
import javax.swing.SwingUtilities;
+import javax.swing.WindowConstants;
import javax.swing.event.HyperlinkEvent;
import javax.swing.event.HyperlinkEvent.EventType;
import javax.swing.event.InternalFrameAdapter;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.gui.QuitHandler.QResponse;
import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
public static HashMap<String, FileWriter> savingFiles = new HashMap<String, FileWriter>();
+ private static int DRAG_MODE = JDesktopPane.OUTLINE_DRAG_MODE;
+
+ public static void setLiveDragMode(boolean b)
+ {
+ DRAG_MODE = b ? JDesktopPane.LIVE_DRAG_MODE
+ : JDesktopPane.OUTLINE_DRAG_MODE;
+ if (desktop != null)
+ desktop.setDragMode(DRAG_MODE);
+ }
+
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
public static boolean nosplash = false;
setIconImages(ChannelProperties.getIconList());
+ // override quit handling when GUI OS close [X] button pressed
+ this.setDefaultCloseOperation(WindowConstants.DO_NOTHING_ON_CLOSE);
addWindowListener(new WindowAdapter()
{
-
@Override
public void windowClosing(WindowEvent ev)
{
- quit();
+ QuitHandler.QResponse ret = desktopQuit(true, true); // ui, disposeFlag
}
});
}
getContentPane().add(desktop, BorderLayout.CENTER);
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);
+ desktop.setDragMode(DRAG_MODE);
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
- this.addWindowListener(new WindowAdapter()
- {
- @Override
- public void windowClosing(WindowEvent evt)
- {
- quit();
- }
- });
-
MouseAdapter ma;
this.addMouseListener(ma = new MouseAdapter()
{
MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- File selectedFile = chooser.getSelectedFile();
- Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ chooser.setResponseHandler(0, () -> {
+ File selectedFile = chooser.getSelectedFile();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- FileFormatI format = chooser.getSelectedFormat();
+ FileFormatI format = chooser.getSelectedFormat();
- /*
- * Call IdentifyFile to verify the file contains what its extension implies.
- * Skip this step for dynamically added file formats, because IdentifyFile does
- * not know how to recognise them.
- */
- if (FileFormats.getInstance().isIdentifiable(format))
+ /*
+ * Call IdentifyFile to verify the file contains what its extension implies.
+ * Skip this step for dynamically added file formats, because IdentifyFile does
+ * not know how to recognise them.
+ */
+ if (FileFormats.getInstance().isIdentifiable(format))
+ {
+ try
{
- try
- {
- format = new IdentifyFile().identify(selectedFile,
- DataSourceType.FILE);
- } catch (FileFormatException e)
- {
- // format = null; //??
- }
+ format = new IdentifyFile().identify(selectedFile,
+ DataSourceType.FILE);
+ } catch (FileFormatException e)
+ {
+ // format = null; //??
}
-
- new FileLoader().LoadFile(viewport, selectedFile,
- DataSourceType.FILE, format);
}
+
+ new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE,
+ format);
+ return null;
});
chooser.showOpenDialog(this);
}
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
- Runnable action = new Runnable()
- {
- @Override
- public void run()
- {
- @SuppressWarnings("unchecked")
- String url = (history instanceof JTextField
- ? ((JTextField) history).getText()
- : ((JComboBox<String>) history).getEditor().getItem()
- .toString().trim());
+ Callable<Void> action = () -> {
+ @SuppressWarnings("unchecked")
+ String url = (history instanceof JTextField
+ ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getEditor().getItem()
+ .toString().trim());
- if (url.toLowerCase(Locale.ROOT).endsWith(".jar"))
+ if (url.toLowerCase(Locale.ROOT).endsWith(".jar"))
+ {
+ if (viewport != null)
{
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- FileFormat.Jalview);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL,
- FileFormat.Jalview);
- }
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ FileFormat.Jalview);
}
else
{
- FileFormatI format = null;
- try
- {
- format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e)
- {
- // TODO revise error handling, distinguish between
- // URL not found and response not valid
- }
+ new FileLoader().LoadFile(url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ }
+ else
+ {
+ FileFormatI format = null;
+ try
+ {
+ format = new IdentifyFile().identify(url, DataSourceType.URL);
+ } catch (FileFormatException e)
+ {
+ // TODO revise error handling, distinguish between
+ // URL not found and response not valid
+ }
- if (format == null)
- {
- String msg = MessageManager
- .formatMessage("label.couldnt_locate", url);
- JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
- MessageManager.getString("label.url_not_found"),
- JvOptionPane.WARNING_MESSAGE);
+ if (format == null)
+ {
+ String msg = MessageManager.formatMessage("label.couldnt_locate",
+ url);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
- return;
- }
+ return null; // Void
+ }
- if (viewport != null)
- {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
- format);
- }
- else
- {
- new FileLoader().LoadFile(url, DataSourceType.URL, format);
- }
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ format);
+ }
+ else
+ {
+ new FileLoader().LoadFile(url, DataSourceType.URL, format);
}
}
+ return null; // Void
};
String dialogOption = MessageManager
.getString("label.input_alignment_from_url");
}
/*
- * Exit the program
+ * Check with user and saving files before actually quitting
*/
- @Override
- public void quit()
+ public void desktopQuit()
{
- Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
- Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
- Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
- storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
- getWidth(), getHeight()));
+ desktopQuit(true, false);
+ }
- if (jconsole != null)
- {
- storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
- jconsole.stopConsole();
- }
- if (jvnews != null)
- {
- storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+ public QuitHandler.QResponse desktopQuit(boolean ui, boolean disposeFlag)
+ {
+ final Callable<Void> doDesktopQuit = () -> {
+ Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
+ Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
+ storeLastKnownDimensions("", new Rectangle(getBounds().x,
+ getBounds().y, getWidth(), getHeight()));
- }
- if (dialogExecutor != null)
- {
- dialogExecutor.shutdownNow();
- }
- closeAll_actionPerformed(null);
+ if (jconsole != null)
+ {
+ storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
+ jconsole.stopConsole();
+ }
- if (groovyConsole != null)
- {
- // suppress a possible repeat prompt to save script
- groovyConsole.setDirty(false);
- groovyConsole.exit();
- }
+ if (jvnews != null)
+ {
+ storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
+
+ }
+
+ if (dialogExecutor != null)
+ {
+ dialogExecutor.shutdownNow();
+ }
+
+ closeAll_actionPerformed(null);
+
+ if (groovyConsole != null)
+ {
+ // suppress a possible repeat prompt to save script
+ groovyConsole.setDirty(false);
+ groovyConsole.exit();
+ }
+
+ if (QuitHandler.gotQuitResponse() == QResponse.FORCE_QUIT)
+ {
+ // note that shutdown hook will not be run
+ jalview.bin.Console.debug("Force Quit selected by user");
+ Runtime.getRuntime().halt(0);
+ }
+
+ jalview.bin.Console.debug("Quit selected by user");
+ if (disposeFlag)
+ {
+ instance.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+ // instance.dispose();
+ }
+ instance.quit();
+
+ return null; // Void
+ };
+
+ return QuitHandler.getQuitResponse(ui, doDesktopQuit, doDesktopQuit,
+ QuitHandler.defaultCancelQuit);
+ }
+
+ /**
+ * Don't call this directly, use desktopQuit() above. Exits the program.
+ */
+ @Override
+ public void quit()
+ {
+ // this will run the shutdownHook but QuitHandler.getQuitResponse() should
+ // not run a second time if gotQuitResponse flag has been set (i.e. user
+ // confirmed quit of some kind).
System.exit(0);
}
saveState_actionPerformed(true);
}
- private void setProjectFile(File choice)
+ protected void setProjectFile(File choice)
{
this.projectFile = choice;
}
// allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
+ chooser.setResponseHandler(0, () -> {
+ File selectedFile = chooser.getSelectedFile();
+ setProjectFile(selectedFile);
+ String choice = selectedFile.getAbsolutePath();
+ Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
+ new Thread(new Runnable()
{
- File selectedFile = chooser.getSelectedFile();
- setProjectFile(selectedFile);
- String choice = selectedFile.getAbsolutePath();
- Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- new Thread(new Runnable()
+ @Override
+ public void run()
{
- @Override
- public void run()
+ try
{
- try
- {
- new Jalview2XML().loadJalviewAlign(selectedFile);
- } catch (OutOfMemoryError oom)
- {
- new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex)
- {
- jalview.bin.Console.error(
- "Problems whilst loading project from " + choice, ex);
- JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage(
- "label.error_whilst_loading_project_from",
- new Object[]
- { choice }),
- MessageManager
- .getString("label.couldnt_load_project"),
- JvOptionPane.WARNING_MESSAGE);
- }
+ new Jalview2XML().loadJalviewAlign(selectedFile);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst loading project from " + choice, oom);
+ } catch (Exception ex)
+ {
+ jalview.bin.Console.error(
+ "Problems whilst loading project from " + choice, ex);
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager.getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
}
- }, "Project Loader").start();
- }
+ }
+ }, "Project Loader").start();
+ return null;
});
chooser.showOpenDialog(this);
@Override
public void actionPerformed(ActionEvent e)
{
- quit();
+ desktopQuit();
}
});
}
*/
package jalview.gui;
-import jalview.util.MessageManager;
-
import java.awt.FlowLayout;
import java.awt.Font;
+import java.util.concurrent.Callable;
import javax.swing.BoxLayout;
import javax.swing.JButton;
import javax.swing.JPanel;
import javax.swing.JTextField;
+import jalview.util.MessageManager;
+
/**
* A dialog where a name and description may be edited
*/
*
* @param action
*/
- public void showDialog(JComponent parent, String title, Runnable action)
+ public void showDialog(JComponent parent, String title, Callable action)
{
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
import java.awt.event.MouseEvent;
import java.util.ArrayList;
import java.util.List;
+import java.util.concurrent.Callable;
import javax.swing.JComboBox;
import javax.swing.JLabel;
*/
public void showDialog()
{
- Runnable okAction = forCreate ? getCreateAction() : getAmendAction();
- Runnable cancelAction = getCancelAction();
+ Callable<Void> okAction = forCreate ? getCreateAction()
+ : getAmendAction();
+ Callable<Void> cancelAction = getCancelAction();
/*
* set dialog action handlers for OK (create/Amend) and Cancel options
*
* @return
*/
- protected Runnable getCancelAction()
+ protected Callable getCancelAction()
{
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- ap.highlightSearchResults(null);
- ap.paintAlignment(false, false);
- }
+ Callable<Void> okAction = () -> {
+ ap.highlightSearchResults(null);
+ ap.paintAlignment(false, false);
+ return null;
};
return okAction;
}
*
* @return
*/
- protected Runnable getCreateAction()
+ protected Callable getCreateAction()
{
- Runnable okAction = new Runnable()
+ Callable<Void> okAction = new Callable()
{
boolean useLastDefaults = features.get(0).getType() == null;
@Override
- public void run()
+ public Void call()
{
final String enteredType = name.getText().trim();
final String enteredGroup = group.getText().trim();
repaintPanel();
}
+ return null;
}
};
return okAction;
*
* @return
*/
- protected Runnable getDeleteAction()
+ protected Callable getDeleteAction()
{
- Runnable deleteAction = new Runnable()
- {
- @Override
- public void run()
- {
- SequenceFeature sf = features.get(featureIndex);
- sequences.get(0).getDatasetSequence().deleteFeature(sf);
- fr.featuresAdded();
- ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
- ap.paintAlignment(true, true);
- }
+ Callable<Void> deleteAction = () -> {
+ SequenceFeature sf = features.get(featureIndex);
+ sequences.get(0).getDatasetSequence().deleteFeature(sf);
+ fr.featuresAdded();
+ ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
+ ap.paintAlignment(true, true);
+ return null;
};
return deleteAction;
}
*
* @return
*/
- protected Runnable getAmendAction()
+ protected Callable getAmendAction()
{
- Runnable okAction = new Runnable()
+ Callable<Void> okAction = new Callable()
{
boolean useLastDefaults = features.get(0).getType() == null;
String featureGroup = group.getText();
@Override
- public void run()
+ public Void call()
{
final String enteredType = name.getText().trim();
final String enteredGroup = group.getText().trim();
fr.featuresAdded();
}
repaintPanel();
+ return null;
}
};
return okAction;
*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Set;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JInternalFrame;
import javax.swing.JLabel;
import javax.swing.JLayeredPane;
{
frame = new JInternalFrame();
frame.setContentPane(this);
+ frame.setFrameIcon(null);
Rectangle bounds = af.getFeatureSettingsGeometry();
String title;
if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels(
chooser.setDialogTitle(
MessageManager.getString("label.load_feature_colours"));
chooser.setToolTipText(MessageManager.getString("action.load"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- File file = chooser.getSelectedFile();
- load(file);
- }
+ chooser.setResponseHandler(0, () -> {
+ File file = chooser.getSelectedFile();
+ load(file);
+ return null;
});
chooser.showOpenDialog(this);
}
focusFixed = fixedFocus;
finders = new HashMap<>();
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
frame.addInternalFrameListener(new InternalFrameAdapter()
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.jbgui.GFontChooser;
-import jalview.util.MessageManager;
-
import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.geom.Rectangle2D;
import javax.swing.JInternalFrame;
import javax.swing.JLayeredPane;
+import jalview.bin.Cache;
+import jalview.jbgui.GFontChooser;
+import jalview.util.MessageManager;
+
/**
* DOCUMENT ME!
*
void init()
{
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
smoothFont.setSelected(ap.av.antiAlias);
*/
package jalview.gui;
+import java.awt.Component;
+import java.awt.Graphics;
+import java.io.File;
+import java.util.concurrent.Callable;
+import java.util.concurrent.atomic.AtomicBoolean;
+
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.io.JalviewFileChooser;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import java.awt.Component;
-import java.awt.Graphics;
-import java.io.File;
-import java.util.concurrent.atomic.AtomicBoolean;
-
/**
* A class that marshals steps in exporting a view in image graphics format
* <ul>
&& !Jalview.isHeadlessMode())
{
final File chosenFile = file;
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- exportImage(chosenFile, !textSelected.get(), width, height,
- messageId);
- }
+ Callable<Void> okAction = () -> {
+ exportImage(chosenFile, !textSelected.get(), width, height,
+ messageId);
+ return null;
};
LineartOptions epsOption = new LineartOptions(TYPE.EPS.getName(),
textSelected);
- epsOption.setResponseAction(1, new Runnable()
+ epsOption.setResponseAction(1, new Callable<Void>()
{
@Override
- public void run()
+ public Void call()
{
setStatus(MessageManager.formatMessage(
"status.cancelled_image_export_operation",
imageType.getName()), messageId);
+ return null;
}
});
epsOption.setResponseAction(0, okAction);
* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.gui;
+import java.awt.AWTEvent;
+import java.awt.ActiveEvent;
import java.awt.Component;
+import java.awt.Container;
import java.awt.Dialog.ModalityType;
+import java.awt.EventQueue;
import java.awt.HeadlessException;
+import java.awt.MenuComponent;
+import java.awt.Toolkit;
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseMotionAdapter;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.concurrent.Callable;
import java.util.concurrent.Executors;
import javax.swing.Icon;
import javax.swing.JButton;
import javax.swing.JDialog;
+import javax.swing.JFrame;
import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
import javax.swing.UIManager;
+import javax.swing.event.InternalFrameEvent;
+import javax.swing.event.InternalFrameListener;
+import jalview.util.ChannelProperties;
import jalview.util.Platform;
import jalview.util.dialogrunner.DialogRunnerI;
private Component parentComponent;
- private Map<Object, Runnable> callbacks = new HashMap<>();
+ private Map<Object, Callable<Void>> callbacks = new HashMap<>();
/*
- * JalviewJS reports user choice in the dialog as the selected
- * option (text); this list allows conversion to index (int)
+ * JalviewJS reports user choice in the dialog as the selected option (text);
+ * this list allows conversion to index (int)
*/
List<Object> ourOptions;
public JvOptionPane(final Component parent)
{
this.parentComponent = Platform.isJS() ? this : parent;
+ this.setIcon(null);
}
public static int showConfirmDialog(Component parentComponent,
* @param string2
* @return
*/
+ public static JvOptionPane newOptionDialog()
+ {
+ return new JvOptionPane(null);
+ }
+
public static JvOptionPane newOptionDialog(Component parentComponent)
{
return new JvOptionPane(parentComponent);
initialValue, true);
}
- public void showDialog(String message, String title, int optionType,
+ public void showDialog(Object message, String title, int optionType,
int messageType, Icon icon, Object[] options, Object initialValue,
boolean modal)
{
+ showDialog(message, title, optionType, messageType, icon, options,
+ initialValue, modal, null);
+ }
+
+ public void showDialog(Object message, String title, int optionType,
+ int messageType, Icon icon, Object[] options, Object initialValue,
+ boolean modal, JButton[] buttons)
+ {
if (!isInteractiveMode())
{
handleResponse(getMockResponse());
+ return;
}
// two uses:
//
if (modal)
{
+ boolean useButtons = false;
+ Object initialValueButton = null;
+ NOTNULL: if (buttons != null)
+ {
+ if (buttons.length != options.length)
+ {
+ jalview.bin.Console.error(
+ "Supplied buttons array not the same length as supplied options array.");
+ break NOTNULL;
+ }
+ int[] buttonActions = { JOptionPane.YES_OPTION,
+ JOptionPane.NO_OPTION, JOptionPane.CANCEL_OPTION };
+ for (int i = 0; i < options.length; i++)
+ {
+ Object o = options[i];
+ jalview.bin.Console.debug(
+ "Setting button " + i + " to '" + o.toString() + "'");
+ JButton jb = buttons[i];
+
+ if (o.equals(initialValue))
+ initialValueButton = jb;
+
+ int buttonAction = buttonActions[i];
+ Callable<Void> action = callbacks.get(buttonAction);
+ jb.setText((String) o);
+ jb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+
+ Object obj = e.getSource();
+ if (obj == null || !(obj instanceof Component))
+ {
+ jalview.bin.Console.debug(
+ "Could not find Component source of event object "
+ + obj);
+ return;
+ }
+ Object joptionpaneObject = SwingUtilities.getAncestorOfClass(
+ JOptionPane.class, (Component) obj);
+ if (joptionpaneObject == null
+ || !(joptionpaneObject instanceof JOptionPane))
+ {
+ jalview.bin.Console.debug(
+ "Could not find JOptionPane ancestor of event object "
+ + obj);
+ return;
+ }
+ JOptionPane joptionpane = (JOptionPane) joptionpaneObject;
+ joptionpane.setValue(buttonAction);
+ if (action != null)
+ Executors.newSingleThreadExecutor().submit(action);
+ joptionpane.transferFocusBackward();
+ joptionpane.setVisible(false);
+ // put focus and raise parent window if possible, unless cancel or
+ // no button pressed
+ boolean raiseParent = (parentComponent != null);
+ if (buttonAction == JOptionPane.CANCEL_OPTION)
+ raiseParent = false;
+ if (optionType == JOptionPane.YES_NO_OPTION
+ && buttonAction == JOptionPane.NO_OPTION)
+ raiseParent = false;
+ if (raiseParent)
+ {
+ parentComponent.requestFocus();
+ if (parentComponent instanceof JInternalFrame)
+ {
+ JInternalFrame jif = (JInternalFrame) parentComponent;
+ jif.show();
+ jif.moveToFront();
+ jif.grabFocus();
+ }
+ else if (parentComponent instanceof Window)
+ {
+ Window w = (Window) parentComponent;
+ w.toFront();
+ w.requestFocus();
+ }
+ }
+ joptionpane.setVisible(false);
+ }
+ });
+
+ }
+ useButtons = true;
+ }
// use a JOptionPane as usual
int response = JOptionPane.showOptionDialog(parentComponent, message,
- title, optionType, messageType, icon, options, initialValue);
+ title, optionType, messageType, icon,
+ useButtons ? buttons : options,
+ useButtons ? initialValueButton : initialValue);
/*
- * In Java, the response is returned to this thread and handled here;
- * (for Javascript, see propertyChange)
+ * In Java, the response is returned to this thread and handled here; (for
+ * Javascript, see propertyChange)
*/
if (!Platform.isJS())
/**
else
{
/*
- * This is java similar to the swingjs handling, with the callbacks
- * attached to the button press of the dialog. This means we can use
- * a non-modal JDialog for the confirmation without blocking the GUI.
+ * This is java similar to the swingjs handling, with the callbacks attached to
+ * the button press of the dialog. This means we can use a non-modal JDialog for
+ * the confirmation without blocking the GUI.
*/
JOptionPane joptionpane = new JOptionPane();
// Make button options
ArrayList<JButton> options_btns = new ArrayList<>();
Object initialValue_btn = null;
- if (!Platform.isJS()) // JalviewJS already uses callback, don't need to add them here
+ if (!Platform.isJS()) // JalviewJS already uses callback, don't need to
+ // add them here
{
for (int i = 0; i < options.length && i < 3; i++)
{
Object o = options[i];
int buttonAction = buttonActions[i];
- Runnable action = callbacks.get(buttonAction);
+ Callable<Void> action = callbacks.get(buttonAction);
JButton jb = new JButton();
jb.setText((String) o);
jb.addActionListener(new ActionListener()
{
joptionpane.setValue(buttonAction);
if (action != null)
- Executors.defaultThreadFactory().newThread(action).start();
+ Executors.newSingleThreadExecutor().submit(action);
// joptionpane.transferFocusBackward();
joptionpane.transferFocusBackward();
joptionpane.setVisible(false);
Platform.isJS() ? initialValue : initialValue_btn);
JDialog dialog = joptionpane.createDialog(parentComponent, title);
+ dialog.setIconImages(ChannelProperties.getIconList());
dialog.setModalityType(modal ? ModalityType.APPLICATION_MODAL
: ModalityType.MODELESS);
dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
handleResponse(getMockResponse());
}
+ // need to set these separately so we can set the title bar icon later
+ this.setOptionType(yesNoCancelOption);
+ this.setMessageType(questionMessage);
+ this.setIcon(icon);
+ this.setInitialValue(initresponse);
+ this.setOptions(options);
+ this.setMessage(mainPanel);
+
ourOptions = Arrays.asList(options);
int response;
if (parentComponent != this)
{
- response = JOptionPane.showInternalOptionDialog(parentComponent,
- mainPanel, title, yesNoCancelOption, questionMessage, icon,
- options, initresponse);
+ JInternalFrame jif = this.createInternalFrame(parentComponent, title);
+ jif.setFrameIcon(null);
+ jif.addInternalFrameListener(new InternalFrameListener()
+ {
+ @Override
+ public void internalFrameActivated(InternalFrameEvent arg0)
+ {
+ }
+
+ @Override
+ public void internalFrameClosed(InternalFrameEvent arg0)
+ {
+ JvOptionPane.this.internalDialogHandleResponse();
+ }
+
+ @Override
+ public void internalFrameClosing(InternalFrameEvent arg0)
+ {
+ }
+
+ @Override
+ public void internalFrameDeactivated(InternalFrameEvent arg0)
+ {
+ }
+
+ @Override
+ public void internalFrameDeiconified(InternalFrameEvent arg0)
+ {
+ }
+
+ @Override
+ public void internalFrameIconified(InternalFrameEvent arg0)
+ {
+ }
+
+ @Override
+ public void internalFrameOpened(InternalFrameEvent arg0)
+ {
+ }
+ });
+ jif.setVisible(true);
+ startModal(jif);
+ return;
}
else
{
- response = JOptionPane.showOptionDialog(parentComponent, mainPanel,
- title, yesNoCancelOption, questionMessage, icon, options,
- initresponse);
+ JDialog dialog = this.createDialog(parentComponent, title);
+ dialog.setIconImages(ChannelProperties.getIconList());
+ dialog.setVisible(true); // blocking
+ this.internalDialogHandleResponse();
+ return;
}
+ }
+
+ private void internalDialogHandleResponse()
+ {
+ String responseString = (String) this.getValue();
+ int response = ourOptions.indexOf(responseString);
+
if (!Platform.isJS())
/**
* Java only
}
}
+ /*
+ * @Override public JvOptionPane setResponseHandler(Object response, Runnable
+ * action) { callbacks.put(response, new Callable<Void>() {
+ *
+ * @Override public Void call() { action.run(); return null; } }); return this;
+ * }
+ */
@Override
- public JvOptionPane setResponseHandler(Object response, Runnable action)
+ public JvOptionPane setResponseHandler(Object response,
+ Callable<Void> action)
{
callbacks.put(response, action);
return this;
}
/**
+ * showDialogOnTop will create a dialog that (attempts to) come to top of OS
+ * desktop windows
+ */
+ public static int showDialogOnTop(String label, String actionString,
+ int JOPTIONPANE_OPTION, int JOPTIONPANE_MESSAGETYPE)
+ {
+ if (!isInteractiveMode())
+ {
+ return (int) getMockResponse();
+ }
+ // Ensure Jalview window is brought to front (primarily for Quit
+ // confirmation window to be visible)
+
+ // This method of raising the Jalview window is broken in java
+ // jalviewDesktop.setVisible(true);
+ // jalviewDesktop.toFront();
+
+ // A better hack which works is to create a new JFrame parent with
+ // setAlwaysOnTop(true)
+ JFrame dialogParent = new JFrame();
+ dialogParent.setIconImages(ChannelProperties.getIconList());
+ dialogParent.setAlwaysOnTop(true);
+
+ int answer = JOptionPane.showConfirmDialog(dialogParent, label,
+ actionString, JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE);
+
+ dialogParent.setAlwaysOnTop(false);
+ dialogParent.dispose();
+
+ return answer;
+ }
+
+ public void showDialogOnTopAsync(String label, String actionString,
+ int JOPTIONPANE_OPTION, int JOPTIONPANE_MESSAGETYPE, Icon icon,
+ Object[] options, Object initialValue, boolean modal)
+ {
+ JFrame frame = new JFrame();
+ frame.setIconImages(ChannelProperties.getIconList());
+ showDialogOnTopAsync(frame, label, actionString, JOPTIONPANE_OPTION,
+ JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal);
+ }
+
+ public void showDialogOnTopAsync(JFrame dialogParent, Object label,
+ String actionString, int JOPTIONPANE_OPTION,
+ int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
+ Object initialValue, boolean modal)
+ {
+ showDialogOnTopAsync(dialogParent, label, actionString,
+ JOPTIONPANE_OPTION, JOPTIONPANE_MESSAGETYPE, icon, options,
+ initialValue, modal, null);
+ }
+
+ public void showDialogOnTopAsync(JFrame dialogParent, Object label,
+ String actionString, int JOPTIONPANE_OPTION,
+ int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
+ Object initialValue, boolean modal, JButton[] buttons)
+ {
+ if (!isInteractiveMode())
+ {
+ handleResponse(getMockResponse());
+ return;
+ }
+ // Ensure Jalview window is brought to front (primarily for Quit
+ // confirmation window to be visible)
+
+ // This method of raising the Jalview window is broken in java
+ // jalviewDesktop.setVisible(true);
+ // jalviewDesktop.toFront();
+
+ // A better hack which works is to create a new JFrame parent with
+ // setAlwaysOnTop(true)
+ dialogParent.setAlwaysOnTop(true);
+ parentComponent = dialogParent;
+
+ showDialog(label, actionString, JOPTIONPANE_OPTION,
+ JOPTIONPANE_MESSAGETYPE, icon, options, initialValue, modal,
+ buttons);
+
+ dialogParent.setAlwaysOnTop(false);
+ dialogParent.dispose();
+ }
+
+ /**
* JalviewJS signals option selection by a property change event for the
* option e.g. "OK". This methods responds to that by running the response
* action that corresponds to that option.
public void handleResponse(Object response)
{
/*
- * this test is for NaN in Chrome
- */
+ * this test is for NaN in Chrome
+ */
if (response != null && !response.equals(response))
{
return;
}
- Runnable action = callbacks.get(response);
+ Callable<Void> action = callbacks.get(response);
if (action != null)
{
- action.run();
- parentComponent.requestFocus();
+ try
+ {
+ action.call();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ if (parentComponent != null)
+ parentComponent.requestFocus();
+ }
+ }
+
+ /**
+ * Create a non-modal confirm dialog
+ */
+ public JDialog createDialog(Component parentComponent, Object message,
+ String title, int optionType, int messageType, Icon icon,
+ Object[] options, Object initialValue, boolean modal)
+ {
+ return createDialog(parentComponent, message, title, optionType,
+ messageType, icon, options, initialValue, modal, null);
+ }
+
+ public JDialog createDialog(Component parentComponent, Object message,
+ String title, int optionType, int messageType, Icon icon,
+ Object[] options, Object initialValue, boolean modal,
+ JButton[] buttons)
+ {
+ if (!isInteractiveMode())
+ {
+ handleResponse(getMockResponse());
+ return null;
+ }
+ JButton[] optionsButtons = null;
+ Object initialValueButton = null;
+ JOptionPane joptionpane = new JOptionPane();
+ // Make button options
+ int[] buttonActions = { JOptionPane.YES_OPTION, JOptionPane.NO_OPTION,
+ JOptionPane.CANCEL_OPTION };
+
+ // we need the strings to make the buttons with actionEventListener
+ if (options == null)
+ {
+ ArrayList<String> options_default = new ArrayList<>();
+ options_default.add(UIManager.getString("OptionPane.yesButtonText"));
+ if (optionType == JOptionPane.YES_NO_OPTION
+ || optionType == JOptionPane.YES_NO_CANCEL_OPTION)
+ {
+ options_default.add(UIManager.getString("OptionPane.noButtonText"));
+ }
+ if (optionType == JOptionPane.YES_NO_CANCEL_OPTION)
+ {
+ options_default
+ .add(UIManager.getString("OptionPane.cancelButtonText"));
+ }
+ options = options_default.toArray();
+ }
+ if (!Platform.isJS()) // JalviewJS already uses callback, don't need to
+ // add them here
+ {
+ if (((optionType == JOptionPane.YES_OPTION
+ || optionType == JOptionPane.NO_OPTION
+ || optionType == JOptionPane.CANCEL_OPTION
+ || optionType == JOptionPane.OK_OPTION
+ || optionType == JOptionPane.DEFAULT_OPTION)
+ && options.length < 1)
+ || ((optionType == JOptionPane.YES_NO_OPTION
+ || optionType == JOptionPane.OK_CANCEL_OPTION)
+ && options.length < 2)
+ || (optionType == JOptionPane.YES_NO_CANCEL_OPTION
+ && options.length < 3))
+ {
+ jalview.bin.Console
+ .debug("JvOptionPane: not enough options for dialog type");
+ }
+ optionsButtons = new JButton[options.length];
+ for (int i = 0; i < options.length && i < 3; i++)
+ {
+ Object o = options[i];
+ int buttonAction = buttonActions[i];
+ Callable<Void> action = callbacks.get(buttonAction);
+ JButton jb;
+ if (buttons != null && buttons.length > i && buttons[i] != null)
+ {
+ jb = buttons[i];
+ }
+ else
+ {
+ jb = new JButton();
+ }
+ jb.setText((String) o);
+ jb.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ joptionpane.setValue(buttonAction);
+ if (action != null)
+ Executors.newSingleThreadExecutor().submit(action);
+ // joptionpane.transferFocusBackward();
+ joptionpane.transferFocusBackward();
+ joptionpane.setVisible(false);
+ // put focus and raise parent window if possible, unless cancel
+ // button pressed
+ boolean raiseParent = (parentComponent != null);
+ if (buttonAction == JOptionPane.CANCEL_OPTION)
+ raiseParent = false;
+ if (optionType == JOptionPane.YES_NO_OPTION
+ && buttonAction == JOptionPane.NO_OPTION)
+ raiseParent = false;
+ if (raiseParent)
+ {
+ parentComponent.requestFocus();
+ if (parentComponent instanceof JInternalFrame)
+ {
+ JInternalFrame jif = (JInternalFrame) parentComponent;
+ jif.show();
+ jif.moveToFront();
+ jif.grabFocus();
+ }
+ else if (parentComponent instanceof Window)
+ {
+ Window w = (Window) parentComponent;
+ w.toFront();
+ w.requestFocus();
+ }
+ }
+ joptionpane.setVisible(false);
+ }
+ });
+ optionsButtons[i] = jb;
+ if (o.equals(initialValue))
+ initialValueButton = jb;
+ }
+ }
+ joptionpane.setMessage(message);
+ joptionpane.setMessageType(messageType);
+ joptionpane.setOptionType(optionType);
+ joptionpane.setIcon(icon);
+ joptionpane.setOptions(Platform.isJS() ? options : optionsButtons);
+ joptionpane.setInitialValue(
+ Platform.isJS() ? initialValue : initialValueButton);
+
+ JDialog dialog = joptionpane.createDialog(parentComponent, title);
+ dialog.setIconImages(ChannelProperties.getIconList());
+ dialog.setModalityType(
+ modal ? ModalityType.APPLICATION_MODAL : ModalityType.MODELESS);
+ dialog.setDefaultCloseOperation(JDialog.DISPOSE_ON_CLOSE);
+ return dialog;
+ }
+
+ /**
+ * Utility to programmatically click a button on a JOptionPane (as a JFrame)
+ *
+ * returns true if button was found
+ */
+ public static boolean clickButton(JFrame frame, int buttonType)
+ {
+
+ return false;
+ }
+
+ /**
+ * This helper method makes the JInternalFrame wait until it is notified by an
+ * InternalFrameClosing event. This method also adds the given JOptionPane to
+ * the JInternalFrame and sizes it according to the JInternalFrame's preferred
+ * size.
+ *
+ * @param f
+ * The JInternalFrame to make modal.
+ */
+ private static void startModal(JInternalFrame f)
+ {
+ // We need to add an additional glasspane-like component directly
+ // below the frame, which intercepts all mouse events that are not
+ // directed at the frame itself.
+ JPanel modalInterceptor = new JPanel();
+ modalInterceptor.setOpaque(false);
+ JLayeredPane lp = JLayeredPane.getLayeredPaneAbove(f);
+ lp.setLayer(modalInterceptor, JLayeredPane.MODAL_LAYER.intValue());
+ modalInterceptor.setBounds(0, 0, lp.getWidth(), lp.getHeight());
+ modalInterceptor.addMouseListener(new MouseAdapter()
+ {
+ });
+ modalInterceptor.addMouseMotionListener(new MouseMotionAdapter()
+ {
+ });
+ lp.add(modalInterceptor);
+ f.toFront();
+
+ // We need to explicitly dispatch events when we are blocking the event
+ // dispatch thread.
+ EventQueue queue = Toolkit.getDefaultToolkit().getSystemEventQueue();
+ try
+ {
+ while (!f.isClosed())
+ {
+ if (EventQueue.isDispatchThread())
+ {
+ // The getNextEventMethod() issues wait() when no
+ // event is available, so we don't need do explicitly wait().
+ AWTEvent ev = queue.getNextEvent();
+ // This mimics EventQueue.dispatchEvent(). We can't use
+ // EventQueue.dispatchEvent() directly, because it is
+ // protected, unfortunately.
+ if (ev instanceof ActiveEvent)
+ ((ActiveEvent) ev).dispatch();
+ else if (ev.getSource() instanceof Component)
+ ((Component) ev.getSource()).dispatchEvent(ev);
+ else if (ev.getSource() instanceof MenuComponent)
+ ((MenuComponent) ev.getSource()).dispatchEvent(ev);
+ // Other events are ignored as per spec in
+ // EventQueue.dispatchEvent
+ }
+ else
+ {
+ // Give other threads a chance to become active.
+ Thread.yield();
+ }
+ }
+ } catch (InterruptedException ex)
+ {
+ // If we get interrupted, then leave the modal state.
+ } finally
+ {
+ // Clean up the modal interceptor.
+ lp.remove(modalInterceptor);
+
+ // Remove the internal frame from its parent, so it is no longer
+ // lurking around and clogging memory.
+ Container parent = f.getParent();
+ if (parent != null)
+ parent.remove(f);
}
}
}
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.util.MessageManager;
-
import java.awt.FlowLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.util.concurrent.Callable;
import java.util.concurrent.atomic.AtomicBoolean;
import javax.swing.BorderFactory;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
/**
* A dialog where the user may choose Text or Lineart rendering, and optionally
* save this as a preference ("Don't ask me again")
*
* @param action
*/
- public void setResponseAction(Object response, Runnable action)
+ public void setResponseAction(Object response, Callable action)
{
dialog.setResponseHandler(response, action);
}
*/
package jalview.gui;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.awt.print.PrinterJob;
+
+import javax.swing.ButtonGroup;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.AlignViewportI;
import jalview.api.analysis.ScoreModelI;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.Graphics;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.print.PageFormat;
-import java.awt.print.Printable;
-import java.awt.print.PrinterException;
-import java.awt.print.PrinterJob;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JMenuItem;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.event.InternalFrameAdapter;
-import javax.swing.event.InternalFrameEvent;
-
/**
* The panel holding the Principal Component Analysis 3-D visualisation
*/
SimilarityParamsI params)
{
super();
+ this.setFrameIcon(null);
this.av = alignPanel.av;
this.ap = alignPanel;
boolean nucleotide = av.getAlignment().isNucleotide();
*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.SortedMap;
MessageManager.getString("label.group_description"));
dialog.showDialog(ap.alignFrame,
MessageManager.getString("label.edit_group_name_description"),
- new Runnable()
- {
- @Override
- public void run()
- {
- sg.setName(dialog.getName());
- sg.setDescription(dialog.getDescription());
- refresh();
- }
+ () -> {
+ sg.setName(dialog.getName());
+ sg.setDescription(dialog.getDescription());
+ refresh();
+ return null;
});
}
sequence.getDescription(),
MessageManager.getString("label.sequence_name"),
MessageManager.getString("label.sequence_description"));
- dialog.showDialog(ap.alignFrame, MessageManager.getString(
- "label.edit_sequence_name_description"), new Runnable()
- {
- @Override
- public void run()
+ dialog.showDialog(ap.alignFrame, MessageManager
+ .getString("label.edit_sequence_name_description"), () -> {
+ if (dialog.getName() != null)
{
- if (dialog.getName() != null)
+ if (dialog.getName().indexOf(" ") > -1)
{
- if (dialog.getName().indexOf(" ") > -1)
- {
- JvOptionPane.showMessageDialog(ap,
- MessageManager.getString(
- "label.spaces_converted_to_underscores"),
- MessageManager.getString(
- "label.no_spaces_allowed_sequence_name"),
- JvOptionPane.WARNING_MESSAGE);
- }
- sequence.setName(dialog.getName().replace(' ', '_'));
- ap.paintAlignment(false, false);
+ JvOptionPane.showMessageDialog(ap,
+ MessageManager.getString(
+ "label.spaces_converted_to_underscores"),
+ MessageManager.getString(
+ "label.no_spaces_allowed_sequence_name"),
+ JvOptionPane.WARNING_MESSAGE);
}
- sequence.setDescription(dialog.getDescription());
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ sequence.setName(dialog.getName().replace(' ', '_'));
+ ap.paintAlignment(false, false);
}
+ sequence.setDescription(dialog.getDescription());
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ return null;
});
}
seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
null, MessageManager.getString("label.edit_sequence"), null);
dialog.showDialog(ap.alignFrame,
- MessageManager.getString("label.edit_sequence"),
- new Runnable()
- {
- @Override
- public void run()
- {
- EditCommand editCommand = new EditCommand(
- MessageManager.getString("label.edit_sequences"),
- Action.REPLACE,
- dialog.getName().replace(' ',
- ap.av.getGapCharacter()),
- sg.getSequencesAsArray(
- ap.av.getHiddenRepSequences()),
- sg.getStartRes(), sg.getEndRes() + 1,
- ap.av.getAlignment());
- ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
- }
+ MessageManager.getString("label.edit_sequence"), () -> {
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE,
+ dialog.getName().replace(' ',
+ ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(
+ ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
+ ap.alignFrame.addHistoryItem(editCommand);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ return null;
});
}
}
{
super();
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
if (!Platform.isJS())
/**
--- /dev/null
+package jalview.gui;
+
+import java.io.File;
+import java.util.List;
+import java.util.concurrent.Callable;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.TimeUnit;
+import java.util.concurrent.TimeoutException;
+
+import javax.swing.JButton;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JTextPane;
+
+import com.formdev.flatlaf.extras.FlatDesktop;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.BackupFiles;
+import jalview.project.Jalview2XML;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+public class QuitHandler
+{
+ private static final int MIN_WAIT_FOR_SAVE = 1000;
+
+ private static final int MAX_WAIT_FOR_SAVE = 20000;
+
+ private static boolean interactive = true;
+
+ public static enum QResponse
+ {
+ NULL, QUIT, CANCEL_QUIT, FORCE_QUIT
+ };
+
+ private static ExecutorService executor = Executors.newFixedThreadPool(3);
+
+ public static QResponse setQuitHandler()
+ {
+ FlatDesktop.setQuitHandler(response -> {
+ Callable<Void> performQuit = () -> {
+ response.performQuit();
+ setResponse(QResponse.QUIT);
+ return null;
+ };
+ Callable<Void> performForceQuit = () -> {
+ response.performQuit();
+ setResponse(QResponse.FORCE_QUIT);
+ return null;
+ };
+ Callable<Void> cancelQuit = () -> {
+ response.cancelQuit();
+ // reset
+ setResponse(QResponse.NULL);
+ return null;
+ };
+ getQuitResponse(true, performQuit, performForceQuit, cancelQuit);
+ });
+
+ return gotQuitResponse();
+ }
+
+ private static QResponse gotQuitResponse = QResponse.NULL;
+
+ protected static QResponse setResponse(QResponse qresponse)
+ {
+ gotQuitResponse = qresponse;
+ return qresponse;
+ }
+
+ public static QResponse gotQuitResponse()
+ {
+ return gotQuitResponse;
+ }
+
+ public static final Callable<Void> defaultCancelQuit = () -> {
+ Console.debug("QuitHandler: (default) Quit action CANCELLED by user");
+ // reset
+ setResponse(QResponse.CANCEL_QUIT);
+ return null;
+ };
+
+ public static final Callable<Void> defaultOkQuit = () -> {
+ Console.debug("QuitHandler: (default) Quit action CONFIRMED by user");
+ setResponse(QResponse.QUIT);
+ return null;
+ };
+
+ public static final Callable<Void> defaultForceQuit = () -> {
+ Console.debug("QuitHandler: (default) Quit action FORCED by user");
+ // note that shutdown hook will not be run
+ Runtime.getRuntime().halt(0);
+ setResponse(QResponse.FORCE_QUIT); // this line never reached!
+ return null;
+ };
+
+ public static QResponse getQuitResponse(boolean ui)
+ {
+ return getQuitResponse(ui, defaultOkQuit, defaultForceQuit,
+ defaultCancelQuit);
+ }
+
+ public static QResponse getQuitResponse(boolean ui, Callable<Void> okQuit,
+ Callable<Void> forceQuit, Callable<Void> cancelQuit)
+ {
+ QResponse got = gotQuitResponse();
+ if (got != QResponse.NULL && got != QResponse.CANCEL_QUIT)
+ {
+ // quit has already been selected, continue with calling quit method
+ return got;
+ }
+
+ interactive = ui && !Platform.isHeadless();
+ // confirm quit if needed and wanted
+ boolean confirmQuit = true;
+
+ if (!interactive)
+ {
+ Console.debug("Non interactive quit -- not confirming");
+ confirmQuit = false;
+ }
+ else if (Jalview2XML.allSavedUpToDate())
+ {
+ Console.debug("Nothing changed -- not confirming quit");
+ confirmQuit = false;
+ }
+ else
+ {
+ confirmQuit = jalview.bin.Cache
+ .getDefault(jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT, true);
+ Console.debug("Jalview property '"
+ + jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT
+ + "' is/defaults to " + confirmQuit + " -- "
+ + (confirmQuit ? "" : "not ") + "confirming quit");
+ }
+ got = confirmQuit ? QResponse.NULL : QResponse.QUIT;
+ setResponse(got);
+
+ if (confirmQuit)
+ {
+ JvOptionPane.newOptionDialog()
+ .setResponseHandler(JOptionPane.YES_OPTION, defaultOkQuit)
+ .setResponseHandler(JOptionPane.NO_OPTION, cancelQuit)
+ .showDialogOnTopAsync(
+ new StringBuilder(MessageManager
+ .getString("label.quit_jalview"))
+ .append("\n")
+ .append(MessageManager
+ .getString("label.unsaved_changes"))
+ .toString(),
+ MessageManager.getString("action.quit"),
+ JOptionPane.YES_NO_OPTION,
+ JOptionPane.QUESTION_MESSAGE, null, new Object[]
+ { MessageManager.getString("action.quit"),
+ MessageManager.getString("action.cancel") },
+ MessageManager.getString("action.quit"), true);
+ }
+
+ got = gotQuitResponse();
+ boolean wait = false;
+ if (got == QResponse.CANCEL_QUIT)
+ {
+ // reset
+ Console.debug("Cancelling quit. Resetting response to NULL");
+ setResponse(QResponse.NULL);
+ // but return cancel
+ return QResponse.CANCEL_QUIT;
+ }
+ else if (got == QResponse.QUIT)
+ {
+ if (Cache.getDefault("WAIT_FOR_SAVE", true)
+ && BackupFiles.hasSavesInProgress())
+ {
+ waitQuit(interactive, okQuit, forceQuit, cancelQuit);
+ QResponse waitResponse = gotQuitResponse();
+ wait = waitResponse == QResponse.QUIT;
+ }
+ }
+
+ Callable<Void> next = null;
+ switch (gotQuitResponse())
+ {
+ case QUIT:
+ next = okQuit;
+ break;
+ case FORCE_QUIT: // not actually an option at this stage
+ next = forceQuit;
+ break;
+ default:
+ next = cancelQuit;
+ break;
+ }
+ try
+ {
+ executor.submit(next).get();
+ got = gotQuitResponse();
+ } catch (InterruptedException | ExecutionException e)
+ {
+ jalview.bin.Console
+ .debug("Exception during quit handling (final choice)", e);
+ }
+ setResponse(got);
+
+ if (gotQuitResponse() == QResponse.CANCEL_QUIT)
+ {
+ // reset if cancelled
+ setResponse(QResponse.NULL);
+ return QResponse.CANCEL_QUIT;
+ }
+ return gotQuitResponse();
+ }
+
+ private static QResponse waitQuit(boolean interactive,
+ Callable<Void> okQuit, Callable<Void> forceQuit,
+ Callable<Void> cancelQuit)
+ {
+ // check for saves in progress
+ if (!BackupFiles.hasSavesInProgress())
+ return QResponse.QUIT;
+
+ int size = 0;
+ AlignFrame[] afArray = Desktop.getAlignFrames();
+ if (!(afArray == null || afArray.length == 0))
+ {
+ for (int i = 0; i < afArray.length; i++)
+ {
+ AlignFrame af = afArray[i];
+ List<? extends AlignmentViewPanel> avpList = af.getAlignPanels();
+ for (AlignmentViewPanel avp : avpList)
+ {
+ AlignmentI a = avp.getAlignment();
+ List<SequenceI> sList = a.getSequences();
+ for (SequenceI s : sList)
+ {
+ size += s.getLength();
+ }
+ }
+ }
+ }
+ int waitTime = Math.min(MAX_WAIT_FOR_SAVE,
+ Math.max(MIN_WAIT_FOR_SAVE, size / 2));
+ Console.debug("Set waitForSave to " + waitTime);
+
+ int iteration = 0;
+ boolean doIterations = true; // note iterations not used in the gui now,
+ // only one pass without the "Wait" button
+ while (doIterations && BackupFiles.hasSavesInProgress()
+ && iteration++ < (interactive ? 100 : 5))
+ {
+ // future that returns a Boolean when all files are saved
+ CompletableFuture<Boolean> filesAllSaved = new CompletableFuture<>();
+
+ // callback as each file finishes saving
+ for (CompletableFuture<Boolean> cf : BackupFiles
+ .savesInProgressCompletableFutures(false))
+ {
+ // if this is the last one then complete filesAllSaved
+ cf.whenComplete((ret, e) -> {
+ if (!BackupFiles.hasSavesInProgress())
+ {
+ filesAllSaved.complete(true);
+ }
+ });
+ }
+ try
+ {
+ filesAllSaved.get(waitTime, TimeUnit.MILLISECONDS);
+ } catch (InterruptedException | ExecutionException e1)
+ {
+ Console.debug(
+ "Exception whilst waiting for files to save before quit",
+ e1);
+ } catch (TimeoutException e2)
+ {
+ // this Exception to be expected
+ }
+
+ if (interactive && BackupFiles.hasSavesInProgress())
+ {
+ boolean showForceQuit = iteration > 0; // iteration > 1 to not show
+ // force quit the first time
+ JFrame parent = new JFrame();
+ JButton[] buttons = { new JButton(), new JButton() };
+ JvOptionPane waitDialog = JvOptionPane.newOptionDialog();
+ JTextPane messagePane = new JTextPane();
+ messagePane.setBackground(waitDialog.getBackground());
+ messagePane.setBorder(null);
+ messagePane.setText(waitingForSaveMessage());
+ // callback as each file finishes saving
+ for (CompletableFuture<Boolean> cf : BackupFiles
+ .savesInProgressCompletableFutures(false))
+ {
+ cf.whenComplete((ret, e) -> {
+ if (BackupFiles.hasSavesInProgress())
+ {
+ // update the list of saving files as they save too
+ messagePane.setText(waitingForSaveMessage());
+ }
+ else
+ {
+ if (!(QuitHandler.gotQuitResponse() == QResponse.CANCEL_QUIT
+ || QuitHandler.gotQuitResponse() == QResponse.NULL))
+ {
+ for (int i = 0; i < buttons.length; i++)
+ {
+ Console.debug("DISABLING BUTTON " + buttons[i].getText());
+ buttons[i].setEnabled(false);
+ buttons[i].setVisible(false);
+ }
+ // if this is the last one then close the dialog
+ messagePane.setText(new StringBuilder()
+ .append(MessageManager.getString("label.all_saved"))
+ .append("\n")
+ .append(MessageManager
+ .getString("label.quitting_bye"))
+ .toString());
+ messagePane.setEditable(false);
+ try
+ {
+ Thread.sleep(1500);
+ } catch (InterruptedException e1)
+ {
+ }
+ parent.dispose();
+ }
+ }
+ });
+ }
+
+ String[] options;
+ int dialogType = -1;
+ if (showForceQuit)
+ {
+ options = new String[2];
+ options[0] = MessageManager.getString("action.force_quit");
+ options[1] = MessageManager.getString("action.cancel_quit");
+ dialogType = JOptionPane.YES_NO_OPTION;
+ waitDialog.setResponseHandler(JOptionPane.YES_OPTION, forceQuit)
+ .setResponseHandler(JOptionPane.NO_OPTION, cancelQuit);
+ }
+ else
+ {
+ options = new String[1];
+ options[0] = MessageManager.getString("action.cancel_quit");
+ dialogType = JOptionPane.YES_OPTION;
+ waitDialog.setResponseHandler(JOptionPane.YES_OPTION, cancelQuit);
+ }
+ waitDialog.showDialogOnTopAsync(parent, messagePane,
+ MessageManager.getString("label.wait_for_save"), dialogType,
+ JOptionPane.WARNING_MESSAGE, null, options,
+ MessageManager.getString("action.cancel_quit"), true,
+ buttons);
+
+ parent.dispose();
+ final QResponse thisWaitResponse = gotQuitResponse();
+ switch (thisWaitResponse)
+ {
+ case QUIT: // wait -- do another iteration
+ break;
+ case FORCE_QUIT:
+ doIterations = false;
+ break;
+ case CANCEL_QUIT:
+ doIterations = false;
+ break;
+ case NULL: // already cancelled
+ doIterations = false;
+ break;
+ default:
+ }
+ } // end if interactive
+
+ } // end while wait iteration loop
+ return gotQuitResponse();
+ };
+
+ private static String waitingForSaveMessage()
+ {
+ StringBuilder messageSB = new StringBuilder();
+
+ messageSB.append(MessageManager.getString("label.save_in_progress"));
+ List<File> files = BackupFiles.savesInProgressFiles(false);
+ boolean any = files.size() > 0;
+ if (any)
+ {
+ for (File file : files)
+ {
+ messageSB.append("\n\u2022 ").append(file.getName());
+ }
+ }
+ else
+ {
+ messageSB.append(MessageManager.getString("label.unknown"));
+ }
+ messageSB.append("\n\n")
+ .append(MessageManager.getString("label.quit_after_saving"));
+ return messageSB.toString();
+ }
+
+ public static void abortQuit()
+ {
+ setResponse(QResponse.CANCEL_QUIT);
+ }
+}
\ No newline at end of file
*/
package jalview.gui;
-import jalview.analysis.AlignSeq;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.jbgui.GSliderPanel;
-import jalview.util.MessageManager;
-
import java.awt.event.ActionEvent;
import java.util.ArrayList;
import java.util.List;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.analysis.AlignSeq;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GSliderPanel;
+import jalview.util.MessageManager;
+
/**
* DOCUMENT ME!
*
worker.start();
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
Desktop.addInternalFrame(frame,
MessageManager
frame = new JInternalFrame();
frame.setContentPane(this);
+ frame.setFrameIcon(null);
Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
Platform.isAMacAndNotJS() ? 240 : 180);
}
{
sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
conservationSlider = new JInternalFrame();
+ conservationSlider.setFrameIcon(null);
conservationSlider.setContentPane(sliderPanel);
conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
{
sliderPanel = new SliderPanel(ap, threshold, false, rs);
PIDSlider = new JInternalFrame();
+ PIDSlider.setFrameIcon(null);
PIDSlider.setContentPane(sliderPanel);
PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
}
*/
protected void init()
{
+ setFrameIcon(null);
getTopFrame().setSplitFrame(this);
getBottomFrame().setSplitFrame(this);
getTopFrame().setVisible(true);
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;
};
// fetch db refs if OK pressed
- final Runnable discoverCanonicalDBrefs = new Runnable()
- {
- @Override
- public void run()
+ final Callable discoverCanonicalDBrefs = () -> {
+ btn_queryTDB.setEnabled(false);
+ populateSeqsWithoutSourceDBRef();
+
+ final int y = seqsWithoutSourceDBRef.size();
+ if (y > 0)
{
- btn_queryTDB.setEnabled(false);
- populateSeqsWithoutSourceDBRef();
+ 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
- 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();
- }
+ 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
public StructureViewerBase()
{
super();
+ setFrameIcon(null);
}
/**
if (confirm == JvOptionPane.CANCEL_OPTION
|| confirm == JvOptionPane.CLOSED_OPTION)
{
+ // abort possible quit handling if CANCEL chosen
+ if (confirm == JvOptionPane.CANCEL_OPTION)
+ QuitHandler.abortQuit();
return;
}
forceClose = confirm == JvOptionPane.YES_OPTION;
import java.awt.event.MouseEvent;
import java.util.HashMap;
import java.util.Map;
+import java.util.concurrent.Callable;
import javax.swing.BorderFactory;
import javax.swing.JLabel;
MessageManager.getString("action.cancel") };
String title = MessageManager
.getString("label.adjust_foreground_text_colour_threshold");
- Runnable action = new Runnable() // response for 1 = Cancel
+ Callable<Void> action = () -> // response for 1 = Cancel
{
- @Override
- public void run()
- {
- restoreInitialSettings();
- }
+ restoreInitialSettings();
+ return null;
};
JvOptionPane.newOptionDialog(alignPanel.alignFrame)
.setResponseHandler(1, action).showInternalDialog(bigpanel,
*/
package jalview.gui;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.List;
import java.util.Locale;
+import javax.swing.ButtonGroup;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+import org.jibble.epsgraphics.EpsGraphics2D;
+
import jalview.analysis.AlignmentSorter;
import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
-import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.ButtonGroup;
-import javax.swing.JMenuItem;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.event.InternalFrameAdapter;
-import javax.swing.event.InternalFrameEvent;
-
-import org.jibble.epsgraphics.EpsGraphics2D;
-
/**
* DOCUMENT ME!
*
SimilarityParamsI options)
{
super();
+ this.setFrameIcon(null);
this.similarityParams = options;
initTreePanel(ap, type, modelName, null, null);
String theTitle, AlignmentView inputData)
{
super();
+ this.setFrameIcon(null);
this.treeTitle = theTitle;
initTreePanel(alignPanel, null, null, newtree, inputData);
}
*/
package jalview.gui;
-import java.util.Locale;
-
-import jalview.bin.Cache;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GUserDefinedColours;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemeLoader;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.util.ColorUtils;
-import jalview.util.Format;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.xml.binding.jalview.JalviewUserColours;
-import jalview.xml.binding.jalview.JalviewUserColours.Colour;
-import jalview.xml.binding.jalview.ObjectFactory;
-
import java.awt.Color;
import java.awt.Font;
import java.awt.Insets;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
+import java.util.Locale;
import javax.swing.JButton;
import javax.swing.JInternalFrame;
import javax.xml.bind.JAXBContext;
import javax.xml.bind.Marshaller;
+import jalview.bin.Cache;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GUserDefinedColours;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import jalview.util.Format;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.xml.binding.jalview.JalviewUserColours;
+import jalview.xml.binding.jalview.JalviewUserColours.Colour;
+import jalview.xml.binding.jalview.ObjectFactory;
+
/**
* This panel allows the user to assign colours to Amino Acid residue codes, and
* save the colour scheme.
{
colorChooser.getSelectionModel().addChangeListener(this);
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
Desktop.addInternalFrame(frame,
MessageManager.getString("label.user_defined_colours"),
chooser.setDialogTitle(
MessageManager.getString("label.load_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.load"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- File choice = chooser.getSelectedFile();
- Cache.setProperty(LAST_DIRECTORY, choice.getParent());
-
- UserColourScheme ucs = ColourSchemeLoader
- .loadColourScheme(choice.getAbsolutePath());
- Color[] colors = ucs.getColours();
- schemeName.setText(ucs.getSchemeName());
+ chooser.setResponseHandler(0, () -> {
+ File choice = chooser.getSelectedFile();
+ Cache.setProperty(LAST_DIRECTORY, choice.getParent());
- if (ucs.getLowerCaseColours() != null)
- {
- caseSensitive.setSelected(true);
- lcaseColour.setEnabled(true);
- resetButtonPanel(true);
- for (int i = 0; i < lowerCaseButtons.size(); i++)
- {
- JButton button = lowerCaseButtons.get(i);
- button.setBackground(ucs.getLowerCaseColours()[i]);
- }
- }
- else
- {
- caseSensitive.setSelected(false);
- lcaseColour.setEnabled(false);
- resetButtonPanel(false);
- }
+ UserColourScheme ucs = ColourSchemeLoader
+ .loadColourScheme(choice.getAbsolutePath());
+ Color[] colors = ucs.getColours();
+ schemeName.setText(ucs.getSchemeName());
- for (int i = 0; i < upperCaseButtons.size(); i++)
+ if (ucs.getLowerCaseColours() != null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
{
- JButton button = upperCaseButtons.get(i);
- button.setBackground(colors[i]);
+ JButton button = lowerCaseButtons.get(i);
+ button.setBackground(ucs.getLowerCaseColours()[i]);
}
+ }
+ else
+ {
+ caseSensitive.setSelected(false);
+ lcaseColour.setEnabled(false);
+ resetButtonPanel(false);
+ }
- addNewColourScheme(choice.getPath());
+ for (int i = 0; i < upperCaseButtons.size(); i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ button.setBackground(colors[i]);
}
+
+ addNewColourScheme(choice.getPath());
+ return null;
});
chooser.showOpenDialog(this);
*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.RenderingHints;
import java.awt.event.ActionEvent;
import java.awt.image.BufferedImage;
+import java.util.Locale;
import java.util.Vector;
import javax.swing.JComponent;
boolean makeVisible)
{
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
Desktop.addInternalFrame(frame, title, makeVisible, width, height);
frame.setClosable(false);
true, false);
((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
.getComponent(0))
- .setText(ensureHtmlTagged(
- txt + getHtmlFragment(text, false, true)));
+ .setText(ensureHtmlTagged(
+ txt + getHtmlFragment(text, false, true)));
}
else
{
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
import java.util.TreeMap;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
import jalview.bin.Cache;
import jalview.bin.Console;
private static final String oldTempFileSuffix = "_oldfile_tobedeleted";
+ // thread pool used for completablefutures
+ private static final ExecutorService executorService = Executors
+ .newFixedThreadPool(3);
+
+ private static List<BackupFiles> savesInProgress = new ArrayList<>();
+
+ private CompletableFuture<Boolean> myFuture = null;
+
+ private boolean addSaveInProgress()
+ {
+ if (savesInProgress.contains(this))
+ {
+ return false;
+ }
+ else
+ {
+ this.setMyFuture();
+ savesInProgress.add(this);
+ return true;
+ }
+ }
+
+ private boolean removeSaveInProgress(boolean ret)
+ {
+ if (savesInProgress.contains(this))
+ {
+ this.getMyFuture().complete(ret);
+ // remove all occurrences
+ while (savesInProgress.remove(this))
+ {
+ }
+ return true;
+ }
+ return false;
+ }
+
+ private static CompletableFuture<Boolean> getNewFuture()
+ {
+ return new CompletableFuture<Boolean>()
+ {
+ };
+ }
+
+ private CompletableFuture<Boolean> getMyFuture()
+ {
+ return this.myFuture;
+ }
+
+ private void setMyFuture()
+ {
+ this.myFuture = getNewFuture();
+ }
+
+ public static boolean hasSavesInProgress()
+ {
+ boolean has = false;
+ for (CompletableFuture cf : savesInProgressCompletableFutures(true))
+ {
+ has |= !cf.isDone();
+ }
+ return has;
+ }
+
+ public static List<File> savesInProgressFiles(boolean all)
+ {
+ List<File> files = new ArrayList<>();
+ for (BackupFiles bfile : savesInProgress)
+ {
+ if (all || !bfile.getMyFuture().isDone())
+ files.add(bfile.getFile());
+ }
+ return files;
+ }
+
+ public static List<CompletableFuture<Boolean>> savesInProgressCompletableFutures(
+ boolean all)
+ {
+ List<CompletableFuture<Boolean>> cfs = new ArrayList<>();
+ for (BackupFiles bfile : savesInProgress)
+ {
+ if (all || !bfile.getMyFuture().isDone())
+ cfs.add(bfile.getMyFuture());
+ }
+ return cfs;
+ }
+
+ public static Future<Boolean> allSaved()
+ {
+ CompletableFuture<Boolean> f = new CompletableFuture<>();
+
+ executorService.submit(() -> {
+ for (BackupFiles buf : savesInProgress)
+ {
+ boolean allSaved = true;
+ try
+ {
+ allSaved &= buf.getMyFuture().get();
+ } catch (InterruptedException e)
+ {
+ Console.debug("InterruptedException waiting for files to save",
+ e);
+ } catch (ExecutionException e)
+ {
+ Console.debug("ExecutionException waiting for files to save", e);
+ }
+ f.complete(allSaved);
+ }
+ });
+ return f;
+ }
+
public BackupFiles(String filename)
{
this(new File(filename));
{
classInit();
this.file = file;
+
+ // add this file from the save in progress stack
+ addSaveInProgress();
+
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
this.suffix = bfpe.suffix;
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
+ tempdir.mkdirs();
Console.trace(
"BACKUPFILES [file!=null] attempting to create temp file for "
+ tempfilename + " in dir " + tempdir);
tidyUpFiles();
}
+ // remove this file from the save in progress stack
+ removeSaveInProgress(rename);
+
return rename;
}
return ret;
}
+ public File getFile()
+ {
+ return file;
+ }
+
public static boolean moveFileToFile(File oldFile, File newFile)
{
Console.initLogger();
{
alignFrame.setFileName(file, format);
alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
+ alignFrame.getViewport().setSavedUpToDate(true);
}
if (proxyColourScheme != null)
{
*/
package jalview.io;
-import jalview.bin.Cache;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.LineartOptions;
-import jalview.gui.OOMWarning;
-import jalview.math.AlignmentDimension;
-import jalview.util.MessageManager;
-
import java.awt.Graphics;
import java.awt.print.PrinterException;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
+import java.util.concurrent.Callable;
import java.util.concurrent.atomic.AtomicBoolean;
import org.jfree.graphics2d.svg.SVGGraphics2D;
import org.jfree.graphics2d.svg.SVGHints;
+import jalview.bin.Cache;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.LineartOptions;
+import jalview.gui.OOMWarning;
+import jalview.math.AlignmentDimension;
+import jalview.util.MessageManager;
+
public class HtmlSvgOutput extends HTMLOutput
{
public HtmlSvgOutput(AlignmentPanel ap)
/*
* configure the action to run on OK in the dialog
*/
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- doOutput(textOption.get());
- }
+ Callable<Void> okAction = () -> {
+ doOutput(textOption.get());
+ return null;
};
/*
if (renderStyle.equalsIgnoreCase("Prompt each time") && !isHeadless())
{
LineartOptions svgOption = new LineartOptions("HTML", textOption);
- svgOption.setResponseAction(1, new Runnable()
- {
- @Override
- public void run()
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.cancelled_image_export_operation",
- getDescription()));
- }
+ svgOption.setResponseAction(1, () -> {
+ setProgressMessage(MessageManager.formatMessage(
+ "status.cancelled_image_export_operation",
+ getDescription()));
+ return null;
});
svgOption.setResponseAction(0, okAction);
svgOption.showDialog();
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
+import java.util.concurrent.Callable;
import javax.swing.BoxLayout;
import javax.swing.DefaultListCellRenderer;
import javax.swing.JCheckBox;
+import javax.swing.JDialog;
import javax.swing.JFileChooser;
import javax.swing.JList;
+import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.SpringLayout;
import javax.swing.filechooser.FileFilter;
import javax.swing.plaf.basic.BasicFileChooserUI;
+import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
+import jalview.util.ChannelProperties;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.dialogrunner.DialogRunnerI;
+
/**
* Enhanced file chooser dialog box.
*
{
private static final long serialVersionUID = 1L;
- private Map<Object, Runnable> callbacks = new HashMap<>();
+ private Map<Object, Callable> callbacks = new HashMap<>();
File selectedFile = null;
if (selectedFile.exists())
{
- int confirm = JvOptionPane.showConfirmDialog(this,
- MessageManager.getString("label.overwrite_existing_file"),
- MessageManager.getString("label.file_already_exists"),
- JvOptionPane.YES_NO_OPTION);
+ int confirm = Cache.getDefault("CONFIRM_OVERWRITE_FILE", true)
+ ? JvOptionPane.showConfirmDialog(this,
+ MessageManager
+ .getString("label.overwrite_existing_file"),
+ MessageManager.getString("label.file_already_exists"),
+ JvOptionPane.YES_NO_OPTION)
+ : JOptionPane.YES_OPTION;
if (confirm != JvOptionPane.YES_OPTION)
{
}
+ /*
@Override
- public DialogRunnerI setResponseHandler(Object response, Runnable action)
+ public JalviewFileChooser setResponseHandler(Object response,
+ Runnable action)
+ {
+ callbacks.put(response, new Callable<Void>()
+ {
+ @Override
+ public Void call()
+ {
+ action.run();
+ return null;
+ }
+ });
+ return this;
+ }
+ */
+
+ @Override
+ public DialogRunnerI setResponseHandler(Object response, Callable action)
{
callbacks.put(response, action);
return this;
{
return;
}
- Runnable action = callbacks.get(response);
+ Callable action = callbacks.get(response);
if (action != null)
{
- action.run();
+ try
+ {
+ action.call();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
}
}
break;
}
}
+
+ @Override
+ protected JDialog createDialog(Component parent) throws HeadlessException
+ {
+ JDialog dialog = super.createDialog(parent);
+ dialog.setIconImages(ChannelProperties.getIconList());
+ return dialog;
+ }
+
}
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
+import jalview.gui.APQHandlers;
+import jalview.gui.Desktop;
import jalview.io.FileFormatException;
import jalview.util.MessageManager;
import jalview.util.Platform;
*/
private void jbInit() throws Exception
{
- boolean apqHandlersSet = false;
/**
* APQHandlers sets handlers for About, Preferences and Quit actions
* peculiar to macOS's application menu. APQHandlers will check to see if a
*/
try
{
- apqHandlersSet = APQHandlers.setAPQHandlers(this);
+ APQHandlers.setAPQHandlers((Desktop) this);
} catch (Exception e)
{
System.out.println("Cannot set APQHandlers");
@Override
public void actionPerformed(ActionEvent e)
{
- quit();
+ if (Desktop.instance != null)
+ Desktop.instance.desktopQuit();
}
});
aboutMenuItem.setText(MessageManager.getString("label.about"));
private static final String UTF_8 = "UTF-8";
/**
+ * used in decision if quit confirmation should be issued
+ */
+ private static boolean stateSavedUpToDate = false;
+
+ /**
* prefix for recovering datasets for alignments with multiple views where
* non-existent dataset IDs were written for some views
*/
{
AlignFrame[] frames = Desktop.getAlignFrames();
+ setStateSavedUpToDate(true);
+
+ if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
+ {
+ int n = debugDelaySave;
+ int i = 0;
+ while (i < n)
+ {
+ Console.debug("***** debugging save sleep " + i + "/" + n);
+ try
+ {
+ Thread.sleep(1000);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ i++;
+ }
+ }
+
if (frames == null)
{
return;
FileOutputStream fos = new FileOutputStream(
doBackup ? backupfiles.getTempFilePath() : jarFile);
+ if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
+ {
+ int n = debugDelaySave;
+ int i = 0;
+ while (i < n)
+ {
+ Console.debug("***** debugging save sleep " + i + "/" + n);
+ try
+ {
+ Thread.sleep(1000);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ i++;
+ }
+ }
+
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
return colour;
}
+
+ public static void setStateSavedUpToDate(boolean s)
+ {
+ Console.debug("Setting overall stateSavedUpToDate to " + s);
+ stateSavedUpToDate = s;
+ }
+
+ public static boolean stateSavedUpToDate()
+ {
+ Console.debug("Returning overall stateSavedUpToDate value: "
+ + stateSavedUpToDate);
+ return stateSavedUpToDate;
+ }
+
+ public static boolean allSavedUpToDate()
+ {
+ if (stateSavedUpToDate()) // nothing happened since last project save
+ return true;
+
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames != null)
+ {
+ for (int i = 0; i < frames.length; i++)
+ {
+ if (frames[i] == null)
+ continue;
+ if (!frames[i].getViewport().savedUpToDate())
+ return false; // at least one alignment is not individually saved
+ }
+ }
+ return true;
+ }
+
+ // used for debugging and tests
+ private static int debugDelaySave = 20;
+
+ public static void setDebugDelaySave(int n)
+ {
+ debugDelaySave = n;
+ }
}
Turn("Turn Propensity", TurnColourScheme.class),
Buried("Buried Index", BuriedColourScheme.class),
Nucleotide("Nucleotide", NucleotideColourScheme.class),
+ NucleotideAmbiguity("Nucleotide Ambiguity",
+ NucleotideAmbiguityColourScheme.class),
PurinePyrimidine("Purine/Pyrimidine", PurinePyrimidineColourScheme.class),
RNAHelices("RNA Helices", RNAHelicesColour.class),
TCoffee("T-Coffee Scores", TCoffeeColourScheme.class),
- IdColour("Sequence ID", IdColourScheme.class);
+ IdColour("Sequence ID", IdColourScheme.class),;
// RNAInteraction("RNA Interaction type", RNAInteractionColourScheme.class)
private String name;
--- /dev/null
+package jalview.schemes;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AnnotatedCollectionI;
+
+public class NucleotideAmbiguityColourScheme extends ResidueColourScheme
+{
+ /**
+ * Creates a new NucleotideColourScheme object.
+ */
+ public NucleotideAmbiguityColourScheme()
+ {
+ super(ResidueProperties.nucleotideIndex,
+ ResidueProperties.nucleotideAmbiguity);
+ }
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return JalviewColourScheme.NucleotideAmbiguity.toString();
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new NucleotideAmbiguityColourScheme();
+ }
+
+}
*/
package jalview.schemes;
-import java.util.Locale;
-
-import jalview.analysis.GeneticCodes;
-
import java.awt.Color;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
+import jalview.analysis.GeneticCodes;
+
public class ResidueProperties
{
// Stores residue codes/names and colours and other things
public static final Map<String, String> nucleotideName = new HashMap<>();
+ public static final Map<String, String> nucleotideAmbiguityName = new HashMap<>();
+
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
public static final Map<String, String> modifications = new HashMap<>();
/**
* maximum (gap) index for matrices involving nucleotide alphabet
*/
- public final static int maxNucleotideIndex = 10;
+ // public final static int maxNucleotideIndex = 10;
+ public final static int maxNucleotideIndex;
static
{
+ String[][] namesArray = { { "a", "Adenine" }, { "c", "Cytosine" },
+ { "g", "Guanine" },
+ { "t", "Thymine" },
+ { "u", "Uracil" },
+ { "i", "Inosine" },
+ { "x", "Xanthine" },
+ { "r", "Unknown Purine" },
+ { "y", "Unknown Pyrimidine" },
+ { "w", "Weak nucleotide (A or T)" },
+ { "s", "Strong nucleotide (G or C)" },
+ { "m", "Amino (A or C)" },
+ { "k", "Keto (G or T)" },
+ { "b", "Not A (G or C or T)" },
+ { "h", "Not G (A or C or T)" },
+ { "d", "Not C (A or G or T)" },
+ { "v", "Not T (A or G or C)" },
+ { "n", "Unknown" } };
+ // "gap" index
+ maxNucleotideIndex = namesArray.length;
+
nucleotideIndex = new int[255];
for (int i = 0; i < 255; i++)
{
- nucleotideIndex[i] = 10; // non-nucleotide symbols are all non-gap gaps.
+ nucleotideIndex[i] = maxNucleotideIndex; // non-nucleotide symbols are all
+ // non-gap gaps.
}
- nucleotideIndex['A'] = 0;
- nucleotideIndex['a'] = 0;
- nucleotideIndex['C'] = 1;
- nucleotideIndex['c'] = 1;
- nucleotideIndex['G'] = 2;
- nucleotideIndex['g'] = 2;
- nucleotideIndex['T'] = 3;
- nucleotideIndex['t'] = 3;
- nucleotideIndex['U'] = 4;
- nucleotideIndex['u'] = 4;
- nucleotideIndex['I'] = 5;
- nucleotideIndex['i'] = 5;
- nucleotideIndex['X'] = 6;
- nucleotideIndex['x'] = 6;
- nucleotideIndex['R'] = 7;
- nucleotideIndex['r'] = 7;
- nucleotideIndex['Y'] = 8;
- nucleotideIndex['y'] = 8;
- nucleotideIndex['N'] = 9;
- nucleotideIndex['n'] = 9;
-
- nucleotideName.put("A", "Adenine");
- nucleotideName.put("a", "Adenine");
- nucleotideName.put("G", "Guanine");
- nucleotideName.put("g", "Guanine");
- nucleotideName.put("C", "Cytosine");
- nucleotideName.put("c", "Cytosine");
- nucleotideName.put("T", "Thymine");
- nucleotideName.put("t", "Thymine");
- nucleotideName.put("U", "Uracil");
- nucleotideName.put("u", "Uracil");
- nucleotideName.put("I", "Inosine");
- nucleotideName.put("i", "Inosine");
- nucleotideName.put("X", "Xanthine");
- nucleotideName.put("x", "Xanthine");
- nucleotideName.put("R", "Unknown Purine");
- nucleotideName.put("r", "Unknown Purine");
- nucleotideName.put("Y", "Unknown Pyrimidine");
- nucleotideName.put("y", "Unknown Pyrimidine");
- nucleotideName.put("N", "Unknown");
- nucleotideName.put("n", "Unknown");
- nucleotideName.put("W", "Weak nucleotide (A or T)");
- nucleotideName.put("w", "Weak nucleotide (A or T)");
- nucleotideName.put("S", "Strong nucleotide (G or C)");
- nucleotideName.put("s", "Strong nucleotide (G or C)");
- nucleotideName.put("M", "Amino (A or C)");
- nucleotideName.put("m", "Amino (A or C)");
- nucleotideName.put("K", "Keto (G or T)");
- nucleotideName.put("k", "Keto (G or T)");
- nucleotideName.put("B", "Not A (G or C or T)");
- nucleotideName.put("b", "Not A (G or C or T)");
- nucleotideName.put("H", "Not G (A or C or T)");
- nucleotideName.put("h", "Not G (A or C or T)");
- nucleotideName.put("D", "Not C (A or G or T)");
- nucleotideName.put("d", "Not C (A or G or T)");
- nucleotideName.put("V", "Not T (A or G or C");
- nucleotideName.put("v", "Not T (A or G or C");
+ for (int i = 0; i < namesArray.length; i++)
+ {
+ char c = namesArray[i][0].charAt(0);
+ nucleotideIndex[c] = i;
+ // Character.toUpperCase is Locale insensitive
+ nucleotideIndex[Character.toUpperCase(c)] = i;
+ nucleotideName.put(namesArray[i][0], namesArray[i][1]);
+ nucleotideName.put(namesArray[i][0].toUpperCase(Locale.ROOT),
+ namesArray[i][1]);
+ }
}
Color.white, // R
Color.white, // Y
Color.white, // N
+ Color.white, // w
+ Color.white, // s
+ Color.white, // m
+ Color.white, // k
+ Color.white, // b
+ Color.white, // h
+ Color.white, // d
+ Color.white, // v
+ Color.white, // Gap
+ };
+
+ // this colour scheme devised by sduce
+ public static final Color[] nucleotideAmbiguity = {
+ Color.decode("#f0fff0"), // a
+ Color.decode("#f0fff0"), // c
+ Color.decode("#f0fff0"), // g
+ Color.decode("#f0fff0"), // t
+ Color.decode("#f0fff0"), // u
+ Color.decode("#ffffff"), // i
+ Color.decode("#4f6f6f"), // x
+ Color.decode("#CD5C5C"), // r
+ Color.decode("#008000"), // y
+ Color.decode("#4682B4"), // w
+ Color.decode("#FF8C00"), // s
+ Color.decode("#9ACD32"), // m
+ Color.decode("#9932CC"), // k
+ Color.decode("#8b4513"), // b
+ Color.decode("#808080"), // h
+ Color.decode("#483D8B"), // d
+ Color.decode("#b8860b"), // v
+ Color.decode("#2f4f4f"), // n
Color.white, // Gap
};
*/
package jalview.util;
-import jalview.datamodel.SequenceI;
-
import java.util.ArrayList;
import java.util.List;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.SequenceI;
+
/**
* Assorted methods for analysing or comparing sequences.
*/
{
private static final int EIGHTY_FIVE = 85;
- private static final int TO_UPPER_CASE = 'a' - 'A';
+ private static final int NUCLEOTIDE_COUNT_PERCENT;
+
+ private static final int NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT;
+
+ private static final int NUCLEOTIDE_COUNT_SHORT_SEQUENCE;
+
+ private static final int NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE;
+
+ private static final boolean NUCLEOTIDE_AMBIGUITY_DETECTION;
public static final char GAP_SPACE = ' ';
new char[]
{ GAP_SPACE, GAP_DOT, GAP_DASH });
+ static
+ {
+ // these options read only at start of session
+ NUCLEOTIDE_COUNT_PERCENT = Cache.getDefault("NUCLEOTIDE_COUNT_PERCENT",
+ 55);
+ NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT = Cache.getDefault(
+ "NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT", 95);
+ NUCLEOTIDE_COUNT_SHORT_SEQUENCE = Cache
+ .getDefault("NUCLEOTIDE_COUNT_SHORT", 100);
+ NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE = Cache
+ .getDefault("NUCLEOTIDE_COUNT_VERY_SHORT", 4);
+ NUCLEOTIDE_AMBIGUITY_DETECTION = Cache
+ .getDefault("NUCLEOTIDE_AMBIGUITY_DETECTION", true);
+ }
+
/**
* DOCUMENT ME!
*
jlen--;
}
- int count = 0;
int match = 0;
float pid = -1;
{
match++;
}
-
- count++;
}
pid = (float) match / (float) ilen * 100;
{
match++;
}
-
- count++;
}
pid = (float) match / (float) jlen * 100;
*/
public static final boolean isGap(char c)
{
- return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : false;
+ return c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE;
}
/**
*/
public static final boolean isNucleotide(SequenceI seq)
{
- if (seq == null)
+ if (seq == null || seq.getLength() == 0)
{
return false;
}
- long ntCount = 0;
- long aaCount = 0;
- long nCount = 0;
+ long ntCount = 0; // nucleotide symbol count (does not include ntaCount)
+ long aaCount = 0; // non-nucleotide, non-gap symbol count (includes nCount
+ // and ntaCount)
+ long nCount = 0; // "Unknown" (N) symbol count
+ long xCount = 0; // Also used as "Unknown" (X) symbol count
+ long ntaCount = 0; // nucleotide ambiguity symbol count
int len = seq.getLength();
for (int i = 0; i < len; i++)
{
char c = seq.getCharAt(i);
- if (isNucleotide(c) || isX(c))
+ if (isNucleotide(c))
{
ntCount++;
}
{
nCount++;
}
+ else
+ {
+ if (isX(c))
+ {
+ xCount++;
+ }
+ if (isNucleotideAmbiguity(c))
+ {
+ ntaCount++;
+ }
+ }
}
}
- /*
- * Check for nucleotide count > 85% of total count (in a form that evades
- * int / float conversion or divide by zero).
- */
- if ((ntCount + nCount) * 100 > EIGHTY_FIVE * (ntCount + aaCount))
+ long allCount = ntCount + aaCount;
+
+ if (NUCLEOTIDE_AMBIGUITY_DETECTION)
{
- return ntCount > 0; // all N is considered protein. Could use a threshold
- // here too
+ Console.debug("Performing new nucleotide detection routine");
+ if (allCount > NUCLEOTIDE_COUNT_SHORT_SEQUENCE)
+ {
+ // a long sequence.
+ // check for at least 55% nucleotide, and nucleotide and ambiguity codes
+ // (including N) must make up 95%
+ return ntCount * 100 > NUCLEOTIDE_COUNT_PERCENT * allCount
+ && 100 * (ntCount + nCount
+ + ntaCount) > NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT
+ * allCount;
+ }
+ else if (allCount > NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE)
+ {
+ // a short sequence.
+ // check if a short sequence is at least 55% nucleotide and the rest of
+ // the symbols are all X or all N
+ if (ntCount * 100 > NUCLEOTIDE_COUNT_PERCENT * allCount
+ && (nCount == aaCount || xCount == aaCount))
+ {
+ return true;
+ }
+
+ // a short sequence.
+ // check for at least x% nucleotide and all the rest nucleotide
+ // ambiguity codes (including N), where x slides from 75% for sequences
+ // of length 4 (i.e. only one non-nucleotide) to 55% for sequences of
+ // length 100
+ return myShortSequenceNucleotideProportionCount(ntCount, allCount)
+ && nCount + ntaCount == aaCount;
+ }
+ else
+ {
+ // a very short sequence. (<4)
+ // all bases must be nucleotide
+ return ntCount > 0 && ntCount == allCount;
+ }
}
else
{
- return false;
+ Console.debug("Performing old nucleotide detection routine");
+ /*
+ * Check for nucleotide count > 85% of total count (in a form that evades
+ * int / float conversion or divide by zero).
+ */
+ if ((ntCount + nCount) * 100 > EIGHTY_FIVE * allCount)
+ {
+ return ntCount > 0; // all N is considered protein. Could use a
+ // threshold here too
+ }
}
+ return false;
+ }
+
+ protected static boolean myShortSequenceNucleotideProportionCount(
+ long ntCount, long allCount)
+ {
+ /**
+ * this method is valid only for NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE <=
+ * allCount <= NUCLEOTIDE_COUNT_SHORT_SEQUENCE
+ */
+ // the following is a simplified integer version of:
+ //
+ // a := allCount # the number of bases in the sequence
+ // n : = ntCount # the number of definite nucleotide bases
+ // vs := NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE
+ // s := NUCLEOTIDE_COUNT_SHORT_SEQUENCE
+ // lp := NUCLEOTIDE_COUNT_LOWER_PERCENT
+ // vsp := 1 - (1/a) # this is the proportion of required definite
+ // nucleotides
+ // # in a VERY_SHORT Sequence (4 bases).
+ // # This should be equivalent to all but one base in the sequence.
+ // p := (a - vs)/(s - vs) # proportion of the way between
+ // # VERY_SHORT and SHORT thresholds.
+ // tp := vsp + p * (lp/100 - vsp) # the proportion of definite nucleotides
+ // # required for this length of sequence.
+ // minNt := tp * a # the minimum number of definite nucleotide bases
+ // # required for this length of sequence.
+ //
+ // We are then essentially returning:
+ // # ntCount >= 55% of allCount and the rest are all nucleotide ambiguity:
+ // ntCount >= tp * allCount && nCount + ntaCount == aaCount
+ // but without going into float/double land
+ long LHS = 100 * allCount
+ * (NUCLEOTIDE_COUNT_SHORT_SEQUENCE
+ - NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE)
+ * (ntCount - allCount + 1);
+ long RHS = allCount * (allCount - NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE)
+ * (allCount * NUCLEOTIDE_COUNT_PERCENT - 100 * allCount + 100);
+ return LHS >= RHS;
}
/**
*/
public static boolean isNucleotide(char c)
{
- if ('a' <= c && c <= 'z')
- {
- c -= TO_UPPER_CASE;
- }
- switch (c)
+ return isNucleotide(c, false);
+ }
+
+ /**
+ * includeAmbiguity = true also includes Nucleotide Ambiguity codes
+ */
+ public static boolean isNucleotide(char c, boolean includeAmbiguity)
+ {
+ char C = Character.toUpperCase(c);
+ switch (C)
{
case 'A':
case 'C':
case 'U':
return true;
}
+ if (includeAmbiguity)
+ {
+ boolean ambiguity = isNucleotideAmbiguity(C);
+ if (ambiguity)
+ return true;
+ }
return false;
}
- public static boolean isN(char c)
+ /**
+ * Tests *only* nucleotide ambiguity codes (and not definite nucleotide codes)
+ */
+ public static boolean isNucleotideAmbiguity(char c)
{
- switch (c)
+ switch (Character.toUpperCase(c))
{
- case 'N':
- case 'n':
+ case 'I':
+ case 'X':
+ case 'R':
+ case 'Y':
+ case 'W':
+ case 'S':
+ case 'M':
+ case 'K':
+ case 'B':
+ case 'H':
+ case 'D':
+ case 'V':
return true;
+ case 'N': // not counting N as nucleotide
}
return false;
}
+ public static boolean isN(char c)
+ {
+ return 'n' == Character.toLowerCase(c);
+ }
+
public static boolean isX(char c)
{
- switch (c)
- {
- case 'X':
- case 'x':
- return true;
- }
- return false;
+ return 'x' == Character.toLowerCase(c);
}
/**
*/
public static boolean isNucleotideSequence(String s, boolean allowGaps)
{
+ return isNucleotideSequence(s, allowGaps, false);
+ }
+
+ public static boolean isNucleotideSequence(String s, boolean allowGaps,
+ boolean includeAmbiguous)
+ {
if (s == null)
{
return false;
for (int i = 0; i < s.length(); i++)
{
char c = s.charAt(i);
- if (!isNucleotide(c))
+ if (!isNucleotide(c, includeAmbiguous))
{
if (!allowGaps || !isGap(c))
{
public static boolean isSameResidue(char c1, char c2,
boolean caseSensitive)
{
- if (caseSensitive)
- {
- return (c1 == c2);
- }
- else
- {
- return Character.toUpperCase(c1) == Character.toUpperCase(c2);
- }
+ return caseSensitive ? c1 == c2
+ : Character.toUpperCase(c1) == Character.toUpperCase(c2);
}
}
import com.stevesoft.pat.Regex;
+import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.Mapping;
// toPromote.add(cand);
if (!cand.isPrimaryCandidate())
{
- System.out.println(
- "Warning: Couldn't promote dbref " + cand.toString()
- + " for sequence " + sequence.toString());
+ if (Console.isDebugEnabled())
+ {
+ Console.debug(
+ "Warning: Couldn't promote dbref " + cand.toString()
+ + " for sequence " + sequence.toString());
+ }
}
}
}
*/
package jalview.util.dialogrunner;
+import java.util.concurrent.Callable;
+
/**
* An interface for blocking dialog response handling. This is motivated by
* JalviewJS - when running as Javascript, there is only a single thread, and
* @param action
* @return
*/
- DialogRunnerI setResponseHandler(Object response, Runnable action);
+ DialogRunnerI setResponseHandler(Object response, Callable<Void> action);
+
+ // DialogRunnerI setResponseHandler(Object response, Runnable action);
/**
* Runs the registered handler (if any) for the given response. The default
*/
package jalview.viewmodel;
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.project.Jalview2XML;
import jalview.renderer.ResidueShader;
import jalview.renderer.ResidueShaderI;
import jalview.schemes.ColourSchemeI;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-
/**
* base class holding visualization and analysis attributes and common logic for
* an active alignment view displayed in the GUI
protected Deque<CommandI> redoList = new ArrayDeque<>();
/**
+ * used to determine if quit should be confirmed
+ */
+ private boolean savedUpToDate = false;
+
+ /**
* alignment displayed in the viewport. Please use get/setter
*/
protected AlignmentI alignment;
{
this.historyList.push(command);
broadcastCommand(command, false);
+ setSavedUpToDate(false);
+ Jalview2XML.setStateSavedUpToDate(false);
}
}
return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
false));
}
+
+ public void setSavedUpToDate(boolean s)
+ {
+ Console.debug(
+ "Setting " + this.getViewId() + " setSavedUpToDate to " + s);
+ savedUpToDate = s;
+ }
+
+ public boolean savedUpToDate()
+ {
+ Console.debug("Returning " + this.getViewId() + " savedUpToDate value: "
+ + savedUpToDate);
+ return savedUpToDate;
+ }
}
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.Alignment;
import jalview.util.MapList;
import jalview.ws.SequenceFetcher;
import jalview.ws.SequenceFetcherFactory;
-import jalview.ws.params.InvalidArgumentException;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
public class CrossRefTest
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @BeforeMethod(alwaysRun = true)
+ public void loadProperties()
+ {
+ Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+ }
+
@Test(groups = { "Functional" })
public void testFindXDbRefs()
{
AlignmentI al = new Alignment(new SequenceI[] { emblSeq, uniprotSeq });
Alignment xrefs = new CrossRef(new SequenceI[] { emblSeq }, al)
.findXrefSequences("UNIPROT", true);
+ System.err.println("xrefs=" + xrefs);
assertEquals(1, xrefs.getHeight());
assertSame(uniprotSeq, xrefs.getSequenceAt(0));
}
*/
package jalview.datamodel;
-import java.util.Locale;
-
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.analysis.AlignmentGenerator;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.PDBEntry.Type;
-import jalview.gui.JvOptionPane;
-import jalview.util.MapList;
-import jalview.ws.params.InvalidArgumentException;
-
import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
+import java.util.Locale;
import java.util.Vector;
import org.testng.Assert;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+import jalview.analysis.AlignmentGenerator;
+import jalview.bin.Cache;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
+import jalview.util.MapList;
import junit.extensions.PA;
public class SequenceTest
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @BeforeMethod(alwaysRun = true)
+ public void loadProperties()
+ {
+ Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+ }
+
Sequence seq;
@BeforeMethod(alwaysRun = true)
assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
// test DNA with X
assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
+ // short sequence is nucleotide only if 50% is nucleotide and remaining N/X
+ // is either N or X only
+ assertTrue(new Sequence("prot", "ACGTACGTACGTXN").isProtein());
// test DNA with N
assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
// test RNA with X
+ assertFalse(new Sequence("prot", "ACGUACGUACGUACTGACAXX").isProtein());
assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
}
--- /dev/null
+package jalview.gui;
+
+import static org.testng.Assert.assertNotNull;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.gui.QuitHandler.QResponse;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileLoader;
+import jalview.project.Jalview2XML;
+
+@Test(singleThreaded = true)
+public class QuitHandlerTest
+{
+ private static String saveProjectFile = "test-output/tempSaveFile.jvp";
+
+ private static String saveFastaFile = "test-output/tempSaveFile.fa";
+
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ Jalview2XML.setDebugDelaySave(3);
+ }
+
+ /**
+ * @throws java.lang.Exception
+ */
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ Cache.loadProperties("test/jalview/gui/quitProps.jvprops");
+
+ /*
+ * set news feed last read to a future time to ensure no
+ * 'unread' news item is displayed
+ */
+ Date oneHourFromNow = new Date(
+ System.currentTimeMillis() + 3600 * 1000);
+ Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
+
+ Jalview.main(
+ new String[]
+ { "-nowebservicediscovery", "-nosplash", "-nonews" });
+ }
+
+ @AfterClass(alwaysRun = true)
+ public static void resetProps()
+ {
+ // reset quit response
+ QuitHandler.setResponse(QResponse.NULL);
+ // reset mock response
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ // close desktop windows/frames
+ Desktop.instance.closeAll_actionPerformed(null);
+ // reset debug delay
+ Jalview2XML.setDebugDelaySave(20);
+ }
+
+ @BeforeMethod(alwaysRun = true)
+ public static void tearDownAfterClass() throws Exception
+ {
+ // reset quit response
+ QuitHandler.setResponse(QResponse.NULL);
+ // reset mock response
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ // close desktop windows/frames
+ Desktop.instance.closeAll_actionPerformed(null);
+ // reset debug delay
+ Cache.setProperty("DEBUG_DELAY_SAVE", "false");
+ Jalview2XML.setDebugDelaySave(3);
+ // set the project file
+ Desktop.instance.setProjectFile(new File(saveProjectFile));
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public static void cleanup()
+ {
+ // delete save files
+ List<String> files = new ArrayList<>();
+ files.add(saveProjectFile);
+ files.add(saveFastaFile);
+ for (String filename : files)
+ {
+ File file = new File(filename);
+ if (file.exists())
+ {
+ file.delete();
+ }
+ }
+ }
+
+ @Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
+ public void testInstantQuit() throws Exception
+ {
+ String inFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+
+ long start = System.currentTimeMillis();
+
+ // if a save is attempted it will delay 3s
+ Jalview2XML.setDebugDelaySave(3);
+ Cache.setProperty("DEBUG_DELAY_SAVE", "true");
+
+ // loaded file but haven't done anything, should just quit
+ QResponse response = QuitHandler.getQuitResponse(true);
+ long end = System.currentTimeMillis();
+
+ Assert.assertEquals(response, QResponse.QUIT);
+ Assert.assertTrue(end - start < 500,
+ "Quit-with-no-save-needed took too long (" + (end - start)
+ + "ms)");
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = { "Functional" }, singleThreaded = true, priority = 10)
+ public void testWaitForSaveQuit() throws Exception
+ {
+ String inFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+
+ long start = System.currentTimeMillis();
+
+ // start a long save (3s)
+ Jalview2XML.setDebugDelaySave(3);
+ Cache.setProperty("DEBUG_DELAY_SAVE", "true");
+ Desktop.instance.saveState_actionPerformed(false);
+
+ // give the saveState thread time to start!
+ Thread.sleep(500);
+
+ // af.saveAlignment(saveProjectFile, FileFormat.Jalview);
+ QResponse response = QuitHandler.getQuitResponse(true);
+ long end = System.currentTimeMillis();
+
+ Assert.assertEquals(response, QResponse.QUIT);
+ Assert.assertTrue(end - start > 2900,
+ "Quit-whilst-saving was too short (" + (end - start) + "ms)");
+
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = { "Functional" }, singleThreaded = true, priority = 9)
+ public void testSavedProjectChanges() throws Exception
+ {
+ String inFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+ AlignViewport viewport = af.getViewport();
+ // pretend something has happened
+ viewport.setSavedUpToDate(false);
+ Jalview2XML.setStateSavedUpToDate(false);
+
+ // don't want to hang around here
+ Cache.setProperty("DEBUG_DELAY_SAVE", "false");
+ af.saveAlignment(saveProjectFile, FileFormat.Jalview);
+
+ // this is only a two button dialog [Quit] [Cancel] so use NO_OPTION (to
+ // mean [CANCEL] -- file should already be saved so this doesn't happen and
+ // we get a QUIT response)
+ JvOptionPane.setMockResponse(JvOptionPane.NO_OPTION);
+ QResponse response = QuitHandler.getQuitResponse(true);
+
+ // if not saved this would be CANCEL_QUIT
+ Assert.assertEquals(response, QResponse.QUIT);
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = { "Functional" }, singleThreaded = true, priority = 9)
+ public void testSavedAlignmentChanges() throws Exception
+ {
+ String inFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+ AlignViewport viewport = af.getViewport();
+ // pretend something has happened
+ viewport.setSavedUpToDate(false);
+ Jalview2XML.setStateSavedUpToDate(false);
+
+ // no hanging around needed here
+ Cache.setProperty("DEBUG_DELAY_SAVE", "false");
+ af.saveAlignment(saveFastaFile, FileFormat.Fasta);
+
+ // this is only a two button dialog [Quit] [Cancel] so use NO_OPTION
+ JvOptionPane.setMockResponse(JvOptionPane.NO_OPTION);
+ QResponse response = QuitHandler.getQuitResponse(true);
+
+ // if not saved this would be CANCEL_QUIT
+ Assert.assertEquals(response, QResponse.QUIT);
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
+ public void testUnsavedChanges() throws Exception
+ {
+ String inFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+ AlignViewport viewport = af.getViewport();
+ // pretend something has happened
+ viewport.setSavedUpToDate(false);
+ Jalview2XML.setStateSavedUpToDate(false);
+
+ // this is only a two button dialog [Quit] [Cancel] so use NO_OPTION
+ JvOptionPane.setMockResponse(JvOptionPane.NO_OPTION);
+ QResponse response = QuitHandler.getQuitResponse(true);
+
+ Assert.assertEquals(response, QResponse.CANCEL_QUIT);
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = { "Functional" }, singleThreaded = true, priority = 1)
+ public void testNoGUIUnsavedChanges() throws Exception
+ {
+ String inFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+ AlignViewport viewport = af.getViewport();
+ // pretend something has happened
+ viewport.setSavedUpToDate(false);
+ Jalview2XML.setStateSavedUpToDate(false);
+
+ // this is only a two button dialog [Quit] [Cancel] so use NO_OPTION
+ JvOptionPane.setMockResponse(JvOptionPane.NO_OPTION);
+ /*
+ QResponse response = QuitHandler.getQuitResponse(false,
+ QuitHandler.defaultOkQuit, () -> {
+ // set FORCE_QUIT without the force quit
+ QuitHandler.setResponse(QResponse.FORCE_QUIT);
+ return null;
+ }, QuitHandler.defaultCancelQuit);
+ */
+ QResponse response = QuitHandler.getQuitResponse(false);
+
+ Assert.assertEquals(response, QResponse.QUIT);
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = { "Functional" }, singleThreaded = true, priority = 11)
+ public void testForceQuit() throws Exception
+ {
+ String inFile = "examples/uniref50.fa";
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+ DataSourceType.FILE);
+ assertNotNull(af, "Didn't read input file " + inFile);
+
+ long start = System.currentTimeMillis();
+
+ // start a long save (10s)
+ Jalview2XML.setDebugDelaySave(10);
+ Cache.setProperty("DEBUG_DELAY_SAVE", "true");
+ Desktop.instance.saveState_actionPerformed(false);
+
+ // give the saveState thread time to start!
+ Thread.sleep(100);
+
+ // this will select "Force Quit"
+ JvOptionPane.setMockResponse(JvOptionPane.YES_OPTION);
+ QResponse response = QuitHandler.getQuitResponse(true,
+ QuitHandler.defaultOkQuit, () -> {
+ // set FORCE_QUIT without the force quit
+ jalview.bin.Console.debug(
+ "Setting FORCE_QUIT without actually quitting");
+ QuitHandler.setResponse(QResponse.FORCE_QUIT);
+ return null;
+ }, QuitHandler.defaultCancelQuit);
+ long end = System.currentTimeMillis();
+
+ Assert.assertEquals(response, QResponse.FORCE_QUIT);
+ // if the wait (min wait is 1s) wasn't long enough...
+ Assert.assertTrue(end - start > 1000,
+ "Force-Quit-whilst-saving was too short (" + (end - start)
+ + "ms)");
+ // if the wait was too long (probably waited for file to save)
+ Assert.assertTrue(end - start < 9090,
+ "Force-Quit-whilst-saving was too long (" + (end - start)
+ + "ms)");
+
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+}
--- /dev/null
+DEBUG_DELAY_SAVE=true
+BACKUPFILES_ENABLED=true
+BACKUPFILES_FC_INCLUDE=false
+BACKUPFILES_PRESET=1
+CONFIRM_OVERWRITE_FILE=true
+SHOW_STARTUP_FILE=false
+logs.Jalview.level=DEBUG
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNull;
-import jalview.gui.JvOptionPane;
-
import java.util.Collections;
import java.util.List;
import java.util.Map;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.gui.JvOptionPane;
+
public class ResiduePropertiesTest
{
*/
residues = ResidueProperties.getResidues(true, true);
Collections.sort(residues);
- assertEquals("[A, C, G, I, N, R, T, U, X, Y]", residues.toString());
+ assertEquals("[A, B, C, D, G, H, I, K, M, N, R, S, T, U, V, W, X, Y]",
+ residues.toString());
}
@Test(groups = { "Functional" })
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.bin.Cache;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class ComparisonTest
{
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+ @BeforeMethod(alwaysRun = true)
+ public void loadProperties()
+ {
+ Cache.loadProperties("test/jalview/util/comparisonTestProps.jvprops");
+ }
+
@Test(groups = { "Functional" })
public void testIsGap()
{
@Test(groups = { "Functional" })
public void testIsNucleotide_sequences()
{
- SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
+ SequenceI seq = new Sequence("eightypercent+fivepercent", "agctuagcPV");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
assertFalse(
Comparison.isNucleotide(new SequenceI[][]
{ new SequenceI[] { seq } }));
- seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
+ seq = new Sequence("eightyfivepercent+tenpercent",
+ "agctuagcgVagctuagcuVE");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+ seq = new Sequence(">nineyfivepercent+0percent",
+ "aagctuagcgEagctuagcua");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+ seq = new Sequence("nineyfivepercent+0percent", "agctuagcgEagctuagcua");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
- seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
+ seq = new Sequence("nineyfivepercent+fivepercent",
+ "agctuagcgWagctuagcua");
assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
+ seq = new Sequence("nineyfivepercent+tenpercent",
+ "agctuagcgEWWctuagcua");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
+ seq = new Sequence("eightyfivepercent+fifteenpercent",
+ "agctuagcgWWWctuagcua");
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+
seq = new Sequence("eightyfivepercentgapped",
"--agc--tuA--GCPV-a---gct-uA-GC---UV");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
- seq = new Sequence("nineypercentgapped",
- "ag--ct-u-A---GC---g----Vag--c---tuAGCUV");
+ seq = new Sequence("ninetyfivepercentgapped",
+ "ag--ct-u-a---gc---g----aag--c---tuagcuV");
assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("allgap", "---------");
new SequenceI[]
{ seq, seq, seq, seq, seq2, seq2, null } }));
- seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
- // 12/14 = 85.7%
+ String seqString = "aaatatatatgEcctgagtcgt";
+ seq = new Sequence("ShortProteinThatLooksLikeDNA", seqString);
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+ seq = new Sequence("LongProteinThatLooksLikeDNA", seqString.repeat(10));
assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
assertFalse(Comparison.isNucleotide((SequenceI[]) null));
assertFalse(Comparison.isNucleotide('P'));
}
+ @Test(groups = { "Functional" })
+ public void testIsNucleotideAmbiguity()
+ {
+ assertTrue(Comparison.isNucleotide('b', true));
+ assertTrue(Comparison.isNucleotide('B', true));
+ assertTrue(Comparison.isNucleotide('d', true));
+ assertTrue(Comparison.isNucleotide('V', true));
+ assertTrue(Comparison.isNucleotide('M', true));
+ assertTrue(Comparison.isNucleotide('s', true));
+ assertTrue(Comparison.isNucleotide('W', true));
+ assertTrue(Comparison.isNucleotide('x', true));
+ assertTrue(Comparison.isNucleotide('Y', true));
+ assertTrue(Comparison.isNucleotide('r', true));
+ assertTrue(Comparison.isNucleotide('i', true));
+ assertFalse(Comparison.isNucleotide('-', true));
+ assertFalse(Comparison.isNucleotide('n', true));
+ assertFalse(Comparison.isNucleotide('P', true));
+ }
+
/**
* Test the percentage identity calculation for two sequences
*/
assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false));
assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));
+ assertFalse(Comparison.isNucleotideSequence("gatactawgataca", false));
+ // including nucleotide ambiguity
+ assertTrue(
+ Comparison.isNucleotideSequence("gatacaWgataca", true, true));
+ assertFalse(
+ Comparison.isNucleotideSequence("gatacaEgataca", true, true));
+
+ // not quite all nucleotides and ambiguity codes
+ Sequence seq = new Sequence("Ambiguity DNA codes", "gatacagatacabve");
+ assertFalse(Comparison.isNucleotide(seq));
+ // all nucleotide and nucleotide ambiguity codes
+ seq = new Sequence("Ambiguity DNA codes", "gatacagatacabvt");
+ assertFalse(Comparison.isNucleotide(seq));
+ seq = new Sequence("Ambiguity DNA codes", "agatacabb");
+ assertFalse(Comparison.isNucleotide(seq));
+ // 55% nucleotide with only Xs or Ns
+ assertTrue(Comparison
+ .isNucleotide(new Sequence("dnaWithXs", "gatacaXXXX")));
+ assertTrue(Comparison
+ .isNucleotide(new Sequence("dnaWithXs", "gatacaNNNN")));
+ assertFalse(Comparison
+ .isNucleotide(new Sequence("dnaWithXs", "gatacXXXXX")));
+ assertFalse(Comparison
+ .isNucleotide(new Sequence("dnaWithXs", "gatacNNNNN")));
}
@Test(groups = { "Functional" })
assertFalse(Comparison.isSameResidue('a', 'A', true));
assertFalse(Comparison.isSameResidue('A', 'a', true));
}
+
+ @Test(groups = { "Functional" })
+ public void testNucleotideProportion()
+ {
+ assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 3));
+ assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 3));
+ assertFalse(Comparison.myShortSequenceNucleotideProportionCount(2, 4));
+ assertTrue(Comparison.myShortSequenceNucleotideProportionCount(3, 4));
+ assertFalse(
+ Comparison.myShortSequenceNucleotideProportionCount(17, 20));
+ assertTrue(Comparison.myShortSequenceNucleotideProportionCount(18, 20));
+ assertFalse(
+ Comparison.myShortSequenceNucleotideProportionCount(38, 50));
+ assertTrue(Comparison.myShortSequenceNucleotideProportionCount(39, 50));
+ assertFalse(
+ Comparison.myShortSequenceNucleotideProportionCount(54, 100));
+ assertTrue(
+ Comparison.myShortSequenceNucleotideProportionCount(55, 100));
+ }
}
--- /dev/null
+NUCLEOTIDE_AMBIGUITY_DETECTION=true
+NUCLEOTIDE_COUNT_PERCENT=55
+NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT=95
+NUCLEOTIDE_COUNT_SHORT=100
+NUCLEOTIDE_COUNT_VERY_SHORT=4
### Edited to use adoptium domain to gain access to Java 17 (LTS) versions.
BASE=https://api.adoptium.net/v3/binary/latest
+ZULU_BASE=https://cdn.azul.com/zulu/bin
RELEASE_TYPE=ga
JVM_IMPL=hotspot
HEAP_SIZE=normal
VENDOR=eclipse
IMAGE_TYPE=jdk
+TAR=tar
+ZIP=zip
+UNZIP=unzip
+
+STRIP_MAC_APP_BUNDLING=false
+# archives not needed for JDKs
+CREATE_ARCHIVES=""
+# need zip with top-level jre dir for getdown updates. need tgz without top-level jre dir for install4j bundling
RM=/bin/rm
# unzip-strip from https://superuser.com/questions/518347/equivalent-to-tars-strip-components-1-in-unzip
-unzip-strip() (
+unzip-strip() {
local zip=$1
local dest=${2:-.}
- local temp=$(mktemp -d) && unzip -qq -d "$temp" "$zip" && mkdir -p "$dest" &&
+ local temp=$(mktemp -d) && $UNZIP -qq -d "$temp" "$zip" && mkdir -p "$dest" &&
shopt -s dotglob && local f=("$temp"/*) &&
if (( ${#f[@]} == 1 )) && [[ -d "${f[0]}" ]] ; then
mv "$temp"/*/* "$dest"
else
mv "$temp"/* "$dest"
fi && rmdir "$temp"/* "$temp"
-)
+}
+
+dl_zulu() {
+ local OS="$1"
+ local ARCH="$2"
+ local VERSION="$3"
+ local TARFILE="$4"
+ declare -A osmap
+ osmap[mac]=macosx
+ osmap[windows]=win
+ osmap[linux]=linux
+ ZOS="${osmap[$OS]}"
+ echo "- Looking for download from Azul"
+ LATEST_DL_URL_FILE=$(wget -q -O - "${ZULU_BASE}/" | perl -n -e 'm/<a\b[^>]*href="(([^"]*\/)?zulu[^"]*-ca-'"${IMAGE_TYPE}""${VERSION}"'\.[^"]*-'"${ZOS}"'_'"${ARCH}"'.tar.gz)"[^"]*>/ && print "$1\n";' | tail -1)
+ local URL="${ZULU_BASE}/${LATEST_DL_URL_FILE}"
+ if [ -z "${LATEST_DL_URL_FILE}" ]; then
+ echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}' found at Azul"
+ return 1
+ fi
+ echo "- Found at Azul. Downloading '${URL}'"
+ wget -q -O "${TARFILE}" "${URL}" "${TARFILE}"
+ echo RETURN=$?
+ if [ "$?" != 0 ]; then
+ echo "- Download from Azul failed"
+ return 1
+ fi
+ return 0
+}
+
+declare -A DOWNLOAD_SUMMARY
for FEATURE_VERSION in 8 11 17; do
for OS_ARCH in mac:x64 mac:aarch64 windows:x64 linux:x64 linux:arm linux:aarch64; do
ARCH=${OS_ARCH#*:}
NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
TARFILE="${NAME}.tgz"
+ DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="None"
+ STRIP_COMPONENTS=1
+ MAC_STRIP_COMPONENTS=3
echo "* Downloading ${TARFILE}"
URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
wget -q -O "${TARFILE}" "${URL}"
if [ "$?" != 0 ]; then
- echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
+ echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}' at Adoptium"
$RM -f "${TARFILE}"
- continue;
+
+ # Try Azul Zulu (not an API, a bit messier, but has Java 8 JRE for mac:aarch64
+ dl_zulu "${OS}" "${ARCH}" "${FEATURE_VERSION}" "${TARFILE}"
+
+ if [ "$?" != 0 ]; then
+ DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="None"
+ continue;
+ fi
+ STRIP_COMPONENTS=2
+ MAC_STRIP_COMPONENTS=4
+ DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="Azul"
+ echo "Set ${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}=Azul"
+ else
+ DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="Adoptium"
+ echo "Set ${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}=Adoptium"
fi
echo "Unpacking ${TARFILE}"
JREDIR="${NAME}/${IMAGE_TYPE}"
RET=$?
else
echo "using tar"
- tar --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
- RET=$?
+ if [ x$OS = xmac -a x$STRIP_MAC_APP_BUNDLING = xtrue ]; then
+ echo "Running $TAR --strip-components=\"${MAC_STRIP_COMPONENTS}\" -C \"${JREDIR}\" -zxf \"${TARFILE}\" \"*/Contents/Home\""
+ $TAR --strip-components="${MAC_STRIP_COMPONENTS}" -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
+ RET=$?
+ else
+ $TAR --strip-components="${STRIP_COMPONENTS}" -C "${JREDIR}" -zxf "${TARFILE}"
+ RET=$?
+ fi
fi
if [ "$RET" != 0 ]; then
echo "Error unpacking ${TARFILE}"
exit 1
fi
$RM "${TARFILE}"
+ if [ \! -z "$CREATE_ARCHIVES" ]; then
+ for CREATEARCHIVE in ${CREATE_ARCHIVES}; do
+ ARCHIVEDIR=$CREATEARCHIVE
+ case $CREATEARCHIVE in
+ zip)
+ EXT=${CREATEARCHIVE}
+ echo "Creating ${NAME}.${EXT} for getdown updates"
+ [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
+ ABSARCHIVEDIR="${PWD}/$ARCHIVEDIR"
+ ZIPFILE="${ABSARCHIVEDIR}/${NAME}.${CREATEARCHIVE}"
+ [ -e "${ZIPFILE}" ] && $RM "${ZIPFILE}"
+ cd ${NAME}
+ $ZIP -X -r "${ZIPFILE}" "${IMAGE_TYPE}"
+ cd -
+ ;;
+ tgz)
+ EXT=tar.gz
+ echo "Creating ${NAME}.${EXT} for install4j bundling"
+ [ \! -d ${ARCHIVEDIR} ] && mkdir -p "${ARCHIVEDIR}"
+ $TAR -C "${JREDIR}" -zcf "${ARCHIVEDIR}/${NAME}.${EXT}" .
+ # make symbolic link with _ instead of - for install4j9
+ NEWNAME=${NAME//-/_}
+ echo "Linking from ${NEWNAME}.${EXT} for install4j9"
+ [ -e "${ARCHIVEDIR}/${NEWNAME}.${EXT}" ] && $RM "${ARCHIVEDIR}/${NEWNAME}.${EXT}"
+ ln -s "${NAME}.${EXT}" "${ARCHIVEDIR}/${NEWNAME}.${EXT}"
+ ;;
+ *)
+ echo "Archiving as '${CREATEARCHIVE}' file not supported"
+ ;;
+ esac
+ done
+ fi
done
done
+echo ""
+echo "Download Summary"
+for OA in "${!DOWNLOAD_SUMMARY[@]}"; do
+ echo "$OA: ${DOWNLOAD_SUMMARY[$OA]}"
+done
+
### Edited to use adoptium domain to gain access to Java 17 (LTS) versions.
BASE=https://api.adoptium.net/v3/binary/latest
+ZULU_BASE=https://cdn.azul.com/zulu/bin
RELEASE_TYPE=ga
JVM_IMPL=hotspot
HEAP_SIZE=normal
RM=/bin/rm
# unzip-strip from https://superuser.com/questions/518347/equivalent-to-tars-strip-components-1-in-unzip
-unzip-strip() (
+unzip-strip() {
local zip=$1
local dest=${2:-.}
local temp=$(mktemp -d) && $UNZIP -qq -d "$temp" "$zip" && mkdir -p "$dest" &&
else
mv "$temp"/* "$dest"
fi && rmdir "$temp"/* "$temp"
-)
+}
+
+dl_zulu() {
+ local OS="$1"
+ local ARCH="$2"
+ local VERSION="$3"
+ local TARFILE="$4"
+ declare -A osmap
+ osmap[mac]=macosx
+ osmap[windows]=win
+ osmap[linux]=linux
+ ZOS="${osmap[$OS]}"
+ echo "- Looking for download from Azul"
+ LATEST_DL_URL_FILE=$(wget -q -O - "${ZULU_BASE}/" | perl -n -e 'm/<a\b[^>]*href="(([^"]*\/)?zulu[^"]*-ca-'"${IMAGE_TYPE}""${VERSION}"'\.[^"]*-'"${ZOS}"'_'"${ARCH}"'.tar.gz)"[^"]*>/ && print "$1\n";' | tail -1)
+ local URL="${ZULU_BASE}/${LATEST_DL_URL_FILE}"
+ if [ -z "${LATEST_DL_URL_FILE}" ]; then
+ echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}' found at Azul"
+ return 1
+ fi
+ echo "- Found at Azul. Downloading '${URL}'"
+ wget -q -O "${TARFILE}" "${URL}" "${TARFILE}"
+ echo RETURN=$?
+ if [ "$?" != 0 ]; then
+ echo "- Download from Azul failed"
+ return 1
+ fi
+ return 0
+}
+
+declare -A DOWNLOAD_SUMMARY
for FEATURE_VERSION in 8 11 17; do
for OS_ARCH in mac:x64 mac:aarch64 windows:x64 linux:x64 linux:arm linux:aarch64; do
ARCH=${OS_ARCH#*:}
NAME="${IMAGE_TYPE}-${FEATURE_VERSION}-${OS}-${ARCH}"
TARFILE="${NAME}.tgz"
+ DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="None"
+ STRIP_COMPONENTS=1
+ MAC_STRIP_COMPONENTS=3
echo "* Downloading ${TARFILE}"
URL="${BASE}/${FEATURE_VERSION}/${RELEASE_TYPE}/${OS}/${ARCH}/${IMAGE_TYPE}/${JVM_IMPL}/${HEAP_SIZE}/${VENDOR}"
wget -q -O "${TARFILE}" "${URL}"
if [ "$?" != 0 ]; then
- echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}'"
+ echo "- No ${IMAGE_TYPE}-${FEATURE_VERSION} download for ${OS}-${ARCH} '${URL}' at Adoptium"
$RM -f "${TARFILE}"
- continue;
+
+ # Try Azul Zulu (not an API, a bit messier, but has Java 8 JRE for mac:aarch64
+ dl_zulu "${OS}" "${ARCH}" "${FEATURE_VERSION}" "${TARFILE}"
+
+ if [ "$?" != 0 ]; then
+ DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="None"
+ continue;
+ fi
+ STRIP_COMPONENTS=2
+ MAC_STRIP_COMPONENTS=4
+ DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="Azul"
+ echo "Set ${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}=Azul"
+ else
+ DOWNLOAD_SUMMARY["${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}"]="Adoptium"
+ echo "Set ${OS_ARCH}-${IMAGE_TYPE}-${FEATURE_VERSION}=Adoptium"
fi
echo "Unpacking ${TARFILE}"
JREDIR="${NAME}/${IMAGE_TYPE}"
else
echo "using tar"
if [ x$OS = xmac -a x$STRIP_MAC_APP_BUNDLING = xtrue ]; then
- $TAR --strip-components=3 -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
+ echo "Running $TAR --strip-components=\"${MAC_STRIP_COMPONENTS}\" -C \"${JREDIR}\" -zxf \"${TARFILE}\" \"*/Contents/Home\""
+ $TAR --strip-components="${MAC_STRIP_COMPONENTS}" -C "${JREDIR}" -zxf "${TARFILE}" "*/Contents/Home"
RET=$?
else
- $TAR --strip-components=1 -C "${JREDIR}" -zxf "${TARFILE}"
+ $TAR --strip-components="${STRIP_COMPONENTS}" -C "${JREDIR}" -zxf "${TARFILE}"
RET=$?
fi
fi
done
done
+echo ""
+echo "Download Summary"
+for OA in "${!DOWNLOAD_SUMMARY[@]}"; do
+ echo "$OA: ${DOWNLOAD_SUMMARY[$OA]}"
+done
+
--- /dev/null
+#!/usr/bin/env perl
+
+use strict;
+
+my $i4jversion = 10;
+if ($ARGV[0] eq "-v") {
+ shift @ARGV;
+ $i4jversion = shift @ARGV;
+ die("-v i4jversion must be an integer [probably 7 or 8]") unless $i4jversion =~ m/^\d+$/;
+}
+
+my $fileformats = $ARGV[0];
+$fileformats = "../../src/jalview/io/FileFormat.java" unless $fileformats;
+
+# default mimetype will be text/x-$shortname
+# TODO: find an actual extension for mat, see JAL-Xxxxx for outstanding issues too
+# TODO: look up standard mime type used for BLASTfmt matrices, etc
+my $mimetypes = {
+ rnaml => "application/rnaml+xml",
+ biojson => "application/x-jalview-biojson+json",
+ jnet => "application/x-jalview-jnet+text",
+ features => "application/x-jalview-features+text",
+ scorematrix => "application/x-jalview-scorematrix+text",
+ pdb => "chemical/x-pdb",
+ mmcif => "chemical/x-cif",
+ mmcif2 => "chemical/x-mmcif",
+ jalview => "application/x-jalview+xml+zip",
+ jvl => "application/x-jalview-jvl+text",
+ annotations => "application/x-jalview-annotations+text",
+};
+
+my @dontaddshortname = qw(features json);
+my @dontaddextension = qw(html xml json jar mfa fastq);
+my $add_associations = {
+ biojson => {shortname=>"biojson",name=>"BioJSON",extensions=>["biojson"]},
+ gff2 => {shortname=>"gff2",name=>"Generic Features Format v2",extensions=>["gff2"]},
+ gff3 => {shortname=>"gff3",name=>"Generic Features Format v3",extensions=>["gff3"]},
+ features => {shortname=>"features",name=>"Jalview Features",extensions=>["features","jvfeatures"]},
+ annotations => {shortname=>"annotations",name=>"Jalview Annotations",extensions=>["annotations","jvannotations"]},
+ mmcif => {shortname=>"mmcif",name=>"CIF",extensions=>["cif"]},
+ mmcif2 => {shortname=>"mmcif2",name=>"mmCIF",extensions=>["mcif","mmcif"]},
+ jvl => {shortname=>"jvl",name=>"Jalview Launch",extensions=>["jvl"],iconfile=>"jvl_file"},
+ jnet => {shortname=>"jnet",name=>"JnetFile",extensions=>["concise","jnet"]},
+ scorematrix => {shortname=>"scorematrix",name=>"Substitution Matrix",extensions=>["mat"]},
+};
+my $add_extensions = {
+ blc => ["blc"],
+};
+my @put_first = qw(jalview jvl);
+my @owner = @put_first;
+
+my @non_primary = qw(mmcif mmcif2 pdb);
+
+my $v = ($i4jversion >= 8)?$i4jversion:"";
+my $i4jtemplatefile = "file_associations_template-install4j${v}.xml";
+my $i4jtemplate;
+my $mactemplatefile = "file_associations_template-Info_plist.xml";
+my $mactemplate;
+
+open(MT,"<$mactemplatefile") or die("Could not open '$mactemplatefile' for reading");
+while(<MT>){
+ $mactemplate .= $_;
+}
+close(MT);
+open(IT,"<$i4jtemplatefile") or die("Could not open '$i4jtemplatefile' for reading");
+while(<IT>){
+ $i4jtemplate .= $_;
+}
+close(IT);
+my $macauto;
+my $i4jauto;
+
+my $macautofile = $mactemplatefile;
+$macautofile =~ s/template/auto$1/;
+
+my $i4jautofile = $i4jtemplatefile;
+$i4jautofile =~ s/template/auto$1/;
+
+for my $key (sort keys %$add_associations) {
+ my $a = $add_associations->{$key};
+ warn("Known file association for $a->{shortname} (".join(",",@{$a->{extensions}}).")\n");
+}
+
+open(MA,">$macautofile") or die ("Could not open '$macautofile' for writing");
+print MA "<key>CFBundleDocumentTypes</key>\n<array>\n\n";
+
+open(IA,">$i4jautofile") or die ("Could not open '$i4jautofile' for writing");
+
+open(IN, "<$fileformats") or die ("Could not open '$fileformats' for reading");
+my $id = 10000;
+my $file_associations = {};
+while(my $line = <IN>) {
+ $line =~ s/\s+/ /g;
+ $line =~ s/(^ | $)//g;
+ if ($line =~ m/^(\w+) ?\( ?"([^"]*)" ?, ?"([^"]*)" ?, ?(true|false) ?, ?(true|false) ?\)$/i) {
+ my $shortname = lc($1);
+ next if (grep($_ eq $shortname, @dontaddshortname));
+ my $name = $2;
+ my $extensions = $3;
+ $extensions =~ s/\s+//g;
+ my @possextensions = map(lc($_),split(m/,/,$extensions));
+ my @extensions;
+ my $addext = $add_extensions->{$shortname};
+ if (ref($addext) eq "ARRAY") {
+ push(@possextensions, @$addext);
+ }
+ for my $possext (@possextensions) {
+ next if grep($_ eq $possext, @extensions);
+ next if grep($_ eq $possext, @dontaddextension);
+ push(@extensions,$possext);
+ }
+ next unless scalar(@extensions);
+ $file_associations->{$shortname} = {
+ shortname => $shortname,
+ name => $name,
+ extensions => \@extensions
+ };
+ warn("Reading file association for $shortname (".join(",",@extensions).")\n");
+ }
+}
+close(IN);
+
+my %all_associations = (%$file_associations, %$add_associations);
+
+my @ordered = (@put_first, @non_primary);
+for my $key (sort keys %all_associations) {
+ next if grep($_ eq $key, @ordered);
+ push(@ordered, $key);
+}
+my $num = $#ordered + 1;
+
+warn("--\n");
+
+my $i4jcount = 0;
+for my $shortname (@ordered) {
+ my $a = $all_associations{$shortname};
+ next if (ref($a) ne "HASH");
+
+ my $name = $a->{name};
+ my $extensions = $a->{extensions};
+ my $mimetype = $mimetypes->{$shortname};
+ $mimetype = "application/x-$shortname+txt" unless $mimetype;
+
+ my $iconfile = $a->{iconfile};
+ $iconfile = "Jalview-File" unless $iconfile;
+
+ my $owner = grep($_ eq $shortname, @owner);
+ my $primary = (! grep($_ eq $shortname, @non_primary));
+ my $primarystring = $primary?"true":"false";
+ #my $role = $owner?"Owner":($primary?"Editor":"Viewer");
+ my $role = $primary?"Editor":"Viewer";
+ my $rank = $owner?"Owner":($primary?"Default":"Alternate");
+
+ my @extensions = @$extensions;
+
+ my $xname = xml_escape($name);
+ my $xmimetype = xml_escape($mimetype);
+ my $xshortname = xml_escape($shortname);
+ my $xiconfile = xml_escape($iconfile);
+ my $xrole = xml_escape($role);
+ my $xROLE = xml_escape(uc($role));
+ my $xrank = xml_escape($rank);
+ my $xprimarystring = xml_escape($primarystring);
+
+ my $macentry = $mactemplate;
+ $macentry =~ s/\$\$NAME\$\$/$xname/g;
+ $macentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
+ $macentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
+ $macentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
+ $macentry =~ s/\$\$ROLE\$\$/$xrole/g;
+ $macentry =~ s/\$\$RANK\$\$/$xrank/g;
+ $macentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
+ while ($macentry =~ m/\$\$([^\$]*)EXTENSIONS([^\$]*)\$\$/) {
+ my $pre = $1;
+ my $post = $2;
+ my $macextensions;
+ for my $ext (@extensions) {
+ my $xext = xml_escape($ext);
+ $macextensions .= $pre.$xext.$post;
+ }
+ $macentry =~ s/\$\$${pre}EXTENSIONS${post}\$\$/$macextensions/g;
+ }
+ print MA $macentry;
+
+ my $i4jentry = $i4jtemplate;
+ $i4jentry =~ s/\$\$NAME\$\$/$xname/g;
+ $i4jentry =~ s/\$\$SHORTNAME\$\$/$xshortname/g;
+ $i4jentry =~ s/\$\$MIMETYPE\$\$/$xmimetype/g;
+ $i4jentry =~ s/\$\$ICONFILE\$\$/$xiconfile/g;
+ $i4jentry =~ s/\$\$PRIMARY\$\$/$xprimarystring/g;
+ $i4jentry =~ s/\$\$MACASSOCIATIONROLE\$\$/$xROLE/g;
+
+ my $ext = join(",",sort(@extensions));
+ my $xdisplayext = xml_escape(join(", ", map(".$_",sort(@extensions))));
+ my $progresspercent = int(($i4jcount/$num)*100);
+ $progresspercent = 100 if $progresspercent > 100;
+ $i4jcount++;
+ my $xext = xml_escape($ext);
+ my $addunixextension = "true";
+
+ $i4jentry =~ s/\$\$ADDUNIXEXTENSION\$\$/$addunixextension/g;
+ $i4jentry =~ s/\$\$EXTENSION\$\$/$xext/g;
+ $i4jentry =~ s/\$\$DISPLAYEXTENSION\$\$/$xdisplayext/g;
+ $i4jentry =~ s/\$\$PROGRESSPERCENT\$\$/$progresspercent/g;
+ $i4jentry =~ s/\$\$ID\$\$/$id/g;
+ $id++;
+ $i4jentry =~ s/\$\$ID1\$\$/$id/g;
+ $id++;
+ $i4jentry =~ s/\$\$ID2\$\$/$id/g;
+ $id++;
+
+ print IA $i4jentry;
+
+ delete $all_associations{$shortname};
+ warn("Writing entry for $name (".join(",",@$extensions).": $mimetype)\n");
+}
+
+close(IA);
+print MA "</array>\n";
+close(MA);
+
+sub xml_escape {
+ my $x = shift;
+ # stolen from Pod::Simple::XMLOutStream in base distro
+ $x =~ s/([^-\n\t !\#\$\%\(\)\*\+,\.\~\/\:\;=\?\@\[\\\]\^_\`\{\|\}a-zA-Z0-9])/'&#'.(ord($1)).';'/eg;
+ return $x;
+}
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Owner</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-jalview+xml+zip</string>
<string>jvl_file.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Owner</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-jalview-jvl+text</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Viewer</string>
+<key>LSHandlerRank</key>
+<string>Alternate</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>chemical/x-cif</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Viewer</string>
+<key>LSHandlerRank</key>
+<string>Alternate</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>chemical/x-mmcif</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Viewer</string>
+<key>LSHandlerRank</key>
+<string>Alternate</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>chemical/x-pdb</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-amsa+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-jalview-annotations+text</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-jalview-biojson+json</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-blc+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-clustal+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-embl+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-fasta+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-jalview-features+text</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-genbank+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-gff2+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-gff3+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-jalview-jnet+text</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-msf+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-pfam+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-phylip+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-pileup+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-pir+txt</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/rnaml+xml</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-jalview-scorematrix+text</string>
<string>Jalview-File.icns</string>
<key>CFBundleTypeRole</key>
<string>Editor</string>
+<key>LSHandlerRank</key>
+<string>Default</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>application/x-stockholm+txt</string>
--- /dev/null
+<!-- Jalview (.jvp) BEGIN -->
+ <action name="Jalview (.jvp) message" id="10000" customizedId="Jalview-jvp-10000-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Jalview (.jvp)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Jalview (.jvp) progress bar 0" id="10001" customizedId="Jalview-jvp-10001-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="0" />
+ </serializedBean>
+ </action>
+
+ <action name="Jalview (.jvp) file association" id="10002" customizedId="Jalview-jvp-10002-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .jvp file association">
+ <serializedBean>
+ <property name="description" type="string">Jalview File</property>
+ <property name="extension" type="string">jvp</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-jalview+xml+zip</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- Jalview Launch (.jvl) BEGIN -->
+ <action name="Jalview Launch (.jvl) message" id="10003" customizedId="Jalview Launch-jvl-10003-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Jalview Launch (.jvl)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Jalview Launch (.jvl) progress bar 4" id="10004" customizedId="Jalview Launch-jvl-10004-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="4" />
+ </serializedBean>
+ </action>
+
+ <action name="Jalview Launch (.jvl) file association" id="10005" customizedId="Jalview Launch-jvl-10005-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .jvl file association">
+ <serializedBean>
+ <property name="description" type="string">Jalview Launch File</property>
+ <property name="extension" type="string">jvl</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>jvl_file.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>jvl_file.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-jalview-jvl+text</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>jvl_file.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- CIF (.cif) BEGIN -->
+ <action name="CIF (.cif) message" id="10006" customizedId="CIF-cif-10006-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">CIF (.cif)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="CIF (.cif) progress bar 8" id="10007" customizedId="CIF-cif-10007-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="8" />
+ </serializedBean>
+ </action>
+
+ <action name="CIF (.cif) file association" id="10008" customizedId="CIF-cif-10008-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .cif file association">
+ <serializedBean>
+ <property name="description" type="string">CIF File</property>
+ <property name="extension" type="string">cif</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="VIEWER" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="false" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">chemical/x-cif</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- mmCIF (.mcif, .mmcif) BEGIN -->
+ <action name="mmCIF (.mcif, .mmcif) message" id="10009" customizedId="mmCIF-mcif,mmcif-10009-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">mmCIF (.mcif, .mmcif)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="mmCIF (.mcif, .mmcif) progress bar 12" id="10010" customizedId="mmCIF-mcif,mmcif-10010-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="12" />
+ </serializedBean>
+ </action>
+
+ <action name="mmCIF (.mcif, .mmcif) file association" id="10011" customizedId="mmCIF-mcif,mmcif-10011-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .mcif,mmcif file association">
+ <serializedBean>
+ <property name="description" type="string">mmCIF File</property>
+ <property name="extension" type="string">mcif,mmcif</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="VIEWER" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="false" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">chemical/x-mmcif</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- PDB (.ent, .pdb) BEGIN -->
+ <action name="PDB (.ent, .pdb) message" id="10012" customizedId="PDB-ent,pdb-10012-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">PDB (.ent, .pdb)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="PDB (.ent, .pdb) progress bar 16" id="10013" customizedId="PDB-ent,pdb-10013-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="16" />
+ </serializedBean>
+ </action>
+
+ <action name="PDB (.ent, .pdb) file association" id="10014" customizedId="PDB-ent,pdb-10014-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .ent,pdb file association">
+ <serializedBean>
+ <property name="description" type="string">PDB File</property>
+ <property name="extension" type="string">ent,pdb</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="VIEWER" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="false" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">chemical/x-pdb</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- AMSA (.amsa) BEGIN -->
+ <action name="AMSA (.amsa) message" id="10015" customizedId="AMSA-amsa-10015-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">AMSA (.amsa)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="AMSA (.amsa) progress bar 20" id="10016" customizedId="AMSA-amsa-10016-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="20" />
+ </serializedBean>
+ </action>
+
+ <action name="AMSA (.amsa) file association" id="10017" customizedId="AMSA-amsa-10017-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .amsa file association">
+ <serializedBean>
+ <property name="description" type="string">AMSA File</property>
+ <property name="extension" type="string">amsa</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-amsa+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- Jalview Annotations (.annotations, .jvannotations) BEGIN -->
+ <action name="Jalview Annotations (.annotations, .jvannotations) message" id="10018" customizedId="Jalview Annotations-annotations,jvannotations-10018-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Jalview Annotations (.annotations, .jvannotations)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Jalview Annotations (.annotations, .jvannotations) progress bar 24" id="10019" customizedId="Jalview Annotations-annotations,jvannotations-10019-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="24" />
+ </serializedBean>
+ </action>
+
+ <action name="Jalview Annotations (.annotations, .jvannotations) file association" id="10020" customizedId="Jalview Annotations-annotations,jvannotations-10020-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .annotations,jvannotations file association">
+ <serializedBean>
+ <property name="description" type="string">Jalview Annotations File</property>
+ <property name="extension" type="string">annotations,jvannotations</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-jalview-annotations+text</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- BioJSON (.biojson) BEGIN -->
+ <action name="BioJSON (.biojson) message" id="10021" customizedId="BioJSON-biojson-10021-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">BioJSON (.biojson)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="BioJSON (.biojson) progress bar 28" id="10022" customizedId="BioJSON-biojson-10022-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="28" />
+ </serializedBean>
+ </action>
+
+ <action name="BioJSON (.biojson) file association" id="10023" customizedId="BioJSON-biojson-10023-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .biojson file association">
+ <serializedBean>
+ <property name="description" type="string">BioJSON File</property>
+ <property name="extension" type="string">biojson</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-jalview-biojson+json</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- BLC (.blc) BEGIN -->
+ <action name="BLC (.blc) message" id="10024" customizedId="BLC-blc-10024-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">BLC (.blc)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="BLC (.blc) progress bar 32" id="10025" customizedId="BLC-blc-10025-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="32" />
+ </serializedBean>
+ </action>
+
+ <action name="BLC (.blc) file association" id="10026" customizedId="BLC-blc-10026-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .blc file association">
+ <serializedBean>
+ <property name="description" type="string">BLC File</property>
+ <property name="extension" type="string">blc</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-blc+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- Clustal (.aln) BEGIN -->
+ <action name="Clustal (.aln) message" id="10027" customizedId="Clustal-aln-10027-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Clustal (.aln)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Clustal (.aln) progress bar 36" id="10028" customizedId="Clustal-aln-10028-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="36" />
+ </serializedBean>
+ </action>
+
+ <action name="Clustal (.aln) file association" id="10029" customizedId="Clustal-aln-10029-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .aln file association">
+ <serializedBean>
+ <property name="description" type="string">Clustal File</property>
+ <property name="extension" type="string">aln</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-clustal+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- ENA Flatfile (.txt) BEGIN -->
+ <action name="ENA Flatfile (.txt) message" id="10030" customizedId="ENA Flatfile-txt-10030-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">ENA Flatfile (.txt)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="ENA Flatfile (.txt) progress bar 40" id="10031" customizedId="ENA Flatfile-txt-10031-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="40" />
+ </serializedBean>
+ </action>
+
+ <action name="ENA Flatfile (.txt) file association" id="10032" customizedId="ENA Flatfile-txt-10032-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .txt file association">
+ <serializedBean>
+ <property name="description" type="string">ENA Flatfile File</property>
+ <property name="extension" type="string">txt</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-embl+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- Fasta (.fa, .fasta) BEGIN -->
+ <action name="Fasta (.fa, .fasta) message" id="10033" customizedId="Fasta-fa,fasta-10033-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Fasta (.fa, .fasta)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Fasta (.fa, .fasta) progress bar 44" id="10034" customizedId="Fasta-fa,fasta-10034-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="44" />
+ </serializedBean>
+ </action>
+
+ <action name="Fasta (.fa, .fasta) file association" id="10035" customizedId="Fasta-fa,fasta-10035-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fa,fasta file association">
+ <serializedBean>
+ <property name="description" type="string">Fasta File</property>
+ <property name="extension" type="string">fa,fasta</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-fasta+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- Jalview Features (.features, .jvfeatures) BEGIN -->
+ <action name="Jalview Features (.features, .jvfeatures) message" id="10036" customizedId="Jalview Features-features,jvfeatures-10036-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Jalview Features (.features, .jvfeatures)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Jalview Features (.features, .jvfeatures) progress bar 48" id="10037" customizedId="Jalview Features-features,jvfeatures-10037-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="48" />
+ </serializedBean>
+ </action>
+
+ <action name="Jalview Features (.features, .jvfeatures) file association" id="10038" customizedId="Jalview Features-features,jvfeatures-10038-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .features,jvfeatures file association">
+ <serializedBean>
+ <property name="description" type="string">Jalview Features File</property>
+ <property name="extension" type="string">features,jvfeatures</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-jalview-features+text</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- GenBank Flatfile (.gb, .gbk) BEGIN -->
+ <action name="GenBank Flatfile (.gb, .gbk) message" id="10039" customizedId="GenBank Flatfile-gb,gbk-10039-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">GenBank Flatfile (.gb, .gbk)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="GenBank Flatfile (.gb, .gbk) progress bar 52" id="10040" customizedId="GenBank Flatfile-gb,gbk-10040-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="52" />
+ </serializedBean>
+ </action>
+
+ <action name="GenBank Flatfile (.gb, .gbk) file association" id="10041" customizedId="GenBank Flatfile-gb,gbk-10041-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .gb,gbk file association">
+ <serializedBean>
+ <property name="description" type="string">GenBank Flatfile File</property>
+ <property name="extension" type="string">gb,gbk</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-genbank+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- Generic Features Format v2 (.gff2) BEGIN -->
+ <action name="Generic Features Format v2 (.gff2) message" id="10042" customizedId="Generic Features Format v2-gff2-10042-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Generic Features Format v2 (.gff2)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Generic Features Format v2 (.gff2) progress bar 56" id="10043" customizedId="Generic Features Format v2-gff2-10043-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="56" />
+ </serializedBean>
+ </action>
+
+ <action name="Generic Features Format v2 (.gff2) file association" id="10044" customizedId="Generic Features Format v2-gff2-10044-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .gff2 file association">
+ <serializedBean>
+ <property name="description" type="string">Generic Features Format v2 File</property>
+ <property name="extension" type="string">gff2</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-gff2+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- Generic Features Format v3 (.gff3) BEGIN -->
+ <action name="Generic Features Format v3 (.gff3) message" id="10045" customizedId="Generic Features Format v3-gff3-10045-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Generic Features Format v3 (.gff3)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Generic Features Format v3 (.gff3) progress bar 60" id="10046" customizedId="Generic Features Format v3-gff3-10046-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="60" />
+ </serializedBean>
+ </action>
+
+ <action name="Generic Features Format v3 (.gff3) file association" id="10047" customizedId="Generic Features Format v3-gff3-10047-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .gff3 file association">
+ <serializedBean>
+ <property name="description" type="string">Generic Features Format v3 File</property>
+ <property name="extension" type="string">gff3</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-gff3+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- JnetFile (.concise, .jnet) BEGIN -->
+ <action name="JnetFile (.concise, .jnet) message" id="10048" customizedId="JnetFile-concise,jnet-10048-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">JnetFile (.concise, .jnet)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="JnetFile (.concise, .jnet) progress bar 64" id="10049" customizedId="JnetFile-concise,jnet-10049-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="64" />
+ </serializedBean>
+ </action>
+
+ <action name="JnetFile (.concise, .jnet) file association" id="10050" customizedId="JnetFile-concise,jnet-10050-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .concise,jnet file association">
+ <serializedBean>
+ <property name="description" type="string">JnetFile File</property>
+ <property name="extension" type="string">concise,jnet</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-jalview-jnet+text</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- MSF (.msf) BEGIN -->
+ <action name="MSF (.msf) message" id="10051" customizedId="MSF-msf-10051-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">MSF (.msf)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="MSF (.msf) progress bar 68" id="10052" customizedId="MSF-msf-10052-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="68" />
+ </serializedBean>
+ </action>
+
+ <action name="MSF (.msf) file association" id="10053" customizedId="MSF-msf-10053-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .msf file association">
+ <serializedBean>
+ <property name="description" type="string">MSF File</property>
+ <property name="extension" type="string">msf</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-msf+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- PFAM (.pfam) BEGIN -->
+ <action name="PFAM (.pfam) message" id="10054" customizedId="PFAM-pfam-10054-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">PFAM (.pfam)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="PFAM (.pfam) progress bar 72" id="10055" customizedId="PFAM-pfam-10055-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="72" />
+ </serializedBean>
+ </action>
+
+ <action name="PFAM (.pfam) file association" id="10056" customizedId="PFAM-pfam-10056-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .pfam file association">
+ <serializedBean>
+ <property name="description" type="string">PFAM File</property>
+ <property name="extension" type="string">pfam</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-pfam+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- PHYLIP (.phy) BEGIN -->
+ <action name="PHYLIP (.phy) message" id="10057" customizedId="PHYLIP-phy-10057-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">PHYLIP (.phy)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="PHYLIP (.phy) progress bar 76" id="10058" customizedId="PHYLIP-phy-10058-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="76" />
+ </serializedBean>
+ </action>
+
+ <action name="PHYLIP (.phy) file association" id="10059" customizedId="PHYLIP-phy-10059-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .phy file association">
+ <serializedBean>
+ <property name="description" type="string">PHYLIP File</property>
+ <property name="extension" type="string">phy</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-phylip+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- PileUp (.pileup) BEGIN -->
+ <action name="PileUp (.pileup) message" id="10060" customizedId="PileUp-pileup-10060-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">PileUp (.pileup)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="PileUp (.pileup) progress bar 80" id="10061" customizedId="PileUp-pileup-10061-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="80" />
+ </serializedBean>
+ </action>
+
+ <action name="PileUp (.pileup) file association" id="10062" customizedId="PileUp-pileup-10062-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .pileup file association">
+ <serializedBean>
+ <property name="description" type="string">PileUp File</property>
+ <property name="extension" type="string">pileup</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-pileup+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- PIR (.pir) BEGIN -->
+ <action name="PIR (.pir) message" id="10063" customizedId="PIR-pir-10063-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">PIR (.pir)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="PIR (.pir) progress bar 84" id="10064" customizedId="PIR-pir-10064-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="84" />
+ </serializedBean>
+ </action>
+
+ <action name="PIR (.pir) file association" id="10065" customizedId="PIR-pir-10065-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .pir file association">
+ <serializedBean>
+ <property name="description" type="string">PIR File</property>
+ <property name="extension" type="string">pir</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-pir+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- RNAML (.rnaml) BEGIN -->
+ <action name="RNAML (.rnaml) message" id="10066" customizedId="RNAML-rnaml-10066-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">RNAML (.rnaml)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="RNAML (.rnaml) progress bar 88" id="10067" customizedId="RNAML-rnaml-10067-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="88" />
+ </serializedBean>
+ </action>
+
+ <action name="RNAML (.rnaml) file association" id="10068" customizedId="RNAML-rnaml-10068-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .rnaml file association">
+ <serializedBean>
+ <property name="description" type="string">RNAML File</property>
+ <property name="extension" type="string">rnaml</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/rnaml+xml</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- Substitution Matrix (.mat) BEGIN -->
+ <action name="Substitution Matrix (.mat) message" id="10069" customizedId="Substitution Matrix-mat-10069-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Substitution Matrix (.mat)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Substitution Matrix (.mat) progress bar 92" id="10070" customizedId="Substitution Matrix-mat-10070-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="92" />
+ </serializedBean>
+ </action>
+
+ <action name="Substitution Matrix (.mat) file association" id="10071" customizedId="Substitution Matrix-mat-10071-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .mat file association">
+ <serializedBean>
+ <property name="description" type="string">Substitution Matrix File</property>
+ <property name="extension" type="string">mat</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-jalview-scorematrix+text</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
+<!-- Stockholm (.stk, .sto) BEGIN -->
+ <action name="Stockholm (.stk, .sto) message" id="10072" customizedId="Stockholm-stk,sto-10072-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">Stockholm (.stk, .sto)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="Stockholm (.stk, .sto) progress bar 96" id="10073" customizedId="Stockholm-stk,sto-10073-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="96" />
+ </serializedBean>
+ </action>
+
+ <action name="Stockholm (.stk, .sto) file association" id="10074" customizedId="Stockholm-stk,sto-10074-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .stk,sto file association">
+ <serializedBean>
+ <property name="description" type="string">Stockholm File</property>
+ <property name="extension" type="string">stk,sto</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="EDITOR" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="true" />
+ <property name="unix" type="boolean" value="true" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">application/x-stockholm+txt</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>Jalview-File.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
<string>$$ICONFILE$$.icns</string>
<key>CFBundleTypeRole</key>
<string>$$ROLE$$</string>
+<key>LSHandlerRank</key>
+<string>$$RANK$$</string>
<key>CFBundleTypeMIMETypes</key>
<array>
<string>$$MIMETYPE$$</string>
--- /dev/null
+<!-- $$NAME$$ ($$DISPLAYEXTENSION$$) BEGIN -->
+ <action name="$$NAME$$ ($$DISPLAYEXTENSION$$) message" id="$$ID$$" customizedId="$$NAME$$-$$EXTENSION$$-$$ID$$-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="detailMessage" type="string">$$NAME$$ ($$DISPLAYEXTENSION$$)</property>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+
+ <action name="$$NAME$$ ($$DISPLAYEXTENSION$$) progress bar $$PROGRESSPERCENT$$" id="$$ID1$$" customizedId="$$NAME$$-$$EXTENSION$$-$$ID1$$-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="$$PROGRESSPERCENT$$" />
+ </serializedBean>
+ </action>
+
+ <action name="$$NAME$$ ($$DISPLAYEXTENSION$$) file association" id="$$ID2$$" customizedId="$$NAME$$-$$EXTENSION$$-$$ID2$$-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .$$EXTENSION$$ file association">
+ <serializedBean>
+ <property name="description" type="string">$$NAME$$ File</property>
+ <property name="extension" type="string">$$EXTENSION$$</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <!--<property name="macIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>$$ICONFILE$$.icns</string>
+ </object>
+ </property>
+ <property name="macRole" type="enum" class="com.install4j.runtime.beans.actions.desktop.MacAssociationRole" value="$$MACASSOCIATIONROLE$$" />-->
+ <property name="restartFinder" type="boolean" value="true" />
+ <property name="selected" type="boolean" value="$$PRIMARY$$" />
+ <property name="unix" type="boolean" value="$$ADDUNIXEXTENSION$$" />
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>$$ICONFILE$$.png</string>
+ </object>
+ </property>
+ <property name="unixMimeType" type="string">$$MIMETYPE$$</property>
+ <property name="windowsIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>$$ICONFILE$$.ico</string>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
+<!-- END -->
+
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<install4j version="10.0.4" transformSequenceNumber="10">
+ <directoryPresets config="bin/jalview" />
+ <application name="${compiler:JALVIEW_APPLICATION_NAME}" applicationId="${compiler:WINDOWS_APPLICATION_ID}" mediaDir="${compiler:BUILD_DIR}" lzmaCompression="true" shortName="${compiler:INTERNAL_ID}" publisher="University of Dundee" publisherWeb="https://www.jalview.org/" version="${compiler:JALVIEW_VERSION}" allPathsRelative="true" macVolumeId="5aac4968c304f65" javaMinVersion="${compiler:JAVA_MIN_VERSION}" javaMaxVersion="${compiler:JAVA_MAX_VERSION}" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
+ <searchSequence>
+ <directory location="${compiler:JRE_DIR}" />
+ <registry />
+ <envVar name="JAVA_HOME" />
+ </searchSequence>
+ <variables>
+ <variable name="JALVIEW_NAME" value="Jalview" />
+ <variable name="JALVIEW_APPLICATION_NAME" value="Jalview" />
+ <variable name="JALVIEW_DIR" value="../.." />
+ <variable name="BUILD_DIR" value="${compiler:JALVIEW_DIR}/build/install4j" />
+ <variable name="OSX_KEYSTORE" />
+ <variable name="OSX_APPLEID" />
+ <variable name="JSIGN_SH" value="echo" />
+ <variable name="JRE_DIR" value="jre" description="The folder under the app folder that the JRE will be either copied or unpacked into" />
+ <variable name="INSTALLER_TEMPLATE_VERSION" value="DEVELOPMENT_default" />
+ <variable name="JALVIEW_VERSION" value="DEVELOPMENT" />
+ <variable name="JAVA_MIN_VERSION" value="11" />
+ <variable name="JAVA_MAX_VERSION" value="11" />
+ <variable name="JAVA_VERSION" value="11" />
+ <variable name="JAVA_INTEGER_VERSION" value="11" />
+ <variable name="VERSION" value="DEVELOPMENT" />
+ <variable name="MACOS_X64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-mac-x64/jre" />
+ <variable name="MACOS_AARCH64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-mac-aarch64/jre" />
+ <variable name="WINDOWS_X64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-windows-x64/jre" />
+ <variable name="LINUX_X64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-linux-x64/jre" />
+ <variable name="LINUX_AARCH64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-linux-aarch64/jre" />
+ <variable name="MACOS_X64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_mac_x64.tar.gz" />
+ <variable name="MACOS_AARCH64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_mac_aarch64.tar.gz" />
+ <variable name="WINDOWS_X64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_windows_x64.tar.gz" />
+ <variable name="LINUX_X64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_linux_x64.tar.gz" />
+ <variable name="LINUX_AARCH64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_linux_aarch64.tar.gz" />
+ <variable name="COPYRIGHT_MESSAGE" value="..." />
+ <variable name="BUNDLE_ID" value="org.jalview.jalview-desktop" />
+ <variable name="INTERNAL_ID" value="Jalview" />
+ <variable name="WINDOWS_APPLICATION_ID" value="6595-2347-1923-0725" />
+ <variable name="MACOS_DMG_DS_STORE" value="utils/channels/default/images/jalview_default_dmg_DS_Store" />
+ <variable name="MACOS_DMG_BG_IMAGE" value="utils/channels/default/images/jalview_default_dmg_background-72dpi.png" />
+ <variable name="WRAPPER_LINK" value="jalview" />
+ <variable name="BASH_WRAPPER_SCRIPT" value="jalview.sh" />
+ <variable name="WRAPPER_SCRIPT_BIN_DIR" value="bin" />
+ <variable name="INSTALLER_NAME" value="Jalview Installer" />
+ <variable name="INSTALL4J_UTILS_DIR" value="utils/install4j" />
+ <variable name="GETDOWN_CHANNEL_DIR" value="build/website/docroot/getdown/default" />
+ <variable name="GETDOWN_FILES_DIR" value="getdown/files" />
+ <variable name="GETDOWN_RESOURCE_DIR" value="resource" />
+ <variable name="GETDOWN_DIST_DIR" value="dist" />
+ <variable name="GETDOWN_ALT_DIR" value="alt" />
+ <variable name="GETDOWN_INSTALL_DIR" value="install" />
+ <variable name="INFO_PLIST_FILE_ASSOCIATIONS_FILE" value="file_associations_auto-Info_plist.xml" />
+ <variable name="APPLICATION_CATEGORIES" value="Science;Biology;Java;" />
+ <variable name="APPLICATION_FOLDER" value="Jalview" />
+ <variable name="UNIX_APPLICATION_FOLDER" value="jalview" />
+ <variable name="EXECUTABLE_NAME" value="jalview" />
+ <variable name="EXTRA_SCHEME" value="jalviewx" />
+ <variable name="MAC_ICONS_FILE" value="utils/channels/release/images/jalview_logo.icns" />
+ <variable name="WINDOWS_ICONS_FILE" value="utils/channels/release/images/jalview_logo.ico" />
+ <variable name="PNG_ICON_FILE" value="utils/channels/release/images/jalview_logo.png" />
+ <variable name="BACKGROUND" value="utils/channels/release/images/jalview_logo_background_fade-640x480.png" />
+ </variables>
+ <codeSigning macEnabled="true" macPkcs12File="${compiler:OSX_KEYSTORE}" macNotarize="true" appleId="${compiler:OSX_APPLEID}">
+ <macAdditionalBinaries>
+ <entry>*.dylib</entry>
+ <entry>*.so</entry>
+ <entry>*.jnilib</entry>
+ <entry>unpack200</entry>
+ <entry>tnameserv</entry>
+ <entry>servertool</entry>
+ <entry>rmiregistry</entry>
+ <entry>rmid</entry>
+ <entry>policytool</entry>
+ <entry>pack200</entry>
+ <entry>orbd</entry>
+ <entry>keytool</entry>
+ <entry>jjs</entry>
+ <entry>java</entry>
+ <entry>jspawnhelper</entry>
+ <entry>libfreetype.dylib.6</entry>
+ <entry>applet</entry>
+ <entry>jaotc</entry>
+ <entry>jfr</entry>
+ <entry>jrunscript</entry>
+ <entry>libjli.dylib</entry>
+ </macAdditionalBinaries>
+ </codeSigning>
+ </application>
+ <files defaultUninstallMode="2">
+ <filesets>
+ <fileset name="Full file set" id="734" customizedId="FULL_FILE_SET" />
+ <fileset name="macOS x64 JVM" id="2801" customizedId="MACOS_X64_JVM" />
+ <fileset name="macOS aarch64 JVM" id="2803" customizedId="MACOS_AARCH64_JVM" />
+ </filesets>
+ <roots>
+ <root id="735" fileset="734" />
+ <root id="2802" fileset="2801" />
+ <root id="2804" fileset="2803" />
+ </roots>
+ <mountPoints>
+ <mountPoint id="736" root="735" />
+ <mountPoint id="2805" root="2802" />
+ <mountPoint id="2806" root="2804" />
+ </mountPoints>
+ <entries>
+ <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_CHANNEL_DIR}/${compiler:JAVA_VERSION}" uninstallMode="2" overrideOverwriteMode="true" overrideUninstallMode="true" subDirectory="files">
+ <exclude>
+ <entry location="${compiler:WRAPPER_SCRIPT_BIN_DIR}" />
+ </exclude>
+ </dirEntry>
+ <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/examples" overwriteMode="1" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="examples" />
+ <dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_CHANNEL_DIR}/${compiler:JAVA_VERSION}/${compiler:WRAPPER_SCRIPT_BIN_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:WRAPPER_SCRIPT_BIN_DIR}" overrideDirMode="true" />
+ <dirEntry mountPoint="2805" file="${compiler:MACOS_X64_JAVA_VM_DIR}" overwriteMode="1" fileMode="755" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
+ <dirEntry mountPoint="2806" file="${compiler:MACOS_AARCH64_JAVA_VM_DIR}" overwriteMode="1" fileMode="755" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
+ </entries>
+ <components>
+ <component name="jalview_getdown" id="1031">
+ <include>
+ <entry filesetId="734" />
+ </include>
+ </component>
+ </components>
+ </files>
+ <launchers>
+ <launcher name="Jalview Launcher" id="737" customizedId="JALVIEW" menuName="${compiler:JALVIEW_APPLICATION_NAME}" icnsFile="${compiler:JALVIEW_DIR}/${compiler:MAC_ICONS_FILE}" customMacBundleIdentifier="true" macBundleIdentifier="${compiler:BUNDLE_ID}" fileset="734" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:JALVIEW_APPLICATION_NAME}">
+ <executable name="${compiler:EXECUTABLE_NAME}" iconSet="true" iconFile="${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}" redirectStdout="true" executableMode="gui" changeWorkingDirectory="false" singleInstance="true" checkConsoleParameter="true">
+ <versionInfo include="true" fileDescription="${compiler:sys.fullName}" legalCopyright="${compiler:COPYRIGHT_MESSAGE}" internalName="${compiler:INTERNAL_ID}" productName="${compiler:sys.fullName}" />
+ </executable>
+ <splashScreen width="640" height="480" bitmapFile="${compiler:JALVIEW_DIR}/${compiler:BACKGROUND}" textOverlay="true">
+ <text>
+ <statusLine x="85" y="81" text="${compiler:sys.shortName}" fontSize="18" />
+ <versionLine x="85" y="109" text="version ${compiler:sys.version}" />
+ </text>
+ </splashScreen>
+ <java mainClass="com.threerings.getdown.launcher.GetdownApp" vmParameters="-Dinstaller_template_version=${compiler:INSTALLER_TEMPLATE_VERSION}" arguments=""${launcher:sys.launcherDirectory}" jalview">
+ <classPath>
+ <archive location="getdown-launcher.jar" />
+ <archive location="${compiler:GETDOWN_INSTALL_DIR}/getdown-launcher.jar" failOnError="false" />
+ </classPath>
+ <nativeLibraryDirectories>
+ <directory name="${compiler:JRE_DIR}/bin" />
+ <directory name="${compiler:GETDOWN_DIST_DIR}" />
+ </nativeLibraryDirectories>
+ </java>
+ <infoPlist>${compiler:file("${compiler:INFO_PLIST_FILE_ASSOCIATIONS_FILE}")}</infoPlist>
+ <iconImageFiles>
+ <file path="${compiler:JALVIEW_DIR}/${compiler:PNG_ICON_FILE}" />
+ </iconImageFiles>
+ <macStaticAssociations>
+ <urlHandler scheme="jalview" />
+ <urlHandler scheme="jalviews" />
+ <urlHandler scheme="${compiler:EXTRA_SCHEME}" />
+ </macStaticAssociations>
+ </launcher>
+ </launchers>
+ <installerGui autoUpdateDescriptorUrl="https://www.jalview.org/install4j/updates.xml">
+ <applications>
+ <application id="installer" beanClass="com.install4j.runtime.beans.applications.InstallerApplication" styleId="35" customIcnsFile="${compiler:JALVIEW_DIR}/${compiler:MAC_ICONS_FILE}" customIcoFile="${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}">
+ <serializedBean>
+ <property name="useCustomIcon" type="boolean" value="true" />
+ </serializedBean>
+ <styleOverrides>
+ <styleOverride name="Customize banner image" enabled="true">
+ <group id="146" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup" useExternalParametrization="true" externalParametrizationName="Customize banner image" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="backgroundColor">
+ <object class="com.install4j.runtime.beans.LightOrDarkColor">
+ <object class="java.awt.Color">
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ </object>
+ <object class="java.awt.Color">
+ <int>49</int>
+ <int>52</int>
+ <int>53</int>
+ <int>255</int>
+ </object>
+ </object>
+ </property>
+ <property name="borderSides">
+ <object class="com.install4j.runtime.beans.formcomponents.BorderSides">
+ <property name="bottom" type="boolean" value="true" />
+ </object>
+ </property>
+ <property name="imageEdgeBackgroundColor">
+ <object class="java.awt.Color">
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ </object>
+ </property>
+ <property name="imageEdgeBorder" type="boolean" value="true" />
+ <property name="imageFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:BACKGROUND}</string>
+ </object>
+ </property>
+ <property name="insets">
+ <object class="java.awt.Insets">
+ <int>5</int>
+ <int>10</int>
+ <int>10</int>
+ <int>10</int>
+ </object>
+ </property>
+ </serializedBean>
+ <externalParametrizationPropertyNames>
+ <propertyName>imageAnchor</propertyName>
+ <propertyName>imageEdgeBackgroundColor</propertyName>
+ <propertyName>imageFile</propertyName>
+ </externalParametrizationPropertyNames>
+ </group>
+ </styleOverride>
+ <styleOverride name="Jalview" enabled="true">
+ <formComponent name="Watermark" id="352" beanClass="com.install4j.runtime.beans.formcomponents.SeparatorComponent" insetTop="0" insetLeft="5" insetBottom="0" useExternalParametrization="true" externalParametrizationName="Jalview" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="enabledTitleText" type="boolean" value="false" />
+ </serializedBean>
+ <externalParametrizationPropertyNames>
+ <propertyName>labelText</propertyName>
+ </externalParametrizationPropertyNames>
+ </formComponent>
+ </styleOverride>
+ </styleOverrides>
+ <startup>
+ <screen id="1" beanClass="com.install4j.runtime.beans.screens.StartupScreen" rollbackBarrierExitCode="0">
+ <actions>
+ <action id="22" beanClass="com.install4j.runtime.beans.actions.misc.RequestPrivilegesAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="obtainIfAdminWin" type="boolean" value="false" />
+ </serializedBean>
+ </action>
+ <action name="Set unixUserBinDir (Linux or Unix)" id="2738" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">String userHome = (String)context.getVariable("sys.userHome");
+
+ArrayList<String> tryPaths = new ArrayList<> ();
+tryPaths.add(userHome + File.separator + "bin");
+tryPaths.add(userHome + File.separator + ".local" + File.separator + "bin");
+tryPaths.add(userHome + File.separator + "local" + File.separator + "bin");
+tryPaths.add(userHome + File.separator + "opt" + File.separator + "bin");
+
+if (Util.isMacOS()) { // && root permission?
+ tryPaths.add(File.separator + "usr" + File.separator + "local" + File.separator + "bin");
+}
+
+for (int i = 0; i < tryPaths.size(); i++) {
+ String tryPath = tryPaths.get(i);
+ File unixUserBinDir = new File(tryPath);
+ if (unixUserBinDir.exists()) {
+ return tryPath;
+ }
+}
+
+return null;
+</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">unixUserBinDir</property>
+ </serializedBean>
+ <condition>Util.isLinux() || Util.isUnixInstaller() || Util.isMacOS()</condition>
+ </action>
+ <action name="Set macWrapperLinkLocation (macOS)" id="2745" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">String javaHome = System.getProperty("java.home");
+String appName = ((String)context.getCompilerVariable("JALVIEW_APPLICATION_NAME")) + ".app";
+int i = javaHome.indexOf(appName);
+String wrapperLink = null;
+if (i > -1) {
+ wrapperLink = javaHome.substring(0, i) + appName + File.separator + "Contents" + File.separator + "MacOS" + File.separator + ((String)context.getCompilerVariable("WRAPPER_LINK"));
+}
+return wrapperLink;
+</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">macWrapperLinkLocation</property>
+ </serializedBean>
+ <condition>Util.isMacOS()</condition>
+ </action>
+ </actions>
+ </screen>
+ </startup>
+ <screens>
+ <screen id="2" beanClass="com.install4j.runtime.beans.screens.WelcomeScreen" rollbackBarrierExitCode="0">
+ <styleOverrides>
+ <styleOverride name="Customize banner image" enabled="true">
+ <group id="145" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup" useExternalParametrization="true" externalParametrizationName="Customize banner image" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="backgroundColor">
+ <object class="com.install4j.runtime.beans.LightOrDarkColor">
+ <object class="java.awt.Color">
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ </object>
+ <object class="java.awt.Color">
+ <int>49</int>
+ <int>52</int>
+ <int>53</int>
+ <int>255</int>
+ </object>
+ </object>
+ </property>
+ <property name="borderSides">
+ <object class="com.install4j.runtime.beans.formcomponents.BorderSides">
+ <property name="bottom" type="boolean" value="true" />
+ </object>
+ </property>
+ <property name="imageEdgeBackgroundColor">
+ <object class="com.install4j.runtime.beans.LightOrDarkColor">
+ <object class="java.awt.Color">
+ <int>25</int>
+ <int>143</int>
+ <int>220</int>
+ <int>255</int>
+ </object>
+ <object class="java.awt.Color">
+ <int>0</int>
+ <int>74</int>
+ <int>151</int>
+ <int>255</int>
+ </object>
+ </object>
+ </property>
+ <property name="imageEdgeBorder" type="boolean" value="true" />
+ <property name="imageFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:BACKGROUND}</string>
+ </object>
+ </property>
+ <property name="insets">
+ <object class="java.awt.Insets">
+ <int>5</int>
+ <int>10</int>
+ <int>10</int>
+ <int>10</int>
+ </object>
+ </property>
+ </serializedBean>
+ <externalParametrizationPropertyNames>
+ <propertyName>imageAnchor</propertyName>
+ <propertyName>imageEdgeBackgroundColor</propertyName>
+ <propertyName>imageFile</propertyName>
+ </externalParametrizationPropertyNames>
+ </group>
+ </styleOverride>
+ </styleOverrides>
+ <actions>
+ <action id="7" beanClass="com.install4j.runtime.beans.actions.misc.LoadResponseFileAction" rollbackBarrierExitCode="0" multiExec="true">
+ <serializedBean>
+ <property name="excludedVariables" type="array" elementType="string" length="1">
+ <element index="0">sys.installationDir</element>
+ </property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("sys.confirmedUpdateInstallation")</condition>
+ </action>
+ </actions>
+ <formComponents>
+ <formComponent id="3" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent">
+ <serializedBean>
+ <property name="labelText" type="string">${form:welcomeMessage}</property>
+ </serializedBean>
+ <visibilityScript>!context.isConsole()</visibilityScript>
+ </formComponent>
+ <formComponent id="4" beanClass="com.install4j.runtime.beans.formcomponents.ConsoleHandlerFormComponent">
+ <serializedBean>
+ <property name="consoleScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">String message = context.getMessage("ConsoleWelcomeLabel", context.getApplicationName());
+return console.askOkCancel(message, true);
+</property>
+ </object>
+ </property>
+ </serializedBean>
+ </formComponent>
+ <formComponent id="5" beanClass="com.install4j.runtime.beans.formcomponents.UpdateAlertComponent" useExternalParametrization="true" externalParametrizationName="Update Alert" externalParametrizationMode="include">
+ <externalParametrizationPropertyNames>
+ <propertyName>updateCheck</propertyName>
+ </externalParametrizationPropertyNames>
+ </formComponent>
+ <formComponent id="6" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetTop="20">
+ <serializedBean>
+ <property name="labelText" type="string">${i18n:ClickNext}</property>
+ </serializedBean>
+ </formComponent>
+ </formComponents>
+ </screen>
+ <screen id="8" beanClass="com.install4j.runtime.beans.screens.InstallationDirectoryScreen" rollbackBarrierExitCode="0">
+ <condition>!context.getBooleanVariable("sys.confirmedUpdateInstallation")</condition>
+ <actions>
+ <action id="11" beanClass="com.install4j.runtime.beans.actions.misc.LoadResponseFileAction" rollbackBarrierExitCode="0" multiExec="true">
+ <serializedBean>
+ <property name="excludedVariables" type="array" elementType="string" length="1">
+ <element index="0">sys.installationDir</element>
+ </property>
+ </serializedBean>
+ <condition>context.getVariable("sys.responseFile") == null</condition>
+ </action>
+ </actions>
+ <formComponents>
+ <formComponent id="9" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetBottom="25">
+ <serializedBean>
+ <property name="labelText" type="string">${i18n:SelectDirLabel(${compiler:sys.fullName})}</property>
+ </serializedBean>
+ </formComponent>
+ <formComponent id="10" beanClass="com.install4j.runtime.beans.formcomponents.InstallationDirectoryChooserComponent" useExternalParametrization="true" externalParametrizationName="Installation Directory Chooser" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="requestFocus" type="boolean" value="true" />
+ </serializedBean>
+ <externalParametrizationPropertyNames>
+ <propertyName>allowSpacesOnUnix</propertyName>
+ <propertyName>checkFreeSpace</propertyName>
+ <propertyName>checkWritable</propertyName>
+ <propertyName>existingDirWarning</propertyName>
+ <propertyName>manualEntryAllowed</propertyName>
+ <propertyName>showFreeDiskSpace</propertyName>
+ <propertyName>showRequiredDiskSpace</propertyName>
+ <propertyName>standardValidation</propertyName>
+ <propertyName>suggestAppDir</propertyName>
+ <propertyName>validateApplicationId</propertyName>
+ <propertyName>validationScript</propertyName>
+ </externalParametrizationPropertyNames>
+ </formComponent>
+ </formComponents>
+ </screen>
+ <screen id="12" beanClass="com.install4j.runtime.beans.screens.ComponentsScreen" enabled="false" rollbackBarrierExitCode="0">
+ <formComponents>
+ <formComponent id="13" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent">
+ <serializedBean>
+ <property name="labelText" type="string">${i18n:SelectComponentsLabel2}</property>
+ </serializedBean>
+ <visibilityScript>!context.isConsole()</visibilityScript>
+ </formComponent>
+ <formComponent id="14" beanClass="com.install4j.runtime.beans.formcomponents.ComponentSelectorComponent" useExternalParametrization="true" externalParametrizationName="Installation Components" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="fillVertical" type="boolean" value="true" />
+ </serializedBean>
+ <externalParametrizationPropertyNames>
+ <propertyName>selectionChangedScript</propertyName>
+ </externalParametrizationPropertyNames>
+ </formComponent>
+ </formComponents>
+ </screen>
+ <screen id="1692" beanClass="com.install4j.runtime.beans.screens.FileAssociationsScreen" rollbackBarrierExitCode="0">
+ <formComponents>
+ <formComponent id="1693" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent">
+ <serializedBean>
+ <property name="labelText" type="string">${i18n:SelectAssociationsLabel}</property>
+ </serializedBean>
+ </formComponent>
+ <formComponent id="1694" beanClass="com.install4j.runtime.beans.formcomponents.FileAssociationsComponent" useExternalParametrization="true" externalParametrizationName="File Associations" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="fillVertical" type="boolean" value="true" />
+ <property name="selectionButtonPosition" type="enum" class="com.install4j.runtime.beans.formcomponents.VerticalDockingPosition" value="TOP" />
+ <property name="showSelectionButtons" type="boolean" value="true" />
+ </serializedBean>
+ <externalParametrizationPropertyNames>
+ <propertyName>showSelectionButtons</propertyName>
+ <propertyName>selectionButtonPosition</propertyName>
+ </externalParametrizationPropertyNames>
+ </formComponent>
+ </formComponents>
+ </screen>
+ <screen id="15" beanClass="com.install4j.runtime.beans.screens.InstallationScreen" rollbackBarrier="true" rollbackBarrierExitCode="0">
+ <actions>
+ <action id="17" beanClass="com.install4j.runtime.beans.actions.InstallFilesAction" actionElevationType="elevated" rollbackBarrierExitCode="0" failureStrategy="quit" errorMessage="${i18n:FileCorrupted}" />
+ <action name="Create program group (RELEASE)" id="18" customizedId="PROGRAM_GROUP_RELEASE" beanClass="com.install4j.runtime.beans.actions.desktop.CreateProgramGroupAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="allUsers" type="boolean" value="false" />
+ <property name="categories" type="string">${compiler:APPLICATION_CATEGORIES}</property>
+ <property name="programGroupEntryConfigs">
+ <add>
+ <object class="com.install4j.runtime.beans.screens.components.ProgramGroupFileConfig">
+ <property name="name" type="string">Examples</property>
+ <property name="target">
+ <object class="java.io.File">
+ <string>examples</string>
+ </object>
+ </property>
+ </object>
+ </add>
+ </property>
+ <property name="programGroupName" type="string">${compiler:JALVIEW_NAME}</property>
+ <property name="uninstallerMenuName" type="string">${i18n:UninstallerMenuEntry(${compiler:sys.fullName})}</property>
+ </serializedBean>
+ <condition>!context.getBooleanVariable("sys.programGroupDisabled")</condition>
+ </action>
+ <action name="Create program group (NON-RELEASE)" id="2730" customizedId="PROGRAM_GROUP_NON_RELEASE" beanClass="com.install4j.runtime.beans.actions.desktop.CreateProgramGroupAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="allUsers" type="boolean" value="false" />
+ <property name="categories" type="string">${compiler:APPLICATION_CATEGORIES}</property>
+ <property name="programGroupName" type="string">${compiler:JALVIEW_NAME}</property>
+ <property name="uninstallerMenuName" type="string">${i18n:UninstallerMenuEntry(${compiler:sys.fullName})}</property>
+ </serializedBean>
+ <condition>!context.getBooleanVariable("sys.programGroupDisabled")</condition>
+ </action>
+ <action id="19" beanClass="com.install4j.runtime.beans.actions.desktop.RegisterAddRemoveAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="itemName" type="string">${compiler:sys.fullName} ${compiler:sys.version}</property>
+ </serializedBean>
+ </action>
+ <action id="124" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" enabled="false" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string" />
+ </object>
+ </property>
+ <property name="variableName" type="string" />
+ </serializedBean>
+ <condition>true</condition>
+ </action>
+ <action id="134" beanClass="com.install4j.runtime.beans.actions.misc.AddVmOptionsAction" enabled="false" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">121</property>
+ <property name="vmOptions" type="array" elementType="string" length="0" />
+ </serializedBean>
+ </action>
+ <group name="File Associations" id="2251" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
+ <beans>
+ <action id="2253" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="statusMessage" type="string">Creating file associations...</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+ <action id="2254" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="progressChangeType" type="enum" class="com.install4j.runtime.beans.actions.control.ProgressChangeType" value="SET_INDETERMINATE" />
+ </serializedBean>
+ </action>
+ <group name="File Associations Replacement Group" id="2753" customizedId="EXTENSIONS_REPLACED_BY_GRADLE_PARENT_GROUP" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
+ <beans>
+ <action name="EXTENSIONS_REPLACED_BY_GRADLE" id="1691" customizedId="EXTENSIONS" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="description" type="string">This action, identified by its name "EXTENSIONS_REPLACED_BY_GRADLE", will be replaced by gradle with the contents of file 'file_associations_auto_install4j.xml'.</property>
+ <property name="extension" type="string">extensions_to_be_replaced_by_gradle</property>
+ <property name="launcherId" type="string">JALVIEW</property>
+ </serializedBean>
+ </action>
+ </beans>
+ </group>
+ <action id="2542" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="statusMessage" type="string">Finished creating file associations</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+ <action id="2541" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="100" />
+ </serializedBean>
+ </action>
+ </beans>
+ </group>
+ <action id="2350" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <property name="scheme" type="string">jalview</property>
+ </serializedBean>
+ </action>
+ <action id="2450" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <property name="scheme" type="string">jalviews</property>
+ </serializedBean>
+ </action>
+ <action id="2641" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">JALVIEW</property>
+ <property name="scheme" type="string">${compiler:EXTRA_SCHEME}</property>
+ </serializedBean>
+ </action>
+ </actions>
+ <formComponents>
+ <formComponent id="16" beanClass="com.install4j.runtime.beans.formcomponents.ProgressComponent">
+ <serializedBean>
+ <property name="initialStatusMessage" type="string">${i18n:WizardPreparing}</property>
+ </serializedBean>
+ </formComponent>
+ </formComponents>
+ </screen>
+ <screen id="20" beanClass="com.install4j.runtime.beans.screens.FinishedScreen" rollbackBarrierExitCode="0" finishScreen="true">
+ <actions>
+ <action id="2012" beanClass="com.install4j.runtime.beans.actions.desktop.CreateStartMenuEntryAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="allUsers" type="boolean" value="false" />
+ <property name="categories" type="string">${compiler:APPLICATION_CATEGORIES}</property>
+ <property name="entryName" type="string">${compiler:JALVIEW_APPLICATION_NAME}</property>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${installer:sys.contentDir}/${compiler:EXECUTABLE_NAME}</string>
+ </object>
+ </property>
+ <property name="icon">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}</string>
+ </object>
+ </property>
+ <property name="programGroupName" type="string">${compiler:JALVIEW_NAME}</property>
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:PNG_ICON_FILE}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>!context.getBooleanVariable("sys.programGroupDisabled")</condition>
+ </action>
+ <action id="573" beanClass="com.install4j.runtime.beans.actions.desktop.CreateDesktopLinkAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make desktop link">
+ <serializedBean>
+ <property name="allUsers" type="boolean" value="false" />
+ <property name="description" type="string">${compiler:JALVIEW_APPLICATION_NAME}</property>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${installer:sys.contentDir}/${compiler:EXECUTABLE_NAME}</string>
+ </object>
+ </property>
+ <property name="name" type="string">${compiler:JALVIEW_APPLICATION_NAME}</property>
+ <property name="unixIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:PNG_ICON_FILE}</string>
+ </object>
+ </property>
+ <property name="winIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:WINDOWS_ICONS_FILE}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("createDesktopLinkAction")</condition>
+ </action>
+ <action id="576" beanClass="com.install4j.runtime.beans.actions.desktop.AddToDockAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="executable">
+ <object class="java.io.File">
+ <string>${compiler:JALVIEW_APPLICATION_NAME}.app</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("addToDockAction")</condition>
+ </action>
+ <action name="Linux/Unix symlink" id="2733" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make symlink to wrapper script">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>Util.isLinux() || Util.isUnixInstaller() || Util.isMacOS()</condition>
+ </action>
+ <action name="Add Jalview bin to the user's path (Windows)" id="2740" beanClass="com.install4j.runtime.beans.actions.misc.ModifyEnvironmentVariableAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not add "${installer:sys.contentDir}\${compiler:WRAPPER_SCRIPT_BIN_DIR}" to the Path environment variable">
+ <serializedBean>
+ <property name="type" type="enum" class="com.install4j.runtime.beans.actions.misc.ModifyStringType" value="APPEND" />
+ <property name="value" type="string">${installer:sys.contentDir}\${compiler:WRAPPER_SCRIPT_BIN_DIR}</property>
+ <property name="variableName" type="string">Path</property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("appendToPathAction")</condition>
+ </action>
+ <action name="Create Linux/Unix symbolic link to jalview.sh in user's local bin" id="2739" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixUserBinDir}">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${installer:sys.contentDir}/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${installer:unixUserBinDir}/${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("makeSymbolicLinkAction") && ( Util.isLinux() || Util.isUnixInstaller() ) && ( context.getVariable("unixUserBinDir") != null )</condition>
+ </action>
+ <action name="Create macOS symbolic link to jalview in user's local bin" id="2743" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixUserBinDir}">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${installer:macWrapperLinkLocation}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${installer:unixUserBinDir}/${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("makeSymbolicLinkAction") && Util.isMacOS() && ( context.getVariable("unixUserBinDir") != null ) && ( context.getVariable("macWrapperLinkLocation") != null )</condition>
+ </action>
+ </actions>
+ <formComponents>
+ <formComponent id="21" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetBottom="10">
+ <serializedBean>
+ <property name="labelText" type="string">${form:finishedMessage}</property>
+ </serializedBean>
+ </formComponent>
+ <formComponent name="Add a desktop link" id="574" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">${i18n:CreateDesktopIcon}</property>
+ <property name="initiallySelected" type="boolean" value="true" />
+ <property name="variableName" type="string">createDesktopLinkAction</property>
+ </serializedBean>
+ <visibilityScript>!Util.isMacOS()</visibilityScript>
+ </formComponent>
+ <formComponent name="Add an executable to the dock" id="577" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">${i18n:AddToDock}</property>
+ <property name="initiallySelected" type="boolean" value="true" />
+ <property name="variableName" type="string">addToDockAction</property>
+ </serializedBean>
+ <visibilityScript>Util.isMacOS()</visibilityScript>
+ </formComponent>
+ <formComponent name="Add jalview bin to the user's Path environment variable (Windows)" id="2734" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">Add ${compiler:JALVIEW_APPLICATION_NAME}'s bin folder to the Path environment variable</property>
+ <property name="initiallySelected" type="boolean" value="true" />
+ <property name="variableName" type="string">appendToPathAction</property>
+ </serializedBean>
+ <visibilityScript>Util.isWindows()</visibilityScript>
+ </formComponent>
+ <formComponent name="Make a symbolic link to jalview.sh bash script in the user's local bin (Linux or Unix)" id="2736" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">Make a ${compiler:WRAPPER_LINK} symbolic link in ${installer:unixUserBinDir}</property>
+ <property name="initiallySelected" type="boolean" value="true" />
+ <property name="variableName" type="string">makeSymbolicLinkAction</property>
+ </serializedBean>
+ <visibilityScript>( Util.isLinux() || Util.isUnixInstaller() || ( Util.isMacOS() && ( context.getVariable("macWrapperLinkLocation") != null ) ) ) && ( context.getVariable("unixUserBinDir") != null )</visibilityScript>
+ </formComponent>
+ </formComponents>
+ </screen>
+ </screens>
+ </application>
+ <application id="uninstaller" beanClass="com.install4j.runtime.beans.applications.UninstallerApplication" styleId="35">
+ <serializedBean>
+ <property name="customMacosExecutableName" type="string">${i18n:UninstallerMenuEntry(${compiler:sys.fullName})}</property>
+ <property name="useCustomMacosExecutableName" type="boolean" value="true" />
+ </serializedBean>
+ <styleOverrides>
+ <styleOverride name="Customize banner image" enabled="true">
+ <group id="147" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup" useExternalParametrization="true" externalParametrizationName="Customize banner image" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="backgroundColor">
+ <object class="com.install4j.runtime.beans.LightOrDarkColor">
+ <object class="java.awt.Color">
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ </object>
+ <object class="java.awt.Color">
+ <int>49</int>
+ <int>52</int>
+ <int>53</int>
+ <int>255</int>
+ </object>
+ </object>
+ </property>
+ <property name="borderSides">
+ <object class="com.install4j.runtime.beans.formcomponents.BorderSides">
+ <property name="bottom" type="boolean" value="true" />
+ </object>
+ </property>
+ <property name="imageEdgeBackgroundColor">
+ <object class="java.awt.Color">
+ <int>192</int>
+ <int>192</int>
+ <int>192</int>
+ <int>255</int>
+ </object>
+ </property>
+ <property name="imageEdgeBorder" type="boolean" value="true" />
+ <property name="imageFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:BACKGROUND}</string>
+ </object>
+ </property>
+ <property name="insets">
+ <object class="java.awt.Insets">
+ <int>5</int>
+ <int>10</int>
+ <int>10</int>
+ <int>10</int>
+ </object>
+ </property>
+ </serializedBean>
+ <externalParametrizationPropertyNames>
+ <propertyName>imageAnchor</propertyName>
+ <propertyName>imageEdgeBackgroundColor</propertyName>
+ <propertyName>imageFile</propertyName>
+ </externalParametrizationPropertyNames>
+ </group>
+ </styleOverride>
+ </styleOverrides>
+ <startup>
+ <screen id="23" beanClass="com.install4j.runtime.beans.screens.StartupScreen" rollbackBarrierExitCode="0">
+ <actions>
+ <action id="33" beanClass="com.install4j.runtime.beans.actions.misc.LoadResponseFileAction" rollbackBarrierExitCode="0" />
+ <action id="34" beanClass="com.install4j.runtime.beans.actions.misc.RequireInstallerPrivilegesAction" actionElevationType="none" rollbackBarrierExitCode="0" />
+ </actions>
+ </screen>
+ </startup>
+ <screens>
+ <screen id="24" beanClass="com.install4j.runtime.beans.screens.UninstallWelcomeScreen" rollbackBarrierExitCode="0">
+ <formComponents>
+ <formComponent id="25" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetBottom="10">
+ <serializedBean>
+ <property name="labelText" type="string">${form:welcomeMessage}</property>
+ </serializedBean>
+ <visibilityScript>!context.isConsole()</visibilityScript>
+ </formComponent>
+ <formComponent id="26" beanClass="com.install4j.runtime.beans.formcomponents.ConsoleHandlerFormComponent">
+ <serializedBean>
+ <property name="consoleScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">String message = context.getMessage("ConfirmUninstall", context.getApplicationName());
+return console.askYesNo(message, true);
+</property>
+ </object>
+ </property>
+ </serializedBean>
+ </formComponent>
+ </formComponents>
+ </screen>
+ <screen id="27" beanClass="com.install4j.runtime.beans.screens.UninstallationScreen" rollbackBarrierExitCode="0">
+ <actions>
+ <action id="659" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="progressChangeType" type="enum" class="com.install4j.runtime.beans.actions.control.ProgressChangeType" value="SET_INDETERMINATE" />
+ </serializedBean>
+ </action>
+ <action id="29" beanClass="com.install4j.runtime.beans.actions.UninstallFilesAction" actionElevationType="elevated" rollbackBarrierExitCode="0" />
+ <action id="660" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" enabled="false" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="95" />
+ </serializedBean>
+ </action>
+ <action id="1525" beanClass="com.install4j.runtime.beans.actions.files.DeleteFileAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="files" type="array" class="java.io.File" length="40">
+ <element index="0">
+ <object class="java.io.File">
+ <string>jre</string>
+ </object>
+ </element>
+ <element index="1">
+ <object class="java.io.File">
+ <string>jre.jar</string>
+ </object>
+ </element>
+ <element index="2">
+ <object class="java.io.File">
+ <string>.install4j</string>
+ </object>
+ </element>
+ <element index="3">
+ <object class="java.io.File">
+ <string>getdown-launcher.jar</string>
+ </object>
+ </element>
+ <element index="4">
+ <object class="java.io.File">
+ <string>getdown-launcher-old.jar</string>
+ </object>
+ </element>
+ <element index="5">
+ <object class="java.io.File">
+ <string>getdown-launcher-new.jar</string>
+ </object>
+ </element>
+ <element index="6">
+ <object class="java.io.File">
+ <string>gettingdown.lock</string>
+ </object>
+ </element>
+ <element index="7">
+ <object class="java.io.File">
+ <string>jre.zip</string>
+ </object>
+ </element>
+ <element index="8">
+ <object class="java.io.File">
+ <string>digest.txt</string>
+ </object>
+ </element>
+ <element index="9">
+ <object class="java.io.File">
+ <string>digest2.txt</string>
+ </object>
+ </element>
+ <element index="10">
+ <object class="java.io.File">
+ <string>getdown-launcher.jarv</string>
+ </object>
+ </element>
+ <element index="11">
+ <object class="java.io.File">
+ <string>getdown-launcher-new.jarv</string>
+ </object>
+ </element>
+ <element index="12">
+ <object class="java.io.File">
+ <string>launcher.log</string>
+ </object>
+ </element>
+ <element index="13">
+ <object class="java.io.File">
+ <string>proxy.txt</string>
+ </object>
+ </element>
+ <element index="14">
+ <object class="java.io.File">
+ <string>build_properties</string>
+ </object>
+ </element>
+ <element index="15">
+ <object class="java.io.File">
+ <string>channel_launch*.jvl</string>
+ </object>
+ </element>
+ <element index="16">
+ <object class="java.io.File">
+ <string>jalview*.jvl</string>
+ </object>
+ </element>
+ <element index="17">
+ <object class="java.io.File">
+ <string>*.jarv</string>
+ </object>
+ </element>
+ <element index="18">
+ <object class="java.io.File">
+ <string>*.log</string>
+ </object>
+ </element>
+ <element index="19">
+ <object class="java.io.File">
+ <string>*.txt</string>
+ </object>
+ </element>
+ <element index="20">
+ <object class="java.io.File">
+ <string>*_new</string>
+ </object>
+ </element>
+ <element index="21">
+ <object class="java.io.File">
+ <string>hs_err_*.*</string>
+ </object>
+ </element>
+ <element index="22">
+ <object class="java.io.File">
+ <string>${compiler:GETDOWN_DIST_DIR}</string>
+ </object>
+ </element>
+ <element index="23">
+ <object class="java.io.File">
+ <string>${compiler:GETDOWN_ALT_DIR}</string>
+ </object>
+ </element>
+ <element index="24">
+ <object class="java.io.File">
+ <string>${compiler:GETDOWN_RESOURCE_DIR}</string>
+ </object>
+ </element>
+ <element index="25">
+ <object class="java.io.File">
+ <string>META-INF</string>
+ </object>
+ </element>
+ <element index="26">
+ <object class="java.io.File">
+ <string>install</string>
+ </object>
+ </element>
+ <element index="27">
+ <object class="java.io.File">
+ <string>resource</string>
+ </object>
+ </element>
+ <element index="28">
+ <object class="java.io.File">
+ <string>dist</string>
+ </object>
+ </element>
+ <element index="29">
+ <object class="java.io.File">
+ <string>release</string>
+ </object>
+ </element>
+ <element index="30">
+ <object class="java.io.File">
+ <string>alt</string>
+ </object>
+ </element>
+ <element index="31">
+ <object class="java.io.File">
+ <string>dev</string>
+ </object>
+ </element>
+ <element index="32">
+ <object class="java.io.File">
+ <string>build</string>
+ </object>
+ </element>
+ <element index="33">
+ <object class="java.io.File">
+ <string>alt_*</string>
+ </object>
+ </element>
+ <element index="34">
+ <object class="java.io.File">
+ <string>dev_*</string>
+ </object>
+ </element>
+ <element index="35">
+ <object class="java.io.File">
+ <string>build_*</string>
+ </object>
+ </element>
+ <element index="36">
+ <object class="java.io.File">
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}</string>
+ </object>
+ </element>
+ <element index="37">
+ <object class="java.io.File">
+ <string>bin</string>
+ </object>
+ </element>
+ <element index="38">
+ <object class="java.io.File">
+ <string>channel.props</string>
+ </object>
+ </element>
+ <element index="39">
+ <object class="java.io.File">
+ <string>channel.propsv</string>
+ </object>
+ </element>
+ </property>
+ <property name="recursive" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+ <action id="1791" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="100" />
+ </serializedBean>
+ </action>
+ </actions>
+ <formComponents>
+ <formComponent id="28" beanClass="com.install4j.runtime.beans.formcomponents.ProgressComponent">
+ <serializedBean>
+ <property name="initialStatusMessage" type="string">${i18n:UninstallerPreparing}</property>
+ </serializedBean>
+ </formComponent>
+ </formComponents>
+ </screen>
+ <screen id="32" beanClass="com.install4j.runtime.beans.screens.UninstallFailureScreen" rollbackBarrierExitCode="0" finishScreen="true" />
+ <screen id="30" beanClass="com.install4j.runtime.beans.screens.UninstallSuccessScreen" styleId="41" rollbackBarrierExitCode="0" finishScreen="true">
+ <formComponents>
+ <formComponent id="31" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetBottom="10">
+ <serializedBean>
+ <property name="labelText" type="string">${form:successMessage}</property>
+ </serializedBean>
+ </formComponent>
+ </formComponents>
+ </screen>
+ </screens>
+ </application>
+ <application name="MacOS Setup" id="2746" beanClass="com.install4j.runtime.beans.applications.CustomApplication" fileset="734" macEntitlementsFile="${compiler:JALVIEW_DIR}/utils/osx_signing/entitlements.txt">
+ <serializedBean>
+ <property name="executableDirectory">
+ <object class="java.io.File">
+ <string>.</string>
+ </object>
+ </property>
+ <property name="executableName" type="string">${compiler:WRAPPER_LINK}_setup</property>
+ <property name="windowTitle" type="string">${compiler:sys.fullName}</property>
+ </serializedBean>
+ <startup>
+ <screen id="2747" beanClass="com.install4j.runtime.beans.screens.StartupScreen" rollbackBarrierExitCode="0">
+ <actions>
+ <link id="2749" targetId="22" />
+ <link id="2750" targetId="2738" />
+ <link id="2751" targetId="2745" />
+ </actions>
+ </screen>
+ </startup>
+ <screens>
+ <screen id="2772" beanClass="com.install4j.runtime.beans.screens.FormScreen" rollbackBarrierExitCode="0" backButton="hidden" finishScreen="true">
+ <serializedBean>
+ <property name="title" type="string">Running ${i18n:SetupAppTitle}</property>
+ </serializedBean>
+ <actions>
+ <link id="2778" targetId="576" />
+ <link id="2779" targetId="2743" />
+ </actions>
+ <formComponents>
+ <formComponent id="2773" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetBottom="10">
+ <serializedBean>
+ <property name="labelText" type="string">${i18n:FinishedLabel(${compiler:JALVIEW_APPLICATION_NAME})}</property>
+ </serializedBean>
+ </formComponent>
+ <formComponent name="Add an executable to the dock" id="2775" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">${i18n:AddToDock}</property>
+ <property name="initiallySelected" type="boolean" value="true" />
+ <property name="variableName" type="string">addToDockAction</property>
+ </serializedBean>
+ <visibilityScript>Util.isMacOS()</visibilityScript>
+ </formComponent>
+ <formComponent name="Make a symbolic link to jalview.sh bash script in the user's local bin (Linux or Unix)" id="2777" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">Make a ${compiler:WRAPPER_LINK} symbolic link in ${installer:unixUserBinDir}</property>
+ <property name="initiallySelected" type="boolean" value="true" />
+ <property name="variableName" type="string">makeSymbolicLinkAction</property>
+ </serializedBean>
+ <visibilityScript>( Util.isLinux() || Util.isUnixInstaller() || ( Util.isMacOS() && ( context.getVariable("macWrapperLinkLocation") != null ) ) ) && ( context.getVariable("unixUserBinDir") != null )</visibilityScript>
+ </formComponent>
+ <formComponent id="2780" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent">
+ <serializedBean>
+ <property name="labelText" type="string">
+${i18n:ClickFinish}
+
+${compiler:JALVIEW_APPLICATION_NAME} will now launch.</property>
+ </serializedBean>
+ </formComponent>
+ </formComponents>
+ </screen>
+ </screens>
+ </application>
+ </applications>
+ <styles defaultStyleId="35">
+ <style name="Standard" id="35" beanClass="com.install4j.runtime.beans.styles.FormStyle">
+ <formComponents>
+ <formComponent name="Header" id="36" beanClass="com.install4j.runtime.beans.styles.NestedStyleComponent" insetTop="0" insetBottom="0">
+ <serializedBean>
+ <property name="styleId" type="string">48</property>
+ </serializedBean>
+ </formComponent>
+ <group name="Main" id="37" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup">
+ <serializedBean>
+ <property name="imageEdgeAxisType" type="enum" class="com.install4j.runtime.beans.formcomponents.AxisType" value="HORIZONTAL" />
+ <property name="imageEdgeBackgroundColor">
+ <object class="java.awt.Color">
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ </object>
+ </property>
+ <property name="imageFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:BACKGROUND}</string>
+ </object>
+ </property>
+ <property name="imageOverlap" type="boolean" value="true" />
+ </serializedBean>
+ <beans>
+ <formComponent id="38" beanClass="com.install4j.runtime.beans.styles.ContentComponent" insetTop="10" insetLeft="20" insetBottom="10" insetRight="20" />
+ <formComponent name="Watermark" id="39" beanClass="com.install4j.runtime.beans.formcomponents.SeparatorComponent" insetTop="0" insetLeft="5" insetBottom="0" useExternalParametrization="true" externalParametrizationName="${compiler:JALVIEW_APPLICATION_NAME}" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="enabledTitleText" type="boolean" value="false" />
+ </serializedBean>
+ <externalParametrizationPropertyNames>
+ <propertyName>labelText</propertyName>
+ </externalParametrizationPropertyNames>
+ </formComponent>
+ <formComponent name="Footer" id="40" beanClass="com.install4j.runtime.beans.styles.NestedStyleComponent" insetTop="0" insetBottom="0">
+ <serializedBean>
+ <property name="styleId" type="string">52</property>
+ </serializedBean>
+ </formComponent>
+ </beans>
+ </group>
+ </formComponents>
+ </style>
+ <style name="Banner" id="41" beanClass="com.install4j.runtime.beans.styles.FormStyle">
+ <formComponents>
+ <group id="42" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup" useExternalParametrization="true" externalParametrizationName="Customize banner image" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="backgroundColor">
+ <object class="com.install4j.runtime.beans.LightOrDarkColor">
+ <object class="java.awt.Color">
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ </object>
+ <object class="java.awt.Color">
+ <int>49</int>
+ <int>52</int>
+ <int>53</int>
+ <int>255</int>
+ </object>
+ </object>
+ </property>
+ <property name="borderSides">
+ <object class="com.install4j.runtime.beans.formcomponents.BorderSides">
+ <property name="bottom" type="boolean" value="true" />
+ </object>
+ </property>
+ <property name="imageEdgeBackgroundColor">
+ <object class="com.install4j.runtime.beans.LightOrDarkColor">
+ <object class="java.awt.Color">
+ <int>25</int>
+ <int>143</int>
+ <int>220</int>
+ <int>255</int>
+ </object>
+ <object class="java.awt.Color">
+ <int>0</int>
+ <int>74</int>
+ <int>151</int>
+ <int>255</int>
+ </object>
+ </object>
+ </property>
+ <property name="imageEdgeBorder" type="boolean" value="true" />
+ <property name="imageFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:sys.install4jHome}/resource/styles/wizard.png</string>
+ </object>
+ </property>
+ <property name="insets">
+ <object class="java.awt.Insets">
+ <int>5</int>
+ <int>10</int>
+ <int>10</int>
+ <int>10</int>
+ </object>
+ </property>
+ </serializedBean>
+ <beans>
+ <formComponent id="43" beanClass="com.install4j.runtime.beans.styles.ScreenTitleComponent" insetTop="0">
+ <serializedBean>
+ <property name="labelFontSizePercent" type="int" value="130" />
+ <property name="labelFontStyle" type="enum" class="com.install4j.runtime.beans.formcomponents.FontStyle" value="BOLD" />
+ <property name="labelFontType" type="enum" class="com.install4j.runtime.beans.formcomponents.FontType" value="DERIVED" />
+ </serializedBean>
+ </formComponent>
+ <formComponent id="44" beanClass="com.install4j.runtime.beans.formcomponents.SeparatorComponent" />
+ <formComponent id="45" beanClass="com.install4j.runtime.beans.styles.ContentComponent" insetTop="10" insetBottom="0" />
+ </beans>
+ <externalParametrizationPropertyNames>
+ <propertyName>imageAnchor</propertyName>
+ <propertyName>imageEdgeBackgroundColor</propertyName>
+ <propertyName>imageFile</propertyName>
+ </externalParametrizationPropertyNames>
+ </group>
+ <formComponent id="46" beanClass="com.install4j.runtime.beans.styles.NestedStyleComponent" insetBottom="0">
+ <serializedBean>
+ <property name="styleId" type="string">52</property>
+ </serializedBean>
+ </formComponent>
+ </formComponents>
+ </style>
+ <group name="Style components" id="47" beanClass="com.install4j.runtime.beans.groups.StyleGroup">
+ <beans>
+ <style name="Standard header" id="48" beanClass="com.install4j.runtime.beans.styles.FormStyle">
+ <serializedBean>
+ <property name="fillVertical" type="boolean" value="false" />
+ <property name="standalone" type="boolean" value="false" />
+ <property name="verticalAnchor" type="enum" class="com.install4j.api.beans.Anchor" value="NORTH" />
+ </serializedBean>
+ <formComponents>
+ <group id="49" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup" useExternalParametrization="true" externalParametrizationName="Customize title bar" externalParametrizationMode="include">
+ <serializedBean>
+ <property name="backgroundColor">
+ <object class="com.install4j.runtime.beans.LightOrDarkColor">
+ <object class="java.awt.Color">
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ <int>255</int>
+ </object>
+ <object class="java.awt.Color">
+ <int>49</int>
+ <int>52</int>
+ <int>53</int>
+ <int>255</int>
+ </object>
+ </object>
+ </property>
+ <property name="borderSides">
+ <object class="com.install4j.runtime.beans.formcomponents.BorderSides">
+ <property name="bottom" type="boolean" value="true" />
+ </object>
+ </property>
+ <property name="imageAnchor" type="enum" class="com.install4j.api.beans.Anchor" value="NORTHEAST" />
+ <property name="imageEdgeBorderWidth" type="int" value="2" />
+ <property name="imageFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>icon:${installer:sys.installerApplicationMode}_header.png</string>
+ </object>
+ </property>
+ <property name="imageInsets">
+ <object class="java.awt.Insets">
+ <int>0</int>
+ <int>5</int>
+ <int>1</int>
+ <int>1</int>
+ </object>
+ </property>
+ <property name="insets">
+ <object class="java.awt.Insets">
+ <int>0</int>
+ <int>20</int>
+ <int>0</int>
+ <int>10</int>
+ </object>
+ </property>
+ </serializedBean>
+ <beans>
+ <formComponent name="Title" id="50" beanClass="com.install4j.runtime.beans.styles.ScreenTitleComponent">
+ <serializedBean>
+ <property name="labelFontStyle" type="enum" class="com.install4j.runtime.beans.formcomponents.FontStyle" value="BOLD" />
+ <property name="labelFontType" type="enum" class="com.install4j.runtime.beans.formcomponents.FontType" value="DERIVED" />
+ </serializedBean>
+ </formComponent>
+ <formComponent name="Subtitle" id="51" beanClass="com.install4j.runtime.beans.styles.ScreenTitleComponent" insetLeft="8">
+ <serializedBean>
+ <property name="titleType" type="enum" class="com.install4j.runtime.beans.styles.TitleType" value="SUB_TITLE" />
+ </serializedBean>
+ </formComponent>
+ </beans>
+ <externalParametrizationPropertyNames>
+ <propertyName>backgroundColor</propertyName>
+ <propertyName>foregroundColor</propertyName>
+ <propertyName>imageAnchor</propertyName>
+ <propertyName>imageFile</propertyName>
+ <propertyName>imageOverlap</propertyName>
+ </externalParametrizationPropertyNames>
+ </group>
+ </formComponents>
+ </style>
+ <style name="Standard footer" id="52" beanClass="com.install4j.runtime.beans.styles.FormStyle">
+ <serializedBean>
+ <property name="fillVertical" type="boolean" value="false" />
+ <property name="standalone" type="boolean" value="false" />
+ <property name="verticalAnchor" type="enum" class="com.install4j.api.beans.Anchor" value="SOUTH" />
+ </serializedBean>
+ <formComponents>
+ <group id="53" beanClass="com.install4j.runtime.beans.groups.HorizontalFormComponentGroup">
+ <serializedBean>
+ <property name="alignFirstLabel" type="boolean" value="false" />
+ <property name="insets">
+ <object class="java.awt.Insets">
+ <int>3</int>
+ <int>5</int>
+ <int>8</int>
+ <int>5</int>
+ </object>
+ </property>
+ </serializedBean>
+ <beans>
+ <formComponent id="54" beanClass="com.install4j.runtime.beans.formcomponents.SpringComponent" />
+ <formComponent name="Back button" id="55" beanClass="com.install4j.runtime.beans.styles.StandardControlButtonComponent">
+ <serializedBean>
+ <property name="buttonText" type="string">< ${i18n:ButtonBack}</property>
+ <property name="controlButtonType" type="enum" class="com.install4j.api.context.ControlButtonType" value="PREVIOUS" />
+ </serializedBean>
+ </formComponent>
+ <formComponent name="Next button" id="56" beanClass="com.install4j.runtime.beans.styles.StandardControlButtonComponent">
+ <serializedBean>
+ <property name="buttonText" type="string">${i18n:ButtonNext} ></property>
+ <property name="controlButtonType" type="enum" class="com.install4j.api.context.ControlButtonType" value="NEXT" />
+ </serializedBean>
+ </formComponent>
+ <formComponent name="Cancel button" id="57" beanClass="com.install4j.runtime.beans.styles.StandardControlButtonComponent" insetLeft="5">
+ <serializedBean>
+ <property name="buttonText" type="string">${i18n:ButtonCancel}</property>
+ <property name="controlButtonType" type="enum" class="com.install4j.api.context.ControlButtonType" value="CANCEL" />
+ </serializedBean>
+ </formComponent>
+ </beans>
+ </group>
+ </formComponents>
+ </style>
+ </beans>
+ </group>
+ </styles>
+ </installerGui>
+ <mediaSets>
+ <windows name="Windows x64 EXE Installer" id="743" customizedId="WINDOWS-X64-EXE" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:APPLICATION_FOLDER}" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" customInstallBaseDir="~/AppData/Local" architecture="64">
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
+ <exclude>
+ <entry defaultFileset="true" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
+ </exclude>
+ <jreBundle jreBundleSource="preCreated" includedJre="${compiler:WINDOWS_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
+ </windows>
+ <macosArchive name="macOS x64 Disk Image" id="878" customizedId="MACOS-X64-DMG" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-macOS-x64-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" volumeName="${compiler:INSTALLER_NAME}" launcherId="737" setupAppId="2746">
+ <exclude>
+ <entry defaultFileset="true" />
+ <entry filesetId="2803" />
+ </exclude>
+ <jreBundle jreBundleSource="none" includedJre="${compiler:MACOS_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
+ <topLevelFiles>
+ <symlink name="" "" target="/Applications" />
+ <file name=".background/jalview_dmg_background.png" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_BG_IMAGE}" />
+ <file name=".DS_Store" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_DS_STORE}" />
+ <file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/Jalview-File.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Jalview-File.icns" />
+ <file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/jvl_file.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/jvl_file.icns" />
+ <symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/${compiler:WRAPPER_LINK}" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}" />
+ </topLevelFiles>
+ </macosArchive>
+ <macosArchive name="macOS aarch64 Disk Image" id="2796" customizedId="MACOS-AARCH64-DMG" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-macOS-aarch64-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" volumeName="${compiler:INSTALLER_NAME}" architecture="aarch64" launcherId="737" setupAppId="2746">
+ <exclude>
+ <entry defaultFileset="true" />
+ <entry filesetId="2801" />
+ </exclude>
+ <jreBundle jreBundleSource="none" />
+ <topLevelFiles>
+ <symlink name="" "" target="/Applications" />
+ <file name=".background/jalview_dmg_background.png" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_BG_IMAGE}" />
+ <file name=".DS_Store" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_DS_STORE}" />
+ <file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/Jalview-File.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Jalview-File.icns" />
+ <file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/jvl_file.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/jvl_file.icns" />
+ <symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/${compiler:WRAPPER_LINK}" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}" />
+ </topLevelFiles>
+ </macosArchive>
+ <unixInstaller name="Linux x64 Shell Installer" id="1595" customizedId="LINUX-X64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux-x64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
+ <exclude>
+ <entry defaultFileset="true" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
+ </exclude>
+ <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
+ </unixInstaller>
+ <unixInstaller name="Linux aarch64 Shell Installer" id="2782" customizedId="LINUX-AARCH64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux-aarch64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
+ <exclude>
+ <entry defaultFileset="true" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
+ </exclude>
+ <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_AARCH64_JAVA_VM_TGZ}" manualJreEntry="true" />
+ </unixInstaller>
+ <unixArchive name="Unix .tar.gz Archive" id="1596" customizedId="UNIX--TGZ" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}">
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
+ <exclude>
+ <entry defaultFileset="true" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
+ </exclude>
+ <jreBundle jreBundleSource="none" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
+ </unixArchive>
+ <unixInstaller name="Unix Shell Installer" id="2639" customizedId="UNIX--SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
+ <exclude>
+ <entry defaultFileset="true" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
+ </exclude>
+ <jreBundle jreBundleSource="none" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
+ </unixInstaller>
+ </mediaSets>
+ <buildIds>
+ <mediaSet refId="743" />
+ <mediaSet refId="878" />
+ <mediaSet refId="2796" />
+ <mediaSet refId="1595" />
+ <mediaSet refId="2782" />
+ <mediaSet refId="1596" />
+ <mediaSet refId="2639" />
+ </buildIds>
+</install4j>
<?xml version="1.0" encoding="UTF-8"?>
-<install4j version="9.0.5" transformSequenceNumber="9">
+<install4j version="9.0.7" transformSequenceNumber="9">
<directoryPresets config="bin/jalview" />
<application name="${compiler:JALVIEW_APPLICATION_NAME}" applicationId="${compiler:WINDOWS_APPLICATION_ID}" mediaDir="${compiler:BUILD_DIR}" lzmaCompression="true" shortName="${compiler:INTERNAL_ID}" publisher="University of Dundee" publisherWeb="https://www.jalview.org/" version="${compiler:JALVIEW_VERSION}" allPathsRelative="true" macVolumeId="5aac4968c304f65" javaMinVersion="${compiler:JAVA_MIN_VERSION}" javaMaxVersion="${compiler:JAVA_MAX_VERSION}" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
<searchSequence>
<variable name="JAVA_VERSION" value="11" />
<variable name="JAVA_INTEGER_VERSION" value="11" />
<variable name="VERSION" value="DEVELOPMENT" />
- <variable name="MACOS_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-mac-x64/jre" />
- <variable name="WINDOWS_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-windows-x64/jre" />
- <variable name="LINUX_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-linux-x64/jre" />
- <variable name="MACOS_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_mac_x64.tar.gz" />
- <variable name="WINDOWS_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_windows_x64.tar.gz" />
- <variable name="LINUX_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_linux_x64.tar.gz" />
+ <variable name="MACOS_X64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-mac-x64/jre" />
+ <variable name="MACOS_AARCH64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-mac-aarch64/jre" />
+ <variable name="WINDOWS_X64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-windows-x64/jre" />
+ <variable name="LINUX_X64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-linux-x64/jre" />
+ <variable name="LINUX_AARCH64_JAVA_VM_DIR" value="${compiler:env.HOME}/buildtools/jre/jre-${compiler:JAVA_INTEGER_VERSION}-linux-aarch64/jre" />
+ <variable name="MACOS_X64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_mac_x64.tar.gz" />
+ <variable name="MACOS_AARCH64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_mac_aarch64.tar.gz" />
+ <variable name="WINDOWS_X64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_windows_x64.tar.gz" />
+ <variable name="LINUX_X64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_linux_x64.tar.gz" />
+ <variable name="LINUX_AARCH64_JAVA_VM_TGZ" value="${compiler:env.HOME}/buildtools/jre/tgz/jre_${compiler:JAVA_INTEGER_VERSION}_linux_aarch64.tar.gz" />
<variable name="COPYRIGHT_MESSAGE" value="..." />
<variable name="BUNDLE_ID" value="org.jalview.jalview-desktop" />
<variable name="INTERNAL_ID" value="Jalview" />
<variable name="WINDOWS_APPLICATION_ID" value="6595-2347-1923-0725" />
- <variable name="MACOS_DMG_DS_STORE" value="jalview_dmg_DS_Store" />
- <variable name="MACOS_DMG_BG_IMAGE" value="jalview_dmg_background-72dpi.png" />
+ <variable name="MACOS_DMG_DS_STORE" value="utils/channels/default/images/jalview_default_dmg_DS_Store" />
+ <variable name="MACOS_DMG_BG_IMAGE" value="utils/channels/default/images/jalview_default_dmg_background-72dpi.png" />
<variable name="WRAPPER_LINK" value="jalview" />
<variable name="BASH_WRAPPER_SCRIPT" value="jalview.sh" />
<variable name="WRAPPER_SCRIPT_BIN_DIR" value="bin" />
<files defaultUninstallMode="2" preserveSymlinks="false">
<filesets>
<fileset name="Full file set" id="734" customizedId="FULL_FILE_SET" />
- <fileset name="Mac OS X JRE" id="880" />
- <fileset name="Windows JRE" id="882" />
- <fileset name="Jalview application" id="1873" />
+ <fileset name="macOS x64 JVM" id="2801" customizedId="MACOS_X64_JVM" />
+ <fileset name="macOS aarch64 JVM" id="2803" customizedId="MACOS_AARCH64_JVM" />
</filesets>
<roots>
<root id="735" fileset="734" />
- <root id="881" fileset="880" />
- <root id="883" fileset="882" />
- <root id="1874" fileset="1873" />
+ <root id="2802" fileset="2801" />
+ <root id="2804" fileset="2803" />
</roots>
<mountPoints>
- <mountPoint id="454" />
<mountPoint id="736" root="735" />
- <mountPoint id="884" root="881" />
- <mountPoint id="885" root="883" />
- <mountPoint id="1875" root="1874" />
+ <mountPoint id="2805" root="2802" />
+ <mountPoint id="2806" root="2804" />
</mountPoints>
<entries>
- <dirEntry mountPoint="454" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_FILES_DIR}/${compiler:JAVA_VERSION}" uninstallMode="2" overrideOverwriteMode="true" overrideUninstallMode="true" subDirectory="files" />
<dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_CHANNEL_DIR}/${compiler:JAVA_VERSION}" uninstallMode="2" overrideOverwriteMode="true" overrideUninstallMode="true" subDirectory="files">
<exclude>
<entry location="${compiler:WRAPPER_SCRIPT_BIN_DIR}" />
</dirEntry>
<dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/examples" overwriteMode="1" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="examples" />
<dirEntry mountPoint="736" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_CHANNEL_DIR}/${compiler:JAVA_VERSION}/${compiler:WRAPPER_SCRIPT_BIN_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:WRAPPER_SCRIPT_BIN_DIR}" overrideDirMode="true" />
- <dirEntry mountPoint="884" file="${compiler:MACOS_JAVA_VM_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
- <dirEntry mountPoint="885" file="${compiler:WINDOWS_JAVA_VM_DIR}" fileMode="755" overrideFileMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
- <dirEntry mountPoint="1875" file="${compiler:JALVIEW_DIR}/${compiler:GETDOWN_CHANNEL_DIR}/${compiler:JAVA_VERSION}/${compiler:GETDOWN_DIST_DIR}" overwriteMode="1" uninstallMode="2" overrideFileMode="true" overrideOverwriteMode="true" overrideUninstallMode="true" entryMode="subdir" subDirectory="${compiler:GETDOWN_DIST_DIR}" overrideDirMode="true" />
+ <dirEntry mountPoint="2805" file="${compiler:MACOS_X64_JAVA_VM_DIR}" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
+ <dirEntry mountPoint="2806" file="${compiler:MACOS_AARCH64_JAVA_VM_DIR}" entryMode="subdir" subDirectory="${compiler:JRE_DIR}" />
</entries>
<components>
<component name="jalview_getdown" id="1031">
<entry filesetId="734" />
</include>
</component>
- <component name="macos_java_vm" id="1155">
- <include>
- <entry filesetId="880" />
- </include>
- </component>
- <component name="windows_java_vm" id="1156">
- <include>
- <entry filesetId="882" />
- </include>
- </component>
- <component name="getdown" id="1276">
- <include>
- <entry defaultFileset="true" />
- </include>
- </component>
- <component name="jalview" id="1881">
- <include>
- <entry filesetId="1873" />
- </include>
- </component>
</components>
</files>
<launchers>
</installerGui>
<mediaSets>
<windows name="Windows x64 EXE Installer" id="743" customizedId="WINDOWS-X64-EXE" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:APPLICATION_FOLDER}" runPostProcessor="true" postProcessor="${compiler:JSIGN_SH} $EXECUTABLE" customInstallBaseDir="~/AppData/Local">
- <excludedComponents>
- <component id="1155" />
- <component id="1156" />
- <component id="1276" />
- <component id="1881" />
- </excludedComponents>
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
<exclude>
<entry defaultFileset="true" />
- <entry filesetId="880" />
- <entry filesetId="882" />
- <entry filesetId="1873" />
- <entry filesetId="2105" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
</exclude>
- <jreBundle jreBundleSource="preCreated" includedJre="${compiler:WINDOWS_JAVA_VM_TGZ}" manualJreEntry="true" />
+ <jreBundle jreBundleSource="preCreated" includedJre="${compiler:WINDOWS_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
</windows>
- <macosArchive name="macOS Disk Image" id="878" customizedId="MACOS-X64-DMG" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" volumeName="${compiler:INSTALLER_NAME}" launcherId="737" executeSetupApp="true" setupAppId="2746">
- <excludedComponents>
- <component id="1156" />
- <component id="1276" />
- <component id="1881" />
- </excludedComponents>
+ <macosArchive name="macOS x64 Disk Image" id="878" customizedId="MACOS-X64-DMG" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-macOS-x64-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" volumeName="${compiler:INSTALLER_NAME}" launcherId="737" setupAppId="2746">
+ <exclude>
+ <entry defaultFileset="true" />
+ <entry filesetId="2803" />
+ </exclude>
+ <jreBundle jreBundleSource="none" includedJre="${compiler:MACOS_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
+ <topLevelFiles>
+ <symlink name="" "" target="/Applications" />
+ <file name=".background/jalview_dmg_background.png" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_BG_IMAGE}" />
+ <file name=".DS_Store" file="${compiler:JALVIEW_DIR}/${compiler:MACOS_DMG_DS_STORE}" />
+ <file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/Jalview-File.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/Jalview-File.icns" />
+ <file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/jvl_file.icns" file="${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/jvl_file.icns" />
+ <symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/${compiler:WRAPPER_LINK}" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}" />
+ </topLevelFiles>
+ </macosArchive>
+ <macosArchive name="macOS aarch64 Disk Image" id="2796" customizedId="MACOS-AARCH64-DMG" mediaFileName="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-macOS-aarch64-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" volumeName="${compiler:INSTALLER_NAME}" architecture="aarch64" launcherId="737" setupAppId="2746">
<exclude>
<entry defaultFileset="true" />
- <entry filesetId="882" />
- <entry filesetId="1873" />
+ <entry filesetId="2801" />
</exclude>
<jreBundle jreBundleSource="none" />
<topLevelFiles>
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/${compiler:WRAPPER_LINK}" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}" />
</topLevelFiles>
</macosArchive>
- <unixInstaller name="Linux x64 Shell Installer" id="1595" customizedId="LINUX-X64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux_x64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
- <excludedComponents>
- <component id="1155" />
- <component id="1156" />
- <component id="1276" />
- <component id="1881" />
- </excludedComponents>
+ <unixInstaller name="Linux x64 Shell Installer" id="1595" customizedId="LINUX-X64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux-x64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
+ <exclude>
+ <entry defaultFileset="true" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
+ </exclude>
+ <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
+ </unixInstaller>
+ <unixInstaller name="Linux aarch64 Shell Installer" id="2782" customizedId="LINUX-AARCH64-SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-linux-aarch64-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
<exclude>
<entry defaultFileset="true" />
- <entry filesetId="880" />
- <entry filesetId="882" />
- <entry filesetId="1873" />
- <entry filesetId="2105" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
</exclude>
- <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_JAVA_VM_TGZ}" manualJreEntry="true" />
+ <jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_AARCH64_JAVA_VM_TGZ}" manualJreEntry="true" />
</unixInstaller>
<unixArchive name="Unix .tar.gz Archive" id="1596" customizedId="UNIX--TGZ" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}">
- <excludedComponents>
- <component id="1155" />
- <component id="1156" />
- <component id="1276" />
- <component id="1881" />
- </excludedComponents>
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
<exclude>
<entry defaultFileset="true" />
- <entry filesetId="880" />
- <entry filesetId="882" />
- <entry filesetId="1873" />
- <entry filesetId="2105" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
</exclude>
- <jreBundle jreBundleSource="none" includedJre="${compiler:LINUX_JAVA_VM_TGZ}" manualJreEntry="true" />
+ <jreBundle jreBundleSource="none" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
</unixArchive>
<unixInstaller name="Unix Shell Installer" id="2639" customizedId="UNIX--SH" mediaFileName="${compiler:UNIX_APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-java_${compiler:JAVA_INTEGER_VERSION}" installDir="${compiler:UNIX_APPLICATION_FOLDER}" customInstallBaseDir="~/opt/">
- <excludedComponents>
- <component id="1155" />
- <component id="1156" />
- <component id="1276" />
- <component id="1881" />
- </excludedComponents>
+ <excludedBeans>
+ <bean refId="2746" />
+ </excludedBeans>
<exclude>
<entry defaultFileset="true" />
- <entry filesetId="880" />
- <entry filesetId="882" />
- <entry filesetId="1873" />
- <entry filesetId="2105" />
+ <entry filesetId="2801" />
+ <entry filesetId="2803" />
</exclude>
- <jreBundle jreBundleSource="none" includedJre="${compiler:LINUX_JAVA_VM_TGZ}" manualJreEntry="true" />
+ <jreBundle jreBundleSource="none" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
</unixInstaller>
</mediaSets>
<buildIds>
<mediaSet refId="743" />
<mediaSet refId="878" />
+ <mediaSet refId="2796" />
<mediaSet refId="1595" />
+ <mediaSet refId="2782" />
<mediaSet refId="1596" />
<mediaSet refId="2639" />
</buildIds>
git://source.jalview.org / jalview.git / commitdiff