dependencies {
classpath "com.vladsch.flexmark:flexmark-all:0.62.0"
classpath "org.jsoup:jsoup:1.14.3"
- classpath "com.eowise:gradle-imagemagick:0.5.1"
classpath 'ru.vyarus:gradle-use-python-plugin:4.0.0'
}
}
}
repositories {
- jcenter()
mavenCentral()
mavenLocal()
}
}
getdownWebsiteResourceFilenames += file(channelPropsFile).getName()
- // set some getdownTxt_ properties then go through all properties looking for getdownTxt_...
+ // set some getdownTxt_ properties then go through all properties looking for getdown_txt_...
def props = project.properties.sort { it.key }
if (getdownAltJavaMinVersion != null && getdownAltJavaMinVersion.length() > 0) {
props.put("getdown_txt_java_min_version", getdownAltJavaMinVersion)
into getdownResourceDir
}
}
-
- def getdownWrapperScripts = [ getdown_bash_wrapper_script, getdown_powershell_wrapper_script, getdown_batch_wrapper_script ]
+
+ def getdownWrapperScripts = [
+ getdown_bash_wrapper_script,
+ getdown_powershell_wrapper_script,
+ getdown_bash_update_script,
+ getdown_powershell_update_script,
+ ]
+ def run_powershell = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${getdown_run_powershell}" )
+ def run_other_script = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${getdown_run_other_script}" )
getdownWrapperScripts.each{ script ->
def s = file( "${jalviewDir}/utils/getdown/${getdown_wrapper_script_dir}/${script}" )
if (s.exists()) {
}
getdownTextLines += "xresource = ${getdown_wrapper_script_dir}/${script}"
}
+ def ext = script.toLowerCase(Locale.ROOT).substring(script.lastIndexOf(".") + 1)
+ if ("ps1".equals(ext)) {
+ def base = script.take(script.lastIndexOf("."))
+ def newbase = "update".equals(base) ? "${install4jUnixApplicationFolder}_update" : install4jUnixApplicationFolder
+ if (!newbase.equals(base)) {
+ copy {
+ from run_other_script
+ rename(run_other_script.getName(), "${newbase}.${ext}")
+ into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
+ getdownTextLines += "xresource = ${getdown_wrapper_script_dir}/${newbase}.${ext}"
+ filter(ReplaceTokens,
+ beginToken: '__',
+ endToken: '__',
+ tokens: [
+ 'OTHERSCRIPT': script
+ ]
+ ) }
+ }
+ copy {
+ from run_powershell
+ rename(run_powershell.getName(), "${newbase}.bat")
+ into "${getdownAppBaseDir}/${getdown_wrapper_script_dir}"
+ getdownTextLines += "xresource = ${getdown_wrapper_script_dir}/${newbase}.bat"
+ }
+ }
}
def codeFiles = []
dependsOn install4jCustomiseDS_StoreAarch64
}
+task install4jDMGVmoptionsFile(type: Copy) {
+ def inputDir = "${jalviewDir}/${install4j_utils_dir}"
+ def outputDir = "${jalviewDir}/${install4j_build_dir}/tmp"
+
+ def installDateTime = getDate("yyyy-MM-dd HH:mm:ss") + " (build time)"
+
+ from(inputDir) {
+ include(string("${install4j_default_vmoptions}"))
+ rename(string("${install4j_default_vmoptions}"), string("${install4j_default_vmoptions}.X64"))
+
+ filter(ReplaceTokens,
+ beginToken: '__',
+ endToken: '__',
+ tokens: [
+ 'INSTALLERFILENAME': string("${install4jmacOSArchiveX64DMGFilename}.dmg"),
+ 'INSTALLDATETIME': installDateTime
+ ]
+ )
+
+ }
+
+ from(inputDir) {
+ include(string("${install4j_default_vmoptions}"))
+ rename(string("${install4j_default_vmoptions}"), string("${install4j_default_vmoptions}.AARCH64"))
+
+ filter(ReplaceTokens,
+ beginToken: '__',
+ endToken: '__',
+ tokens: [
+ 'INSTALLERFILENAME': string("${install4jmacOSArchiveAarch64DMGFilename}.dmg"),
+ 'INSTALLDATETIME': installDateTime
+ ]
+ )
+ }
+
+ into outputDir
+
+ inputs.file("${inputDir}/${install4j_default_vmoptions}")
+ outputs.file("${outputDir}/${install4j_default_vmoptions}.X64")
+ outputs.file("${outputDir}/${install4j_default_vmoptions}.AARCH64")
+}
+
task install4jDMGProcesses {
dependsOn install4jDMGBackgroundImageProcess
dependsOn install4jCustomiseDS_Store
+ dependsOn install4jDMGVmoptionsFile
}
task installerFiles(type: com.install4j.gradle.Install4jTask) {
'WRAPPER_LINK': getdownWrapperLink,
'BASH_WRAPPER_SCRIPT': getdown_bash_wrapper_script,
'POWERSHELL_WRAPPER_SCRIPT': getdown_powershell_wrapper_script,
- 'BATCH_WRAPPER_SCRIPT': getdown_batch_wrapper_script,
+ 'BASH_UPDATE_SCRIPT': getdown_bash_update_script,
+ 'POWERSHELL_UPDATE_SCRIPT': getdown_powershell_update_script,
'WRAPPER_SCRIPT_BIN_DIR': getdown_wrapper_script_dir,
'MACOSARCHIVE_X64_NAME': install4jmacOSArchiveX64Name,
'MACOSARCHIVE_AARCH64_NAME': install4jmacOSArchiveAarch64Name,
'GETDOWN_ALT_DIR': getdown_app_dir_alt,
'GETDOWN_INSTALL_DIR': getdown_install_dir,
'INFO_PLIST_FILE_ASSOCIATIONS_FILE': install4j_info_plist_file_associations,
- 'BUILD_DIR': install4jBuildDir,
+ 'BUILD_DIR': install4j_build_dir,
'APPLICATION_CATEGORIES': install4j_application_categories,
'APPLICATION_FOLDER': install4jApplicationFolder,
'UNIX_APPLICATION_FOLDER': install4jUnixApplicationFolder,
'INSTALLER_ICON': "${getdownImagesDir}/${install4j_installer_icon}",
'INSTALLER_MAC_ICON': "${getdownImagesDir}/${install4j_installer_mac_icon}",
'INSTALLER_WINDOWS_ICON': "${getdownImagesDir}/${install4j_installer_windows_icon}",
+ 'TITLE_ICON': "${getdownImagesDir}/${install4j_title_icon}",
'LOG_FILE': "${install4jUnixApplicationFolder}.log",
]
-1.8.3-1.5.0_FJVL
+1.8.3-1.5.3_FJVL
-1.8.3-1.5.0_JVL
+1.8.3-1.5.3_JVL
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.5.0_FJVL</version>
+ <version>1.8.3-1.5.3_FJVL</version>
</parent>
<artifactId>getdown-ant</artifactId>
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.5.0_FJVL</version>
+ <version>1.8.3-1.5.3_FJVL</version>
</parent>
<artifactId>getdown-core</artifactId>
import java.nio.file.StandardCopyOption;
import java.security.*;
import java.security.cert.Certificate;
-import java.util.*;
import java.util.concurrent.*;
+import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.zip.GZIPInputStream;
args.add("-Dlauncher.version=" + Build.version());
addSystemPropertyIfNotNull(args, "installer.appdir");
// add the marker indicating the app is running in getdown
- args.add("-D" + Properties.GETDOWN + "=true");
+ args.add("-D" + com.threerings.getdown.data.Properties.GETDOWN + "=true");
args.add("-Dsys.install4jVersion=" + Application.i4jVersion);
addSystemPropertyIfNotNull(args, "installer.template_version");
addSystemPropertyIfNotNull(args, "installer.logfile");
}
}
+ final String installerPropsFilename = "installer.properties";
+ log.info("Creating " + installerPropsFilename);
+ java.util.Properties installerProps = new java.util.Properties();
+ installerProps.setProperty("installer.appdir", applicationAppDir.getAbsolutePath());
+ installerProps.setProperty("installer.appdirhash", EnvConfig.getAppDirHash());
+ for ( String key: new String[] {"installer.template_version", "installer.application_folder", "installer.icon", "installer.mac_icons", "installer.logfile", "installer.logfile_append"}) {
+ String val = System.getProperty(key);
+ if (val != null) {
+ installerProps.put(key, val);
+ }
+ }
+ for (String prop: installerProps.stringPropertyNames()) {
+ log.info("Adding property '" + prop + "'='" + installerProps.getProperty(prop) + "' to " + installerPropsFilename);
+ }
+ File installerPropsFile = new File(userAppDir, installerPropsFilename);
+ try {
+ installerProps.store(new FileOutputStream(installerPropsFile.getAbsolutePath()), "Created by installer launcher in " + applicationAppDir);
+ } catch (IOException e) {
+ log.warning("Could not write installer properties file '" + installerPropsFile.getAbsolutePath() + "'");
+ }
+
MessageDigest md = Digest.getMessageDigest(Digest.VERSION);
for (Resource rsc: copyResources) {
String digestHash = digest2.getDigest(rsc);
package com.threerings.getdown.data;
+import static java.nio.charset.StandardCharsets.UTF_8;
+
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
String appIdProv = null;
String appBase = null;
String appBaseProv = null;
- applicationFolder = System.getProperty("installer.application_folder");
- installerAppdir = System.getProperty(APPLICATION_APPDIR_PROPERTY);
-
- appName = System.getProperty("channel.app_name");
+ setVarsFromProperties();
// start with bootstrap.properties config, if avaialble
try {
}
// forced by system property to not use user default appdir
- if (SysProps.noUpdate() && Boolean.valueOf(System.getProperty("no" + USER_DEFAULT_APPDIR_PROPERTY))) {
+ if (appDir == null && Boolean.valueOf(System.getProperty("no" + USER_DEFAULT_APPDIR_PROPERTY))) {
appDir = installerAppdir;
- appDirProv = "no user default";
+ appDirProv = "installer appdir";
userAppDir = false;
+ notes.add(Note.info("Not using " + USER_DEFAULT_APPDIR_PROPERTY + ", resorting to " + appDirProv + " '" + appDir +"'"));
} else if (userAppDir && installerAppdir != null) {
// we're going to try and use a different appdir, check if newer getdown-launcher.jar found there, and restart using that one
final String getdown = "getdown-launcher.jar";
// ensure that we were able to find an app dir
if (appDir == null) {
+ if (!SysProps.noUpdate()) {
+ notes.add(Note.error("No appDir could be determined. You may need to set -Dsilent=noupdate -Dno"+USER_DEFAULT_APPDIR_PROPERTY));
+ }
return null; // caller will report problem to user
}
this.appArgs = appArgs;
}
- private static final String getUserAppdir() {
+ /**
+ * compute a hash for the given path string using the getdown digest
+ * @param install_app_dir
+ * @return 8-character hex hash
+ */
+ public static final String getFullPathToDirectoryHash(String install_app_dir)
+ {
+ MessageDigest md = Digest.getMessageDigest(Digest.VERSION);
+ byte[] contents = install_app_dir.getBytes(UTF_8);
+ String hash = StringUtil.hexlate(md.digest(contents));
+ return hash.substring(0,8);
+ }
+
+ public static final String getUserAppdir() {
final String noUseDefaultAppDirProperty = "no" + USER_DEFAULT_APPDIR_PROPERTY;
if (Boolean.valueOf(System.getProperty(noUseDefaultAppDirProperty))) {
System.err.println("Not using default user appdir because property '" + noUseDefaultAppDirProperty + "' is '" + System.getProperty(noUseDefaultAppDirProperty) + "'");
}
String appdirname = applicationFolder == null || applicationFolder.length() == 0 ? ChannelProperties.FALLBACK_APPNAME : applicationFolder;
String home = System.getProperty("user.home");
+ // for times when using this method without running GetdownApp
+ if (appName == null) {
+ appName = System.getProperty("channel.app_name");
+ }
+ if (installerAppdir == null) {
+ installerAppdir = System.getProperty(APPLICATION_APPDIR_PROPERTY);
+ }
String appname = StringUtil.isBlank(appName) ? ChannelProperties.FALLBACK_APPNAME : appName;
final String FS = File.separator;
+ try {
+ setAppDirHash(installerAppdir);
+ } catch (IOException ioex) {
+ System.err.println("Unable to resolve '"+installerAppdir+"' as a proper path on this system.\nNot generating a user local appdir - getdown may fail to update!");
+ return null;
+ }
+
String appDataPath;
String append;
+ boolean addHome = true;
if (LaunchUtil.isMacOS()) {
appDataPath = osAppDataPathMap.get("macos");
append = appname;
appDataPath = osAppDataPathMap.get("other");
append = appdirname.toLowerCase(Locale.ROOT);
}
- String returnString = home + FS + appDataPath + FS + append + FS + "app";
- return returnString;
+ String setUserAppDirPath = System.getProperty(SET_USER_APPDIR_PATH);
+ // do not use a setUserAppDirPath with ".." in it
+ if (!StringUtil.isBlank(setUserAppDirPath) && setUserAppDirPath.indexOf("..") == -1) {
+ if (setUserAppDirPath.startsWith("~" + FS)) {
+ setUserAppDirPath = home + setUserAppDirPath.substring(1);
+ }
+ appDataPath = setUserAppDirPath.replaceAll("%u", System.getProperty("user.name")).replaceAll("%h", home);
+ addHome = false;
+ }
+
+ StringBuilder sb = new StringBuilder();
+ if (addHome) {
+ sb.append(home).append(FS);
+ }
+ sb.append(appDataPath).append(FS);
+ sb.append(append).append(FS);
+ sb.append(getAppDirHash()).append(FS);
+ sb.append("app");
+ return sb.toString();
}
public static void setRelaunched(boolean b) {
return appName;
}
+ public static void setVarsFromProperties() {
+ applicationFolder = System.getProperty("installer.application_folder");
+ installerAppdir = System.getProperty(APPLICATION_APPDIR_PROPERTY);
+ appName = System.getProperty("channel.app_name");
+ }
+
+ public static String getAppDirHash() {
+ return appDirHash;
+ }
+
+ public static void setAppDirHash(String path) throws IOException {
+ appDirHash = getFullPathToDirectoryHash(new File(path).getCanonicalPath());
+ }
+
private static boolean relaunched = false;
private static final String USER_HOME_KEY = "${user.home}";
private static String appName = null;
- private static final String USER_DEFAULT_APPDIR_PROPERTY = "userdefaultappdir";
+ private static String appDirHash = null;
+
+ public static final String USER_DEFAULT_APPDIR_PROPERTY = "userdefaultappdir";
+
+ protected static final String APPLICATION_APPDIR_PROPERTY = "installer.appdir";
- private static final String APPLICATION_APPDIR_PROPERTY = "installer.appdir";
+ protected static final String POPULATE_DEFAULT_APPDIR_PROPERTY = "populatedefaultappdir";
- private static final String POPULATE_DEFAULT_APPDIR_PROPERTY= "populatedefaultappdir";
+ protected static final String SET_USER_APPDIR_PATH = "setuserappdirpath";
private static final Map<String,String> osAppDataPathMap;
import java.nio.file.Paths;
import java.util.Locale;
-import javax.xml.bind.DatatypeConverter;
-
import java.security.MessageDigest;
import jalview.util.ChannelProperties;
MessageDigest md = MessageDigest.getInstance(algo);
md.update(Files.readAllBytes(Paths.get(file.getAbsolutePath())));
byte[] digest = md.digest();
- checksum = DatatypeConverter.printHexBinary(digest).toUpperCase(Locale.ROOT);
+ checksum = printHexBinary(digest).toUpperCase(Locale.ROOT);
} catch (Exception e) {
System.out.println("Couldn't create "+algo+" digest of "+file.getPath());
}
// can't grab system properties; we'll just pretend we're not on any of these OSes
}
}
+
+ private static String printHexBinary(byte[] bytes) {
+ if (bytes == null) {
+ return null;
+ }
+ StringBuilder sb = new StringBuilder();
+ for (int i = 0; i < bytes.length; i++) {
+ sb.append(byteToHex(bytes[i]));
+ }
+ return sb.toString();
+ }
+
+ private static String byteToHex(byte num) {
+ char[] hexDigits = new char[2];
+ hexDigits[0] = Character.forDigit((num >> 4) & 0xF, 16);
+ hexDigits[1] = Character.forDigit((num & 0xF), 16);
+ return new String(hexDigits);
+ }
+
}
--- /dev/null
+/*
+ * 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.
+ */
+package jalview.bin;
+
+import java.io.File;
+
+import com.threerings.getdown.data.EnvConfig;
+import com.threerings.getdown.util.LaunchUtil;
+
+public class GetdownLauncherUpdate
+{
+ public static void main(String[] args)
+ {
+ EnvConfig.setVarsFromProperties();
+
+ String appdir = args.length > 0 ? args[0] : null;
+ if (appdir == null || appdir.length() == 0)
+ {
+ appdir = System.getProperty("launcher.appdir", null);
+ }
+ if (appdir == null)
+ {
+ appdir = EnvConfig.getUserAppdir();
+ }
+ if (appdir == null)
+ {
+ System.err.println("Not running upgradeGetdown");
+ return;
+ }
+ boolean debug = false;
+ for (int i = 0; i < args.length; i++)
+ {
+ if ("--debug".equals(args[i]))
+ {
+ debug = true;
+ break;
+ }
+ }
+ if (debug)
+ {
+ System.err.println("Running upgradeGetdown");
+ }
+ File appdirFile = new File(appdir);
+ if (!appdirFile.exists())
+ {
+ System.err.println("Directory '" + appdirFile.getAbsolutePath()
+ + "' doesn't exist, cannot update getdown-launcher.jar.");
+ if (Boolean.valueOf(System.getProperty("launcher.update")))
+ {
+ System.exit(1);
+ }
+ }
+ LaunchUtil.upgradeGetdown(new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+}
+/*
+ * 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.
+ */
package jalview.util;
import java.lang.reflect.InvocationTargetException;
private static String prefix = null;
+ private static boolean quiet = false;
+
public static void setHasConsole(boolean b)
{
hasConsole = b;
}
+ public static void setQuiet(boolean b)
+ {
+ quiet = b;
+ }
+
public static void setPrefix(String s)
{
prefix = s;
public static void println(String message0, boolean err,
boolean thisHasConsole)
{
+ if (!err && quiet)
+ {
+ return;
+ }
String message = prefix == null ? message0 : prefix + message0;
if (thisHasConsole && hasConsole)
{
}
String v0 = getJarImplementationVersion(f0);
String v1 = getJarImplementationVersion(f1);
- syserr(true, false,
+ syserr(v0 != null && !v0.equals(v1), false,
"Got launcher versions '" + v0 + "' and '" + v1 + "'");
return compareGetdownLauncherJarVersions(v0, v1);
}
checkAppBase(cfg, TESTBASE);
checkNoAppArgs(cfg);
}
+
+ /**
+ * check that the appdir hash distinguishes between different base-app paths
+ */
+ @Test public void testDifferentUserappdirHash() {
+ String envhash1 = EnvConfig.getFullPathToDirectoryHash("/Applications/Getdown.app/");
+ String envhash2 = EnvConfig.getFullPathToDirectoryHash("/Applications/Getdown 1.app/");
+ assertTrue(!envhash1.equals(envhash2));
+ }
+
+ /**
+ * check whether userdefaultappdir can be overrridden by nouserdefaultappdir
+ */
+ @Test public void checkUserAppDir() {
+ List<EnvConfig.Note> notes = new ArrayList<>();
+ System.getProperties().setProperty(EnvConfig.APPLICATION_APPDIR_PROPERTY, "/Applications/Getdown.app");
+ System.getProperties().setProperty("userdefaultappdir","true");
+ EnvConfig cfg = sysPropsConfig(notes, "appdir", CWD);
+ assertTrue(cfg!=null);
+ hasUserAppDir();
+
+ System.getProperties().setProperty("nouserdefaultappdir","true");
+ cfg = sysPropsConfig(notes, "appdir", CWD);
+ assertTrue(cfg!=null);
+ noUserAppDir();
+
+ System.getProperties().remove("nouserdefaultappdir");
+ cfg = sysPropsConfig(notes, "appdir", CWD);
+ assertTrue(cfg!=null);
+ hasUserAppDir();
+ }
+
+ public void noUserAppDir() {
+ assertTrue(EnvConfig.getUserAppdir()==null);
+ }
+ public void hasUserAppDir() {
+ assertTrue(EnvConfig.getUserAppdir()!=null && !"".equals(EnvConfig.getUserAppdir()));
+ }
}
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.5.0_FJVL</version>
+ <version>1.8.3-1.5.3_FJVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
// determine whether or not we can write to our install directory
File instdir = _app.getLocalPath("");
- if (!instdir.canWrite()) {
+ if (!instdir.canWrite() && !SysProps.noUpdate()) {
String path = instdir.getPath();
if (path.equals(".")) {
path = System.getProperty("user.dir");
public static Getdown start (String[] argv) throws Exception {
jalview.util.ErrorLog.setHasConsole(false);
jalview.util.ErrorLog.setPrefix("LAUNCHER: ");
- jalview.util.ErrorLog.outPrintln("start of logging");
+ if (SysProps.silent() && !SysProps.launchInSilent() && "true".equals(System.getProperty("launcher.update", "false"))) {
+ jalview.util.ErrorLog.outPrintln("Running update only");
+ } else {
+ jalview.util.ErrorLog.outPrintln("Start of logging");
+ }
List<EnvConfig.Note> notes = new ArrayList<>();
boolean append = false;
EnvConfig envc = EnvConfig.create(argv, notes, GetdownApp.class);
import ca.beq.util.win32.registry.RootKey;
import com.threerings.getdown.data.Application;
+import com.threerings.getdown.data.SysProps;
import com.threerings.getdown.spi.ProxyAuth;
import com.threerings.getdown.util.Config;
import com.threerings.getdown.util.ConnectionUtil;
public static void configProxy (Application app, String host, String port,
String username, String password) {
// save our proxy host and port in a local file
- saveProxy(app, host, port);
+ if (!SysProps.noUpdate()) {
+ saveProxy(app, host, port);
+ }
// save our credentials via the SPI
if (!StringUtil.isBlank(username) && !StringUtil.isBlank(password)) {
public static void initProxy (Application app, String host, String port,
String username, String password)
{
-System.out.println("**** initProxy(app, '"+host+"', "+port+", '"+username+"', "+(password==null?"null":"*x"+password.length())+")");
+ log.info("initProxy:", "app", app, "host", host, "port", port, "username", username, "password", "("+(password==null?"null":"*x"+password.length())+")");
// check whether we have saved proxy credentials
String appDir = app.getAppDir().getAbsolutePath();
ServiceLoader<ProxyAuth> loader = ServiceLoader.load(ProxyAuth.class);
+++ /dev/null
-//
-// Getdown - application installer, patcher and launcher
-// Copyright (C) 2004-2018 Getdown authors
-// https://github.com/threerings/getdown/blob/master/LICENSE
-
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
- <modelVersion>4.0.0</modelVersion>
- <groupId>jregistrykey</groupId>
- <artifactId>jregistrykey</artifactId>
- <version>1.0</version>
- <description>POM was created from install:install-file</description>
-</project>
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<metadata>
- <groupId>jregistrykey</groupId>
- <artifactId>jregistrykey</artifactId>
- <version>1.0</version>
- <versioning>
- <versions>
- <version>1.0</version>
- </versions>
- <lastUpdated>20101118155146</lastUpdated>
- </versioning>
-</metadata>
+++ /dev/null
-Main-Class: com.threerings.getdown.launcher.Getdown
-Permissions: all-permissions
-Application-Name: Getdown
-Codebase: *
-Application-Library-Allowable-Codebase: *
-Caller-Allowable-Codebase: *
if [ x$JVLVERSION != x ]; then
export VERSION=$JVLVERSION
else
- export VERSION=1.8.3-1.5.0_JVL
+ export VERSION=1.8.3-1.5.3_JVL
fi
if [ x${VERSION%_JVL} = x$VERSION ]; then
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
<packaging>pom</packaging>
- <version>1.8.3-1.5.0_FJVL</version>
+ <version>1.8.3-1.5.3_FJVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
getdown_launcher = getdown-launcher.jar
getdown_launcher_local = getdown-launcher-local.jar
getdown_launcher_new = getdown-launcher-new.jar
-getdown_core = getdown/lib/getdown-core.jar
getdown_build_properties = build_properties
getdown_launch_jvl_name = channel_launch
getdown_images_dir = utils/getdown
# now got better (dynamic) defaults when jvmmem* not set
#getdown_txt_jalview.jvmmempc = 90
#getdown_txt_jalview.jvmmemmax = 32G
+getdown_txt_resource = getdown/lib/getdown-core.jar
getdown_txt_strict_comments = true
getdown_txt_ui.progress_sync_before_shown = true
getdown_txt_ui.progress_sync_after_shown = false
install4j_installer_icon = jalview_installer.png
install4j_installer_mac_icon = jalview_installer.icns
install4j_installer_windows_icon = jalview_installer.ico
+install4j_default_vmoptions = default.vmoptions
jalview_customise_ds_store = utils/macos_dmg/jalview_customise_dsstore.py
getdown_wrapper_script_dir = bin
getdown_bash_wrapper_script = jalview.sh
getdown_powershell_wrapper_script = jalview.ps1
-getdown_batch_wrapper_script = jalview.bat
+getdown_bash_update_script = update.sh
+getdown_powershell_update_script = update.ps1
+getdown_run_other_script = run_other_script.ps1
+getdown_run_powershell = run_powershell.bat
OSX_KEYSTORE =
OSX_KEYPASS =
---
version: 2.11.4.0
-date: 2024-06-30
+date: 2024-09-03
channel: "develop"
---
## New Features
+- <!-- JAL-4159,JAL-4390 --> Calculate PASiMap projection for sequences - ported by Thomas Morell ( U. Konstanz)
- <!-- JAL-4392 --> Consensus secondary structure visualization for alignments
+- <!-- JAL-4411 --> Show data source for 'reference annotation' from 3D structure (e.g. Secondary Structure)
- <!-- JAL-4386 --> Calculate tree or PCA using secondary structure annotation
-- <!-- JAL-4159 --> Calculate PASiMap projection for sequences - ported by Thomas Morell ( U. Konstanz)
- <!-- JAL-789,JAL-4257 --> allow adjustment of gap opening, extension, and score model for built in pairwise alignment
+### Experimental Features (enable via Desktop's tools menu)
+
+- <!-- JAL-4420 --> Jalview sensibly handles opening or a drag'n'drop of several .features, .annotations and .newick files onto an alignment
+<!-- not yet! - -- JAL-4366 Linked visualisation of Foldseek 3Di MSAs with corresponding 3D structures -->
### development and deployment
+- <!-- JAL-3830 --> Add a command-line wrapper script to macOS bundle, linux and Windows installations (bash, powershell and .bat wrappers)
+- <!-- JAL-3384 --> Redirect stdout and stderr to file when launched from getdown
+- <!-- JAL-3845 --> Add error message when launched directly from Jalview Installer DMG volume
+- <!-- JAL-3631,JAL-4104 --> Allow jalview auto-updates to download to and work from separate user-space directory
+- <!-- JAL-3978, JAL-3196 --> Gradle build with install4j launchers
+- <!-- JAL-4409, JAL-4160 --> Implement in Jalview (and getdown for JVL) the use of specific scheme names for different channels (e.g. jalviewd://)
+- <!-- JAL-4428 --> integrate OSX codesigning scripts in jalview's repository
+- <!-- JAL-3063 --> new documentation describing how jalview project XML schema is maintained (in doc/jalview-projects.md)
+- <!-- JAL-3018,JAL-4449, JAL-4328 --> updated Jalview's Ensembl's client for v15.8 of the REST API - change in BRAF query returned by ensembl Genes for chicken for GRCg7b (now ENSGALG00010013466, was ENSGALG00000012865)
## Issues Resolved
+- <!-- JAL-1054 --> jalview does not fetch from a URL containing a redirect
+- <!-- JAL-4414 --> HTTP errors are often interpreted to the user as a file format error - and FileNotFound errors are not propagated from Web or Local file import
+- <!-- JAL-3409 --> launcher.log from jalview runtime missing newlines and also lacks stdout/stderr reported in Jalview Console
+- <!-- JAL-4072 --> Possible "Zip Slip Vulnerability" in getdown
+- <!-- JAL-4417 --> jalview.bin.CommandsTest.headlessOrGuiImageOutputTest produces different images for --gui and --headless when using certain .jalview_properties
+- <!-- JAL-4421 --> Release installer DMG does not display the background image
+- <!-- JAL-4358 --> Getdown splash screen should disappear as soon as the Jalview Desktop is created/visible
+### development and deployment
-### New Known Issues
+- <!-- JAL-4111 --> removed gradle build's dependency on gradle-imagemagick plugin to allow building on windows (still need imagemagick installed on path for splashscreen commit watermark)
+- <!-- JAL-4397 --> fixed inconsistencies in test suite on different platforms
+- <!-- JAL-4398 --> The rendering of the text "Window" for the Window menu item is different to the other menus when testing in Linux
+### New Known Issues
+- <!-- JAL-4443 --> PaSiMap not available in JalviewJS
+- <!-- JAL-4100 --> Jalview ignores ncrna genes when importing from genbank format files
+- <!-- JAL-4450 --> Sequence letter aspect ratio not set correctly when aspect ratio is very narrow after middle-mouse drag
// jalview.bin.Console.outPrintln(elapsed);
}
-
public static final ProfilesI calculateSS(List<SequenceI> list, int start,
int end, String source)
{
return calculateSS(list, start, end, false, source);
}
-
+
public static final ProfilesI calculateSS(List<SequenceI> sequences,
int start, int end, boolean profile, String source)
{
return reply;
}
}
-
+
public static final ProfilesI calculateSS(final SequenceI[] sequences,
int width, int start, int end, boolean saveFullProfile, String source)
{
int seqCount = sequences.length;
int seqWithSSCount = 0;
-
+
ProfileI[] result = new ProfileI[width];
for (int column = start; column < end; column++)
{
-
+
int ssCount = 0;
-
+
SecondaryStructureCount ssCounts = new SecondaryStructureCount();
for (int row = 0; row < seqCount; row++)
"WARNING: Consensus skipping null sequence - possible race condition.");
continue;
}
-
+
char c = sequences[row].getCharAt(column);
List<AlignmentAnnotation> annots = AlignmentUtils.getAlignmentAnnotationForSource(sequences[row], source);
if(annots!=null) {
ProfileI profile = new Profile(maxSS, ssCount, gapCount,
maxSSCount, seqWithSSCount);
-
if (saveFullProfile)
{
profile.setSSCounts(ssCounts);
// long elapsed = System.currentTimeMillis() - now;
// jalview.bin.Console.outPrintln(-elapsed);
}
-
-
- public static void completeSSConsensus(AlignmentAnnotation ssConsensus,
- ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
- boolean showSequenceLogo, long nseq)
- {
- // long now = System.currentTimeMillis();
- if (ssConsensus == null || ssConsensus.annotations == null
- || ssConsensus.annotations.length < endCol)
- {
- /*
+
+ public static void completeSSConsensus(AlignmentAnnotation ssConsensus,
+ ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps,
+ boolean showSequenceLogo, long nseq)
+ {
+ // long now = System.currentTimeMillis();
+ if (ssConsensus == null || ssConsensus.annotations == null
+ || ssConsensus.annotations.length < endCol)
+ {
+ /*
* called with a bad alignment annotation row
* wait for it to be initialised properly
*/
- return;
- }
+ return;
+ }
- for (int i = startCol; i < endCol; i++)
- {
- ProfileI profile = profiles.get(i);
- if (profile == null)
- {
- /*
+ for (int i = startCol; i < endCol; i++)
+ {
+ ProfileI profile = profiles.get(i);
+ if (profile == null)
+ {
+ /*
* happens if sequences calculated over were
* shorter than alignment width
*/
final int dp = getPercentageDp(nseq);
- float value = profile.getSSPercentageIdentity(ignoreGaps);
+ float value = profile.getSSPercentageIdentity(ignoreGaps);
- String description = getSSTooltip(profile, value, showSequenceLogo,
- ignoreGaps, dp);
+ String description = getSSTooltip(profile, value, showSequenceLogo,
+ ignoreGaps, dp);
String modalSS = profile.getModalSS();
if ("".equals(modalSS))
}
return description;
}
-
+
static String getSSTooltip(ProfileI profile, float pid,
boolean showSequenceLogo, boolean ignoreGaps, int dp)
{
{
char[] symbols;
int[] values;
-
+
if (profile.getCounts() != null)
{
ResidueCount counts = profile.getCounts();
SymbolCounts symbolCounts = counts.getSymbolCounts();
symbols = symbolCounts.symbols;
values = symbolCounts.values;
-
+
}
- else if(profile.getSSCounts() != null)
+ else if (profile.getSSCounts() != null)
{
SecondaryStructureCount counts = profile.getSSCounts();
// to do
- SecondaryStructureCount.SymbolCounts symbolCounts = counts.getSymbolCounts();
+ SecondaryStructureCount.SymbolCounts symbolCounts = counts
+ .getSymbolCounts();
symbols = symbolCounts.symbols;
values = symbolCounts.values;
}
- else {
+ else
+ {
return null;
}
-
QuickSort.sort(values, symbols);
int totalPercentage = 0;
private static final int DEFAULT_OPENCOST = 120;
private static final int DEFAULT_EXTENDCOST = 20;
-
- private int GAP_OPEN_COST=DEFAULT_OPENCOST;
- private int GAP_EXTEND_COST=DEFAULT_EXTENDCOST;
+ private int GAP_OPEN_COST = DEFAULT_OPENCOST;
+
+ private int GAP_EXTEND_COST = DEFAULT_EXTENDCOST;
private static final int GAP_INDEX = -1;
int[] aseq1;
int[] aseq2;
-
+
/*
* matches in alignment
*/
- int match=-1;
+ int match = -1;
public String astr1 = "";
public float maxscore;
- public float meanScore; //needed for PaSiMap
+ public float meanScore; // needed for PaSiMap
- public int hypotheticMaxScore; // needed for PaSiMap
+ public int hypotheticMaxScore; // needed for PaSiMap
int prev = 0;
GAP_OPEN_COST = opencost;
GAP_EXTEND_COST = extcost;
}
+
public AlignSeq(SequenceI s1, SequenceI s2, String type)
{
seqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(),
public AlignSeq(SequenceI s1, SequenceI s2, String type, int opencost,
int extcost)
{
- this(s1,s2,type);
- GAP_OPEN_COST=opencost;
- GAP_EXTEND_COST=extcost;
+ this(s1, s2, type);
+ GAP_OPEN_COST = opencost;
+ GAP_EXTEND_COST = extcost;
}
public AlignSeq(SequenceI s12, String string1, SequenceI s22,
String string2, String type2, int defaultOpencost,
int defaultExtendcost)
{
- this(s12,string1,s22,string2,type2);
- GAP_OPEN_COST=defaultOpencost;
- GAP_EXTEND_COST=defaultExtendcost;
+ this(s12, string1, s22, string2, type2);
+ GAP_OPEN_COST = defaultOpencost;
+ GAP_EXTEND_COST = defaultExtendcost;
}
/**
}
/**
- * returns the overall score of the alignment
- *
- * @return
- */
+ * returns the overall score of the alignment
+ *
+ * @return
+ */
public float getAlignmentScore()
{
return alignmentScore;
s2.getDatasetSequence() == null ? s2 : s2.getDatasetSequence());
return alSeq2;
}
+
/**
* fraction of seq2 matched in the alignment
+ *
* @return NaN or [0..1]
*/
public double getS2Coverage()
{
- if (match>=0)
+ if (match >= 0)
{
- return ((double)match)/((double)s2.getEnd()-s2.getStart()+1);
+ return ((double) match) / ((double) s2.getEnd() - s2.getStart() + 1);
}
return Double.NaN;
}
+
/**
* fraction of seq1 matched in the alignment
+ *
* @return NaN or [0..1]
*/
public double getS1Coverage()
{
- if (match>=0)
+ if (match >= 0)
{
- return ((double)match)/((double)s1.getEnd()-s1.getStart()+1);
+ return ((double) match) / ((double) s1.getEnd() - s1.getStart() + 1);
}
return Double.NaN;
}
public void seqInit(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
{
- seqInit(s1,string1,s2,string2,type,GAP_OPEN_COST,GAP_EXTEND_COST);
+ seqInit(s1, string1, s2, string2, type, GAP_OPEN_COST, GAP_EXTEND_COST);
}
+
public void seqInit(SequenceI s1, String string1, SequenceI s2,
- String string2, String type, int opening,int extension)
+ String string2, String type, int opening, int extension)
{
- GAP_OPEN_COST=opening;
- GAP_EXTEND_COST=extension;
+ GAP_OPEN_COST = opening;
+ GAP_EXTEND_COST = extension;
this.s1 = s1;
this.s2 = s2;
setDefaultParams(type);
aseq1 = new int[seq1.length + seq2.length];
aseq2 = new int[seq1.length + seq2.length];
- match=0;
+ match = 0;
StringBuilder sb1 = new StringBuilder(aseq1.length);
StringBuilder sb2 = new StringBuilder(aseq2.length);
count = (seq1.length + seq2.length) - 1;
-
while (i > 0 && j > 0)
{
aseq1[count] = seq1[i];
{
aseq2[count] = seq2[j];
sb2.append(s2str.charAt(j));
- if (aseq1[count]!=GAP_INDEX) {
+ if (aseq1[count] != GAP_INDEX)
+ {
match++;
}
}
-
/*
* we built the character strings backwards, so now
* reverse them to convert to sequence strings
int trace;
maxscore = score[i][j] / 10f;
- //prepare trailing gaps
+ // prepare trailing gaps
while ((i < seq1.length - 1) || (j < seq2.length - 1))
{
i++;
count = (seq1.length + seq2.length) - 1;
- //get trailing gaps
+ // get trailing gaps
while ((i >= seq1.length) || (j >= seq2.length))
{
if (i >= seq1.length)
{
- aseq1[count] = GAP_INDEX;
- sb1.append("-");
- aseq2[count] = seq2[j];
- sb2.append(s2str.charAt(j));
- } else if (j >= seq2.length) {
- aseq1[count] = seq1[i];
- sb1.append(s1str.charAt(i));
- aseq2[count] = GAP_INDEX;
- sb2.append("-");
+ aseq1[count] = GAP_INDEX;
+ sb1.append("-");
+ aseq2[count] = seq2[j];
+ sb2.append(s2str.charAt(j));
+ }
+ else if (j >= seq2.length)
+ {
+ aseq1[count] = seq1[i];
+ sb1.append(s1str.charAt(i));
+ aseq2[count] = GAP_INDEX;
+ sb2.append("-");
}
i--;
j--;
aseq2[count] = seq2[j];
sb2.append(s2str.charAt(j));
- //get initial gaps
+ // get initial gaps
while (j > 0 || i > 0)
{
if (j > 0)
{
- j--;
- sb1.append("-");
- sb2.append(s2str.charAt(j));
- } else if (i > 0) {
- i--;
- sb1.append(s1str.charAt(i));
- sb2.append("-");
+ j--;
+ sb1.append("-");
+ sb2.append(s2str.charAt(j));
+ }
+ else if (i > 0)
+ {
+ i--;
+ sb1.append(s1str.charAt(i));
+ sb2.append("-");
}
}
{
int n = seq1.length;
int m = seq2.length;
- final int GAP_EX_COST=GAP_EXTEND_COST;
+ final int GAP_EX_COST = GAP_EXTEND_COST;
final int GAP_OP_COST = GAP_OPEN_COST;
// top left hand element
score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0),
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
s2str.charAt(j));
- score[0][j] = max(pairwiseScore * 10, -GAP_OP_COST,
- -GAP_EX_COST);
+ score[0][j] = max(pairwiseScore * 10, -GAP_OP_COST, -GAP_EX_COST);
traceback[0][j] = 1;
}
public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
String type)
{
- return doGlobalNWAlignment(s1, s2, type, DEFAULT_OPENCOST,DEFAULT_EXTENDCOST);
+ return doGlobalNWAlignment(s1, s2, type, DEFAULT_OPENCOST,
+ DEFAULT_EXTENDCOST);
}
+
public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2,
- String type, int opencost,int extcost)
+ String type, int opencost, int extcost)
{
-
- AlignSeq as = new AlignSeq(s1, s2, type,opencost,extcost);
+
+ AlignSeq as = new AlignSeq(s1, s2, type, opencost, extcost);
as.calcScoreMatrix();
as.traceAlignment();
}
/**
- * calculate the mean score of the alignment
- * mean score is equal to the score of an alignmenet of two sequences with randomly shuffled AA sequence composited of the same AA as the two original sequences
- *
- */
+ * calculate the mean score of the alignment mean score is equal to the score
+ * of an alignmenet of two sequences with randomly shuffled AA sequence
+ * composited of the same AA as the two original sequences
+ *
+ */
public void meanScore()
{
- int length = indelfreeAstr1.length(); //both have the same length
- //create HashMap for counting residues in each sequence
+ int length = indelfreeAstr1.length(); // both have the same length
+ // create HashMap for counting residues in each sequence
HashMap<Character, Integer> seq1ResCount = new HashMap<Character, Integer>();
HashMap<Character, Integer> seq2ResCount = new HashMap<Character, Integer>();
- // for both sequences (String indelfreeAstr1 or 2) create a key for the residue and add 1 each time its encountered
- for (char residue: indelfreeAstr1.toCharArray())
+ // for both sequences (String indelfreeAstr1 or 2) create a key for the
+ // residue and add 1 each time its encountered
+ for (char residue : indelfreeAstr1.toCharArray())
{
seq1ResCount.putIfAbsent(residue, 0);
seq1ResCount.replace(residue, seq1ResCount.get(residue) + 1);
}
- for (char residue: indelfreeAstr2.toCharArray())
+ for (char residue : indelfreeAstr2.toCharArray())
{
seq2ResCount.putIfAbsent(residue, 0);
seq2ResCount.replace(residue, seq2ResCount.get(residue) + 1);
}
- // meanscore = for each residue pair get the number of appearance and add (countA * countB * pairwiseScore(AB))
+ // meanscore = for each residue pair get the number of appearance and add
+ // (countA * countB * pairwiseScore(AB))
// divide the meanscore by the sequence length afterwards
float _meanscore = 0;
for (char resA : seq1ResCount.keySet())
{
for (char resB : seq2ResCount.keySet())
{
- int countA = seq1ResCount.get(resA);
- int countB = seq2ResCount.get(resB);
+ int countA = seq1ResCount.get(resA);
+ int countB = seq2ResCount.get(resB);
float scoreAB = scoreMatrix.getPairwiseScore(resA, resB);
- _meanscore += countA * countB * scoreAB;
+ _meanscore += countA * countB * scoreAB;
}
}
_meanscore /= length;
}
/**
- * calculate the hypothetic max score using the self-alignment of the sequences
- */
+ * calculate the hypothetic max score using the self-alignment of the
+ * sequences
+ */
public void hypotheticMaxScore()
{
int _hmsA = 0;
int _hmsB = 0;
- for (char residue: indelfreeAstr1.toCharArray())
+ for (char residue : indelfreeAstr1.toCharArray())
{
_hmsA += scoreMatrix.getPairwiseScore(residue, residue);
}
- for (char residue: indelfreeAstr2.toCharArray())
+ for (char residue : indelfreeAstr2.toCharArray())
{
_hmsB += scoreMatrix.getPairwiseScore(residue, residue);
}
- this.hypotheticMaxScore = (_hmsA < _hmsB) ? _hmsA : _hmsB; // take the lower self alignment
+ this.hypotheticMaxScore = (_hmsA < _hmsB) ? _hmsA : _hmsB; // take the lower
+ // self alignment
}
}
/**
- * create strings based of astr1 and astr2 but without gaps
- */
+ * create strings based of astr1 and astr2 but without gaps
+ */
public void getIndelfreeAstr()
{
- int n = astr1.length(); // both have the same length
+ int n = astr1.length(); // both have the same length
for (int i = 0; i < n; i++)
{
- if (Character.isLetter(astr1.charAt(i)) && Character.isLetter(astr2.charAt(i))) // if both sequences dont have a gap -> add to indelfreeAstr
+ if (Character.isLetter(astr1.charAt(i))
+ && Character.isLetter(astr2.charAt(i))) // if both sequences dont
+ // have a gap -> add to
+ // indelfreeAstr
{
- this.indelfreeAstr1 += astr1.charAt(i);
- this.indelfreeAstr2 += astr2.charAt(i);
+ this.indelfreeAstr1 += astr1.charAt(i);
+ this.indelfreeAstr2 += astr2.charAt(i);
}
}
}
/**
- * calculates the overall score of the alignment
- * preprescore = sum of all scores - all penalties
- * if preprescore < 1 ~ alignmentScore = Float.NaN >
- * alignmentScore = ((preprescore - meanScore) / (hypotheticMaxScore - meanScore)) * coverage
- */
+ * calculates the overall score of the alignment preprescore = sum of all
+ * scores - all penalties if preprescore < 1 ~ alignmentScore = Float.NaN >
+ * alignmentScore = ((preprescore - meanScore) / (hypotheticMaxScore -
+ * meanScore)) * coverage
+ */
public void scoreAlignment()
{
char char2 = indelfreeAstr2.charAt(i);
boolean aIsLetter = Character.isLetter(char1);
boolean bIsLetter = Character.isLetter(char2);
- if (aIsLetter && bIsLetter) // if pair -> get score
+ if (aIsLetter && bIsLetter) // if pair -> get score
{
score += scoreMatrix.getPairwiseScore(char1, char2);
- } else if (!aIsLetter && !bIsLetter) { // both are gap -> skip
- } else if ((!aIsLetter && aGapOpen) || (!bIsLetter && bGapOpen)) { // one side gapopen -> score - gap_extend
- score -= GAP_EXTEND_COST;
- } else { // no gap open -> score - gap_open
- score -= GAP_OPEN_COST;
+ }
+ else if (!aIsLetter && !bIsLetter)
+ { // both are gap -> skip
+ }
+ else if ((!aIsLetter && aGapOpen) || (!bIsLetter && bGapOpen))
+ { // one side gapopen -> score - gap_extend
+ score -= GAP_EXTEND_COST;
+ }
+ else
+ { // no gap open -> score - gap_open
+ score -= GAP_OPEN_COST;
}
// adjust GapOpen status in both sequences
aGapOpen = (!aIsLetter) ? true : false;
bGapOpen = (!bIsLetter) ? true : false;
}
- float preprescore = score; // if this score < 1 --> alignment score = Float.NaN
- score = (score - this.meanScore) / (this.hypotheticMaxScore - this.meanScore);
- int[] _max = MiscMath.findMax(new int[]{astr1.replace("-","").length(), astr2.replace("-","").length()}); // {index of max, max}
- float coverage = (float) n / (float) _max[1]; // indelfreeAstr length / longest sequence length
- float prescore = score; // only debug
+ float preprescore = score; // if this score < 1 --> alignment score =
+ // Float.NaN
+ score = (score - this.meanScore)
+ / (this.hypotheticMaxScore - this.meanScore);
+ int[] _max = MiscMath
+ .findMax(new int[]
+ { astr1.replace("-", "").length(),
+ astr2.replace("-", "").length() }); // {index of max, max}
+ float coverage = (float) n / (float) _max[1]; // indelfreeAstr length /
+ // longest sequence length
+ float prescore = score; // only debug
score *= coverage;
- //System.out.println(String.format("prepre-score: %f, pre-score: %f, longlength: %d\nscore: %1.16f, mean: %f, max: %d", preprescore, prescore, _max[1], score, this.meanScore, this.hypotheticMaxScore));
+ // System.out.println(String.format("prepre-score: %f, pre-score: %f,
+ // longlength: %d\nscore: %1.16f, mean: %f, max: %d", preprescore, prescore,
+ // _max[1], score, this.meanScore, this.hypotheticMaxScore));
float minScore = 0f;
this.alignmentScore = (score <= minScore) ? Float.NaN : score;
}
public void setScoreMatrix(ScoreMatrix sm)
{
- if (sm != null) {
- scoreMatrix = sm;
- }
+ if (sm != null)
+ {
+ scoreMatrix = sm;
+ }
}
}
{
private static final int CODON_LENGTH = 3;
- private static final String SEQUENCE_VARIANT = "sequence_variant:";
+ private static final String SEQUENCE_VARIANT = "sequence_variant:";
/*
* the 'id' attribute is provided for variant features fetched from
}
}
}
-
-
- public static boolean isSSAnnotationPresent( Map<SequenceI, List<AlignmentAnnotation>> annotations) {
-
+
+ public static boolean isSSAnnotationPresent(
+ Map<SequenceI, List<AlignmentAnnotation>> annotations)
+ {
+
for (SequenceI seq : annotations.keySet())
{
- if(isSecondaryStructurePresent(annotations.get(seq).toArray(new AlignmentAnnotation[0])))
+ if (isSecondaryStructurePresent(
+ annotations.get(seq).toArray(new AlignmentAnnotation[0])))
{
return true;
}
return ssPresent;
}
-
+
public static Color getSecondaryStructureAnnotationColour(char symbol)
{
}
return Color.white;
+
}
- public static char findSSAnnotationForGivenSeqposition(AlignmentAnnotation aa,
- int seqPosition)
+ public static char findSSAnnotationForGivenSeqposition(
+ AlignmentAnnotation aa, int seqPosition)
{
char ss = '*';
return ssAlignmentAnnotationForSequences;
}
-
+
+
+ // to do set priority for labels
+ public static AlignmentAnnotation getDisplayedAlignmentAnnotation(
+ SequenceI seq)
+ {
+
+ for (String ssLabel : Constants.SECONDARY_STRUCTURE_LABELS.keySet())
+ {
+
+ AlignmentAnnotation[] aa = seq.getAnnotation(ssLabel);
+ if (aa != null)
+ {
+
+ for (AlignmentAnnotation annot : aa)
+ {
+ if (annot.visible)
+ {
+ return annot;
+ }
+ }
+ }
+ }
+
+ return null;
+
+ }
+
}
public class ConnectivityException extends RuntimeException
{
private String sequence;
+
private int connection;
+
private byte dim;
public ConnectivityException(String sequence, int connection, byte dim)
this("Insufficient number of connections", sequence, connection, dim);
}
- public ConnectivityException(String message, String sequence, int connection, byte dim)
+ public ConnectivityException(String message, String sequence,
+ int connection, byte dim)
{
- super(String.format("%s for %s (%d, should be %d or more)", message, sequence, connection, dim));
+ super(String.format("%s for %s (%d, should be %d or more)", message,
+ sequence, connection, dim));
this.sequence = sequence;
this.connection = connection;
this.dim = dim;
}
else
{
- //allFeatures = sf.getAllFeatures(null);
+ // allFeatures = sf.getAllFeatures(null);
allFeatures = sf.getAllFeatures();
}
// so we can check we are advancing when debugging
/**
* Performs Principal Component Analysis on given sequences
- * @AUTHOR MorellThomas
+ *
+ * @AUTHOR MorellThomas
*/
public class PaSiMap implements Runnable
{
* @param sm
* @param options
*/
- public PaSiMap(AlignmentViewport sequences, ScoreModelI sm, PairwiseAlignPanel pap)
+ public PaSiMap(AlignmentViewport sequences, ScoreModelI sm,
+ PairwiseAlignPanel pap)
{
this.seqs = sequences;
- if (sm!=null && sm instanceof ScoreMatrix)
+ if (sm != null && sm instanceof ScoreMatrix)
{
this.scoreMatrix = ((ScoreMatrix) sm);
- } else {
+ }
+ else
+ {
this.scoreMatrix = null;
}
* DOCUMENT ME!
* @param mm
* DOCUMENT ME!
- * @param factor ~ is 1
+ * @param factor
+ * ~ is 1
*
* @return DOCUMENT ME!
*/
}
/**
- * Answers a formatted text report of the PaSiMap calculation results (matrices
- * and eigenvalues) suitable for display
+ * Answers a formatted text report of the PaSiMap calculation results
+ * (matrices and eigenvalues) suitable for display
*
* @return
*/
/**
* Performs the PaSiMap calculation
*
- * creates a new gui/PairwiseAlignPanel with the input sequences (AlignmentViewport)
- * uses analysis/AlignSeq to creatue the pairwise alignments and calculate the AlignmentScores (float for each pair)
+ * creates a new gui/PairwiseAlignPanel with the input sequences
+ * (AlignmentViewport)
+ *
+ * uses analysis/AlignSeq to creatue the pairwise alignments and calculate the
+ * AlignmentScores (float for each pair)
+ *
* gets all float[][] scores from the gui/PairwiseAlignPanel
- * checks the connections for each sequence with AlignmentViewport seqs.calculateConnectivity(float[][] scores, int dim) (from analysis/Connectivity) -- throws an Exception if insufficient
+ *
+ * checks the connections for each sequence with AlignmentViewport
+ * seqs.calculateConnectivity(float[][] scores, int dim) (from
+ * analysis/Connectivity) -- throws an Exception if insufficient
+ *
* creates a math/MatrixI pairwiseScores of the float[][] scores
- * copys the scores and fills the diagonal to create a symmetric matrix using math/Matrix.fillDiagonal()
+ *
+ * copys the scores and fills the diagonal to create a symmetric matrix using
+ * math/Matrix.fillDiagonal()
+ *
* performs the analysis/ccAnalysis with the symmetric matrix
+ *
* gets the eigenmatrix and the eigenvalues using math/Matrix.tqli()
*/
@Override
{
try
{
- //alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
+ // alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
alignment.calculate(scoreMatrix);
- float[][] scores = alignment.getAlignmentScores(); //bigger index first -- eg scores[14][13]
+ float[][] scores = alignment.getAlignmentScores(); // bigger index first
+ // -- eg scores[14][13]
SequenceI[] iseqs = alignment.getInputSequences();
Connectivity.getConnectivity(iseqs, scores, dim);
/**
* A class to model rectangular matrices of double values and operations on them
*/
-public class ccAnalysis
+public class ccAnalysis
{
- private byte dim = 0; //dimensions
+ private byte dim = 0; // dimensions
- private MatrixI scoresOld; //input scores
+ private MatrixI scoresOld; // input scores
public ccAnalysis(MatrixI scores, byte dim)
{
{
for (int j = 0; j < scores.width(); j++)
{
- if (!Double.isNaN(scores.getValue(i,j)))
- {
- scores.setValue(i, j, (double) Math.round(scores.getValue(i,j) * (int) 10000) / 10000);
- }
+ if (!Double.isNaN(scores.getValue(i, j)))
+ {
+ scores.setValue(i, j,
+ (double) Math.round(scores.getValue(i, j) * (int) 10000)
+ / 10000);
+ }
}
}
this.scoresOld = scores;
this.dim = dim;
}
- /**
- * Initialise a distrust-score for each hypothesis (h) of hSigns
- * distrust = conHypNum - proHypNum
- *
- * @param hSigns ~ hypothesis signs (+/-) for each sequence
- * @param scores ~ input score matrix
- *
- * @return distrustScores
- */
+ /**
+ * Initialise a distrust-score for each hypothesis (h) of hSigns distrust =
+ * conHypNum - proHypNum
+ *
+ * @param hSigns
+ * ~ hypothesis signs (+/-) for each sequence
+ * @param scores
+ * ~ input score matrix
+ *
+ * @return distrustScores
+ */
private int[] initialiseDistrusts(byte[] hSigns, MatrixI scores)
{
int[] distrustScores = new int[scores.width()];
-
+
// loop over symmetric matrix
for (int i = 0; i < scores.width(); i++)
{
for (int j = 0; j < scores.width(); j++)
{
- double cell = scores.getRow(i)[j]; // value at [i][j] in scores
- byte hBSign = hSigns[j];
- if (!Double.isNaN(cell))
- {
- byte cellSign = (byte) Math.signum(cell); //check if sign of matrix value fits hyptohesis
- if (cellSign == hASign * hBSign)
- {
- proHypNum++;
- } else {
- conHypNum++;
- }
- }
+ double cell = scores.getRow(i)[j]; // value at [i][j] in scores
+ byte hBSign = hSigns[j];
+ if (!Double.isNaN(cell))
+ {
+ byte cellSign = (byte) Math.signum(cell); // check if sign of matrix
+ // value fits hyptohesis
+ if (cellSign == hASign * hBSign)
+ {
+ proHypNum++;
+ }
+ else
+ {
+ conHypNum++;
+ }
+ }
}
- distrustScores[i] = conHypNum - proHypNum; //create distrust score for each sequence
+ distrustScores[i] = conHypNum - proHypNum; // create distrust score for
+ // each sequence
}
return distrustScores;
}
/**
- * Optemise hypothesis concerning the sign of the hypothetical value for each hSigns by interpreting the pairwise correlation coefficients as scalar products
- *
- * @param hSigns ~ hypothesis signs (+/-)
- * @param distrustScores
- * @param scores ~ input score matrix
- *
- * @return hSigns
- */
- private byte[] optimiseHypothesis(byte[] hSigns, int[] distrustScores, MatrixI scores)
+ * Optimise hypothesis concerning the sign of the hypothetical value for each
+ * hSigns by interpreting the pairwise correlation coefficients as scalar
+ * products
+ *
+ * @param hSigns
+ * ~ hypothesis signs (+/-)
+ * @param distrustScores
+ * @param scores
+ * ~ input score matrix
+ *
+ * @return hSigns
+ */
+ private byte[] optimiseHypothesis(byte[] hSigns, int[] distrustScores,
+ MatrixI scores)
{
// get maximum distrust score
int[] maxes = MiscMath.findMax(distrustScores);
// if hypothesis is not optimal yet
if (maxDistrust > 0)
{
- //toggle sign for hI with maximum distrust
+ // toggle sign for hI with maximum distrust
hSigns[maxDistrustIndex] *= -1;
// update distrust at same position
distrustScores[maxDistrustIndex] *= -1;
byte hASign = hSigns[maxDistrustIndex];
for (int NOTmaxDistrustIndex = 0; NOTmaxDistrustIndex < distrustScores.length; NOTmaxDistrustIndex++)
{
- if (NOTmaxDistrustIndex != maxDistrustIndex)
- {
- byte hBSign = hSigns[NOTmaxDistrustIndex];
- double cell = scores.getValue(maxDistrustIndex, NOTmaxDistrustIndex);
-
- // distrust only changed if not NaN
- if (!Double.isNaN(cell))
- {
- byte cellSign = (byte) Math.signum(cell);
- // if sign of cell matches hypothesis decrease distrust by 2 because 1 more value supporting and 1 less contradicting
- // else increase by 2
- if (cellSign == hASign * hBSign)
- {
- distrustScores[NOTmaxDistrustIndex] -= 2;
- } else {
- distrustScores[NOTmaxDistrustIndex] += 2;
- }
- }
- }
+ if (NOTmaxDistrustIndex != maxDistrustIndex)
+ {
+ byte hBSign = hSigns[NOTmaxDistrustIndex];
+ double cell = scores.getValue(maxDistrustIndex,
+ NOTmaxDistrustIndex);
+
+ // distrust only changed if not NaN
+ if (!Double.isNaN(cell))
+ {
+ byte cellSign = (byte) Math.signum(cell);
+ // if sign of cell matches hypothesis decrease distrust by 2 because
+ // 1 more value supporting and 1 less contradicting
+ // else increase by 2
+ if (cellSign == hASign * hBSign)
+ {
+ distrustScores[NOTmaxDistrustIndex] -= 2;
+ }
+ else
+ {
+ distrustScores[NOTmaxDistrustIndex] += 2;
+ }
+ }
+ }
}
- //further optimisation necessary
+ // further optimisation necessary
return optimiseHypothesis(hSigns, distrustScores, scores);
- } else {
+ }
+ else
+ {
return hSigns;
}
}
- /**
- * takes the a symmetric MatrixI as input scores which may contain Double.NaN
- * approximate the missing values using hypothesis optimisation
- *
- * runs analysis
- *
- * @param scores ~ score matrix
- *
- * @return
- */
- public MatrixI run () throws Exception
+ /**
+ * takes the a symmetric MatrixI as input scores which may contain Double.NaN
+ * approximate the missing values using hypothesis optimisation
+ *
+ * runs analysis
+ *
+ * @param scores
+ * ~ score matrix
+ *
+ * @return
+ */
+ public MatrixI run() throws Exception
{
- //initialse eigenMatrix and repMatrix
+ // initialse eigenMatrix and repMatrix
MatrixI eigenMatrix = scoresOld.copy();
MatrixI repMatrix = scoresOld.copy();
try
{
- /*
- * Calculate correction factor for 2nd and higher eigenvalue(s).
- * This correction is NOT needed for the 1st eigenvalue, because the
- * unknown (=NaN) values of the matrix are approximated by presuming
- * 1-dimensional vectors as the basis of the matrix interpretation as dot
- * products.
- */
-
- System.out.println("Input correlation matrix:");
- eigenMatrix.print(System.out, "%1.4f ");
-
- int matrixWidth = eigenMatrix.width(); // square matrix, so width == height
- int matrixElementsTotal = (int) Math.pow(matrixWidth, 2); //total number of elemts
-
- float correctionFactor = (float) (matrixElementsTotal - eigenMatrix.countNaN()) / (float) matrixElementsTotal;
-
- /*
- * Calculate hypothetical value (1-dimensional vector) h_i for each
- * dataset by interpreting the given correlation coefficients as scalar
- * products.
- */
-
- /*
- * Memory for current hypothesis concerning sign of each h_i.
- * List of signs for all h_i in the encoding:
+ /*
+ * Calculate correction factor for 2nd and higher eigenvalue(s).
+ * This correction is NOT needed for the 1st eigenvalue, because the
+ * unknown (=NaN) values of the matrix are approximated by presuming
+ * 1-dimensional vectors as the basis of the matrix interpretation as dot
+ * products.
+ */
+
+ System.out.println("Input correlation matrix:");
+ eigenMatrix.print(System.out, "%1.4f ");
+
+ int matrixWidth = eigenMatrix.width(); // square matrix, so width ==
+ // height
+ int matrixElementsTotal = (int) Math.pow(matrixWidth, 2); // total number
+ // of elemts
+
+ float correctionFactor = (float) (matrixElementsTotal
+ - eigenMatrix.countNaN()) / (float) matrixElementsTotal;
+
+ /*
+ * Calculate hypothetical value (1-dimensional vector) h_i for each
+ * dataset by interpreting the given correlation coefficients as scalar
+ * products.
+ */
+
+ /*
+ * Memory for current hypothesis concerning sign of each h_i.
+ * List of signs for all h_i in the encoding:
* * 1: positive
* * 0: zero
* * -1: negative
- * Initial hypothesis: all signs are positive.
- */
- byte[] hSigns = new byte[matrixWidth];
- Arrays.fill(hSigns, (byte) 1);
-
- //Estimate signs for each h_i by refining hypothesis on signs.
- hSigns = optimiseHypothesis(hSigns, initialiseDistrusts(hSigns, eigenMatrix), eigenMatrix);
-
-
- //Estimate absolute values for each h_i by determining sqrt of mean of
- //non-NaN absolute values for every row.
- double[] hAbs = MiscMath.sqrt(eigenMatrix.absolute().meanRow());
-
- //Combine estimated signs with absolute values in obtain total value for
- //each h_i.
- double[] hValues = MiscMath.elementwiseMultiply(hSigns, hAbs);
-
- /*Complement symmetric matrix by using the scalar products of estimated
- *values of h_i to replace NaN-cells.
- *Matrix positions that have estimated values
- *(only for diagonal and upper off-diagonal values, due to the symmetry
- *the positions of the lower-diagonal values can be inferred).
- List of tuples (row_idx, column_idx).*/
-
- ArrayList<int[]> estimatedPositions = new ArrayList<int[]>();
-
- // for off-diagonal cells
- for (int rowIndex = 0; rowIndex < matrixWidth - 1; rowIndex++)
- {
- for (int columnIndex = rowIndex + 1; columnIndex < matrixWidth; columnIndex++)
+ * Initial hypothesis: all signs are positive.
+ */
+ byte[] hSigns = new byte[matrixWidth];
+ Arrays.fill(hSigns, (byte) 1);
+
+ // Estimate signs for each h_i by refining hypothesis on signs.
+ hSigns = optimiseHypothesis(hSigns,
+ initialiseDistrusts(hSigns, eigenMatrix), eigenMatrix);
+
+ // Estimate absolute values for each h_i by determining sqrt of mean of
+ // non-NaN absolute values for every row.
+ double[] hAbs = MiscMath.sqrt(eigenMatrix.absolute().meanRow());
+
+ // Combine estimated signs with absolute values in obtain total value for
+ // each h_i.
+ double[] hValues = MiscMath.elementwiseMultiply(hSigns, hAbs);
+
+ /*Complement symmetric matrix by using the scalar products of estimated
+ *values of h_i to replace NaN-cells.
+ *Matrix positions that have estimated values
+ *(only for diagonal and upper off-diagonal values, due to the symmetry
+ *the positions of the lower-diagonal values can be inferred).
+ List of tuples (row_idx, column_idx).*/
+
+ ArrayList<int[]> estimatedPositions = new ArrayList<int[]>();
+
+ // for off-diagonal cells
+ for (int rowIndex = 0; rowIndex < matrixWidth - 1; rowIndex++)
{
- double cell = eigenMatrix.getValue(rowIndex, columnIndex);
- if (Double.isNaN(cell))
- {
- //calculate scalar product as new cell value
- cell = hValues[rowIndex] * hValues[columnIndex];
- //fill in new value in cell and symmetric partner
- eigenMatrix.setValue(rowIndex, columnIndex, cell);
- eigenMatrix.setValue(columnIndex, rowIndex, cell);
- //save positions of estimated values
- estimatedPositions.add(new int[]{rowIndex, columnIndex});
- }
+ for (int columnIndex = rowIndex
+ + 1; columnIndex < matrixWidth; columnIndex++)
+ {
+ double cell = eigenMatrix.getValue(rowIndex, columnIndex);
+ if (Double.isNaN(cell))
+ {
+ // calculate scalar product as new cell value
+ cell = hValues[rowIndex] * hValues[columnIndex];
+ // fill in new value in cell and symmetric partner
+ eigenMatrix.setValue(rowIndex, columnIndex, cell);
+ eigenMatrix.setValue(columnIndex, rowIndex, cell);
+ // save positions of estimated values
+ estimatedPositions.add(new int[] { rowIndex, columnIndex });
+ }
+ }
}
- }
- // for diagonal cells
- for (int diagonalIndex = 0; diagonalIndex < matrixWidth; diagonalIndex++)
+ // for diagonal cells
+ for (int diagonalIndex = 0; diagonalIndex < matrixWidth; diagonalIndex++)
{
double cell = Math.pow(hValues[diagonalIndex], 2);
- eigenMatrix.setValue(diagonalIndex, diagonalIndex, cell);
- estimatedPositions.add(new int[]{diagonalIndex, diagonalIndex});
+ eigenMatrix.setValue(diagonalIndex, diagonalIndex, cell);
+ estimatedPositions.add(new int[] { diagonalIndex, diagonalIndex });
}
- /*Refine total values of each h_i:
- *Initialise h_values of the hypothetical non-existant previous iteration
- *with the correct format but with impossible values.
- Needed for exit condition of otherwise endless loop.*/
- System.out.print("initial values: [ ");
- for (double h : hValues)
- {
- System.out.print(String.format("%1.4f, ", h));
- }
- System.out.println(" ]");
-
-
- double[] hValuesOld = new double[matrixWidth];
-
- int iterationCount = 0;
-
- // repeat unitl values of h do not significantly change anymore
- while (true)
- {
- for (int hIndex = 0; hIndex < matrixWidth; hIndex++)
- {
- double newH = Arrays.stream(MiscMath.elementwiseMultiply(hValues, eigenMatrix.getRow(hIndex))).sum() / Arrays.stream(MiscMath.elementwiseMultiply(hValues, hValues)).sum();
- hValues[hIndex] = newH;
- }
-
- System.out.print(String.format("iteration %d: [ ", iterationCount));
+ /*Refine total values of each h_i:
+ *Initialise h_values of the hypothetical non-existant previous iteration
+ *with the correct format but with impossible values.
+ Needed for exit condition of otherwise endless loop.*/
+ System.out.print("initial values: [ ");
for (double h : hValues)
{
- System.out.print(String.format("%1.4f, ", h));
+ System.out.print(String.format("%1.4f, ", h));
}
System.out.println(" ]");
- //update values of estimated positions
- for (int[] pair : estimatedPositions) // pair ~ row, col
- {
- double newVal = hValues[pair[0]] * hValues[pair[1]];
- eigenMatrix.setValue(pair[0], pair[1], newVal);
- eigenMatrix.setValue(pair[1], pair[0], newVal);
- }
+ double[] hValuesOld = new double[matrixWidth];
- iterationCount++;
+ int iterationCount = 0;
- //exit loop as soon as new values are similar to the last iteration
- if (MiscMath.allClose(hValues, hValuesOld, 0d, 1e-05d, false))
+ // FIXME JAL-4443 - spliterators could be coded out or patched with j2s
+ // annotation
+ // repeat unitl values of h do not significantly change anymore
+ while (true)
{
- break;
+ for (int hIndex = 0; hIndex < matrixWidth; hIndex++)
+ {
+ double newH = Arrays
+ .stream(MiscMath.elementwiseMultiply(hValues,
+ eigenMatrix.getRow(hIndex)))
+ .sum()
+ / Arrays.stream(
+ MiscMath.elementwiseMultiply(hValues, hValues))
+ .sum();
+ hValues[hIndex] = newH;
+ }
+
+ System.out.print(String.format("iteration %d: [ ", iterationCount));
+ for (double h : hValues)
+ {
+ System.out.print(String.format("%1.4f, ", h));
+ }
+ System.out.println(" ]");
+
+ // update values of estimated positions
+ for (int[] pair : estimatedPositions) // pair ~ row, col
+ {
+ double newVal = hValues[pair[0]] * hValues[pair[1]];
+ eigenMatrix.setValue(pair[0], pair[1], newVal);
+ eigenMatrix.setValue(pair[1], pair[0], newVal);
+ }
+
+ iterationCount++;
+
+ // exit loop as soon as new values are similar to the last iteration
+ if (MiscMath.allClose(hValues, hValuesOld, 0d, 1e-05d, false))
+ {
+ break;
+ }
+
+ // save hValues for comparison in the next iteration
+ System.arraycopy(hValues, 0, hValuesOld, 0, hValues.length);
}
- //save hValues for comparison in the next iteration
- System.arraycopy(hValues, 0, hValuesOld, 0, hValues.length);
- }
-
- //-----------------------------
- //Use complemented symmetric matrix to calculate final representative
- //vectors.
-
- //Eigendecomposition.
- eigenMatrix.tred();
- eigenMatrix.tqli();
+ // -----------------------------
+ // Use complemented symmetric matrix to calculate final representative
+ // vectors.
- System.out.println("eigenmatrix");
- eigenMatrix.print(System.out, "%8.2f");
- System.out.println();
- System.out.println("uncorrected eigenvalues");
- eigenMatrix.printD(System.out, "%2.4f ");
- System.out.println();
+ // Eigendecomposition.
+ eigenMatrix.tred();
+ eigenMatrix.tqli();
- double[] eigenVals = eigenMatrix.getD();
+ System.out.println("eigenmatrix");
+ eigenMatrix.print(System.out, "%8.2f");
+ System.out.println();
+ System.out.println("uncorrected eigenvalues");
+ eigenMatrix.printD(System.out, "%2.4f ");
+ System.out.println();
- TreeMap<Double, Integer> eigenPairs = new TreeMap<>(Comparator.reverseOrder());
- for (int i = 0; i < eigenVals.length; i++)
- {
- eigenPairs.put(eigenVals[i], i);
- }
+ double[] eigenVals = eigenMatrix.getD();
- // matrix of representative eigenvectors (each row is a vector)
- double[][] _repMatrix = new double[eigenVals.length][dim];
- double[][] _oldMatrix = new double[eigenVals.length][dim];
- double[] correctedEigenValues = new double[dim];
-
- int l = 0;
- for (Entry<Double, Integer> pair : eigenPairs.entrySet())
- {
- double eigenValue = pair.getKey();
- int column = pair.getValue();
- double[] eigenVector = eigenMatrix.getColumn(column);
- //for 2nd and higher eigenvalues
- if (l >= 1)
+ TreeMap<Double, Integer> eigenPairs = new TreeMap<>(
+ Comparator.reverseOrder());
+ for (int i = 0; i < eigenVals.length; i++)
{
- eigenValue /= correctionFactor;
+ eigenPairs.put(eigenVals[i], i);
}
- correctedEigenValues[l] = eigenValue;
- for (int j = 0; j < eigenVector.length; j++)
- {
- _repMatrix[j][l] = (eigenValue < 0) ? 0.0 : - Math.sqrt(eigenValue) * eigenVector[j];
- double tmpOldScore = scoresOld.getColumn(column)[j];
- _oldMatrix[j][dim - l - 1] = (Double.isNaN(tmpOldScore)) ? 0.0 : tmpOldScore;
- }
- l++;
- if (l >= dim)
- {
- break;
- }
- }
- System.out.println("correctedEigenValues");
- MiscMath.print(correctedEigenValues, "%2.4f ");
-
- repMatrix = new Matrix(_repMatrix);
- repMatrix.setD(correctedEigenValues);
- MatrixI oldMatrix = new Matrix(_oldMatrix);
-
- MatrixI dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
-
- double rmsd = scoresOld.rmsd(dotMatrix);
-
- System.out.println("iteration, rmsd, maxDiff, rmsdDiff");
- System.out.println(String.format("0, %8.5f, -, -", rmsd));
- // Refine representative vectors by minimising sum-of-squared deviates between dotMatrix and original score matrix
- for (int iteration = 1; iteration < 21; iteration++) // arbitrarily set to 20
- {
- MatrixI repMatrixOLD = repMatrix.copy();
- MatrixI dotMatrixOLD = dotMatrix.copy();
+ // matrix of representative eigenvectors (each row is a vector)
+ double[][] _repMatrix = new double[eigenVals.length][dim];
+ double[][] _oldMatrix = new double[eigenVals.length][dim];
+ double[] correctedEigenValues = new double[dim];
- // for all rows/hA in the original matrix
- for (int hAIndex = 0; hAIndex < oldMatrix.height(); hAIndex++)
+ int l = 0;
+ for (Entry<Double, Integer> pair : eigenPairs.entrySet())
{
- double[] row = oldMatrix.getRow(hAIndex);
- double[] hA = repMatrix.getRow(hAIndex);
- hAIndex = hAIndex;
- //find least-squares-solution fo rdifferences between original scores and representative vectors
- double[] hAlsm = leastSquaresOptimisation(repMatrix, scoresOld, hAIndex);
- // update repMatrix with new hAlsm
- for (int j = 0; j < repMatrix.width(); j++)
- {
- repMatrix.setValue(hAIndex, j, hAlsm[j]);
- }
- }
-
- // dot product of representative vecotrs yields a matrix with values approximating the correlation matrix
- dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
- // calculate rmsd between approximation and correlation matrix
- rmsd = scoresOld.rmsd(dotMatrix);
-
- // calculate maximum change of representative vectors of current iteration
- MatrixI diff = repMatrix.subtract(repMatrixOLD).absolute();
- double maxDiff = 0.0;
- for (int i = 0; i < diff.height(); i++)
- {
- for (int j = 0; j < diff.width(); j++)
- {
- maxDiff = (diff.getValue(i, j) > maxDiff) ? diff.getValue(i, j) : maxDiff;
- }
+ double eigenValue = pair.getKey();
+ int column = pair.getValue();
+ double[] eigenVector = eigenMatrix.getColumn(column);
+ // for 2nd and higher eigenvalues
+ if (l >= 1)
+ {
+ eigenValue /= correctionFactor;
+ }
+ correctedEigenValues[l] = eigenValue;
+ for (int j = 0; j < eigenVector.length; j++)
+ {
+ _repMatrix[j][l] = (eigenValue < 0) ? 0.0
+ : -Math.sqrt(eigenValue) * eigenVector[j];
+ double tmpOldScore = scoresOld.getColumn(column)[j];
+ _oldMatrix[j][dim - l - 1] = (Double.isNaN(tmpOldScore)) ? 0.0
+ : tmpOldScore;
+ }
+ l++;
+ if (l >= dim)
+ {
+ break;
+ }
}
- // calculate rmsd between current and previous estimation
- double rmsdDiff = dotMatrix.rmsd(dotMatrixOLD);
+ System.out.println("correctedEigenValues");
+ MiscMath.print(correctedEigenValues, "%2.4f ");
+
+ repMatrix = new Matrix(_repMatrix);
+ repMatrix.setD(correctedEigenValues);
+ MatrixI oldMatrix = new Matrix(_oldMatrix);
- System.out.println(String.format("%d, %8.5f, %8.5f, %8.5f", iteration, rmsd, maxDiff, rmsdDiff));
+ MatrixI dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
- if (!(Math.abs(maxDiff) > 1e-06))
+ double rmsd = scoresOld.rmsd(dotMatrix);
+
+ System.out.println("iteration, rmsd, maxDiff, rmsdDiff");
+ System.out.println(String.format("0, %8.5f, -, -", rmsd));
+ // Refine representative vectors by minimising sum-of-squared deviates
+ // between dotMatrix and original score matrix
+ for (int iteration = 1; iteration < 21; iteration++) // arbitrarily set to
+ // 20
{
- repMatrix = repMatrixOLD.copy();
- break;
+ MatrixI repMatrixOLD = repMatrix.copy();
+ MatrixI dotMatrixOLD = dotMatrix.copy();
+
+ // for all rows/hA in the original matrix
+ for (int hAIndex = 0; hAIndex < oldMatrix.height(); hAIndex++)
+ {
+ double[] row = oldMatrix.getRow(hAIndex);
+ double[] hA = repMatrix.getRow(hAIndex);
+ hAIndex = hAIndex;
+ // find least-squares-solution fo rdifferences between original scores
+ // and representative vectors
+ double[] hAlsm = leastSquaresOptimisation(repMatrix, scoresOld,
+ hAIndex);
+ // update repMatrix with new hAlsm
+ for (int j = 0; j < repMatrix.width(); j++)
+ {
+ repMatrix.setValue(hAIndex, j, hAlsm[j]);
+ }
+ }
+
+ // dot product of representative vecotrs yields a matrix with values
+ // approximating the correlation matrix
+ dotMatrix = repMatrix.postMultiply(repMatrix.transpose());
+ // calculate rmsd between approximation and correlation matrix
+ rmsd = scoresOld.rmsd(dotMatrix);
+
+ // calculate maximum change of representative vectors of current
+ // iteration
+ MatrixI diff = repMatrix.subtract(repMatrixOLD).absolute();
+ double maxDiff = 0.0;
+ for (int i = 0; i < diff.height(); i++)
+ {
+ for (int j = 0; j < diff.width(); j++)
+ {
+ maxDiff = (diff.getValue(i, j) > maxDiff) ? diff.getValue(i, j)
+ : maxDiff;
+ }
+ }
+
+ // calculate rmsd between current and previous estimation
+ double rmsdDiff = dotMatrix.rmsd(dotMatrixOLD);
+
+ System.out.println(String.format("%d, %8.5f, %8.5f, %8.5f",
+ iteration, rmsd, maxDiff, rmsdDiff));
+
+ if (!(Math.abs(maxDiff) > 1e-06))
+ {
+ repMatrix = repMatrixOLD.copy();
+ break;
+ }
}
- }
-
} catch (Exception q)
{
}
/**
- * Create equations system using information on originally known
- * pairwise correlation coefficients (parsed from infile) and the
- * representative result vectors
- *
- * Each equation has the format:
- * hA * hA - pairwiseCC = 0
- * with:
- * hA: unknown variable
- * hB: known representative vector
- * pairwiseCC: known pairwise correlation coefficien
- *
- * The resulting equations system is overdetermined, if there are more
- * equations than unknown elements
- *
- * @param x ~ unknown n-dimensional column-vector
- * (needed for generating equations system, NOT to be specified by user).
- * @param hAIndex ~ index of currently optimised representative result vector.
- * @param h ~ matrix with row-wise listing of representative result vectors.
- * @param originalRow ~ matrix-row of originally parsed pairwise correlation coefficients.
- *
- * @return
- */
- private double[] originalToEquasionSystem(double[] hA, MatrixI repMatrix, MatrixI scoresOld, int hAIndex)
+ * Create equations system using information on originally known pairwise
+ * correlation coefficients (parsed from infile) and the representative result
+ * vectors
+ *
+ * Each equation has the format:
+ *
+ * hA * hA - pairwiseCC = 0
+ *
+ * with:
+ *
+ * hA: unknown variable
+ *
+ * hB: known representative vector
+ *
+ * pairwiseCC: known pairwise correlation coefficien
+ *
+ * The resulting equations system is overdetermined, if there are more
+ * equations than unknown elements
+ *
+ * x is the user input. Remaining parameters are needed for generating
+ * equations system, NOT to be specified by user).
+ *
+ * @param x
+ * ~ unknown n-dimensional column-vector
+ * @param hAIndex
+ * ~ index of currently optimised representative result vector.
+ * @param h
+ * ~ matrix with row-wise listing of representative result vectors.
+ * @param originalRow
+ * ~ matrix-row of originally parsed pairwise correlation
+ * coefficients.
+ *
+ * @return
+ */
+ private double[] originalToEquasionSystem(double[] hA, MatrixI repMatrix,
+ MatrixI scoresOld, int hAIndex)
{
double[] originalRow = scoresOld.getRow(hAIndex);
int nans = MiscMath.countNaN(originalRow);
double[] result = new double[originalRow.length - nans];
- //for all pairwiseCC in originalRow
+ // for all pairwiseCC in originalRow
int resultIndex = 0;
for (int hBIndex = 0; hBIndex < originalRow.length; hBIndex++)
{
if (!Double.isNaN(pairwiseCC))
{
double[] hB = repMatrix.getRow(hBIndex);
- result[resultIndex++] = MiscMath.sum(MiscMath.elementwiseMultiply(hA, hB)) - pairwiseCC;
- } else {
+ result[resultIndex++] = MiscMath
+ .sum(MiscMath.elementwiseMultiply(hA, hB)) - pairwiseCC;
+ }
+ else
+ {
}
}
return result;
}
/**
- * returns the jacobian matrix
- * @param repMatrix ~ matrix of representative vectors
- * @param hAIndex ~ current row index
- *
- * @return
- */
- private MatrixI approximateDerivative(MatrixI repMatrix, MatrixI scoresOld, int hAIndex)
+ * returns the jacobian matrix
+ *
+ * @param repMatrix
+ * ~ matrix of representative vectors
+ * @param hAIndex
+ * ~ current row index
+ *
+ * @return
+ */
+ private MatrixI approximateDerivative(MatrixI repMatrix,
+ MatrixI scoresOld, int hAIndex)
{
- //hA = x0
+ // hA = x0
double[] hA = repMatrix.getRow(hAIndex);
- double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld, hAIndex);
+ double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld,
+ hAIndex);
double[] signX0 = new double[hA.length];
double[] xAbs = new double[hA.length];
for (int i = 0; i < hA.length; i++)
{
signX0[i] = (hA[i] >= 0) ? 1 : -1;
xAbs[i] = (Math.abs(hA[i]) >= 1.0) ? Math.abs(hA[i]) : 1.0;
- }
+ }
double rstep = Math.pow(Math.ulp(1.0), 0.5);
- double[] h = new double [hA.length];
+ double[] h = new double[hA.length];
for (int i = 0; i < hA.length; i++)
{
h[i] = rstep * signX0[i] * xAbs[i];
}
-
+
int m = f0.length;
int n = hA.length;
double[][] jTransposed = new double[n][m];
System.arraycopy(hA, 0, x, 0, h.length);
x[i] += h[i];
double dx = x[i] - hA[i];
- double[] df = originalToEquasionSystem(x, repMatrix, scoresOld, hAIndex);
+ double[] df = originalToEquasionSystem(x, repMatrix, scoresOld,
+ hAIndex);
for (int j = 0; j < df.length; j++)
{
- df[j] -= f0[j];
- jTransposed[i][j] = df[j] / dx;
+ df[j] -= f0[j];
+ jTransposed[i][j] = df[j] / dx;
}
}
MatrixI J = new Matrix(jTransposed).transpose();
}
/**
- * norm of regularized (by alpha) least-squares solution minus Delta
- * @param alpha
- * @param suf
- * @param s
- * @param Delta
- *
- * @return
- */
- private double[] phiAndDerivative(double alpha, double[] suf, double[] s, double Delta)
+ * norm of regularized (by alpha) least-squares solution minus Delta
+ *
+ * @param alpha
+ * @param suf
+ * @param s
+ * @param Delta
+ *
+ * @return
+ */
+ private double[] phiAndDerivative(double alpha, double[] suf, double[] s,
+ double Delta)
{
- double[] denom = MiscMath.elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha);
+ double[] denom = MiscMath
+ .elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha);
double pNorm = MiscMath.norm(MiscMath.elementwiseDivide(suf, denom));
double phi = pNorm - Delta;
// - sum ( suf**2 / denom**3) / pNorm
- double phiPrime = - MiscMath.sum(MiscMath.elementwiseDivide(MiscMath.elementwiseMultiply(suf, suf), MiscMath.elementwiseMultiply(MiscMath.elementwiseMultiply(denom, denom), denom))) / pNorm;
- return new double[]{phi, phiPrime};
+ double phiPrime = -MiscMath.sum(MiscMath.elementwiseDivide(
+ MiscMath.elementwiseMultiply(suf, suf),
+ MiscMath.elementwiseMultiply(
+ MiscMath.elementwiseMultiply(denom, denom), denom)))
+ / pNorm;
+ return new double[] { phi, phiPrime };
}
/**
- * class holding the result of solveLsqTrustRegion
- */
+ * class holding the result of solveLsqTrustRegion
+ */
private class TrustRegion
{
private double[] step;
+
private double alpha;
+
private int iteration;
public TrustRegion(double[] step, double alpha, int iteration)
{
return this.alpha;
}
-
+
public int getIteration()
{
return this.iteration;
}
/**
- * solve a trust-region problem arising in least-squares optimisation
- * @param n ~ number of variables
- * @param m ~ number of residuals
- * @param uf
- * @param s ~ singular values of J
- * @param V ~ transpose of VT
- * @param Delta ~ radius of a trust region
- * @param alpha ~ initial guess for alpha
- *
- * @return
- */
- private TrustRegion solveLsqTrustRegion(int n, int m, double[] uf, double[] s, MatrixI V, double Delta, double alpha)
+ * solve a trust-region problem arising in least-squares optimisation
+ *
+ * @param n
+ * ~ number of variables
+ * @param m
+ * ~ number of residuals
+ * @param uf
+ * @param s
+ * ~ singular values of J
+ * @param V
+ * ~ transpose of VT
+ * @param Delta
+ * ~ radius of a trust region
+ * @param alpha
+ * ~ initial guess for alpha
+ *
+ * @return
+ */
+ private TrustRegion solveLsqTrustRegion(int n, int m, double[] uf,
+ double[] s, MatrixI V, double Delta, double alpha)
{
double[] suf = MiscMath.elementwiseMultiply(s, uf);
- //check if J has full rank and tr Gauss-Newton step
+ // check if J has full rank and tr Gauss-Newton step
boolean fullRank = false;
if (m >= n)
{
}
if (fullRank)
{
- double[] p = MiscMath.elementwiseMultiply(V.sumProduct(MiscMath.elementwiseDivide(uf, s)), -1);
+ double[] p = MiscMath.elementwiseMultiply(
+ V.sumProduct(MiscMath.elementwiseDivide(uf, s)), -1);
if (MiscMath.norm(p) <= Delta)
{
TrustRegion result = new TrustRegion(p, 0.0, 0);
if (fullRank)
{
double[] phiAndPrime = phiAndDerivative(0.0, suf, s, Delta);
- alphaLower = - phiAndPrime[0] / phiAndPrime[1];
+ alphaLower = -phiAndPrime[0] / phiAndPrime[1];
}
- alpha = (!fullRank && alpha == 0.0) ? alpha = Math.max(0.001 * alphaUpper, Math.pow(alphaLower * alphaUpper, 0.5)) : alpha;
+ alpha = (!fullRank && alpha == 0.0)
+ ? alpha = Math.max(0.001 * alphaUpper,
+ Math.pow(alphaLower * alphaUpper, 0.5))
+ : alpha;
int iteration = 0;
- while (iteration < 10) // 10 is default max_iter
+ while (iteration < 10) // 10 is default max_iter
{
- alpha = (alpha < alphaLower || alpha > alphaUpper) ? alpha = Math.max(0.001 * alphaUpper, Math.pow(alphaLower * alphaUpper, 0.5)) : alpha;
+ alpha = (alpha < alphaLower || alpha > alphaUpper)
+ ? alpha = Math.max(0.001 * alphaUpper,
+ Math.pow(alphaLower * alphaUpper, 0.5))
+ : alpha;
double[] phiAndPrime = phiAndDerivative(alpha, suf, s, Delta);
double phi = phiAndPrime[0];
double phiPrime = phiAndPrime[1];
alphaLower = Math.max(alphaLower, alpha - ratio);
alpha -= (phi + Delta) * ratio / Delta;
- if (Math.abs(phi) < 0.01 * Delta) // default rtol set to 0.01
+ if (Math.abs(phi) < 0.01 * Delta) // default rtol set to 0.01
{
- break;
+ break;
}
iteration++;
}
// p = - V.dot( suf / (s**2 + alpha))
- double[] tmp = MiscMath.elementwiseDivide(suf, MiscMath.elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha));
+ double[] tmp = MiscMath.elementwiseDivide(suf, MiscMath
+ .elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha));
double[] p = MiscMath.elementwiseMultiply(V.sumProduct(tmp), -1);
- // Make the norm of p equal to Delta, p is changed only slightly during this.
+ // Make the norm of p equal to Delta, p is changed only slightly during
+ // this.
// It is done to prevent p lie outside of the trust region
p = MiscMath.elementwiseMultiply(p, Delta / MiscMath.norm(p));
}
/**
- * compute values of a quadratic function arising in least squares
- * function: 0.5 * s.T * (J.T * J + diag) * s + g.T * s
- *
- * @param J ~ jacobian matrix
- * @param g ~ gradient
- * @param s ~ steps and rows
- *
- * @return
- */
+ * compute values of a quadratic function arising in least squares function:
+ * 0.5 * s.T * (J.T * J + diag) * s + g.T * s
+ *
+ * @param J
+ * ~ jacobian matrix
+ * @param g
+ * ~ gradient
+ * @param s
+ * ~ steps and rows
+ *
+ * @return
+ */
private double evaluateQuadratic(MatrixI J, double[] g, double[] s)
{
}
/**
- * update the radius of a trust region based on the cost reduction
- *
- * @param Delta
- * @param actualReduction
- * @param predictedReduction
- * @param stepNorm
- * @param boundHit
- *
- * @return
- */
- private double[] updateTrustRegionRadius(double Delta, double actualReduction, double predictedReduction, double stepNorm, boolean boundHit)
+ * update the radius of a trust region based on the cost reduction
+ *
+ * @param Delta
+ * @param actualReduction
+ * @param predictedReduction
+ * @param stepNorm
+ * @param boundHit
+ *
+ * @return
+ */
+ private double[] updateTrustRegionRadius(double Delta,
+ double actualReduction, double predictedReduction,
+ double stepNorm, boolean boundHit)
{
double ratio = 0;
if (predictedReduction > 0)
{
ratio = actualReduction / predictedReduction;
- } else if (predictedReduction == 0 && actualReduction == 0) {
+ }
+ else if (predictedReduction == 0 && actualReduction == 0)
+ {
ratio = 1;
- } else {
+ }
+ else
+ {
ratio = 0;
}
if (ratio < 0.25)
{
Delta = 0.25 * stepNorm;
- } else if (ratio > 0.75 && boundHit) {
+ }
+ else if (ratio > 0.75 && boundHit)
+ {
Delta *= 2.0;
}
- return new double[]{Delta, ratio};
+ return new double[] { Delta, ratio };
}
/**
- * trust region reflective algorithm
- * @param repMatrix ~ Matrix containing representative vectors
- * @param scoresOld ~ Matrix containing initial observations
- * @param index ~ current row index
- * @param J ~ jacobian matrix
- *
- * @return
- */
- private double[] trf(MatrixI repMatrix, MatrixI scoresOld, int index, MatrixI J)
+ * trust region reflective algorithm
+ *
+ * @param repMatrix
+ * ~ Matrix containing representative vectors
+ * @param scoresOld
+ * ~ Matrix containing initial observations
+ * @param index
+ * ~ current row index
+ * @param J
+ * ~ jacobian matrix
+ *
+ * @return
+ */
+ private double[] trf(MatrixI repMatrix, MatrixI scoresOld, int index,
+ MatrixI J)
{
- //hA = x0
+ // hA = x0
double[] hA = repMatrix.getRow(index);
double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld, index);
int nfev = 1;
double[] g = J.transpose().sumProduct(f0);
double Delta = MiscMath.norm(hA);
int maxNfev = hA.length * 100;
- double alpha = 0.0; // "Levenberg-Marquardt" parameter
+ double alpha = 0.0; // "Levenberg-Marquardt" parameter
double gNorm = 0;
boolean terminationStatus = false;
gNorm = MiscMath.norm(g);
if (terminationStatus || nfev == maxNfev)
{
- break;
+ break;
}
- SingularValueDecomposition svd = new SingularValueDecomposition(new Array2DRowRealMatrix(J.asArray()));
+ SingularValueDecomposition svd = new SingularValueDecomposition(
+ new Array2DRowRealMatrix(J.asArray()));
MatrixI U = new Matrix(svd.getU().getData());
- double[] s = svd.getSingularValues();
+ double[] s = svd.getSingularValues();
MatrixI V = new Matrix(svd.getV().getData()).transpose();
double[] uf = U.transpose().sumProduct(f0);
double[] fNew = new double[f0.length];
double costNew = 0;
double stepHnorm = 0;
-
+
while (actualReduction <= 0 && nfev < maxNfev)
{
- TrustRegion trustRegion = solveLsqTrustRegion(n, m, uf, s, V, Delta, alpha);
- double[] stepH = trustRegion.getStep();
- alpha = trustRegion.getAlpha();
- int nIterations = trustRegion.getIteration();
- double predictedReduction = - (evaluateQuadratic(J, g, stepH));
+ TrustRegion trustRegion = solveLsqTrustRegion(n, m, uf, s, V, Delta,
+ alpha);
+ double[] stepH = trustRegion.getStep();
+ alpha = trustRegion.getAlpha();
+ int nIterations = trustRegion.getIteration();
+ double predictedReduction = -(evaluateQuadratic(J, g, stepH));
xNew = MiscMath.elementwiseAdd(hA, stepH);
- fNew = originalToEquasionSystem(xNew, repMatrix, scoresOld, index);
- nfev++;
-
- stepHnorm = MiscMath.norm(stepH);
+ fNew = originalToEquasionSystem(xNew, repMatrix, scoresOld, index);
+ nfev++;
- if (MiscMath.countNaN(fNew) > 0)
- {
- Delta = 0.25 * stepHnorm;
- continue;
- }
+ stepHnorm = MiscMath.norm(stepH);
- // usual trust-region step quality estimation
- costNew = 0.5 * MiscMath.dot(fNew, fNew);
- actualReduction = cost - costNew;
+ if (MiscMath.countNaN(fNew) > 0)
+ {
+ Delta = 0.25 * stepHnorm;
+ continue;
+ }
- double[] updatedTrustRegion = updateTrustRegionRadius(Delta, actualReduction, predictedReduction, stepHnorm, stepHnorm > (0.95 * Delta));
- double DeltaNew = updatedTrustRegion[0];
- double ratio = updatedTrustRegion[1];
+ // usual trust-region step quality estimation
+ costNew = 0.5 * MiscMath.dot(fNew, fNew);
+ actualReduction = cost - costNew;
- // default ftol and xtol = 1e-8
- boolean ftolSatisfied = actualReduction < (1e-8 * cost) && ratio > 0.25;
- boolean xtolSatisfied = stepHnorm < (1e-8 * (1e-8 + MiscMath.norm(hA)));
- terminationStatus = ftolSatisfied || xtolSatisfied;
- if (terminationStatus)
- {
- break;
- }
+ double[] updatedTrustRegion = updateTrustRegionRadius(Delta,
+ actualReduction, predictedReduction, stepHnorm,
+ stepHnorm > (0.95 * Delta));
+ double DeltaNew = updatedTrustRegion[0];
+ double ratio = updatedTrustRegion[1];
- alpha *= Delta / DeltaNew;
- Delta = DeltaNew;
+ // default ftol and xtol = 1e-8
+ boolean ftolSatisfied = actualReduction < (1e-8 * cost)
+ && ratio > 0.25;
+ boolean xtolSatisfied = stepHnorm < (1e-8
+ * (1e-8 + MiscMath.norm(hA)));
+ terminationStatus = ftolSatisfied || xtolSatisfied;
+ if (terminationStatus)
+ {
+ break;
+ }
+
+ alpha *= Delta / DeltaNew;
+ Delta = DeltaNew;
}
if (actualReduction > 0)
{
- hA = xNew;
- f0 = fNew;
- cost = costNew;
+ hA = xNew;
+ f0 = fNew;
+ cost = costNew;
- J = approximateDerivative(repMatrix, scoresOld, index);
+ J = approximateDerivative(repMatrix, scoresOld, index);
g = J.transpose().sumProduct(f0);
- } else {
+ }
+ else
+ {
stepHnorm = 0;
- actualReduction = 0;
+ actualReduction = 0;
}
iteration++;
}
}
/**
- * performs the least squares optimisation
- * adapted from https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.least_squares.html#scipy.optimize.least_squares
- *
- * @param repMatrix ~ Matrix containing representative vectors
- * @param scoresOld ~ Matrix containing initial observations
- * @param index ~ current row index
- *
- * @return
- */
- private double[] leastSquaresOptimisation(MatrixI repMatrix, MatrixI scoresOld, int index)
+ * performs the least squares optimisation adapted from
+ * https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.least_squares.html#scipy.optimize.least_squares
+ *
+ * @param repMatrix
+ * ~ Matrix containing representative vectors
+ * @param scoresOld
+ * ~ Matrix containing initial observations
+ * @param index
+ * ~ current row index
+ *
+ * @return
+ */
+ private double[] leastSquaresOptimisation(MatrixI repMatrix,
+ MatrixI scoresOld, int index)
{
MatrixI J = approximateDerivative(repMatrix, scoresOld, index);
double[] result = trf(repMatrix, scoresOld, index, J);
return similarities;
}
-
+
}
public boolean isProtein()
{
return true;
- }
+ }
@Override
public String toString()
private final ScoreMatrix PAM250;
private final ScoreMatrix DNA;
-
+
private final ScoreMatrix SECONDARYSTRUCTURE;
private static ScoreModels instance;
* <li>PAM250</li>
* <li>PID</li>
* <li>DNA</li>
- * <li>Sequence Feature Similarity</li> *
+ * <li>Sequence Feature Similarity</li> *
* <li>Secondary Structure Similarity</li>
* </ul>
*/
DNA = loadScoreMatrix("scoreModel/dna.scm");
registerScoreModel(new PIDModel());
registerScoreModel(new FeatureDistanceModel());
- SECONDARYSTRUCTURE = loadScoreMatrix("scoreModel/secondarystructure.scm");
- registerScoreModel(new SecondaryStructureDistanceModel());
+ SECONDARYSTRUCTURE = loadScoreMatrix(
+ "scoreModel/secondarystructure.scm");
+ registerScoreModel(new SecondaryStructureDistanceModel());
}
public void registerScoreModel(ScoreModelI sm)
{
- if(sm.getName().equals("SECONDARYSTRUCTURE")) {
+ if (sm.getName().equals("SECONDARYSTRUCTURE"))
+ {
return;
}
ScoreModelI sm2 = models.get(sm.getName());
{
return PAM250;
}
-
+
public ScoreMatrix getSecondaryStructureMatrix()
{
return SECONDARYSTRUCTURE;
private static final String NAME = "Secondary Structure Similarity";
private ScoreMatrix ssRateMatrix;
-
- private String description;
-
+
+ private String description;
+
FeatureRenderer fr;
-
-
+
/**
* Constructor
*/
public SecondaryStructureDistanceModel()
{
-
+
}
-
+
@Override
public ScoreModelI getInstance(AlignmentViewPanel view)
{
fr = view.cloneFeatureRenderer();
return true;
}
-
+
/**
- * Calculates distance score [i][j] between each pair of protein sequences
- * based on their secondary structure annotations (H, E, C).
- * The final score is normalised by the number of
- * alignment columns processed, providing an average similarity score.
+ * Calculates distance score [i][j] between each pair of protein sequences
+ * based on their secondary structure annotations (H, E, C). The final score
+ * is normalised by the number of alignment columns processed, providing an
+ * average similarity score.
* <p>
- * The parameters argument can include settings for handling gap-residue aligned
- * positions and may determine if the score calculation is based on the longer or shorter
- * sequence in each pair. This can be important for handling partial alignments or
- * sequences of significantly different lengths.
+ * The parameters argument can include settings for handling gap-residue
+ * aligned positions and may determine if the score calculation is based on
+ * the longer or shorter sequence in each pair. This can be important for
+ * handling partial alignments or sequences of significantly different
+ * lengths.
*
- * @param seqData The aligned sequence data including secondary structure annotations.
- * @param params Additional parameters for customising the scoring process, such as gap
- * handling and sequence length consideration.
+ * @param seqData
+ * The aligned sequence data including secondary structure
+ * annotations.
+ * @param params
+ * Additional parameters for customising the scoring process, such as
+ * gap handling and sequence length consideration.
*/
@Override
public MatrixI findDistances(AlignmentView seqData,
SimilarityParamsI params)
- {
-
+ {
+
SeqCigar[] seqs = seqData.getSequences();
int noseqs = seqs.length; //no of sequences
int cpwidth = 0;
AlignmentAnnotation[] alignAnnotList = fr.getViewport().getAlignment()
.getAlignmentAnnotation();
-
/*
* Add secondary structure annotations that are added to the annotation track
Map<SequenceI, ArrayList<AlignmentAnnotation>> ssAlignmentAnnotationForSequences
= AlignmentUtils.getSequenceAssociatedAlignmentAnnotations(alignAnnotList, ssSource);
+
/*
* scan each column, compute and add to each similarity[i, j]
* the number of secondary structure annotation that seqi
*/
for (int vc = 0; vc < viscont.length; vc += 2)
{
- //Iterates for each column position
- for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++)
+ // Iterates for each column position
+ for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++)
{
- cpwidth++; //used to normalise the similarity score
+ cpwidth++; // used to normalise the similarity score
/*
* get set of sequences without gap in the current column
*/
- Set<SeqCigar> seqsWithoutGapAtCol = findSeqsWithoutGapAtColumn(seqs, cpos);
+ Set<SeqCigar> seqsWithoutGapAtCol = findSeqsWithoutGapAtColumn(seqs,
+ cpos);
/*
* calculate similarity score for each secondary structure annotation on i'th and j'th
*/
for (int i = 0; i < (noseqs - 1); i++)
{
- //Iterates for each sequences
+ // Iterates for each sequences
for (int j = i + 1; j < noseqs; j++)
{
boolean undefinedSS2 = ssAlignmentAnnotationForSequences.get(seqs[j].getRefSeq()) == null;
// Set similarity to max score if both SS are not defined
- if (undefinedSS1 && undefinedSS2) {
- similarities[i][j] += ssRateMatrix.getMaximumScore();
- continue;
- }
-
- // Set similarity to minimum score if either one SS is not defined
- else if(undefinedSS1 || undefinedSS2) {
- similarities[i][j] += ssRateMatrix.getMinimumScore();
- continue;
+ if (undefinedSS1 && undefinedSS2)
+ {
+ similarities[i][j] += ssRateMatrix.getMaximumScore();
+ continue;
}
//check if the sequence contains gap in the current column
boolean gap2 = !seqsWithoutGapAtCol.contains(seqs[j]);
//Variable to store secondary structure at the current column
+
char ss1 = '*';
char ss2 = '*';
-
- //secondary structure is fetched only if the current column is not
- //gap for the sequence
- if(!gap1 && !undefinedSS1) {
- //fetch the position in sequence for the column and finds the
- //corresponding secondary structure annotation
- //TO DO - consider based on priority and displayed
+
+ // secondary structure is fetched only if the current column is not
+ // gap for the sequence
+ if (!gap1 && !undefinedSS1)
+ {
+ // fetch the position in sequence for the column and finds the
+ // corresponding secondary structure annotation
+ // TO DO - consider based on priority and displayed
int seqPosition = seqs[i].findPosition(cpos);
AlignmentAnnotation aa = ssAlignmentAnnotationForSequences.get(seqs[i].getRefSeq()).get(0);
if(aa!=null)
ss1 =
AlignmentUtils.findSSAnnotationForGivenSeqposition(aa, seqPosition);
+
}
-
- if(!gap2 && !undefinedSS2) {
+
+ if (!gap2 && !undefinedSS2)
+ {
int seqPosition = seqs[j].findPosition(cpos);
AlignmentAnnotation aa = ssAlignmentAnnotationForSequences.get(seqs[j].getRefSeq()).get(0);
if(aa!=null)
AlignmentUtils.findSSAnnotationForGivenSeqposition(aa, seqPosition);
}
+
if ((!gap1 && !gap2) || params.includeGaps())
{
// Calculate similarity score based on the substitution matrix
- double similarityScore = ssRateMatrix.getPairwiseScore(ss1, ss2);
+ double similarityScore = ssRateMatrix.getPairwiseScore(ss1,
+ ss2);
similarities[i][j] += similarityScore;
}
}
* and fill in the bottom half of the matrix
*/
// TODO JAL-2424 cpwidth may be out by 1 - affects scores but not tree shape
-
+
for (int i = 0; i < noseqs; i++)
{
for (int j = i + 1; j < noseqs; j++)
- {
+ {
similarities[i][j] /= cpwidth;
similarities[j][i] = similarities[i][j];
}
}
return ssRateMatrix.similarityToDistance(new Matrix(similarities));
-
+
}
/**
- * Builds and returns a set containing sequences (SeqCigar) which do not
- * have a gap at the given column position.
+ * Builds and returns a set containing sequences (SeqCigar) which do not have
+ * a gap at the given column position.
*
* @param seqs
* @param columnPosition
* (0..)
* @return
*/
- private Set<SeqCigar> findSeqsWithoutGapAtColumn(
- SeqCigar[] seqs, int columnPosition)
+ private Set<SeqCigar> findSeqsWithoutGapAtColumn(SeqCigar[] seqs,
+ int columnPosition)
{
Set<SeqCigar> seqsWithoutGapAtCol = new HashSet<>();
for (SeqCigar seq : seqs)
{
/*
* position is not a gap
- */
+ */
seqsWithoutGapAtCol.add(seq);
}
}
return seqsWithoutGapAtCol;
}
-
@Override
public String getName()
{
@Override
public boolean isDNA()
{
- return false;
+ return false;
}
@Override
{
return false;
}
-
+
@Override
public boolean isSecondaryStructure()
{
private boolean includeGaps;
private boolean denominateByShortestLength;
-
+
private String secondaryStructureSource;
/**
/**
* Justify alignment or currently selected region left or right
- * @param left - true - means justify left
+ *
+ * @param left
+ * - true - means justify left
* @return
*/
boolean justify_Region(boolean left);
List<AlignmentAnnotation> getAlignmentSecondaryStructureConsensusAnnotation();
-
/**
* get the container for alignment gap annotation
*
void setSequenceConsensusHash(ProfilesI hconsensus);
void setSequenceSSConsensusHash(Map<String, ProfilesI> hSSConsesnusProfileMap);
-
/**
* Set the cDNA complement consensus for the viewport
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
+
/**
* notify all concerned that the alignment data has changed and derived data
* needs to be recalculated
public void notifyAlignmentChanged();
/**
- * retrieve a matrix associated with the view's alignment's annotation
+ * retrieve a matrix associated with the view's alignment's annotation
+ *
* @param alignmentAnnotation
* @return contact matrix or NULL
*/
// TODO getName, isDNA, isProtein can be static methods in Java 8
-
default public boolean isSecondaryStructure()
{
return false;
}
/**
- * Answers false by default
- * Answers true if the data has secondary structure (so should be
- * shown in menus in that context)
+ * Answers false by default Answers true if the data has secondary structure
+ * (so should be shown in menus in that context)
*
* @return
*/
-
-
+
/**
* Returns a distance score for the given sequence regions, that is, a matrix
* whose value [i][j] is the distance of sequence i from sequence j by some
* @return
*/
boolean denominateByShortestLength();
-
+
String getSecondaryStructureSource();
void setSecondaryStructureSource(String secondaryStructureSource);
Menu autoAnnMenu = new Menu(
MessageManager.getString("label.autocalculated_annotation"));
- Menu selectSS = new Menu(
- MessageManager.getString("label.select_secondary_structure_source"));
+ Menu selectSS = new Menu(MessageManager
+ .getString("label.select_secondary_structure_source"));
showGroupConsensus.addItemListener(this);
showGroupConservation.addItemListener(this);
showConsensusHistogram.addItemListener(this);
import jalview.util.ChannelProperties;
import jalview.util.ColorUtils;
import jalview.util.HttpUtils;
+import jalview.util.LaunchUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
sb.append(" (");
sb.append(lafClass);
sb.append(")\n");
+ // pid() only available in Java 9+
+ if (LaunchUtils.getJavaVersion() > 8)
+ {
+ sb.append("Java Virtual Machine PID: ");
+ sb.append(ProcessHandle.current().pid());
+ sb.append("\n");
+ }
+
}
appendIfNotNull(sb, "Installer version: ",
System.getProperty("sys.install4jVersion"), "\n", null);
System.getProperty("launcher.distdir"), "\n", null);
appendIfNotNull(sb, "Launcher appbase: ",
System.getProperty("launcher.appbase"), "\n", null);
+ appendIfNotNull(sb, "Launcher script: ",
+ System.getProperty("launcher.script"), "\n", null);
}
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
--- /dev/null
+/*
+ * 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.
+ */
+package jalview.bin;
+
+import java.io.File;
+
+import com.threerings.getdown.data.EnvConfig;
+import com.threerings.getdown.util.LaunchUtil;
+
+public class GetdownLauncherUpdate
+{
+ public static void main(String[] args)
+ {
+ EnvConfig.setVarsFromProperties();
+
+ String appdir = args.length > 0 ? args[0] : null;
+ if (appdir == null || appdir.length() == 0)
+ {
+ appdir = System.getProperty("launcher.appdir", null);
+ }
+ if (appdir == null)
+ {
+ appdir = EnvConfig.getUserAppdir();
+ }
+ if (appdir == null)
+ {
+ System.err.println("Not running upgradeGetdown");
+ return;
+ }
+ boolean debug = false;
+ for (int i = 0; i < args.length; i++)
+ {
+ if ("--debug".equals(args[i]))
+ {
+ debug = true;
+ break;
+ }
+ }
+ if (debug)
+ {
+ System.err.println("Running upgradeGetdown");
+ }
+ File appdirFile = new File(appdir);
+ if (!appdirFile.exists())
+ {
+ System.err.println("Directory '" + appdirFile.getAbsolutePath()
+ + "' doesn't exist, cannot update getdown-launcher.jar.");
+ if (Boolean.valueOf(System.getProperty("launcher.update")))
+ {
+ System.exit(1);
+ }
+ }
+ LaunchUtil.upgradeGetdown(new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+}
import com.formdev.flatlaf.FlatLightLaf;
import com.formdev.flatlaf.themes.FlatMacLightLaf;
import com.formdev.flatlaf.util.SystemInfo;
-import com.threerings.getdown.util.LaunchUtil;
//import edu.stanford.ejalbert.launching.IBrowserLaunching;
import groovy.lang.Binding;
String appdirString = System.getProperty("launcher.appdir");
if (appdirString != null && appdirString.length() > 0)
{
- final File appdir = new File(appdirString);
new Thread()
{
@Override
public void run()
{
- LaunchUtil.upgradeGetdown(
- new File(appdir, "getdown-launcher-old.jar"),
- new File(appdir, "getdown-launcher.jar"),
- new File(appdir, "getdown-launcher-new.jar"));
+ GetdownLauncherUpdate.main(new String[] { appdirString });
}
}.start();
}
PDBEntry[] pdb = new PDBEntry[pdbs.size()];
String[][] chains = new String[pdbs.size()][];
String[] protocols = new String[pdbs.size()];
- for (int pdbsi = 0,
- pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
+ for (int pdbsi = 0, pdbsiSize = pdbs
+ .size(); pdbsi < pdbsiSize; pdbsi++)
{
Object[] o = (Object[]) pdbs.elementAt(pdbsi);
pdb[pdbsi] = (PDBEntry) o[0];
headless = assumeheadless;
}
+ ErrorLog.setQuiet(quiet);
+
final String appName = ChannelProperties.getProperty("app_name");
// if we're using jalview.bin.Launcher we always assume a console is in use
String scalePropertyArg = HiDPISetting.getScalePropertyArg();
if (scalePropertyArg != null)
{
- LaunchUtils.syserr(debug, quiet, "Running " + startClass
- + " with scale setting " + scalePropertyArg);
+ ErrorLog.errPrintln("Running " + startClass + " with scale setting "
+ + scalePropertyArg);
addJvmArgs.add(scalePropertyArg);
}
addJvmArgs, null, null, null, startClass, null, null, arguments,
launcherprint, launcherwait, launcherstop, debug, quiet);
- LaunchUtils.syserr(debug, quiet, "JVM exited with value " + exitValue);
+ ErrorLog.errPrintln("JVM exited with value " + exitValue);
}
}
{
continue;
}
- char[] range = seq.getSequence(from, to+1);
- if (range==null || range.length==0)
+ char[] range = seq.getSequence(from, to + 1);
+ if (range == null || range.length == 0)
{
continue;
}
alseq[gapstart + gp] = gc;
}
- for (int sqp = 0,insp=0; sqp<alseq.length; sqp++)
+ for (int sqp = 0, insp = 0; sqp < alseq.length; sqp++)
{
if (sqp < range.length && !Comparison.isGap(range[sqp]))
{
// Technically we should return false, since view has not changed
return false;
}
-
+
@Override
public boolean justify_Region(boolean left)
{
+/*
+ * 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.
+ */
package jalview.datamodel;
import java.util.Collection;
+/*
+ * 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.
+ */
package jalview.datamodel;
import java.util.Collection;
+/*
+ * 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.
+ */
package jalview.datamodel;
/**
public void setProviderCategory(String providerCategory)
{
- setProperty(PROVIDERCATEGORY, providerCategory);
+ setProperty(PROVIDERCATEGORY, providerCategory);
}
-
+
public String getProviderCategory()
{
return (String) getProperty(PROVIDERCATEGORY);
{
return _hasProperty(PROVIDERCATEGORY);
}
-
+
}
* an object holding counts of symbols in the profile
*/
private ResidueCount counts;
-
+
private SecondaryStructureCount ssCounts;
private int seqWithSSCount = -1;
* the highest count for any residue in the profile
*/
private int maxCount;
+
private int maxSSCount;
-
/*
* the residue (e.g. K) or residues (e.g. KQW) with the
* highest count in the profile
*/
private String modalResidue;
-
+
private String modalSS;
/**
{
this.counts = residueCounts;
}
-
+
@Override
public void setSSCounts(SecondaryStructureCount secondaryStructureCount)
{
}
return pid;
}
-
+
@Override
public float getSSPercentageIdentity(boolean ignoreGaps)
{
{
return counts;
}
-
+
@Override
public SecondaryStructureCount getSSCounts()
{
{
return maxCount;
}
-
+
@Override
public int getMaxSSCount()
{
{
return modalResidue;
}
-
+
@Override
public String getModalSS()
{
* @param residueCounts
*/
public abstract void setCounts(ResidueCount residueCounts);
- public abstract void setSSCounts(SecondaryStructureCount secondaryStructureCount);
-
+
+ public abstract void setSSCounts(
+ SecondaryStructureCount secondaryStructureCount);
/**
* Returns the percentage identity of the profile, i.e. the highest proportion
* @return
*/
public abstract float getPercentageIdentity(boolean ignoreGaps);
-
+
public abstract float getSSPercentageIdentity(boolean ignoreGaps);
/**
* @return
*/
public abstract int getMaxCount();
+
public abstract int getMaxSSCount();
/**
* @return
*/
public abstract String getModalResidue();
+
public abstract String getModalSS();
/**
* @return
*/
public abstract int getNonGapped();
+
SecondaryStructureCount getSSCounts();
}
\ No newline at end of file
*/
private static final String SS_SYMBOLS = "HEC";
-
static final int GAP_COUNT = 0;
/*
*/
public SecondaryStructureCount()
{
- //isSS = true;
+ // isSS = true;
int charsToCount = SS_SYMBOLS.length();
counts = new short[charsToCount + 1];
}
{
if (intCounts[i] == count)
{
- modal.append(
- SS_SYMBOLS.charAt(i - 1));
+ modal.append(SS_SYMBOLS.charAt(i - 1));
}
}
}
{
if (counts[i] == count)
{
- modal.append(
- SS_SYMBOLS.charAt(i - 1));
+ modal.append(SS_SYMBOLS.charAt(i - 1));
}
}
}
* consensus calculation property
*/
private boolean showSequenceLogo = false;
-
/**
* flag indicating if logo should be rendered normalised
private boolean hidecols = false;
AlignmentAnnotation consensus = null;
-
List<AlignmentAnnotation> ssConsensus = null;
AlignmentAnnotation conservation = null;
private boolean showConsensusHistogram;
-
+
private AnnotatedCollectionI context;
public Map<String, ProfilesI> hSSConsensusProfileMap;
hSSConsensusProfileMap.put(ssSource, hSSConsensus);
}
}
-
if (ssConsensus != null)
{
cs.setSSConsensusProfileMap(hSSConsensusProfileMap);
upd = true;
}
-
if ((conservation != null)
|| (cs != null && cs.conservationApplied()))
}
this.showSequenceLogo = showSequenceLogo;
}
-
+
/**
*
* @param showConsHist
this.showConsensusHistogram = showConsHist;
}
+
/**
* @return the showConsensusHistogram
*/
+/*
+ * 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.
+ */
package jalview.datamodel.annotations;
import jalview.datamodel.Annotation;
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
* @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "15.2";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "15.8";
- private static final String LATEST_ENSEMBL_REST_VERSION = "15.2";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "15.8";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
{
viewport.setShowSSConsensus(showSSConsensus.getState());
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
-
}
/*
alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
}
+
/*
* (non-Javadoc)
*
}
showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
true);
+
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", true);
normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
-
+
showSSConsensus = Cache.getDefault("SHOW_SS_CONSENSUS", false);
showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
public boolean isRepainting()
{
- if (renderPanel!=null && renderPanel.isVisible())
+ if (renderPanel != null && renderPanel.isVisible())
{
return renderPanel.repainting;
}
return false;
}
+
/**
* Outputs the Jmol viewer image as an image file, after prompting the user to
* choose a file and (for EPS) choice of Text or Lineart character rendering
{
while (!isRepainting())
{
- try {
+ try
+ {
Thread.sleep(2);
} catch (Exception q)
- {}
+ {
+ }
}
try
{
}
else
{
- repainting=true;
+ repainting = true;
synchronized (jmb)
{
jmb.jmolViewer.renderScreenImage(g, currentSize.width,
currentSize.height);
-
+
}
- repainting=false;
+ repainting = false;
}
}
- volatile boolean repainting=false;
+
+ volatile boolean repainting = false;
}
@Override
import jalview.bin.Cache;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.Color;
pasimapBorderless.setOpaque(false); // false -> stops every pixel inside
// border from being painted
pasimapBorderless.add(pasimap, FlowLayout.LEFT); // add pasimap button to
- // the JPanel
- calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT); // add button with
- // border and
- // everything to
- // the overall
- // ChoicePanel
+ // the JPanel
+ if (!Platform.isJS())
+ {
+ // FIXME JAL-4443
+ calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT); // add button
+ // with
+ // border and
+ // everything to
+ // the overall
+ // ChoicePanel
+ }
treePanel.add(neighbourJoining);
treePanel.add(averageDistance);
ButtonGroup calcTypes = new ButtonGroup();
calcTypes.add(pca);
- calcTypes.add(pasimap);
+ if (!Platform.isJS())
+ {
+ // FIXME JAL-4443
+ calcTypes.add(pasimap);
+ }
calcTypes.add(neighbourJoining);
calcTypes.add(averageDistance);
calcTypes.add(pairwise);
*
* @param nucleotide
* @param forPca
- * @param ssPresent - include secondary structure similarity model
- * @param forPasimap - limit to ScoreMatrix based models - allows use of AlignSeq
+ * @param ssPresent
+ * - include secondary structure similarity model
+ * @param forPasimap
+ * - limit to ScoreMatrix based models - allows use of AlignSeq
* @return
*/
protected static List<ScoreModelI> getApplicableScoreModels(
ScoreModels scoreModels = ScoreModels.getInstance();
for (ScoreModelI sm : scoreModels.getModels())
{
- if ((!forPasimap || sm instanceof ScoreMatrix)
+ if ((!forPasimap || sm instanceof ScoreMatrix)
&& (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA()
|| sm.isSecondaryStructure() && ssPresent))
/**
* set font size of the textarea
+ *
* @param size
*/
public void setFont(Font font)
{
textarea.setFont(font);
}
-
+
/**
* DOCUMENT ME!
*/
{
}
}
-
+
/**
- * show menu for changing the font
- * @param e
- */
+ * show menu for changing the font
+ *
+ * @param e
+ */
@Override
public void fontSizeMenu_actionPerformed(ActionEvent e)
{
}
/**
- * DOCUMENT ME!
- *
- * @param evt
- * DOCUMENT ME!
+ * load all files dropped (2.11.4.0 behaviour)
+ * @return false if any file resulted in an error
*/
- @Override
- public void drop(DropTargetDropEvent evt)
+ public boolean loadDroppedFiles(List<Object> files,
+ List<DataSourceType> protocols, List<Object> failed,
+ List<Exception> failed_exceptions)
{
- boolean success = true;
- // JAL-1552 - acceptDrop required before getTransferable call for
- // Java's Transferable for native dnd
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
- Transferable t = evt.getTransferable();
- List<Object> files = new ArrayList<>();
- List<DataSourceType> protocols = new ArrayList<>();
-
- try
+ for (int i = 0; i < files.size(); i++)
{
- Desktop.transferFromDropTarget(files, protocols, evt, t);
- } catch (Exception e)
+ Object file = files.get(i);
+ try
+ {
+ // BH 2018 File or String
+ String fileName = file.toString();
+ DataSourceType protocol = (protocols == null) ? DataSourceType.FILE
+ : protocols.get(i);
+ FileFormatI format = null;
+
+ if (fileName.endsWith(".jar"))
+ {
+ format = FileFormat.Jalview;
+ }
+ else
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ }
+ if (file instanceof File)
+ {
+ Platform.cacheFileData((File) file);
+ }
+ new FileLoader().LoadFile(null, file, protocol, format);
+ } catch (Exception x)
+ {
+ failed.add(file);
+ failed_exceptions.add(x);
+ jalview.bin.Console.warn(
+ "Unexpected Exception when handling " + file.toString(), x);
+ }
+ }
+ return failed.size()==0; // at least one was loaded.
+ }
+
+ /**
+ * analyse dropped files and process them according to type: load alignments,
+ * add annotation, trees or features to alignments with the same basename
+ *
+ * @return false if any exception was raised
+ */
+ public boolean processAndLoadDroppedFiles(List<Object> files,
+ List<DataSourceType> protocols, List<Object> failed,
+ List<Exception> failed_exceptions)
+ {
+ // map list to list of strings
+ List<String> filenames = new ArrayList<>();
+ for (int i = 0; i < files.size(); i++)
{
- e.printStackTrace();
- success = false;
+ filenames.add(files.get(i).toString());
}
- if (files != null)
+ // processFilenames will take likely associated files OUT of the list of
+ // filenames and return them in a BaseInfo object in the Map
+ Map<String, BaseInfo> baseInfoMap = ArgParserUtils
+ .processFilenames(filenames, false, files);
+ // so we can catch exceptions for this file
+ Object file = null;
+ try
{
- try
+
+ for (int i = 0; i < files.size(); i++)
{
- // map list to list of strings
- List<String> filenames = new ArrayList<>();
- for (int i = 0; i < files.size(); i++)
+ // BH 2018 File or String
+ file = files.get(i);
+ String fileName = file.toString();
+ DataSourceType protocol = (protocols == null) ? DataSourceType.FILE
+ : protocols.get(i);
+ FileFormatI format = null;
+
+ if (fileName.toLowerCase(Locale.ROOT).endsWith(".jar"))
{
- filenames.add(files.get(i).toString());
+ format = FileFormat.Jalview;
}
-
- // processFilenames will take likely associated files OUT of the list of
- // filenames and return them in a BaseInfo object in the Map
- Map<String, BaseInfo> baseInfoMap = ArgParserUtils
- .processFilenames(filenames, false, files);
- for (int i = 0; i < files.size(); i++)
+ else
{
- // BH 2018 File or String
- Object file = files.get(i);
- String fileName = file.toString();
- DataSourceType protocol = (protocols == null)
- ? DataSourceType.FILE
- : protocols.get(i);
- FileFormatI format = null;
-
- if (fileName.toLowerCase(Locale.ROOT).endsWith(".jar"))
- {
- format = FileFormat.Jalview;
- }
- else
+ format = new IdentifyFile().identify(file, protocol);
+ }
+ // If features/annotations/tree file that hasn't been put into the
+ // baseInfoMap, look through titles of opened AlignFrames to add.
+ String ext = FileUtils.getExtension(fileName);
+ boolean isFeatures = ArgParserUtils.featuresExtensions
+ .contains(ext);
+ boolean isAnnotations = ArgParserUtils.annotationsExtensions
+ .contains(ext);
+ boolean isTree = ArgParserUtils.treeExtensions.contains(ext);
+ if (isFeatures || isAnnotations || isTree)
+ {
+ String base = FileUtils.getBase(fileName);
+ AlignFrame matchingAf = null;
+ AlignFrame[] afs = Desktop.instance.getAlignFrames();
+ boolean dontSkip = false;
+ for (AlignFrame af : afs)
{
- format = new IdentifyFile().identify(file, protocol);
+ String afFilename = af.fileName;
+ String afTitle = af.getTitle();
+ /**
+ * don't need to check the matching afFilename or afTitle has an
+ * alignment extenstion. It's obviously an alignment!
+ */
+ /*
+ if ((base.equals(FileUtils.getBase(afFilename))
+ && ArgParserUtils.alignmentExtensions
+ .contains(FileUtils.getExtension(afFilename)))
+ || (base.equals(FileUtils.getBase(afTitle))
+ && ArgParserUtils.alignmentExtensions
+ .contains(FileUtils
+ .getExtension(afTitle))))
+ */
+ if (base.equals(FileUtils.getBase(afFilename))
+ || base.equals(FileUtils.getBase(afTitle)))
+ {
+ matchingAf = af;
+ break;
+ }
}
- // If features/annotations/tree file that hasn't been put into the
- // baseInfoMap, look through titles of opened AlignFrames to add.
- String ext = FileUtils.getExtension(fileName);
- boolean isFeatures = ArgParserUtils.featuresExtensions
- .contains(ext);
- boolean isAnnotations = ArgParserUtils.annotationsExtensions
- .contains(ext);
- boolean isTree = ArgParserUtils.treeExtensions.contains(ext);
- if (isFeatures || isAnnotations || isTree)
+ if (matchingAf != null)
{
- String base = FileUtils.getBase(fileName);
- AlignFrame matchingAf = null;
- AlignFrame[] afs = Desktop.instance.getAlignFrames();
- boolean dontSkip = false;
- for (AlignFrame af : afs)
+ if (isFeatures)
{
- String afFilename = af.fileName;
- String afTitle = af.getTitle();
- /**
- * don't need to check the matching afFilename or afTitle has an
- * alignment extenstion. It's obviously an alignment!
- */
- /*
- if ((base.equals(FileUtils.getBase(afFilename))
- && ArgParserUtils.alignmentExtensions
- .contains(FileUtils.getExtension(afFilename)))
- || (base.equals(FileUtils.getBase(afTitle))
- && ArgParserUtils.alignmentExtensions
- .contains(FileUtils
- .getExtension(afTitle))))
- */
- if (base.equals(FileUtils.getBase(afFilename))
- || base.equals(FileUtils.getBase(afTitle)))
- {
- matchingAf = af;
- break;
- }
+ matchingAf.parseFeaturesFile(fileName,
+ AppletFormatAdapter.checkProtocol(fileName));
+ }
+ else if (isAnnotations)
+ {
+ matchingAf.loadJalviewDataFile(fileName, null, null, null);
}
- if (matchingAf != null)
+ else if (isTree)
{
- if (isFeatures)
+ try
{
- matchingAf.parseFeaturesFile(fileName,
+ NewickFile nf = new NewickFile(fileName,
AppletFormatAdapter.checkProtocol(fileName));
- }
- else if (isAnnotations)
- {
- matchingAf.loadJalviewDataFile(fileName, null, null, null);
- }
- else if (isTree)
- {
- try
- {
- NewickFile nf = new NewickFile(fileName,
- AppletFormatAdapter.checkProtocol(fileName));
- matchingAf.getViewport().setCurrentTree(matchingAf
- .showNewickTree(nf, fileName).getTree());
- } catch (IOException e)
- {
- jalview.bin.Console.warn(
- "Couldn't add potential tree '" + fileName + "'");
- dontSkip = true;
- }
- }
- if (!dontSkip)
+ matchingAf.getViewport().setCurrentTree(
+ matchingAf.showNewickTree(nf, fileName).getTree());
+ } catch (IOException e)
{
- // skip to next file
- continue;
+ jalview.bin.Console.warn(
+ "Couldn't add potential tree '" + fileName + "'");
+ dontSkip = true;
}
}
+ if (!dontSkip)
+ {
+ // skip to next file
+ continue;
+ }
}
+ }
- if (file instanceof File)
+ if (file instanceof File)
+ {
+ Platform.cacheFileData((File) file);
+ }
+ // new FileLoader().LoadFile(null, file, protocol, format);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fileName,
+ protocol, format);
+ // now we add any associated files to the alignframe
+ if (baseInfoMap.containsKey(fileName) && baseInfoMap.get(fileName)
+ .getAssociatedFilesMap() != null)
+ {
+ BaseInfo bi = baseInfoMap.get(fileName);
+ if (bi.getAssociatedFilesMap().containsKey(Arg.FEATURES))
{
- Platform.cacheFileData((File) file);
+ String featuresfile = bi.getAssociatedFilesMap()
+ .get(Arg.FEATURES);
+ af.parseFeaturesFile(featuresfile,
+ AppletFormatAdapter.checkProtocol(featuresfile));
}
- // new FileLoader().LoadFile(null, file, protocol, format);
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fileName,
- protocol, format);
- // now we add any associated files to the alignframe
- if (baseInfoMap.containsKey(fileName) && baseInfoMap.get(fileName)
- .getAssociatedFilesMap() != null)
+ if (bi.getAssociatedFilesMap().containsKey(Arg.ANNOTATIONS))
{
- BaseInfo bi = baseInfoMap.get(fileName);
- if (bi.getAssociatedFilesMap().containsKey(Arg.FEATURES))
- {
- String featuresfile = bi.getAssociatedFilesMap()
- .get(Arg.FEATURES);
- af.parseFeaturesFile(featuresfile,
- AppletFormatAdapter.checkProtocol(featuresfile));
- }
- if (bi.getAssociatedFilesMap().containsKey(Arg.ANNOTATIONS))
+ String annotationsfile = bi.getAssociatedFilesMap()
+ .get(Arg.ANNOTATIONS);
+ af.loadJalviewDataFile(annotationsfile, null, null, null);
+ }
+ if (bi.getAssociatedFilesMap().containsKey(Arg.TREE))
+ {
+ String treefile = bi.getAssociatedFilesMap().get(Arg.TREE);
+ try
{
- String annotationsfile = bi.getAssociatedFilesMap()
- .get(Arg.ANNOTATIONS);
- af.loadJalviewDataFile(annotationsfile, null, null, null);
- }
- if (bi.getAssociatedFilesMap().containsKey(Arg.TREE))
+ NewickFile nf = new NewickFile(treefile,
+ AppletFormatAdapter.checkProtocol(treefile));
+ af.getViewport().setCurrentTree(
+ af.showNewickTree(nf, treefile).getTree());
+ } catch (IOException e)
{
- String treefile = bi.getAssociatedFilesMap().get(Arg.TREE);
- try
- {
- NewickFile nf = new NewickFile(treefile,
- AppletFormatAdapter.checkProtocol(treefile));
- af.getViewport().setCurrentTree(
- af.showNewickTree(nf, treefile).getTree());
- } catch (IOException e)
- {
- jalview.bin.Console.warn(
- "Couldn't add potential tree '" + treefile + "'");
- }
-
+ jalview.bin.Console.warn(
+ "Couldn't add potential tree '" + treefile + "'");
}
}
}
- } catch (Exception ex)
+
+ }
+ } catch (Exception ex)
+ {
+
+ jalview.bin.Console.warn(
+ "Unexpected exception whilst handling drop to Desktop.", ex);
+ failed.add(file);
+ failed_exceptions.add(ex);
+ return false;
+ }
+ return failed.size() == 0; // redundant for 2.11.4.0 implementation
+ }
+
+ @Override
+ public void drop(DropTargetDropEvent evt)
+ {
+ boolean success = true;
+ // JAL-1552 - acceptDrop required before getTransferable call for
+ // Java's Transferable for native dnd
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
+ Transferable t = evt.getTransferable();
+ List<Object> files = new ArrayList<>();
+ List<DataSourceType> protocols = new ArrayList<>();
+
+ try
+ {
+ Desktop.transferFromDropTarget(files, protocols, evt, t);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ success = false;
+ }
+ try
+ {
+ if (files != null)
{
- success = false;
+ List<Object> failed = new ArrayList<Object>();
+ List<Exception> failed_exceptions = new ArrayList<Exception>();
+ if (!showExperimental())
+ {
+ success = loadDroppedFiles(files, protocols, failed,
+ failed_exceptions);
+ }
+ else
+ {
+ success = processAndLoadDroppedFiles(files, protocols, failed,
+ failed_exceptions);
+ }
}
+ } catch (Throwable ex)
+ {
+ jalview.bin.Console.warn(
+ "Unexpected exception whilst handling drop to Desktop.", ex);
+ success = false;
}
evt.dropComplete(success); // need this to ensure input focus is properly
// transfered to any new windows created
if (progressBars.get(Long.valueOf(id)) == null)
return null;
-
+
for (Component c : progressBars.get(Long.valueOf(id)).getComponents())
{
if (c.getClass() == JProgressBar.class)
- return (JProgressBar) c;
+ return (JProgressBar) c;
}
return null;
}
/**
* Creates a new FontChooser for a CutAndPasteTransfer
+ *
* @param cap
- */
+ */
public FontChooser(CutAndPasteTransfer cap)
{
oldFont = new Font("Monospaced", Font.PLAIN, 12);
if (!isCapFont())
{
smoothFont.setSelected(ap.av.antiAlias);
-
+
/*
* Enable 'scale protein as cDNA' in a SplitFrame view. The selection is
* stored in the ViewStyle of both dna and protein Viewport. Also enable
{
return cap != null;
}
+
/**
* DOCUMENT ME!
*/
*/
public PaSiMapPanel(AlignmentPanel alignPanel, String modelName)
{
- super(8); // dim = 8
+ super(8); // dim = 8
this.av = alignPanel.av;
this.ap = alignPanel;
boolean nucleotide = av.getAlignment().isNucleotide();
- //progressBar = new ProgressBar(statusPanel, statusBar);
+ // progressBar = new ProgressBar(statusPanel, statusBar);
addInternalFrameListener(new InternalFrameAdapter()
{
ScoreModelI scoreModel = ScoreModels.getInstance()
.getScoreModel(modelName, ap);
- setPasimapModel(
- new PaSiMapModel(av, seqs, nucleotide, scoreModel));
+ setPasimapModel(new PaSiMapModel(av, seqs, nucleotide, scoreModel));
PaintRefresher.Register(this, av.getSequenceSetId());
setRotatableCanvas(new RotatableCanvas(alignPanel));
}
/**
- * Ensure references to potentially very large objects (the PaSiMap matrices) are
- * nulled when the frame is closed
+ * Ensure references to potentially very large objects (the PaSiMap matrices)
+ * are nulled when the frame is closed
*/
protected void close_actionPerformed()
{
progressBar.setProgressBar(message, progId);
try
{
- SequenceGroup selGroup=av.getSelectionGroup();
-
- if (selGroup==null)
+ SequenceGroup selGroup = av.getSelectionGroup();
+
+ if (selGroup == null)
{
selGroup = new SequenceGroup(av.getAlignment().getSequences());
selGroup.setStartRes(0);
- selGroup.setEndRes(av.getAlignment().getWidth()-1);
+ selGroup.setEndRes(av.getAlignment().getWidth() - 1);
}
-
- if (selGroup.getSize()>MAX_PASIMAP_SEQ)
+
+ if (selGroup.getSize() > MAX_PASIMAP_SEQ)
{
- int start = selGroup.getStartRes(),end=selGroup.getEndRes();
- selGroup = new SequenceGroup(selGroup.getSequences().subList(0, MAX_PASIMAP_SEQ));
- selGroup.setStartRes(start);
- selGroup.setEndRes(end);
- Console.warn("Truncated input sequences for PASIMAP analysis to "+MAX_PASIMAP_SEQ);
+ int start = selGroup.getStartRes(), end = selGroup.getEndRes();
+ selGroup = new SequenceGroup(
+ selGroup.getSequences().subList(0, MAX_PASIMAP_SEQ));
+ selGroup.setStartRes(start);
+ selGroup.setEndRes(end);
+ Console.warn("Truncated input sequences for PASIMAP analysis to "
+ + MAX_PASIMAP_SEQ);
}
-
+
PairwiseAlignPanel pap = new PairwiseAlignPanel(av, selGroup, true,
GAP_OPEN_COST, GAP_EXTEND_COST, false, null);
pap.setDiscardAlignments(true);
pap.setQuiet(true);
-
+
System.out.println(pap != null);
setPairwiseAlignPanel(pap);
getPasimapModel().calculate(pap);
repaint();
if (getParent() == null)
{
- Desktop.addInternalFrame(
- this, MessageManager.formatMessage("label.calc_title",
- "PaSiMap", ap.alignFrame.getTitle()),
+ Desktop.addInternalFrame(this,
+ MessageManager.formatMessage("label.calc_title", "PaSiMap",
+ ap.alignFrame.getTitle()),
475, 450);
this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
}
}
/**
- * Updates the PaSiMap display after a change of component to use for x, y or z
- * axis
+ * Updates the PaSiMap display after a change of component to use for x, y or
+ * z axis
*/
@Override
protected void doDimensionChange()
}
/**
- * Sets the selected checkbox item index for PaSiMap dimension (1, 2, 3...) for
- * the given axis (X/Y/Z)
+ * Sets the selected checkbox item index for PaSiMap dimension (1, 2, 3...)
+ * for the given axis (X/Y/Z)
*
* @param index
* @param axis
}
/**
- * If available, shows the data which formed the inputs for the PaSiMap as a new
- * alignment
+ * If available, shows the data which formed the inputs for the PaSiMap as a
+ * new alignment
*/
@Override
public void originalSeqData_actionPerformed()
}
}
- public void makePaSiMapImage(ImageMaker.TYPE type) throws Exception
+ public void makePaSiMapImage(ImageMaker.TYPE type) throws Exception
{
int width = getRotatableCanvas().getWidth();
int height = getRotatableCanvas().getHeight();
{
cap.setText(getPasimapModel().getAlignmentOutput());
Desktop.addInternalFrame(cap, MessageManager.formatMessage(
- "label.pairwise_alignment_for_params", new String[] { this.getTitle() }), 500, 500);
+ "label.pairwise_alignment_for_params", new String[]
+ { this.getTitle() }), 500, 500);
} catch (OutOfMemoryError oom)
{
new OOMWarning("exporting pairwise alignments", oom);
public void updateProgressBar(int lengthOfTask, int progress)
{
JProgressBar pBar = progressBar.getProgressBar(progId);
- if (pBar==null)
+ if (pBar == null)
{
return;
}
}
updateProgressBar(progress);
}
+
public void updateProgressBar(int progress)
{
JProgressBar pBar = progressBar.getProgressBar(progId);
-
- if (pBar==null)
+
+ if (pBar == null)
{
return;
}
-
+
pBar.setValue(progress);
pBar.repaint();
}
/**
- * adds a listener for a pairwise alignment panel's progress
- * TODO: generalise for anything that can report progress ?
+ * adds a listener for a pairwise alignment panel's progress TODO: generalise
+ * for anything that can report progress ?
+ *
* @param pap
*/
public void setPairwiseAlignPanel(PairwiseAlignPanel pap)
}
/**
- * Answers the selected checkbox item index for PaSiMap dimension for the X, Y or
- * Z axis of the display
+ * Answers the selected checkbox item index for PaSiMap dimension for the X, Y
+ * or Z axis of the display
*
* @param axis
* @return
private float[][] scores;
- private float[][] alignmentScores; // scores used by PaSiMap
+ private float[][] alignmentScores; // scores used by PaSiMap
private int GAP_OPEN_COST;
private String alignmentOutput;
private boolean quiet;
-
+
private boolean discardAlignments;
private boolean endGaps;
private int total;
private int progress;
-
+
private SequenceGroup selection;
+
/**
* input sequences
*/
- private SequenceI[] seqs=null;
+ private SequenceI[] seqs = null;
private ScoreMatrix scoreMatrix;
*
* @param viewport
* contains selected sequences to align
- * @param endGaps ~ toggle gaps and the beginning and end of sequences
+ * @param endGaps
+ * ~ toggle gaps and the beginning and end of sequences
*/
public PairwiseAlignPanel(AlignmentViewport viewport)
{
- this(viewport, null, false, 120, 20, true, null); // default penalties used in AlignSeq
+ this(viewport, null, false, 120, 20, true, null); // default penalties used
+ // in AlignSeq
}
+
public PairwiseAlignPanel(AlignmentViewport viewport, ScoreMatrix params)
{
- this(viewport, null, false, 120, 20, true,params); // default penalties used in AlignSeq
+ this(viewport, null, false, 120, 20, true, params); // default penalties
+ // used in AlignSeq
}
- public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost)
+
+ public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps,
+ int gapOpenCost, int gapExtendCost)
{
this(viewport, null, endGaps, gapOpenCost, gapExtendCost, true, null);
}
/**
- * Create a new pairwise alignpanel with specified parameters and score model, and optionally start the calculation
+ * Create a new pairwise alignpanel with specified parameters and score model,
+ * and optionally start the calculation
+ *
* @param viewport
* @param selection
* @param endGaps
* @param run
* @param scoreMatrix
*/
- public PairwiseAlignPanel(AlignmentViewport viewport, SequenceGroup selection, boolean endGaps,
- int gapOpenCost, int gapExtendCost, boolean run, ScoreMatrix scoreMatrix)
+ public PairwiseAlignPanel(AlignmentViewport viewport,
+ SequenceGroup selection, boolean endGaps, int gapOpenCost,
+ int gapExtendCost, boolean run, ScoreMatrix scoreMatrix)
{
super();
this.av = viewport;
this.selection = selection;
this.total = MiscMath.combinations(av.getAlignment().getHeight(), 2);
this.scoreMatrix = scoreMatrix;
- if (run) {
+ if (run)
+ {
calculate();
}
}
-
+
public void calculate()
{
calculate(scoreMatrix);
}
- public void calculate (ScoreMatrix sm)
+
+ public void calculate(ScoreMatrix sm)
{
StringBuilder sb = new StringBuilder(1024);
sequences = new Vector<SequenceI>();
String[] seqStrings;
- seqs=null;
+ seqs = null;
if (selection != null)
{
seqs = av.getAlignment().getSequencesArray();
}
}
-
+
String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA
: AlignSeq.PEP;
float[][] alignmentScores = new float[seqs.length][seqs.length];
double totscore = 0D;
int count = seqs.length;
-
+
boolean first = true;
progress = 0;
AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST);
- if (sm != null) {
- as.setScoreMatrix(sm);
- }
+ if (sm != null)
+ {
+ as.setScoreMatrix(sm);
+ }
- if (as.s1str.length() == 0 || as.s2str.length() == 0)
+ if (as.s1str.length() == 0 || as.s2str.length() == 0)
{
continue;
}
sb.append(DASHES);
}
first = false;
- if (!discardAlignments) {
+ if (!discardAlignments)
+ {
as.printAlignment(System.out);
}
scores[i][j] = as.getMaxScore() / as.getASeq1().length;
this.scores = scores;
this.alignmentScores = alignmentScores;
- if (count > 2 && !quiet)
+ if (count > 2 && !quiet)
{
printScoreMatrix(seqs, scores, totscore);
}
{
return progress;
}
+
public SequenceI[] getInputSequences()
{
return seqs;
}
+
/**
- * Set to true to suppress output of progress to Console.stdout or GUI
- * @param quiet
+ * Set to true to suppress output of progress to Console.stdout or GUI
+ *
+ * @param quiet
*/
public void setQuiet(boolean quiet)
{
- this.quiet=quiet;
+ this.quiet = quiet;
}
+
/**
* set this if you are only interested in final alignment scores
+ *
* @param discard
*/
public void setDiscardAlignments(boolean discard)
{
- discardAlignments=discard;
+ discardAlignments = discard;
}
}
AlignmentUtils.addReferenceAnnotations(candidates, alignment, null);
if(AlignmentUtils.isSSAnnotationPresent(candidates)) {
-
restartSSConsensusWorker();
ap.validateAnnotationDimensions(true);
ap.fontChanged();
restartSSConsensusWorker();
//ap.alignFrame.getViewport().getCalcManager().restartWorkers();
}
-
}
-
-
- private void restartSSConsensusWorker() {
-
- List<AlignCalcWorkerI> workers = ap.alignFrame.getViewport().getCalcManager()
- .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class);
- if (!workers.isEmpty()) {
-
- ap.alignFrame.getViewport().getCalcManager().startWorker(workers.remove(0));
+
+ private void restartSSConsensusWorker()
+ {
+
+ List<AlignCalcWorkerI> workers = ap.alignFrame.getViewport()
+ .getCalcManager().getRegisteredWorkersOfClass(
+ SecondaryStructureConsensusThread.class);
+ if (!workers.isEmpty())
+ {
+
+ ap.alignFrame.getViewport().getCalcManager()
+ .startWorker(workers.remove(0));
}
-
+
}
-
-
protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
{
public JProgressBar getProgressBar(long id)
{
Container progBar = progressBars.get(id);
- if (progBar==null || progBar.getComponentCount()==0)
+ if (progBar == null || progBar.getComponentCount() == 0)
{
return null;
}
private Point[] axisEndPoints;
// fields for 'select rectangle' (JAL-1124)
- int rectx1;
- int recty1;
- int rectx2;
- int recty2;
+ int rectx1;
+
+ int recty1;
+
+ int rectx2;
+
+ int recty2;
AlignmentViewport av;
}
}
// //Now the rectangle
- if (rectx2 != -1 && recty2 != -1) {
- g.setColor(Color.white);
-
- g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1);
- }
+ if (rectx2 != -1 && recty2 != -1)
+ {
+ g.setColor(Color.white);
+
+ g.drawRect(rectx1, recty1, rectx2 - rectx1, recty2 - recty1);
+ }
}
/**
mouseX = x;
mouseY = y;
- rectx1 = x;
- recty1 = y;
- rectx2 = -1;
- recty2 = -1;
+ rectx1 = x;
+ recty1 = y;
+ rectx2 = -1;
+ recty2 = -1;
SequenceI found = findSequenceAtPoint(x, y);
// Check if this is a rectangle drawing drag
if ((evt.getModifiersEx() & InputEvent.BUTTON3_DOWN_MASK) != 0)
{
- rectx2 = evt.getX();
- recty2 = evt.getY();
- if ((rectx2 != -1) && (recty2 != -1))
- {
- rectSelect(rectx1, recty1, rectx2, recty2);
- }
+ rectx2 = evt.getX();
+ recty2 = evt.getY();
+ if ((rectx2 != -1) && (recty2 != -1))
+ {
+ rectSelect(rectx1, recty1, rectx2, recty2);
+ }
}
else
{
mouseY = yPos;
// findWidths();
}
- repaint();
+ repaint();
}
@Override
{
SequencePoint sp = sequencePoints.get(i);
int tmp1 = (int) (((sp.coord.x - centre[0]) * getScaleFactor())
- * (getWidth() / 3.15)
- + (getWidth() / 2.0));
+ * (getWidth() / 3.15) + (getWidth() / 2.0));
float pre1 = ((sp.coord.x - centre[0]) * getScaleFactor());
int tmp2 = (int) (((sp.coord.y - centre[1]) * getScaleFactor())
- * (getHeight() / 1.70)
- + (getHeight() / 2.0));
+ * (getHeight() / 1.70) + (getHeight() / 2.0));
float pre2 = ((sp.coord.y - centre[1]) * getScaleFactor());
if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2))
String pdbFilename = selectedPdbFileName;
// TODO - tidy up this ugly hack so we call launchStructureViewer too
StructureChooser.openStructureFileForSequence(ssm, sc, ap,
- selectedSequence, true, pdbFilename, tft, paeFilename,false,
- true,false,getTargetedStructureViewer(ssm).getViewerType());
+ selectedSequence, true, pdbFilename, tft, paeFilename,
+ false, true, false,
+ getTargetedStructureViewer(ssm).getViewerType());
}
SwingUtilities.invokeLater(new Runnable()
{
* @param forceHeadless
* @param showRefAnnotations
* @param doXferSettings
- * @param viewerType - when not null means the viewer will be opened, providing forceHeadless/headless is not true
+ * @param viewerType
+ * - when not null means the viewer will be opened, providing
+ * forceHeadless/headless is not true
* @return
*/
public static StructureViewer openStructureFileForSequence(
ssm = ap.getStructureSelectionManager();
StructureSelectionManager.doConfigureStructurePrefs(ssm);
}
-
+
PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq(
sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance,
tft, paeFilename, doXferSettings);
sc.mainFrame.dispose();
- // TODO should honor preferences - only show reference annotation that is requested - JAL-4415 JAL-3124
+ // TODO should honor preferences - only show reference annotation that is
+ // requested - JAL-4415 JAL-3124
if (showRefAnnotations)
{
showReferenceAnnotationsForSequence(ap.alignFrame, seq);
String modelPage = humanUrl < 1 ? null
: (String) restable.getValueAt(row, humanUrl);
- String modelCategory = idx_mcat < 1 ? null :(String) restable.getValueAt(row,idx_mcat);
-
+ String modelCategory = idx_mcat < 1 ? null
+ : (String) restable.getValueAt(row, idx_mcat);
+
String strucFormat = restable.getValueAt(row, modelformat).toString();
SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
- protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
+ protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
{
showConsensusHistogram_actionPerformed(e);
}
-
});
+
showSequenceLogo
.setText(MessageManager.getString("label.show_consensus_logo"));
showSequenceLogo.addActionListener(new ActionListener()
}
});
-
+
JMenu exportImageMenu = new JMenu(
MessageManager.getString("label.export_image"));
JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
ButtonGroup ssButtonGroup)
{
// TODO Auto-generated method stub
-
+
}
}
@Override
public void actionPerformed(ActionEvent e)
{
- fontSizeMenu_actionPerformed(e);
+ fontSizeMenu_actionPerformed(e);
}
});
copyItem.setText(MessageManager.getString("action.copy"));
/**
* shows a menu for changing the font
+ *
* @param e
*/
public void fontSizeMenu_actionPerformed(ActionEvent e)
public class GDesktop extends JFrame
{
- protected static JMenu windowMenu = new JMenu();
+ protected static JMenu windowMenu = null;
JMenuBar desktopMenubar = new JMenuBar();
public GDesktop()
{
super();
+
+ // instantiate here to set same context (e.g. font) as other menus
+ if (windowMenu == null)
+ {
+ windowMenu = new JMenu();
+ }
+
try
{
jbInit();
zCombobox.addItem("dim " + i);
}
}
+
public GPCAPanel(int dim)
{
try
zCombobox.addItem("dim " + i);
}
}
+
public GPaSiMapPanel(int dim)
{
try
}
});
JMenuItem outputAlignment = new JMenuItem();
- outputAlignment.setText(
- MessageManager.getString("label.output_alignment"));
+ outputAlignment
+ .setText(MessageManager.getString("label.output_alignment"));
outputAlignment.addActionListener(new ActionListener()
{
@Override
protected JCheckBox conservation = new JCheckBox();
- protected JCheckBox identity = new JCheckBox();
+ protected JCheckBox identity = new JCheckBox();
protected JCheckBox ssConsensus = new JCheckBox();
if (row != null)
{
value[i] = new double[row.length];
- int j = 0;
- for (float oldValue : row)
- {
- value[i][j] = oldValue;
- j++;
- }
+ int j = 0;
+ for (float oldValue : row)
+ {
+ value[i][j] = oldValue;
+ j++;
+ }
}
i++;
}
*/
for (int k = 0; k < in.width(); k++)
{
- if (!Double.isNaN(in.getValue(i,k)) && !Double.isNaN(this.value[k][j]))
- {
+ if (!Double.isNaN(in.getValue(i, k))
+ && !Double.isNaN(this.value[k][j]))
+ {
tmp[i][j] += (in.getValue(i, k) * this.value[k][j]);
- }
+ }
}
}
}
}
/**
- * returns the matrix as a double[][] array
- *
- * @return
- */
+ * returns the matrix as a double[][] array
+ *
+ * @return
+ */
@Override
public double[][] asArray()
{
/**
* Add d to all entries of this matrix
*
- * @param d ~ value to add
+ * @param d
+ * ~ value to add
*/
@Override
public void add(double d)
}
/**
- * Returns a copy in which every value in the matrix is its absolute
+ * Returns a copy in which every value in the matrix is its absolute
*
* @return
*/
{
if (row != null)
{
- mean[i++] = MiscMath.mean(row);
+ mean[i++] = MiscMath.mean(row);
}
}
return mean;
double[] column = getColumn(j);
if (column != null)
{
- mean[j] = MiscMath.mean(column);
+ mean[j] = MiscMath.mean(column);
}
}
return mean;
}
/**
- * return a flattened matrix containing the sum of each column
- *
- * @return
- */
+ * return a flattened matrix containing the sum of each column
+ *
+ * @return
+ */
@Override
public double[] sumCol()
{
double[] column = getColumn(j);
if (column != null)
{
- sum[j] = MiscMath.sum(column);
+ sum[j] = MiscMath.sum(column);
}
- }
+ }
return sum;
}
/**
- * returns the mean value of the complete matrix
- *
- * @return
- */
+ * returns the mean value of the complete matrix
+ *
+ * @return
+ */
@Override
public double mean()
{
{
for (double col : row)
{
- if (!Double.isNaN(col))
- {
- sum += col;
- } else {
- nanCount++;
- }
+ if (!Double.isNaN(col))
+ {
+ sum += col;
+ }
+ else
+ {
+ nanCount++;
+ }
}
}
return sum / (double) (this.rows * this.cols - nanCount);
}
/**
- * fills up a diagonal matrix with its transposed copy
- * !other side should be filled with 0
- * !keeps Double.NaN found in either side
- *
- * TODO check on which side it was diagonal and only do calculations for the other side
- */
+ * fills up a diagonal matrix with its transposed copy !other side should be
+ * filled with 0 !keeps Double.NaN found in either side
+ *
+ * TODO check on which side it was diagonal and only do calculations for the
+ * other side
+ */
@Override
public void fillDiagonal()
{
int n = this.rows;
int m = this.cols;
- MatrixI copy = this.transpose(); // goes through each element in the matrix and
- for (int i = 0; i < n; i++) // adds the value in the transposed copy to the original value
+ MatrixI copy = this.transpose(); // goes through each element in the matrix
+ // and
+ for (int i = 0; i < n; i++) // adds the value in the transposed copy to the
+ // original value
{
for (int j = 0; j < m; j++)
{
- if (i != j)
- {
- this.addValue(i, j, copy.getValue(i,j));
- }
+ if (i != j)
+ {
+ this.addValue(i, j, copy.getValue(i, j));
+ }
}
}
}
/**
- * counts the number of Double.NaN in the matrix
- *
- * @return
- */
+ * counts the number of Double.NaN in the matrix
+ *
+ * @return
+ */
@Override
public int countNaN()
{
{
for (int j = 0; j < this.cols; j++)
{
- if (Double.isNaN(this.getValue(i,j)))
- {
- NaN++;
- }
+ if (Double.isNaN(this.getValue(i, j)))
+ {
+ NaN++;
+ }
}
}
return NaN;
}
/**
- * performs an element-wise addition of this matrix by another matrix ~ this - m
- * @param m ~ other matrix
- *
- * @return
- */
+ * performs an element-wise addition of this matrix by another matrix ~ this -
+ * m
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public MatrixI add(MatrixI m)
{
if (m.width() != cols || m.height() != rows)
{
- throw new IllegalArgumentException("Can't add a " + m.height() + "x" + m.width() + " to a " + this.rows + "x" + this.cols + " matrix");
+ throw new IllegalArgumentException(
+ "Can't add a " + m.height() + "x" + m.width() + " to a "
+ + this.rows + "x" + this.cols + " matrix");
}
double[][] tmp = new double[this.rows][this.cols];
for (int i = 0; i < this.rows; i++)
{
for (int j = 0; j < this.cols; j++)
{
- tmp[i][j] = this.getValue(i,j) + m.getValue(i,j);
+ tmp[i][j] = this.getValue(i, j) + m.getValue(i, j);
}
}
return new Matrix(tmp);
}
/**
- * performs an element-wise subtraction of this matrix by another matrix ~ this - m
- * @param m ~ other matrix
- *
- * @return
- */
+ * performs an element-wise subtraction of this matrix by another matrix ~
+ * this - m
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public MatrixI subtract(MatrixI m)
{
if (m.width() != cols || m.height() != rows)
{
- throw new IllegalArgumentException("Can't subtract a " + m.height() + "x" + m.width() + " from a " + this.rows + "x" + this.cols + " matrix");
+ throw new IllegalArgumentException("Can't subtract a " + m.height()
+ + "x" + m.width() + " from a " + this.rows + "x" + this.cols
+ + " matrix");
}
double[][] tmp = new double[this.rows][this.cols];
for (int i = 0; i < this.rows; i++)
{
for (int j = 0; j < this.cols; j++)
{
- tmp[i][j] = this.getValue(i,j) - m.getValue(i,j);
+ tmp[i][j] = this.getValue(i, j) - m.getValue(i, j);
}
}
return new Matrix(tmp);
}
/**
- * performs an element-wise multiplication of this matrix by another matrix ~ this * m
- * @param m ~ other matrix
- *
- * @return
- */
+ * performs an element-wise multiplication of this matrix by another matrix ~
+ * this * m
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public MatrixI elementwiseMultiply(MatrixI m)
{
if (m.width() != cols || m.height() != rows)
{
- throw new IllegalArgumentException("Can't multiply a " + this.rows + "x" + this.cols + " by a " + m.height() + "x" + m.width() + " matrix");
+ throw new IllegalArgumentException(
+ "Can't multiply a " + this.rows + "x" + this.cols + " by a "
+ + m.height() + "x" + m.width() + " matrix");
}
double[][] tmp = new double[this.rows][this.cols];
for (int i = 0; i < this.rows; i++)
{
for (int j = 0; j < this.cols; j++)
{
- tmp[i][j] = this.getValue(i, j) * m.getValue(i,j);
+ tmp[i][j] = this.getValue(i, j) * m.getValue(i, j);
}
}
return new Matrix(tmp);
}
/**
- * performs an element-wise division of this matrix by another matrix ~ this / m
- * @param m ~ other matrix
- *
- * @return
- */
+ * performs an element-wise division of this matrix by another matrix ~ this /
+ * m
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public MatrixI elementwiseDivide(MatrixI m)
{
if (m.width() != cols || m.height() != rows)
{
- throw new IllegalArgumentException("Can't divide a " + this.rows + "x" + this.cols + " by a " + m.height() + "x" + m.width() + " matrix");
+ throw new IllegalArgumentException(
+ "Can't divide a " + this.rows + "x" + this.cols + " by a "
+ + m.height() + "x" + m.width() + " matrix");
}
double[][] tmp = new double[this.rows][this.cols];
for (int i = 0; i < this.rows; i++)
{
for (int j = 0; j < this.cols; j++)
{
- tmp[i][j] = this.getValue(i, j) / m.getValue(i,j);
+ tmp[i][j] = this.getValue(i, j) / m.getValue(i, j);
}
}
return new Matrix(tmp);
}
/**
- * calculate the root-mean-square for tow matrices
- * @param m ~ other matrix
- *
- * @return
- */
+ * calculate the root-mean-square for tow matrices
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
@Override
public double rmsd(MatrixI m)
{
}
/**
- * calculates the Frobenius norm of this matrix
- *
- * @return
- */
+ * calculates the Frobenius norm of this matrix
+ *
+ * @return
+ */
@Override
public double norm()
{
{
for (double val : row)
{
- result += Math.pow(val, 2);
+ result += Math.pow(val, 2);
}
}
return Math.sqrt(result);
}
/**
- * returns the sum of all values in this matrix
- *
- * @return
- */
+ * returns the sum of all values in this matrix
+ *
+ * @return
+ */
@Override
public double sum()
{
{
for (double val : row)
{
- sum += (Double.isNaN(val)) ? 0.0 : val;
+ sum += (Double.isNaN(val)) ? 0.0 : val;
}
}
return sum;
}
/**
- * returns the sum-product of this matrix with vector v
- * @param v ~ vector
- *
- * @return
- */
+ * returns the sum-product of this matrix with vector v
+ *
+ * @param v
+ * ~ vector
+ *
+ * @return
+ */
@Override
public double[] sumProduct(double[] v)
{
if (v.length != cols)
{
- throw new IllegalArgumentException("Vector and matrix do not have the same dimension! (" + v.length + " != " + cols + ")");
+ throw new IllegalArgumentException(
+ "Vector and matrix do not have the same dimension! ("
+ + v.length + " != " + cols + ")");
}
double[] result = new double[rows];
for (int i = 0; i < rows; i++)
double sum = 0;
for (int j = 0; j < row.length; j++)
{
- sum += row[j] * v[j];
+ sum += row[j] * v[j];
}
result[i] = sum;
}
}
/**
- * mirrors columns of the matrix
- *
- * @return
- */
+ * mirrors columns of the matrix
+ *
+ * @return
+ */
@Override
public MatrixI mirrorCol()
{
double[][] result = new double[rows][cols];
for (int i = 0; i < rows; i++)
{
- int k = cols - 1; // reverse col
+ int k = cols - 1; // reverse col
for (int j = 0; j < cols; j++)
{
- result[i][k--] = this.getValue(i,j);
+ result[i][k--] = this.getValue(i, j);
}
}
MatrixI resultMatrix = new Matrix(result);
void setValue(int i, int j, double d);
/**
- * Returns the matrix as a double[][] array
- *
- * @return
- */
+ * Returns the matrix as a double[][] array
+ *
+ * @return
+ */
double[][] asArray();
/**
void multiply(double d);
/**
- * Add d to all entries of this matrix
- *
- * @param d ~ value to add
- */
+ * Add d to all entries of this matrix
+ *
+ * @param d
+ * ~ value to add
+ */
void add(double d);
/**
boolean equals(MatrixI m2, double delta);
/**
- * Returns a copy in which every value in the matrix is its absolute
+ * Returns a copy in which every value in the matrix is its absolute
*/
MatrixI absolute();
double[] meanCol();
/**
- * Returns a flattened matrix containing the sum of each column
- *
- * @return
- */
+ * Returns a flattened matrix containing the sum of each column
+ *
+ * @return
+ */
double[] sumCol();
/**
- * returns the mean value of the complete matrix
- */
+ * returns the mean value of the complete matrix
+ */
double mean();
/**
- * fills up a diagonal matrix with its transposed copy
- * !other side should be filled with either 0 or Double.NaN
- */
+ * fills up a diagonal matrix with its transposed copy !other side should be
+ * filled with either 0 or Double.NaN
+ */
void fillDiagonal();
/**
- * counts the number of Double.NaN in the matrix
- *
- * @return
- */
+ * counts the number of Double.NaN in the matrix
+ *
+ * @return
+ */
int countNaN();
/**
- * performs an element-wise addition of this matrix by another matrix
- * !matrices have to be the same size
- * @param m ~ other matrix
- *
- * @return
- * @throws IllegalArgumentException
- * if this and m do not have the same dimensions
- */
+ * performs an element-wise addition of this matrix by another matrix
+ * !matrices have to be the same size
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this and m do not have the same dimensions
+ */
MatrixI add(MatrixI m);
/**
- * performs an element-wise subtraction of this matrix by another matrix
- * !matrices have to be the same size
- * @param m ~ other matrix
- *
- * @return
- * @throws IllegalArgumentException
- * if this and m do not have the same dimensions
- */
+ * performs an element-wise subtraction of this matrix by another matrix
+ * !matrices have to be the same size
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this and m do not have the same dimensions
+ */
MatrixI subtract(MatrixI m);
-
+
/**
- * performs an element-wise multiplication of this matrix by another matrix ~ this * m
- * !matrices have to be the same size
- * @param m ~ other matrix
- *
- * @return
- * @throws IllegalArgumentException
- * if this and m do not have the same dimensions
- */
+ * performs an element-wise multiplication of this matrix by another matrix ~
+ * this * m !matrices have to be the same size
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this and m do not have the same dimensions
+ */
MatrixI elementwiseMultiply(MatrixI m);
/**
- * performs an element-wise division of this matrix by another matrix ~ this / m
- * !matrices have to be the same size
- * @param m ~ other matrix
- *
- * @return
- * @throws IllegalArgumentException
- * if this and m do not have the same dimensions
- */
+ * performs an element-wise division of this matrix by another matrix ~ this /
+ * m !matrices have to be the same size
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this and m do not have the same dimensions
+ */
MatrixI elementwiseDivide(MatrixI m);
/**
- * calculates the root-mean-square for two matrices
- * @param m ~ other matrix
- *
- * @return
- */
+ * calculates the root-mean-square for two matrices
+ *
+ * @param m
+ * ~ other matrix
+ *
+ * @return
+ */
double rmsd(MatrixI m);
/**
- * calculates the Frobenius norm of this matrix
- *
- * @return
- */
+ * calculates the Frobenius norm of this matrix
+ *
+ * @return
+ */
double norm();
-
+
/**
- * returns the sum of all values in this matrix
- *
- * @return
- */
+ * returns the sum of all values in this matrix
+ *
+ * @return
+ */
double sum();
/**
- * returns the sum-product of this matrix with vector v
- * @param v ~ vector
- *
- * @return
- * @throws IllegalArgumentException
- * if this.cols and v do not have the same length
- */
+ * returns the sum-product of this matrix with vector v
+ *
+ * @param v
+ * ~ vector
+ *
+ * @return
+ * @throws IllegalArgumentException
+ * if this.cols and v do not have the same length
+ */
double[] sumProduct(double[] v);
/**
- * mirrors the columns of this matrix
- *
- * @return
- */
+ * mirrors the columns of this matrix
+ *
+ * @return
+ */
MatrixI mirrorCol();
}
/**
* A collection of miscellaneous mathematical operations
+ *
* @AUTHOR MorellThomas
*/
public class MiscMath
{
/**
- * prints an array
- * @param m ~ array
- */
+ * prints an array
+ *
+ * @param m
+ * ~ array
+ */
public static void print(double[] m, String format)
{
System.out.print("[ ");
}
/**
- * calculates the mean of an array
- *
- * @param m ~ array
- * @return
- */
+ * calculates the mean of an array
+ *
+ * @param m
+ * ~ array
+ * @return
+ */
public static double mean(double[] m)
{
double sum = 0;
int nanCount = 0;
for (int i = 0; i < m.length; i++)
{
- if (!Double.isNaN(m[i])) // ignore NaN values in the array
+ if (!Double.isNaN(m[i])) // ignore NaN values in the array
{
sum += m[i];
- } else {
- nanCount++;
+ }
+ else
+ {
+ nanCount++;
}
}
return sum / (double) (m.length - nanCount);
}
/**
- * calculates the sum of an array
- *
- * @param m ~ array
- * @return
- */
+ * calculates the sum of an array
+ *
+ * @param m
+ * ~ array
+ * @return
+ */
public static double sum(double[] m)
{
double sum = 0;
for (int i = 0; i < m.length; i++)
{
- if (!Double.isNaN(m[i])) // ignore NaN values in the array
+ if (!Double.isNaN(m[i])) // ignore NaN values in the array
{
sum += m[i];
}
}
/**
- * calculates the square root of each element in an array
- *
- * @param m ~ array
- *
- * @return
- * TODO
- * make general with function passed -> apply function to each element
- */
+ * calculates the square root of each element in an array
+ *
+ * @param m
+ * ~ array
+ *
+ * @return TODO make general with function passed -> apply function to each
+ * element
+ */
public static double[] sqrt(double[] m)
{
double[] sqrts = new double[m.length];
}
/**
- * calculate element wise multiplication of two arrays with the same length
- *
- * @param a ~ array
- * @param b ~ array
- *
- * @return
- */
- public static double[] elementwiseMultiply(byte[] a, double[] b) throws RuntimeException
+ * calculate element wise multiplication of two arrays with the same length
+ *
+ * @param a
+ * ~ array
+ * @param b
+ * ~ array
+ *
+ * @return
+ */
+ public static double[] elementwiseMultiply(byte[] a, double[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
return result;
}
- public static double[] elementwiseMultiply(double[] a, double[] b) throws RuntimeException
+
+ public static double[] elementwiseMultiply(double[] a, double[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
return result;
}
- public static byte[] elementwiseMultiply(byte[] a, byte[] b) throws RuntimeException
+
+ public static byte[] elementwiseMultiply(byte[] a, byte[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
return result;
}
+
public static double[] elementwiseMultiply(double[] a, double b)
{
double[] result = new double[a.length];
}
/**
- * calculate element wise division of two arrays ~ a / b
- *
- * @param a ~ array
- * @param b ~ array
- *
- * @return
- */
- public static double[] elementwiseDivide(double[] a, double[] b) throws RuntimeException
+ * calculate element wise division of two arrays ~ a / b
+ *
+ * @param a
+ * ~ array
+ * @param b
+ * ~ array
+ *
+ * @return
+ */
+ public static double[] elementwiseDivide(double[] a, double[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
/**
- * calculate element wise addition of two arrays
- *
- * @param a ~ array
- * @param b ~ array
- *
- * @return
- */
- public static double[] elementwiseAdd(double[] a, double[] b) throws RuntimeException
+ * calculate element wise addition of two arrays
+ *
+ * @param a
+ * ~ array
+ * @param b
+ * ~ array
+ *
+ * @return
+ */
+ public static double[] elementwiseAdd(double[] a, double[] b)
+ throws RuntimeException
{
- if (a.length != b.length) // throw exception if the arrays do not have the same length
+ if (a.length != b.length) // throw exception if the arrays do not have the
+ // same length
{
throw new SameLengthException(a.length, b.length);
}
}
return result;
}
+
public static double[] elementwiseAdd(double[] a, double b)
{
double[] result = new double[a.length];
}
/**
- * returns true if two arrays are element wise within a tolerance
- *
- * @param a ~ array
- * @param b ~ array
- * @param rtol ~ relative tolerance
- * @param atol ~ absolute tolerance
- * @param equalNAN ~ whether NaN at the same position return true
- *
- * @return
- */
- public static boolean allClose(double[] a, double[] b, double rtol, double atol, boolean equalNAN)
+ * returns true if two arrays are element wise within a tolerance
+ *
+ * @param a
+ * ~ array
+ * @param b
+ * ~ array
+ * @param rtol
+ * ~ relative tolerance
+ * @param atol
+ * ~ absolute tolerance
+ * @param equalNAN
+ * ~ whether NaN at the same position return true
+ *
+ * @return
+ */
+ public static boolean allClose(double[] a, double[] b, double rtol,
+ double atol, boolean equalNAN)
{
boolean areEqual = true;
for (int i = 0; i < a.length; i++)
{
- if (equalNAN && (Double.isNaN(a[i]) && Double.isNaN(b[i]))) // if equalNAN == true -> skip the NaN pair
+ if (equalNAN && (Double.isNaN(a[i]) && Double.isNaN(b[i]))) // if equalNAN
+ // == true ->
+ // skip the
+ // NaN pair
{
- continue;
+ continue;
}
- if (Math.abs(a[i] - b[i]) > (atol + rtol * Math.abs(b[i]))) // check for the similarity condition -> if not met -> break and return false
+ if (Math.abs(a[i] - b[i]) > (atol + rtol * Math.abs(b[i]))) // check for
+ // the
+ // similarity
+ // condition
+ // -> if not
+ // met ->
+ // break and
+ // return
+ // false
{
- areEqual = false;
- break;
+ areEqual = false;
+ break;
}
}
return areEqual;
}
/**
- * returns the index of the maximum and the maximum value of an array
- *
- * @param a ~ array
- *
- * @return
- */
+ * returns the index of the maximum and the maximum value of an array
+ *
+ * @param a
+ * ~ array
+ *
+ * @return
+ */
public static int[] findMax(int[] a)
{
int max = 0;
{
if (a[i] > max)
{
- max = a[i];
- maxIndex = i;
+ max = a[i];
+ maxIndex = i;
}
}
- return new int[]{maxIndex, max};
+ return new int[] { maxIndex, max };
}
/**
- * returns the dot product of two arrays
- * @param a ~ array a
- * @param b ~ array b
- *
- * @return
- */
+ * returns the dot product of two arrays
+ *
+ * @param a
+ * ~ array a
+ * @param b
+ * ~ array b
+ *
+ * @return
+ */
public static double dot(double[] a, double[] b)
{
if (a.length != b.length)
{
- throw new IllegalArgumentException(String.format("Vectors do not have the same length (%d, %d)!", a.length, b.length));
+ throw new IllegalArgumentException(
+ String.format("Vectors do not have the same length (%d, %d)!",
+ a.length, b.length));
}
double aibi = 0;
}
/**
- * returns the euklidian norm of the vector
- * @param v ~ vector
- *
- * @return
- */
+ * returns the euklidian norm of the vector
+ *
+ * @param v
+ * ~ vector
+ *
+ * @return
+ */
public static double norm(double[] v)
{
double result = 0;
{
result += Math.pow(i, 2);
}
- return Math.sqrt(result);
+ return Math.sqrt(result);
}
/**
- * returns the number of NaN in the vector
- * @param v ~ vector
- *
- * @return
- */
+ * returns the number of NaN in the vector
+ *
+ * @param v
+ * ~ vector
+ *
+ * @return
+ */
public static int countNaN(double[] v)
{
int cnt = 0;
{
if (Double.isNaN(i))
{
- cnt++;
+ cnt++;
}
}
return cnt;
}
/**
- * recursively calculates the permutations of total n items with r items per combination
- * according to n!/(n-r)! by only multiplying the relevant terms
- * @param n
- * @param r
- *
- * @return permutations
- */
+ * recursively calculates the permutations of total n items with r items per
+ * combination according to n!/(n-r)! by only multiplying the relevant terms
+ *
+ * @param n
+ * @param r
+ *
+ * @return permutations
+ */
public static long permutations(int n, int r)
{
if (n < r)
long result = 1l;
for (int i = 0; i < r; i++)
{
- result *= (n-i);
+ result *= (n - i);
}
return result;
}
/**
* calculate all unique combinations of n elements into r sized groups
+ *
* @param n
* @param r
*
int result = 1;
for (int i = 0; i < r; i++)
{
- result *= (n-1);
+ result *= (n - 1);
}
return (int) (result / MiscMath.factorial(r));
}
/**
* calculate the factorial of n (n >= 0)
+ *
* @param n
*
* @return
}
/**
- * Writes PaSiMap viewer attributes and computed values to an XML model object and
- * adds it to the JalviewModel. Any exceptions are reported by logging.
+ * Writes PaSiMap viewer attributes and computed values to an XML model object
+ * and adds it to the JalviewModel. Any exceptions are reported by logging.
* uses the functions from PCA
*/
protected void savePaSiMap(PaSiMapPanel panel, JalviewModel object)
{
- // TODO: this should be merged with above savePCAPanel - otherwise it is essentially redundant code
+ // TODO: this should be merged with above savePCAPanel - otherwise it is
+ // essentially redundant code
try
{
PcaViewer viewer = new PcaViewer();
Console.error("Error saving PaSiMap: " + t.getMessage());
}
}
+
/**
* Stores values from a matrix into an XML element, including (if present) the
* D or E vectors
private boolean isPasimap(PcaViewer viewer)
{
- return viewer.getTitle().toLowerCase(Locale.ROOT)
- .startsWith("pasimap");
+ return viewer.getTitle().toLowerCase(Locale.ROOT).startsWith("pasimap");
}
+
/**
* Loads any saved PaSiMAp viewers using the function from PCA
*
viewer.isIncludeGappedColumns(), viewer.isMatchGaps(),
viewer.isIncludeGaps(),
viewer.isDenominateByShortestLength());
- */
+ */
/*
* create the panel (without computing the PaSiMAp)
PaSiMap pasimap = new PaSiMap(null, scoreModel, null);
PcaDataType pasimapData = viewer.getPcaData();
- MatrixI pairwise = loadDoubleMatrix(pasimapData.getPairwiseMatrix());
+ MatrixI pairwise = loadDoubleMatrix(
+ pasimapData.getPairwiseMatrix());
pasimap.setPairwiseScores(pairwise);
MatrixI result = loadDoubleMatrix(pasimapData.getEigenMatrix());
* {profile type, #values, total count, char1, pct1, char2, pct2...}
*/
int profl[] = getProfileFor(_aa, column);
-
-
// just try to draw the logo if profl is not null
if (profl != null && profl[2] != 0)
}
else
{
-
+
colour = profcolour.findColour(dc[0], column, null);
}
* the consensus data for each column
*/
private ProfilesI consensus;
-
+
/*
* the ss consensus data for each column for each source
*/
private Map<String, ProfilesI> ssConsensusProfileMap;
+
/*
* if true, apply shading of colour by conservation
*/
public void setConsensus(ProfilesI cons)
{
consensus = cons;
-
+
}
/**
return colour;
}
-
+
@Override
public Color findSSColour(char symbol, int position)
{
{
return false;
}
+
public String toRuleRep()
{
makeColours();
- HashMap<String, String> cols=new HashMap();
- for (String res:ResidueProperties.aa) {
+ HashMap<String, String> cols = new HashMap();
+ for (String res : ResidueProperties.aa)
+ {
StringBuilder sb = new StringBuilder();
-
- int rnum=ResidueProperties.aaIndex[res.charAt(0)];
- if (rnum<0 || rnum>=residueColour.length)
+
+ int rnum = ResidueProperties.aaIndex[res.charAt(0)];
+ if (rnum < 0 || rnum >= residueColour.length)
{
continue;
}
-
+
ConsensusColour cc = residueColour[rnum];
- if (cc==null)
+ if (cc == null)
{
continue;
}
- //sb.append("Residue "+res+" ("+rnum+")");
- //sb.append("\t");
+ // sb.append("Residue "+res+" ("+rnum+")");
+ // sb.append("\t");
sb.append(cc.c.toString());
- double f=0;
+ double f = 0;
sb.append("\t");
- for (Consensus cons: cc.cons) {
- if (cons.threshold==0 || f!=cons.threshold)
+ for (Consensus cons : cc.cons)
+ {
+ if (cons.threshold == 0 || f != cons.threshold)
{
- if (f!=0)
+ if (f != 0)
{
- sb.append("}, {");
- } else {
- sb.append("{");
+ sb.append("}, {");
+ }
+ else
+ {
+ sb.append("{");
}
- sb.append(cons.threshold);
- sb.append(",");
- f=cons.threshold;
- } else {
+ sb.append(cons.threshold);
+ sb.append(",");
+ f = cons.threshold;
+ }
+ else
+ {
sb.append(",");
}
sb.append(cons.maskstr);
}
sb.append("}");
- String clxrep=sb.toString();
+ String clxrep = sb.toString();
String xres = cols.get(clxrep);
- if (xres==null) { xres = "";}
- xres+=res;
+ if (xres == null)
+ {
+ xres = "";
+ }
+ xres += res;
cols.put(clxrep, xres);
}
StringBuilder sb = new StringBuilder();
- for (String clxrep:cols.keySet())
+ for (String clxrep : cols.keySet())
{
sb.append(cols.get(clxrep));
sb.append("\t");
sb.append(clxrep);
sb.append("\n");
-
+
}
return sb.toString();
}
public static final int[] nucleotideIndex;
public static final int[] purinepyrimidineIndex;
-
+
public static final int[] secondaryStructureIndex;
public static final Map<String, Integer> aa3Hash = new HashMap<>();
purinepyrimidineIndex['N'] = 2;
purinepyrimidineIndex['n'] = 2;
}
-
+
static
{
secondaryStructureIndex = new int[255];
for (int i = 0; i < 255; i++)
{
- secondaryStructureIndex[i] = 3;
+ secondaryStructureIndex[i] = 3;
}
secondaryStructureIndex['H'] = 0;
Color.white, // all other nucleotides
Color.white // Gap
};
-
- //Secondary structure
- public static final Color[] secondarystructure = { Color.red, // H
- Color.green, // E
- Color.gray // C
- };
+
+ // Secondary structure
+ public static final Color[] secondarystructure = { Color.red, // H
+ Color.green, // E
+ Color.gray // C
+ };
// Zappo
public static final Color[] zappo = { Color.pink, // A
+/*
+ * 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.
+ */
package jalview.util;
import java.util.ArrayList;
*/
public class Constants
{
-
- //character used to represent secondary structures
+
+ // character used to represent secondary structures
public static final char HELIX = 'H';
+
public static final char SHEET = 'E';
+
public static final char COIL = 'C';
- //label in secondary structure annotation data model from 3d structures
+ // label in secondary structure annotation data model from 3d structures
public static final String SS_ANNOTATION_LABEL = "Secondary Structure";
-
- //label in secondary structure annotation data model from JPred
- public static final String SS_ANNOTATION_FROM_JPRED_LABEL = "jnetpred";
-
+
+ // label in secondary structure annotation data model from JPred
+ public static final String SS_ANNOTATION_FROM_JPRED_LABEL = "jnetpred";
+
public static final Map<String, String> SECONDARY_STRUCTURE_LABELS = new HashMap<>();
+
static {
SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_LABEL, "3D Structures");
SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_FROM_JPRED_LABEL, "JPred");
+/*
+ * 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.
+ */
package jalview.util;
import java.lang.reflect.InvocationTargetException;
private static String prefix = null;
+ private static boolean quiet = false;
+
public static void setHasConsole(boolean b)
{
hasConsole = b;
}
+ public static void setQuiet(boolean b)
+ {
+ quiet = b;
+ }
+
public static void setPrefix(String s)
{
prefix = s;
public static void println(String message0, boolean err,
boolean thisHasConsole)
{
+ if (!err && quiet)
+ {
+ return;
+ }
String message = prefix == null ? message0 : prefix + message0;
if (thisHasConsole && hasConsole)
{
import java.net.URL;
import java.net.URLConnection;
+import jalview.bin.Console;
+
public class HttpUtils
{
public final static String JALVIEWSCHEMEPREFIX = "jalview";
}
/**
- * wrapper to follow a URL connection ALLOWING redirects from http to https
+ * wrapper to return a new HttpURLConnection to a new URL when there is a
+ * redirect from http to https, otherwise return the unused original
+ * HttpURLConnection
*
* @param HttpURLConnection
* conn0
throws IOException
{
URL url = conn0.getURL();
- if (url == null)
+ // we are only checking for a redirect from http to https otherwise the java
+ // connection will follow when called (if not unset)
+ if (url == null || !"http".equals(url.getProtocol())
+ || !conn0.getInstanceFollowRedirects())
{
- return null;
+ return conn0;
}
- HttpURLConnection conn = null;
- int response = conn0.getResponseCode();
- boolean followed = false;
- if (response >= 300 && response < 400 && conn0.getFollowRedirects())
+
+ // check the response code
+ HttpURLConnection checkConn = (HttpURLConnection) url.openConnection();
+ httpURLConnectionCopyAttributes(conn0, checkConn);
+
+ boolean redirectToHttps = false;
+ int response = checkConn.getResponseCode();
+ checkConn.disconnect();
+ if (response >= 300 && response < 400)
{
// we are only checking for a redirect from http to https
- if ("http".equals(url.getProtocol()))
+ URL loc = new URL(conn0.getHeaderField("Location"));
+ if (loc != null && "https".equals(loc.getProtocol()))
{
- URL loc = new URL(conn0.getHeaderField("Location"));
- if (loc != null && "https".equals(loc.getProtocol()))
- {
- conn = (HttpURLConnection) loc.openConnection();
- conn.setRequestMethod(conn0.getRequestMethod());
- conn.setDoInput(conn0.getDoInput());
- conn.setUseCaches(conn0.getUseCaches());
- conn.setConnectTimeout(conn0.getConnectTimeout());
- conn.setReadTimeout(conn0.getReadTimeout());
- conn.setInstanceFollowRedirects(
- conn0.getInstanceFollowRedirects());
- followed = true;
- }
+ redirectToHttps = true;
+ url = loc;
}
}
- return followed && conn != null ? conn : conn0;
+
+ if (!redirectToHttps)
+ {
+ return conn0;
+ }
+
+ // We want to return an HttpURLConnection to the new https URL that is
+ // unconnected in case further manipulation of the request is required
+ HttpURLConnection conn = (HttpURLConnection) url.openConnection();
+ httpURLConnectionCopyAttributes(conn0, conn);
+ return conn;
+ }
+
+ private static void httpURLConnectionCopyAttributes(
+ HttpURLConnection conn0, HttpURLConnection conn1)
+ throws ProtocolException
+ {
+ conn1.setRequestMethod(conn0.getRequestMethod());
+ conn1.setDoInput(conn0.getDoInput());
+ conn1.setUseCaches(conn0.getUseCaches());
+ conn1.setConnectTimeout(conn0.getConnectTimeout());
+ conn1.setReadTimeout(conn0.getReadTimeout());
+ conn1.setInstanceFollowRedirects(conn0.getInstanceFollowRedirects());
}
/**
{
if (url == null)
{
+ Console.debug("HttpUtils.openConnection(url) called with null url");
return null;
}
+ Console.debug("HttpUtils.openConnection(url) called with url="
+ + url.toString());
URLConnection conn = null;
String protocol = url.getProtocol();
if ("http".equals(protocol) || "https".equals(protocol))
}
String v0 = getJarImplementationVersion(f0);
String v1 = getJarImplementationVersion(f1);
- syserr(true, false,
+ syserr(v0 != null && !v0.equals(v1), false,
"Got launcher versions '" + v0 + "' and '" + v1 + "'");
return compareGetdownLauncherJarVersions(v0, v1);
}
+/*
+ * 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.
+ */
package jalview.util;
import jalview.bin.Cache;
protected AlignmentAnnotation quality;
protected AlignmentAnnotation[] groupConsensus;
-
+
protected AlignmentAnnotation[] groupSSConsensus;
protected AlignmentAnnotation[] groupConservation;
protected ProfilesI hconsensus = null;
protected Map<String, ProfilesI> hSSConsensusProfileMap = null;
-
-
/**
* results of cDNA complement consensus visible portion of view
{
this.hconsensus = hconsensus;
}
-
+
@Override
public void setSequenceSSConsensusHash(Map<String, ProfilesI> hSSConsensusProfileMap)
{
this.hSSConsensusProfileMap = hSSConsensusProfileMap;
}
-
+
@Override
public void setComplementConsensusHash(
Hashtable<String, Object>[] hconsensus)
return consensus;
}
-
@Override
public List<AlignmentAnnotation> getAlignmentSecondaryStructureConsensusAnnotation()
{
return secondaryStructureConsensus;
}
-
@Override
public AlignmentAnnotation getAlignmentGapAnnotation()
}
}
}
-
-
-
/**
* trigger update of Secondary Structure consensus annotation
if (calculator
.getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class) == null)
{
- calculator.registerWorker(new SecondaryStructureConsensusThread(this, ap));
+ calculator.registerWorker(
+ new SecondaryStructureConsensusThread(this, ap));
}
ap.adjustAnnotationHeight();
* should consensus profile be rendered by default
*/
protected boolean showSequenceLogo = false;
-
+
/**
* should consensus profile be rendered normalised to row height
*/
* should consensus histograms be rendered by default
*/
protected boolean showConsensusHistogram = true;
-
+
/**
* @return the showConsensusProfile
*/
{
return showSequenceLogo;
}
-
+
/**
* @param showSequenceLogo
* the new value
}
this.showSequenceLogo = showSequenceLogo;
}
-
+
/**
* @param showConsensusHistogram
* the showConsensusHistogram to set
protected boolean showQuality = true;
- protected boolean showConsensus = true;
+ protected boolean showConsensus = true;
protected boolean showSSConsensus = true;
}
}
-
/**
* If this is a protein alignment and there are mappings to cDNA, adds the
* cDNA consensus annotation and returns true, else returns false.
* @param modelName
* @param params
*/
- public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc,
- ScoreModelI modelName)
+ public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs,
+ boolean nuc, ScoreModelI modelName)
{
inputData = seqData;
seqs = sqs;
}
/**
- * Performs the PaSiMap calculation (in the same thread) and extracts result data
- * needed for visualisation by PaSiMapPanel
+ * Performs the PaSiMap calculation (in the same thread) and extracts result
+ * data needed for visualisation by PaSiMapPanel
*/
public void calculate(PairwiseAlignPanel pap)
{
top = width;
points = new Vector<>();
- Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3, 1);
+ Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3,
+ 1);
for (int i = 0; i < height; i++)
{
/**
* Updates the 3D coordinates for the list of points to the given dimensions.
* Principal dimension is getTop(). Next greatest eigenvector is getTop()-1.
- * Note - pasimap.getComponents starts counting the spectrum from rank-2 to zero,
- * rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..)
+ * Note - pasimap.getComponents starts counting the spectrum from rank-2 to
+ * zero, rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1
+ * ..)
*
* @param dim1
* @param dim2
csv.append("\"" + seqs[s].getName() + "\"");
if (!transformed)
{
- double[] fl = pasimap.component(s);
- for (int d = fl.length - 1; d >= 0; d--)
- {
- csv.append(",");
- csv.append(fl[d]);
- }
- } else {
+ double[] fl = pasimap.component(s);
+ for (int d = fl.length - 1; d >= 0; d--)
+ {
+ csv.append(",");
+ csv.append(fl[d]);
+ }
+ }
+ else
+ {
Point p = points.get(s).coord;
csv.append(",").append(p.x);
csv.append(",").append(p.y);
*/
protected List<AlignmentAnnotation> getSSConsensusAnnotation()
{
- return alignViewport.getAlignmentSecondaryStructureConsensusAnnotation();
+ return alignViewport
+ .getAlignmentSecondaryStructureConsensusAnnotation();
}
/**
+/*
+ * 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.
+ */
package jalview.ws.datamodel.alphafold;
import java.awt.Color;
+/*
+ * 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.
+ */
package jalview.ws.datamodel.alphafold;
import java.io.File;
String s = "aArRnNzZxX *.-?";
assertArrayEquals(expected, as.indexEncode(s));
}
- @Test(groups= {"Functional"})
+
+ @Test(groups = { "Functional" })
public void testGlobalAlignment()
{
- String seq1="CAGCTAGCG",seq2="CCATACGA";
- Sequence sq1=new Sequence("s1",seq1),sq2=new Sequence("s2",seq2);
+ String seq1 = "CAGCTAGCG", seq2 = "CCATACGA";
+ Sequence sq1 = new Sequence("s1", seq1), sq2 = new Sequence("s2", seq2);
// AlignSeq doesn't report the unaligned regions at either end of sequences
- //String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA";
+ // String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA";
// so we check we have the aligned segment correct only
- String alseq1="CAGCTAGCG",alseq2="CA--TA-CG";
- AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1,sq2,AlignSeq.DNA);
- assertEquals(as.getAStr1()+"\n"+as.getAStr2(),alseq1+"\n"+alseq2);
+ String alseq1 = "CAGCTAGCG", alseq2 = "CA--TA-CG";
+ AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1, sq2, AlignSeq.DNA);
+ assertEquals(as.getAStr1() + "\n" + as.getAStr2(),
+ alseq1 + "\n" + alseq2);
}
}
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", "Secondary Structure",
- new Annotation[] {});
- AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred", "jnetpred",
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure",
new Annotation[] {});
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
+ "jnetpred", new Annotation[] {});
AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
new Annotation[] {});
AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
new Annotation[] {});
-
- AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] {ann1, ann3, ann4};
- AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] {ann2, ann3, ann4};
-
- AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] {ann3, ann4};
-
+ AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] { ann1, ann3,
+ ann4 };
+
+ AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] { ann2, ann3,
+ ann4 };
+
+ AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] { ann3, ann4 };
+
AlignmentAnnotation[] anns4 = new AlignmentAnnotation[0];
-
- AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] {ann1, ann2, ann3, ann4};
+
+ AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] { ann1, ann2,
+ ann3, ann4 };
}
@Test(groups = { "Functional" })
Assert.assertEquals(expectedSSPresent, AlignmentUtils.isSecondaryStructurePresent(annotations));
}
- @DataProvider(name = "SecondaryStructureAnnotations")
- public static Object[][] provideSecondaryStructureAnnotations() {
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", "Secondary Structure", new Annotation[]{});
- AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred", "jnetpred", new Annotation[]{});
- AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp", new Annotation[]{});
- AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp", new Annotation[]{});
-
- List<String> ssSources1 = new ArrayList<>(Arrays.asList("3D Structures"));
- List<String> ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
- List<String> ssSources3 = new ArrayList<>(Arrays.asList("3D Structures", "JPred"));
- List<String> ssSources4 = new ArrayList<>();
-
- return new Object[][]{
- {new AlignmentAnnotation[]{ann1, ann3, ann4}, true, ssSources1},
- {new AlignmentAnnotation[]{ann2, ann3, ann4}, true, ssSources2},
- {new AlignmentAnnotation[]{ann3, ann4}, false, ssSources4},
- {new AlignmentAnnotation[]{}, false, ssSources4},
- {new AlignmentAnnotation[]{ann1, ann2, ann3, ann4}, true, ssSources3}
- };
- }
-
- @Test(dataProvider = "SecondaryStructureAnnotationColours")
- public void testSecondaryStructureAnnotationColour(char symbol, Color expectedColor) {
- Color actualColor = AlignmentUtils.getSecondaryStructureAnnotationColour(symbol);
- Assert.assertEquals(actualColor, expectedColor);
- }
+ @Test(
+ groups = "Functional",
+ dataProvider = "SecondaryStructureAnnotations")
+ public void testSecondaryStructurePresentAndSources(
+ AlignmentAnnotation[] annotations, boolean expectedSSPresent,
+ ArrayList<String> expectedSSSources)
+ {
+ Assert.assertEquals(expectedSSPresent,
+ AlignmentUtils.isSecondaryStructurePresent(annotations));
+ Assert.assertEquals(expectedSSSources,
+ AlignmentUtils.getSecondaryStructureSources(annotations));
+ }
- @DataProvider(name = "SecondaryStructureAnnotationColours")
- public static Object[][] provideSecondaryStructureAnnotationColours() {
- return new Object[][]{
- {'C', Color.gray},
- {'E', Color.green},
- {'H', Color.red},
- {'-', Color.gray}
- };
- }
-
- @Test(dataProvider = "SSAnnotationPresence")
- public void testIsSSAnnotationPresent(Map<SequenceI, List<AlignmentAnnotation>> annotations, boolean expectedPresence) {
- boolean actualPresence = AlignmentUtils.isSSAnnotationPresent(annotations);
- Assert.assertEquals(actualPresence, expectedPresence);
- }
+ @DataProvider(name = "SecondaryStructureAnnotations")
+ public static Object[][] provideSecondaryStructureAnnotations()
+ {
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure",
+ new Annotation[] {});
+ AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
+ "jnetpred", new Annotation[] {});
+ AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
+ new Annotation[] {});
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
+ new Annotation[] {});
- @DataProvider(name = "SSAnnotationPresence")
- public static Object[][] provideSSAnnotationPresence() {
- Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
- SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
- List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
- annotationsList1.add(new AlignmentAnnotation("Secondary Structure", "Secondary Structure", new Annotation[]{}));
- annotations1.put(seq1, annotationsList1); // Annotation present secondary structure for seq1
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
- SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
- List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
- annotationsList2.add(new AlignmentAnnotation("Other Annotation", "Other Annotation", new Annotation[]{}));
- annotations2.put(seq2, annotationsList2); // Annotation not related to any of secondary structure for seq2
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
- // Empty annotation map
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
- SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
- List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
- annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred", new Annotation[]{}));
- annotations4.put(seq4, annotationsList4); // Annotation present from JPred for seq4
-
-
- return new Object[][]{
- {annotations1, true}, // Annotations present secondary structure present
- {annotations2, false}, // No annotations related to any of the secondary structure present
- {annotations3, false}, // Empty annotation map
- {annotations4, true}, // Annotations present from JPred secondary structure present
- };
- }
-
- @Test
- public void testGetSSSourceFromAnnotationDescription(AlignmentAnnotation[] annotations, String expectedSSSource) {
- List<String> actualSSSource = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
- Assert.assertEquals(actualSSSource, expectedSSSource);
- }
-
- @DataProvider(name = "SSSourceFromAnnotationDescription")
- public static Object[][] provideSSSourceFromAnnotationDescription() {
- Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
- SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
- List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
- annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output", new Annotation[]{}));
- annotations1.put(seq1, annotationsList1); // Annotation present from JPred for seq1
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
- SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
- List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
- annotationsList2.add(new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure for af-q43517-f1A", new Annotation[]{}));
- annotations2.put(seq2, annotationsList2); // Annotation present secondary structure from Alphafold for seq2
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
- // Empty annotation map
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
- SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
- List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
- annotationsList4.add(new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure for 4zhpA", new Annotation[]{}));
- annotations4.put(seq4, annotationsList4); // Annotation present secondary structure from pdb for seq4
-
- Map<SequenceI, List<AlignmentAnnotation>> annotations5 = new HashMap<>();
- SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
- List<AlignmentAnnotation> annotationsList5 = new ArrayList<>();
- annotationsList5.add(new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P",
- new Annotation[]{}));
- annotations5.put(seq5, annotationsList5); // Annotation present secondary structure from Swiss model for seq5
-
-
- //JPred Output - JPred
- //Secondary Structure for af-q43517-f1A - Alphafold
- //Secondary Structure for 4zhpA - Experimental
- //Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P - Swiss Model
-
- return new Object[][]{
- {annotations1, "JPred"},
- {annotations2, "Alphafold"},
- {annotations3, null},
- {annotations4, "PDB"},
- {annotations5, "Swiss Model"}
- };
- }
+ List<String> ssSources1 = new ArrayList<>(
+ Arrays.asList("3D Structures"));
+ List<String> ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
+ List<String> ssSources3 = new ArrayList<>(
+ Arrays.asList("3D Structures", "JPred"));
+ List<String> ssSources4 = new ArrayList<>();
+
+ return new Object[][] {
+ { new AlignmentAnnotation[]
+ { ann1, ann3, ann4 }, true, ssSources1 },
+ { new AlignmentAnnotation[]
+ { ann2, ann3, ann4 }, true, ssSources2 },
+ { new AlignmentAnnotation[]
+ { ann3, ann4 }, false, ssSources4 },
+ { new AlignmentAnnotation[] {}, false, ssSources4 },
+ { new AlignmentAnnotation[]
+ { ann1, ann2, ann3, ann4 }, true, ssSources3 } };
+ }
+
+ @Test(dataProvider = "SecondaryStructureAnnotationColours")
+ public void testSecondaryStructureAnnotationColour(char symbol,
+ Color expectedColor)
+ {
+ Color actualColor = AlignmentUtils
+ .getSecondaryStructureAnnotationColour(symbol);
+ Assert.assertEquals(actualColor, expectedColor);
+ }
+
+ @DataProvider(name = "SecondaryStructureAnnotationColours")
+ public static Object[][] provideSecondaryStructureAnnotationColours()
+ {
+ return new Object[][] { { 'C', Color.gray }, { 'E', Color.green },
+ { 'H', Color.red },
+ { '-', Color.gray } };
+ }
+
+ @Test(dataProvider = "SSAnnotationPresence")
+ public void testIsSSAnnotationPresent(
+ Map<SequenceI, List<AlignmentAnnotation>> annotations,
+ boolean expectedPresence)
+ {
+ boolean actualPresence = AlignmentUtils
+ .isSSAnnotationPresent(annotations);
+ Assert.assertEquals(actualPresence, expectedPresence);
+ }
+
+ @DataProvider(name = "SSAnnotationPresence")
+ public static Object[][] provideSSAnnotationPresence()
+ {
+ Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
+ SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+ List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
+ annotationsList1.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure", new Annotation[] {}));
+ annotations1.put(seq1, annotationsList1); // Annotation present secondary
+ // structure for seq1
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
+ SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+ List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
+ annotationsList2.add(new AlignmentAnnotation("Other Annotation",
+ "Other Annotation", new Annotation[] {}));
+ annotations2.put(seq2, annotationsList2); // Annotation not related to any
+ // of secondary structure for seq2
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
+ // Empty annotation map
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
+ SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+ List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
+ annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred",
+ new Annotation[] {}));
+ annotations4.put(seq4, annotationsList4); // Annotation present from JPred
+ // for seq4
+
+ return new Object[][] { { annotations1, true }, // Annotations present
+ // secondary structure
+ // present
+ { annotations2, false }, // No annotations related to any of the
+ // secondary structure present
+ { annotations3, false }, // Empty annotation map
+ { annotations4, true }, // Annotations present from JPred secondary
+ // structure present
+ };
+ }
+
+ @Test
+ public void testGetSSSourceFromAnnotationDescription(
+ AlignmentAnnotation[] annotations, String expectedSSSource)
+ {
+ List<String> actualSSSource = AlignmentUtils
+ .extractSSSourceInAlignmentAnnotation(annotations);
+ Assert.assertEquals(actualSSSource, expectedSSSource);
+ }
+
+ @DataProvider(name = "SSSourceFromAnnotationDescription")
+ public static Object[][] provideSSSourceFromAnnotationDescription()
+ {
+ Map<SequenceI, List<AlignmentAnnotation>> annotations1 = new HashMap<>();
+ SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+ List<AlignmentAnnotation> annotationsList1 = new ArrayList<>();
+ annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output",
+ new Annotation[] {}));
+ annotations1.put(seq1, annotationsList1); // Annotation present from JPred
+ // for seq1
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations2 = new HashMap<>();
+ SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+ List<AlignmentAnnotation> annotationsList2 = new ArrayList<>();
+ annotationsList2.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure for af-q43517-f1A", new Annotation[] {}));
+ annotations2.put(seq2, annotationsList2); // Annotation present secondary
+ // structure from Alphafold for
+ // seq2
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations3 = new HashMap<>();
+ // Empty annotation map
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations4 = new HashMap<>();
+ SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+ List<AlignmentAnnotation> annotationsList4 = new ArrayList<>();
+ annotationsList4.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure for 4zhpA", new Annotation[] {}));
+ annotations4.put(seq4, annotationsList4); // Annotation present secondary
+ // structure from pdb for seq4
+
+ Map<SequenceI, List<AlignmentAnnotation>> annotations5 = new HashMap<>();
+ SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
+ List<AlignmentAnnotation> annotationsList5 = new ArrayList<>();
+ annotationsList5.add(new AlignmentAnnotation("Secondary Structure",
+ "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P",
+ new Annotation[] {}));
+ annotations5.put(seq5, annotationsList5); // Annotation present secondary
+ // structure from Swiss model for
+ // seq5
+
+ // JPred Output - JPred
+ // Secondary Structure for af-q43517-f1A - Alphafold
+ // Secondary Structure for 4zhpA - Experimental
+ // Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P -
+ // Swiss Model
+
+ return new Object[][] { { annotations1, "JPred" },
+ { annotations2, "Alphafold" },
+ { annotations3, null },
+ { annotations4, "PDB" },
+ { annotations5, "Swiss Model" } };
+ }
}
assertFalse(sm instanceof PairwiseScoreModelI);
assertTrue(sm instanceof DistanceScoreModel);
assertEquals(sm.getName(), "Sequence Feature Similarity");
-
+
sm = models.next();
assertFalse(sm instanceof SimilarityScoreModel);
assertFalse(sm instanceof PairwiseScoreModelI);
// This class tests methods in Class SecondaryStructureDistanceModel
public class SecondaryStructureDistanceModelTest
{
-
+
/**
* Verify computed distances of sequences with gap
*/
ScoreModelI sm = new SecondaryStructureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
af.alignPanel);
-
+
/*
* feature distance model always normalises by region width
* gap-gap is always included (but scores zero)
* include gaps
* score = 0 + 0 + 1 + 0 = 1/4
*/
- SimilarityParamsI params = new SimilarityParams(false, true, true, true);
+ SimilarityParamsI params = new SimilarityParams(false, true, true,
+ true);
params.setSecondaryStructureSource("3D Structures");
MatrixI distances = sm.findDistances(view, params);
assertEquals(distances.getValue(0, 0), 1d);
assertEquals(distances.getValue(1, 1), 1d);
- assertEquals(distances.getValue(0, 1), 0d);
+ assertEquals(distances.getValue(0, 1), 0d);
assertEquals(distances.getValue(1, 0), 0d);
-
+
/*
* exclude gaps
* score = 0 + 0 + 0 + 0 = 0/4
*/
-
- SimilarityParamsI params2 = new SimilarityParams(false, true, false, true);
+
+ SimilarityParamsI params2 = new SimilarityParams(false, true, false,
+ true);
params2.setSecondaryStructureSource("3D Structures");
MatrixI distances2 = sm.findDistances(view, params2);
- assertEquals(distances2.getValue(0, 1), 0d);
+ assertEquals(distances2.getValue(0, 1), 0d);
assertEquals(distances2.getValue(1, 0), 0d);
}
-
-
+
/**
* Verify computed distances of sequences with gap
*/
ScoreModelI sm = new SecondaryStructureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
af.alignPanel);
-
+
/*
* feature distance model always normalises by region width
* gap-gap is always included (but scores zero)
* include gaps
* score = 0 + 0 + 2 + 2 = 2/4
*/
- SimilarityParamsI params = new SimilarityParams(false, true, true, true);
+ SimilarityParamsI params = new SimilarityParams(false, true, true,
+ true);
params.setSecondaryStructureSource("3D Structures");
MatrixI distances = sm.findDistances(view, params);
assertEquals(distances.getValue(0, 0), 1d);
assertEquals(distances.getValue(1, 1), 1d);
- assertEquals(distances.getValue(0, 1), 0d);
+ assertEquals(distances.getValue(0, 1), 0d);
assertEquals(distances.getValue(1, 0), 0d);
-
+
/*
* exclude gaps
* score = 0 + 0 + 2 + 2 = 2/4
*/
-
- SimilarityParamsI params2 = new SimilarityParams(false, true, false, true);
+
+ SimilarityParamsI params2 = new SimilarityParams(false, true, false,
+ true);
params2.setSecondaryStructureSource("3D Structures");
MatrixI distances2 = sm.findDistances(view, params2);
- assertEquals(distances2.getValue(0, 1), 0d);
+ assertEquals(distances2.getValue(0, 1), 0d);
assertEquals(distances2.getValue(1, 0), 0d);
}
-
/**
* Verify computed distances of sequences with gap
*/
ScoreModelI sm = new SecondaryStructureDistanceModel();
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
af.alignPanel);
-
+
/*
* feature distance model always normalises by region width
* gap-gap is always included (but scores zero)
* include gaps
* score = 0 + 0 + 2 + 2 = 2/4
*/
- SimilarityParamsI params = new SimilarityParams(false, true, true, true);
+ SimilarityParamsI params = new SimilarityParams(false, true, true,
+ true);
params.setSecondaryStructureSource("3D Structures");
MatrixI distances = sm.findDistances(view, params);
assertEquals(distances.getValue(0, 0), 1d);
assertEquals(distances.getValue(1, 1), 1d);
- assertEquals(distances.getValue(0, 1), 0d);
+ assertEquals(distances.getValue(0, 1), 0d);
assertEquals(distances.getValue(1, 0), 0d);
-
+
/*
* exclude gaps
* score = 0 + 0 + 2 + 2 = 2/4
*/
-
- SimilarityParamsI params2 = new SimilarityParams(false, true, false, true);
+
+ SimilarityParamsI params2 = new SimilarityParams(false, true, false,
+ true);
params2.setSecondaryStructureSource("3D Structures");
MatrixI distances2 = sm.findDistances(view, params2);
- assertEquals(distances2.getValue(0, 1), 0d);
+ assertEquals(distances2.getValue(0, 1), 0d);
assertEquals(distances2.getValue(1, 0), 0d);
}
-
-
/**
* <pre>
* Set up
new SequenceFeature("metal", null, 1, 4, 0f, null));
s2.addSequenceFeature(
new SequenceFeature("Pfam", null, 1, 4, 0f, null));
-
-
+
/*
* Set up secondary structure annotations
*/
- Annotation ssE = new Annotation("","",'E',0);
- Annotation ssH = new Annotation("","",'H',0);
- Annotation ssC = new Annotation(".","",' ',0);
-
+ Annotation ssE = new Annotation("", "", 'E', 0);
+ Annotation ssH = new Annotation("", "", 'H', 0);
+ Annotation ssC = new Annotation(".", "", ' ', 0);
+
Annotation[] anns1;
Annotation[] anns2;
-
+
/* All secondary structure annotations are similar for each column
* Set up
* column 1 2 3 4
* seq s2 F S J L
* ss E H S E
*/
- if(similar == "All Similar") {
-
- anns1 = new Annotation[] { ssE, ssH, ssC, ssE};
- anns2 = new Annotation[] { ssE, ssH, ssC, ssE};
-
+ if (similar == "All Similar")
+ {
+
+ anns1 = new Annotation[] { ssE, ssH, ssC, ssE };
+ anns2 = new Annotation[] { ssE, ssH, ssC, ssE };
+
}
-
+
/* All secondary structure annotations are dissimilar for each column
* Set up
* column 1 2 3 4
* seq s2 F S J L
* ss H E E C
*/
- else if(similar == "Not Similar") {
-
- anns1 = new Annotation[] { ssE, ssE, ssC, ssE};
- anns2 = new Annotation[] { ssH, ssH, ssE, ssC};
-
+ else if (similar == "Not Similar")
+ {
+
+ anns1 = new Annotation[] { ssE, ssE, ssC, ssE };
+ anns2 = new Annotation[] { ssH, ssH, ssE, ssC };
+
}
-
+
/* All secondary structure annotations are dissimilar for each column
* Set up
* column 1 2 3 4
* seq s2 F S J L
* ss H E E C
*/
- else if(similar == "With Coil") {
-
- anns1 = new Annotation[] { ssE, ssE, null, ssE};
- anns2 = new Annotation[] { ssH, ssH, ssE, null};
-
+ else if (similar == "With Coil")
+ {
+
+ anns1 = new Annotation[] { ssE, ssE, null, ssE };
+ anns2 = new Annotation[] { ssH, ssH, ssE, null };
+
}
-
+
/* Set up
* column 1 2 3 4
* seq s1 F R K S
* seq s2 F S J L
* ss H E E C
*/
- else {
-
- anns1 = new Annotation[] { ssH, ssE, ssC, ssE};
- anns2 = new Annotation[] { ssH, ssE, ssE, ssC};
+ else
+ {
+
+ anns1 = new Annotation[] { ssH, ssE, ssC, ssE };
+ anns2 = new Annotation[] { ssH, ssE, ssE, ssC };
}
-
-
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns1);
- AlignmentAnnotation ann2 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns2);
-
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns1);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns2);
+
s1.addAlignmentAnnotation(ann1);
- s2.addAlignmentAnnotation(ann2);
-
+ s2.addAlignmentAnnotation(ann2);
+
AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
AlignFrame af = new AlignFrame(al, 300, 300);
af.setShowSeqFeatures(true);
af.getFeatureRenderer().findAllFeatures(true);
return af;
}
-
/**
* <pre>
*/
protected AlignFrame setupAlignmentViewWithGap()
{
-
+
SequenceI s1 = new Sequence("s1", "FR S");
SequenceI s2 = new Sequence("s2", "FSJL");
new SequenceFeature("metal", null, 1, 4, 0f, null));
s2.addSequenceFeature(
new SequenceFeature("Pfam", null, 1, 4, 0f, null));
-
-
- Annotation ssE = new Annotation("","",'E',0);
- Annotation ssH = new Annotation("","",'H',0);
- Annotation ssC = new Annotation(".","",' ',0);
-
+
+ Annotation ssE = new Annotation("", "", 'E', 0);
+ Annotation ssH = new Annotation("", "", 'H', 0);
+ Annotation ssC = new Annotation(".", "", ' ', 0);
+
Annotation[] anns1;
Annotation[] anns2;
-
- anns1 = new Annotation[] { ssH, ssE, ssC};
- anns2 = new Annotation[] { ssH, ssE, ssE, ssC};
-
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns1);
- AlignmentAnnotation ann2 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns2);
-
+
+ anns1 = new Annotation[] { ssH, ssE, ssC };
+ anns2 = new Annotation[] { ssH, ssE, ssE, ssC };
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns1);
+ AlignmentAnnotation ann2 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns2);
+
s1.addAlignmentAnnotation(ann1);
- s2.addAlignmentAnnotation(ann2);
-
+ s2.addAlignmentAnnotation(ann2);
+
AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
AlignFrame af = new AlignFrame(al, 300, 300);
af.setShowSeqFeatures(true);
af.getFeatureRenderer().findAllFeatures(true);
-
+
return af;
}
-
- protected AlignFrame setupAlignmentViewWithoutSS(String type) {
-
+
+ protected AlignFrame setupAlignmentViewWithoutSS(String type)
+ {
+
SequenceI s1 = new Sequence("s1", "FR S");
SequenceI s2 = new Sequence("s2", "FSJL");
-
+
s1.addSequenceFeature(
new SequenceFeature("chain", null, 1, 3, 0f, null));
s1.addSequenceFeature(
new SequenceFeature("metal", null, 1, 4, 0f, null));
s2.addSequenceFeature(
new SequenceFeature("Pfam", null, 1, 4, 0f, null));
-
- if(!type.equals("both")) {
- Annotation ssE = new Annotation("","",'E',0);
- Annotation ssH = new Annotation("","",'H',0);
- Annotation ssC = new Annotation(".","",' ',0);
-
+
+ if (!type.equals("both"))
+ {
+ Annotation ssE = new Annotation("", "", 'E', 0);
+ Annotation ssH = new Annotation("", "", 'H', 0);
+ Annotation ssC = new Annotation(".", "", ' ', 0);
+
Annotation[] anns1;
-
- anns1 = new Annotation[] { ssH, ssE, ssC};
-
- AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure",
- "Secondary Structure", anns1);
-
- s1.addAlignmentAnnotation(ann1);
+
+ anns1 = new Annotation[] { ssH, ssE, ssC };
+
+ AlignmentAnnotation ann1 = new AlignmentAnnotation(
+ "Secondary Structure", "Secondary Structure", anns1);
+
+ s1.addAlignmentAnnotation(ann1);
}
-
+
AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
AlignFrame af = new AlignFrame(al, 300, 300);
af.setShowSeqFeatures(true);
af.getFeatureRenderer().findAllFeatures(true);
return af;
}
-
-
+
@DataProvider(name = "testData")
- public Object[][] testData() {
- return new Object[][] {
- {"All Similar", 1d, 1d, 0d, 0d / 4},
- {"Partially Similar", 1d, 1d, 0d, 0d},
- {"Not Similar", 1d, 1d, 0d, 0d},
- {"With Coil", 1d, 1d, 0d, 0d},
- };
+ public Object[][] testData()
+ {
+ return new Object[][] { { "All Similar", 1d, 1d, 0d, 0d / 4 },
+ { "Partially Similar", 1d, 1d, 0d, 0d },
+ { "Not Similar", 1d, 1d, 0d, 0d },
+ { "With Coil", 1d, 1d, 0d, 0d }, };
}
@Test(dataProvider = "testData")
- public void testFindDistances(String scenario, double expectedValue00, double expectedValue11,
- double expectedValue01, double expectedValue10) {
- AlignFrame af = setupAlignmentView(scenario);
- AlignViewport viewport = af.getViewport();
- AlignmentView view = viewport.getAlignmentView(false);
-
- ScoreModelI sm = new SecondaryStructureDistanceModel();
- sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
- af.alignPanel);
-
- SimilarityParamsI params = new SimilarityParams(false, true, true, true);
- params.setSecondaryStructureSource("3D Structures");
- MatrixI distances = sm.findDistances(view, params);
-
- assertEquals(distances.getValue(0, 0), expectedValue00);
- assertEquals(distances.getValue(1, 1), expectedValue11);
- assertEquals(distances.getValue(0, 1), expectedValue01);
- assertEquals(distances.getValue(1, 0), expectedValue10);
+ public void testFindDistances(String scenario, double expectedValue00,
+ double expectedValue11, double expectedValue01,
+ double expectedValue10)
+ {
+ AlignFrame af = setupAlignmentView(scenario);
+ AlignViewport viewport = af.getViewport();
+ AlignmentView view = viewport.getAlignmentView(false);
+
+ ScoreModelI sm = new SecondaryStructureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ af.alignPanel);
+
+ SimilarityParamsI params = new SimilarityParams(false, true, true,
+ true);
+ params.setSecondaryStructureSource("3D Structures");
+ MatrixI distances = sm.findDistances(view, params);
+
+ assertEquals(distances.getValue(0, 0), expectedValue00);
+ assertEquals(distances.getValue(1, 1), expectedValue11);
+ assertEquals(distances.getValue(0, 1), expectedValue01);
+ assertEquals(distances.getValue(1, 0), expectedValue10);
}
-
}
assertEquals(10, sf.getBegin());
assertEquals(11, sf.getEnd());
}
+
private SequenceI mkDs(SequenceI as)
{
SequenceI ds = as.createDatasetSequence();
ds.setSequence(ds.getSequenceAsString().toUpperCase(Locale.ROOT));
return ds;
}
+
/**
* Test that mimics 'remove all gapped columns' action. This generates a
* series Delete Gap edits that each act on all sequences that share a gapped
* and check we are preserving data - if the calls below fail, something has broken the Jalview dataset derivation process
*/
assertEquals("ABCDEF", seq1.getDatasetSequence().getSequenceAsString());
- assertEquals(original1,seq1.getSequenceAsString());
- SequenceI seq2 = new Sequence("sq2",original2);
+ assertEquals(original1, seq1.getSequenceAsString());
+ SequenceI seq2 = new Sequence("sq2", original2);
SequenceI ds2 = mkDs(seq2);
SequenceI seq3 = new Sequence("sq3", original3);
SequenceI ds3 = mkDs(seq3);
- List<SequenceI> sqs = Arrays.asList( seq1, seq2, seq3 );
+ List<SequenceI> sqs = Arrays.asList(seq1, seq2, seq3);
Alignment al = new Alignment(sqs.toArray(new SequenceI[0]));
- EditCommand lefj = new JustifyLeftOrRightCommand("Left J", true, sqs, 1, 7, al);
+ EditCommand lefj = new JustifyLeftOrRightCommand("Left J", true, sqs, 1,
+ 7, al);
String exp = "-ABcD---EF";
// check without case conservation
- assertEquals(exp.toUpperCase(Locale.ROOT),seq1.getSequenceAsString().toUpperCase(Locale.ROOT));
+ assertEquals(exp.toUpperCase(Locale.ROOT),
+ seq1.getSequenceAsString().toUpperCase(Locale.ROOT));
// check case
- assertEquals(exp,seq1.getSequenceAsString());
+ assertEquals(exp, seq1.getSequenceAsString());
// and other seqs
- assertEquals("-GHiJ---",seq2.getSequenceAsString());
- assertEquals("-MNoP---Q",seq3.getSequenceAsString());
- lefj.undoCommand(new AlignmentI[] { al});
- assertEquals(original3,seq3.getSequenceAsString());
- assertEquals(original1,seq1.getSequenceAsString());
- assertEquals(original2,seq2.getSequenceAsString());
-
- EditCommand righj = new JustifyLeftOrRightCommand("Right J", false, sqs, 2, 7, al);
- assertEquals("----ABcDEF",seq1.getSequenceAsString());
- assertEquals("-G---HiJ",seq2.getSequenceAsString());
- assertEquals("-M---NoPQ",seq3.getSequenceAsString());
- righj.undoCommand(new AlignmentI[] { al});
- assertEquals(original3,seq3.getSequenceAsString());
- assertEquals(original1,seq1.getSequenceAsString());
- assertEquals(original2,seq2.getSequenceAsString());
-
+ assertEquals("-GHiJ---", seq2.getSequenceAsString());
+ assertEquals("-MNoP---Q", seq3.getSequenceAsString());
+ lefj.undoCommand(new AlignmentI[] { al });
+ assertEquals(original3, seq3.getSequenceAsString());
+ assertEquals(original1, seq1.getSequenceAsString());
+ assertEquals(original2, seq2.getSequenceAsString());
+
+ EditCommand righj = new JustifyLeftOrRightCommand("Right J", false, sqs,
+ 2, 7, al);
+ assertEquals("----ABcDEF", seq1.getSequenceAsString());
+ assertEquals("-G---HiJ", seq2.getSequenceAsString());
+ assertEquals("-M---NoPQ", seq3.getSequenceAsString());
+ righj.undoCommand(new AlignmentI[] { al });
+ assertEquals(original3, seq3.getSequenceAsString());
+ assertEquals(original1, seq1.getSequenceAsString());
+ assertEquals(original2, seq2.getSequenceAsString());
+
}
}
assertTrue(geneIds.contains("ENSRNOG00000010957")); // rat
assertTrue(geneIds.contains("ENSXETG00000004845")); // xenopus
assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
- assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
+ // was ENSGALG00000012865 - which is still the canonical uniprot BRAF cross
+ // reference via GRCg6a
+ assertTrue(geneIds.contains("ENSGALG00010013466")); // chicken BRAF
+ // bGalGal1.mat.broiler.GRCg7b
assertEquals(8, geneIds.size());
}
*/
package jalview.gui;
-
import java.awt.Color;
import java.io.File;
import java.util.Iterator;
+ "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
+ "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
+ "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
- + "DQWNVEVY\n"
- + ">1GAQ|B/1-98\n"
+ + "DQWNVEVY\n" + ">1GAQ|B/1-98\n"
+ "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADG\n"
- + "WVLTCHAYPTSDVVIETHKEEELTGA\n"
- + ">1GAQ|C/19-314\n"
+ + "WVLTCHAYPTSDVVIETHKEEELTGA\n" + ">1GAQ|C/19-314\n"
+ "ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPH\n"
+ "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
+ "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
+ "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
- + "DQWNVEVY\n"
- ,
- DataSourceType.PASTE);
+ + "DQWNVEVY\n", DataSourceType.PASTE);
/*
* wait for Consensus thread to complete
@Test(groups = "Functional")
public void testAssociatePDBFile()
{
- String assoc_file="examples/1gaq.txt";
- for (SequenceI toassoc:af.getViewport().getAlignment().getSequences())
+ String assoc_file = "examples/1gaq.txt";
+ for (SequenceI toassoc : af.getViewport().getAlignment().getSequences())
{
- PDBEntry pe = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(assoc_file,
- DataSourceType.FILE, toassoc, false,
- Desktop.instance);
+ PDBEntry pe = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+ assoc_file, DataSourceType.FILE, toassoc, false,
+ Desktop.instance);
Assert.assertNotNull(pe);
- Assert.assertNotEquals(toassoc.getDatasetSequence().getAnnotation().length,0);
+ Assert.assertNotEquals(
+ toassoc.getDatasetSequence().getAnnotation().length, 0);
}
}
}
* peptide models for PCA
*/
List<ScoreModelI> filtered = CalculationChooser
- .getApplicableScoreModels(false, true, true,false);
+ .getApplicableScoreModels(false, true, true, false);
assertEquals(filtered.size(), 5);
assertSame(filtered.get(0), blosum62);
assertSame(filtered.get(1), pam250);
assertEquals(filtered.get(2).getName(), "PID");
assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
- assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
+ assertEquals(filtered.get(4).getName(),
+ "Secondary Structure Similarity");
/*
* peptide models for Tree are the same
*/
- filtered = CalculationChooser.getApplicableScoreModels(false, false, true,false);
+ filtered = CalculationChooser.getApplicableScoreModels(false, false,
+ true, false);
assertEquals(filtered.size(), 5);
assertSame(filtered.get(0), blosum62);
assertSame(filtered.get(1), pam250);
assertEquals(filtered.get(2).getName(), "PID");
assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
- assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
+ assertEquals(filtered.get(4).getName(),
+ "Secondary Structure Similarity");
/*
* nucleotide models for PCA
*/
- filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
+ filtered = CalculationChooser.getApplicableScoreModels(true, true,
+ false, false);
assertEquals(filtered.size(), 3);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
/*
* nucleotide models for Tree are the same
*/
- filtered = CalculationChooser.getApplicableScoreModels(true, false, false,false);
+ filtered = CalculationChooser.getApplicableScoreModels(true, false,
+ false, false);
assertEquals(filtered.size(), 3);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
/*
* nucleotide models for Tree are unchanged
*/
- filtered = CalculationChooser.getApplicableScoreModels(true, false, true,false);
+ filtered = CalculationChooser.getApplicableScoreModels(true, false,
+ true, false);
assertEquals(filtered.size(), 4);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
- assertEquals(filtered.get(3).getName(), "Secondary Structure Similarity");
+ assertEquals(filtered.get(3).getName(),
+ "Secondary Structure Similarity");
/*
* nucleotide models for PCA add BLOSUM62 as last option
*/
- filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
+ filtered = CalculationChooser.getApplicableScoreModels(true, true,
+ false, false);
assertEquals(filtered.size(), 4);
assertSame(filtered.get(0), dna);
assertEquals(filtered.get(1).getName(), "PID");
assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
assertSame(filtered.get(3), blosum62);
-
- filtered = CalculationChooser.getApplicableScoreModels(true, true, false,true);
+
+ filtered = CalculationChooser.getApplicableScoreModels(true, true,
+ false, true);
assertEquals(filtered.size(), 1); // DNA matrix for DNA pasimap
- for (int i=0; i<=8;i++)
+ for (int i = 0; i <= 8; i++)
{
- boolean isDna = (i & 1) != 0,isPca = (i & 2) != 0,isSS = (i & 4) != 0;
-
- assertEquals(CalculationChooser.getApplicableScoreModels(isDna,isPca,isSS,true).size(), (isDna) ? 1: 2);
+ boolean isDna = (i & 1) != 0, isPca = (i & 2) != 0,
+ isSS = (i & 4) != 0;
+
+ assertEquals(CalculationChooser
+ .getApplicableScoreModels(isDna, isPca, isSS, true).size(),
+ (isDna) ? 1 : 2);
}
}
}
boolean diffseqcols = false, diffgseqcols = false;
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
- for (int p = 0,
- pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
.findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
assertTrue(__rcs.isSeqAssociated(),
"Group Annotation colourscheme wasn't sequence associated");
- for (int p = 0,
- pSize = af.getViewport().getAlignment().getWidth(); p < pSize
- && (!diffseqcols || !diffgseqcols); p++)
+ for (int p = 0, pSize = af.getViewport().getAlignment()
+ .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
{
if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
SecondaryStructureCount secondaryStructureCount)
{
// TODO Auto-generated method stub
-
+
}
@Override
// viewport
// assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
}
+
@Test
public void testDocString()
{
+ d + "' contains '" + notInDirname + "' when it shouldn't");
}
+ /**
+ * these need to be maintained as jalview's source base grows
+ *
+ * @return
+ */
@DataProvider(name = "patternsAndMinNumFiles")
public Object[][] patternsAndMinNumFiles()
{
{ "test/jalview/**/F*.java", 18, 30 }, // 20 at time of writing
{ "test/jalview/util/F**.java", 1, 5 }, // 2 at time of writing
{ "src/jalview/b*/*.java", 14, 19 }, // 15 at time of writing
- { "src/jalview/b**/*.java", 20, 25 }, // 22 at time of writing
+ { "src/jalview/b**/*.java", 23, 26 }, // 22 at time of writing
};
}
install4j_background_image_text_commit_cmd = text 18,170 '%s'
install4j_background_image_text_date_cmd = text 18,190 '%s'
+install4j_title_icon = jalview_logo-64.png
install4j_background_image_text_commit_cmd = text 18,250 '%s'
install4j_background_image_text_date_cmd = text 18,270 '%s'
+install4j_title_icon = jalview_develop_logo-64.png
install4j_background_image_text_commit_cmd = text 18,250 '%s'
install4j_background_image_text_date_cmd = text 18,270 '%s'
+install4j_title_icon = jalview_develop_logo-64.png
install4j_background_image_text_commit_cmd = text 18,170 '%s'
install4j_background_image_text_date_cmd = text 18,190 '%s'
+install4j_title_icon = jalview_logo-64.png
+install4j_title_icon = jalview_logo-64.png
install4j_background_image_text_commit_cmd = text 18,250 '%s'
install4j_background_image_text_date_cmd = text 18,270 '%s'
+install4j_title_icon = jalview_logo-64.png
install4j_background_image_text_commit_cmd = text 18,250 '%s'
install4j_background_image_text_date_cmd = text 18,270 '%s'
+install4j_title_icon = jalview_test-release_logo-64.png
# save args and first parameter
$myArgs = $args.Clone()
-$myArg1 = $args[0]
# setup for powershell version < 6.0
[bool] $myIsWindows = 0
$myIsMacOS = $IsMacOS
}
-# parent dir of this actual script (which should be the getdown appdir/bin). Follow all symlinks. Like GNU readlink -f
+[bool] $headless = 0
+[bool] $gui = 0
+[bool] $help = 0
+[bool] $debug = 0
+Switch -Regex ($args) {
+ "--help|--help-|--version|-h" {
+ $help = 1
+ $headless = 1
+ Continue
+ }
+ "--gui" {
+ $gui = 1
+ Continue
+ }
+ "--headless" {
+ $headless = 1
+ Continue
+ }
+ "--debug" {
+ $debug = 1
+ Continue
+ }
+}
+if ( $help ) {
+ # --help takes precedence
+ $gui = 0
+} elseif ( $gui ) {
+ # --gui takes precedence over --headless
+ $headless = 0
+}
+
+# actual path of this script (which should be the getdown appdir/bin). Follow all symlinks. Like GNU readlink -f
function Readlink-f {
- Param($Link)
- $Return = $null
- $c = 0
- $max = 100 # just in case we end up in a loop
- [bool] $found = 0
- $file = Get-Item -Path $Link
- $prevfile = $null
- While ( $c -lt $max -and "${file}" -ne "${prevfile}" -and -not $found ) {
- $prevfile = $file
- [string] $target = ( $file ).Target
- If ( $target -eq $null -or ( $file ).LinkType -ne "SymbolicLink" ) {
- $Return = $file
- $found = 1
- } Else {
- If ( $( Split-Path -Path $target -IsAbsolute ) ) {
- $file = Get-Item -Path $target
- } Else {
-# symbolic link is relative: combine previous link parent dir with the link target and resolve
- $file = Get-Item -Path ( Join-Path -Path ( Split-Path -Path $prevfile -Parent ) -ChildPath $target -Resolve )
- }
+ Param(
+ [Parameter(mandatory=$true, ValueFromPipeline=$true)]$Link,
+ [Parameter()]$iteration_count = 1
+ )
+ if ( $iteration_count -ge 100 ) {
+ Write-Error "Readlink-f iterated 100 times"
+ return $Link
+ }
+ if ( $Link -eq "" -or $Link -eq $null ) {
+ return $null
+ }
+ $path_components = @()
+ $dir = Get-Item $Link
+ while ( $dir -ne $null ) {
+ while ( $dir.Target -ne $null ) {
+ # [System.IO.Path]::Combine caters for a multitude of sins that it's almost impossible to deal with with Join-Path
+ $dir = Get-Item ([System.IO.Path]::GetFullPath( [System.IO.Path]::Combine( (Split-Path $dir -Parent), $dir.Target )))
}
- $c++
+ $parent = Split-Path -Path $dir -Parent
+ $path_components = @( (Split-Path -Path $dir -Leaf) ) + $path_components
+ $dir = Readlink-f $parent ($iteration_count + 1)
}
- if ( -not $found ) {
- throw "Could not determine path to actual file $( Split-Path -Path $Link -Leaf )"
+ $real = Get-Item "/"
+ foreach ( $component in $path_components) {
+ # [System.IO.Path]::Combine caters for a multitude of sins that it's almost impossible to deal with with Join-Path
+ $real = Get-Item ([System.IO.Path]::GetFullPath( [System.IO.Path]::Combine( $real, $component )))
}
- $Return
+ $real
}
# Avert problem with unix version of powershell and tell user the reason (Windows must always have .ps1 extension)
throw "Script or link to script must have extension .ps1"
}
+# args for the JVM
+$JVMARGS = @()
$CMDPATH = ( Get-Item $MyInvocation.MyCommand.Path )
$SCRIPTPATH = Readlink-f -Link $CMDPATH
+$SCRIPT = $SCRIPTPATH
$DIR = Split-Path -Path $SCRIPTPATH -Parent
-
$APPDIR = If ( ( Split-Path -Path $DIR -Leaf ) -eq "bin" ) { Split-Path -Path $DIR -Parent } Else { $DIR }
$JAVAEXE = If ( $myIsWindows ) { "java.exe" } Else { "java" }
$JAVA = Join-Path -Path $APPDIR -ChildPath ( "jre/" + $( If ( $myIsMacOS ) { "Contents/Home/" } Else { "" } ) + "bin/${JAVAEXE}" )
+
+if ( $headless ) {
+ # not setting java.awt.headless in java invocation of running jalview due to problem with Jmol
+ if ( $help ) {
+ $JVMARGS += "-Djava.awt.headless=true"
+ }
+ # this suppresses the Java icon appearing in the macOS Dock
+ if ( $myIsMacOS ) {
+ $JVMARGS += "-Dapple.awt.UIElement=true"
+ }
+}
+
$GETDOWNTXT = Join-Path -Path $APPDIR -ChildPath "getdown.txt"
# look for getdown.txt -- needed to create classpath
throw "Cannot find ${GETDOWNTXT}"
}
+# launching Jalview with jalview.bin.Launcher instead of getdown-launcher.jar
+$CLASS = "jalview.bin.Launcher"
+
+# get CLASSPATH from the code= entries in getdown.txt
+$CLASSPATH = ( Select-String -Path "${GETDOWNTXT}" -AllMatches -Pattern "code\s*=\s*(.*)$" | foreach { Join-Path -Path $APPDIR -ChildPath $($_.Matches.Groups[1].Value ) } ) -join $( If ( $myIsWindows ) { ";" } Else { ":" } )
+
+# get console width
+$COLUMNS = $Host.UI.RawUI.WindowSize.Width
+$JVMARGS += "-DCONSOLEWIDTH=${COLUMNS}"
+$JVMARGS += "-Dgetdownappdir=${APPDIR}"
+$JVMARGS += "-Dinstaller.appdir=${APPDIR}"
+$JVMARGS += "-Dlauncher.script=${SCRIPT}"
+
# look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
if ( -not ( Test-Path -Path "${JAVA}" ) ) {
- Write-Host "Cannot find bundled ${JAVAEXE}. Using system ${JAVAEXE} and hoping for the best!"
+ Write-Host "Cannot find bundled ${JAVA}. Using system ${JAVAEXE} and hoping for the best!"
$JAVA = $JAVAEXE
}
-$CLASSPATH = ( Select-String -Path "${GETDOWNTXT}" -AllMatches -Pattern "code\s*=\s*(.*)$" | foreach { Join-Path -Path $APPDIR -ChildPath $($_.Matches.Groups[1].Value ) } ) -join $( If ( $myIsWindows ) { ";" } Else { ":" } )
-
-# get console width
-$CONSOLEWIDTH = $Host.UI.RawUI.WindowSize.Width
+# we should always have at least one JVMARGS so this is okay
+$myJvmArgsString = '"' + $($JVMARGS -join '" "') + '"'
-# quote the args and the command (in case of spaces) with escape chars (`) and precede with & to indicate command not string
+# quote the args and the command (in case of spaces) with escape chars (`) and precede with & to indicate a command not string
if ( $myArgs.count -eq 0 ) {
- Invoke-Expression -Command "& `"${JAVA}`" `"-DCONSOLEWIDTH=${CONSOLEWIDTH}`" `"-Dgetdownappdir=${APPDIR}`" -cp `"${CLASSPATH}`" jalview.bin.Launcher"
+ $COMMAND = "& `"${JAVA}`" ${myJvmArgsString} -cp `"${CLASSPATH}`" $CLASS"
} else {
$myArgsString = '"' + $($myArgs -join '" "') + '"'
- Invoke-Expression -Command "& `"${JAVA}`" `"-DCONSOLEWIDTH=${CONSOLEWIDTH}`" `"-Dgetdownappdir=${APPDIR}`" -cp `"${CLASSPATH}`" jalview.bin.Launcher ${myArgsString}"
+ $COMMAND = "& `"${JAVA}`" ${myJvmArgsString} -cp `"${CLASSPATH}`" $CLASS ${myArgsString}"
}
+if ( $debug -or $help ) {
+ Write-Error -Message "Shell running: ${COMMAND}"
+}
+
+Invoke-Expression -Command ${COMMAND}
+
declare -a ARGS=("${@}")
-# this whole next part is because there's no readlink -f in Darwin
-function readlinkf() {
- FINDFILE="$1"
- FILE="${FINDFILE}"
- PREVFILE=""
- C=0
- MAX=100 # just in case we end up in a loop
- FOUND=0
- while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
- PREVFILE="${FILE}"
- FILE="$(readlink "${FILE}")"
- if [ -z "${FILE}" ]; then
- # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
- FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
- FOUND=1
- elif [ "${FILE#/}" = "${FILE}" ]; then
- # FILE is not an absolute path link, we need to add the relative path to the previous dir
- FILE="$(dirname "${PREVFILE}")/${FILE}"
- fi
- C=$((C+1))
- done
- if [ "${FOUND}" -ne 1 ]; then
- echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
- exit 1
- fi
- echo "${FILE}"
-}
-
ISMACOS=0
if [ "$( uname -s )" = "Darwin" ]; then
ISMACOS=1
;;
--help|--help-*|--version|-h)
HELP=1
+ HEADLESS=1
;;
--gui)
GUI=1
DEBUG=1
;;
esac
-
- if [ "${HELP}" = 1 ]; then
- # --help takes precedence
- HEADLESS=1
- GUI=0
- elif [ "${GUI}" = 1 ]; then
- # --gui takes precedence over --headless
- HEADLESS=0
- fi
done
+if [ "${HELP}" = 1 ]; then
+ # --help takes precedence
+ GUI=0
+elif [ "${GUI}" = 1 ]; then
+ # --gui takes precedence over --headless
+ HEADLESS=0
+fi
+
+# this whole next part is because there's no readlink -f in Darwin
+function readlinkf() {
+ FINDFILE="$1"
+ FILE="${FINDFILE}"
+ PREVFILE=""
+ C=0
+ MAX=100 # just in case we end up in a loop
+ FOUND=0
+ while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
+ PREVFILE="${FILE}"
+ FILE="$(readlink "${FILE}")"
+ if [ -z "${FILE}" ]; then
+ # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
+ FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
+ FOUND=1
+ elif [ "${FILE#/}" = "${FILE}" ]; then
+ # FILE is not an absolute path link, we need to add the relative path to the previous dir
+ FILE="$(dirname "${PREVFILE}")/${FILE}"
+ fi
+ C=$((C+1))
+ done
+ if [ "${FOUND}" -ne 1 ]; then
+ echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
+ exit 1
+ fi
+ echo "${FILE}"
+}
+# args for the JVM
declare -a JVMARGS=()
+JAVABIN=""
# set vars for being inside the macos App Bundle
if [ "${ISMACOS}" = 1 ]; then
# MACOS ONLY
- DIR="$(dirname "$(readlinkf "$0")")"
+ SCRIPT="$(readlinkf "$0")"
+ DIR="$(dirname "${SCRIPT}")"
APPDIR="${DIR%/bin}"
- JAVA="${APPDIR}/jre/Contents/Home/bin/java"
- JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
+
+ if [ -d "${APPDIR}/jre" ]; then
+ JREDIR="${APPDIR}/jre"
+ elif [ -e "${APPDIR}/installer.properties" ]; then
+ INSTALLERAPPDIR="$( grep -E "^installer.appdir[[:space:]]*=[[:space:]]*" "${APPDIR}/installer.properties" | sed -E 's/^installer.appdir[[:space:]]*=[[:space:]]*//' )"
+ if [ -d "${INSTALLERAPPDIR}/jre" ]; then
+ JREDIR="${INSTALLERAPPDIR}/jre"
+ fi
+ fi
+ if [ ! -z "$JREDIR" ]; then
+ JAVABIN="${JREDIR}/Contents/Home/bin"
+ fi
+ if [ "${HEADLESS}" != 1 ]; then
+ JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${APPDIR}/resource/jalview_logo.png" )
+ fi
else
# NOT MACOS
- DIR="$(dirname "$(readlink -f "$0")")"
+ SCRIPT="$(readlink -f "$0")"
+ DIR="$(dirname "${SCRIPT}")"
APPDIR="${DIR%/bin}"
- JAVA="${APPDIR}/jre/bin/java"
+ if [ -d "${APPDIR}/jre" ]; then
+ JAVABIN="${APPDIR}/jre/bin"
+ elif [ -e "${APPDIR}/installer.properties" ]; then
+ INSTALLERAPPDIR="$( grep -E "^installer.appdir[[:space:]]*=[[:space:]]*" "${APPDIR}/installer.properties" | sed -E 's/^installer.appdir[[:space:]]*=[[:space:]]*//' )"
+ if [ ! -z "$INSTALLERAPPDIR" -a -d "${INSTALLERAPPDIR}/jre" ]; then
+ JAVABIN="${INSTALLERAPPDIR}/jre/bin"
+ fi
+ fi
fi
+JAVA="${JAVABIN}/java"
+# headless java arguments
if [ "${HEADLESS}" = 1 ]; then
# not setting java.awt.headless in java invocation of running jalview due to problem with Jmol
if [ "${HELP}" = 1 ]; then
SYSJAVA=java
GETDOWNTXT="${APPDIR}/getdown.txt"
+CHANNELPROPS="${APPDIR}/channel.props"
+NAME="$( grep app_name= "${CHANNELPROPS}" | cut -d= -f2 )"
CLASSPATH=""
# save an array of JAR paths in case we're in WSL (see later)
declare -a JARPATHS=()
-if [ -e "${GETDOWNTXT}" ]; then
- # always check grep and sed regexes on macos -- they're not the same
-for JAR in $(grep -e '^code[[:space:]]*=[[:space:]]*' "${GETDOWNTXT}" | while read -r line; do echo $line | sed -E -e 's/code[[:space:]]*=[[:space:]]*//;'; done);
- do
- [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
- CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
- JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
- done
-else
- echo "Cannot find getdown.txt" >&2
+
+# look for getdown.txt -- needed to create classpath
+if [ ! -e "${GETDOWNTXT}" ]; then
+ echo "Cannot find ${GETDOWNTXT}" >&2
exit 3
fi
-# WINDOWS ONLY (Cygwin or WSL)
-# change paths for Cygwin or Windows Subsystem for Linux (WSL)
+# launching Jalview with jalview.bin.Launcher instead of getdown-launcher.jar
+CLASS="jalview.bin.Launcher"
+
+# get classpath from the code= entries in getdown.txt
+# always check grep and sed regexes on macos -- they're not the same
+for JAR in $(grep -e '^code[[:space:]]*=[[:space:]]*' "${GETDOWNTXT}" | while read -r line; do echo $line | sed -E -e 's/code[[:space:]]*=[[:space:]]*//;'; done);
+do
+ [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH}:"
+ CLASSPATH="${CLASSPATH}${APPDIR}/${JAR}"
+ JARPATHS=( "${JARPATHS[@]}" "${APPDIR}/${JAR}" )
+done
+
+COLUMNS=80
+# get console width -- three ways to try, just in case (not needed for update)
+if command -v tput 2>&1 >/dev/null; then
+ COLUMNS=$(tput cols) 2>/dev/null
+elif command -v stty 2>&1 >/dev/null; then
+ COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
+elif command -v resize 2>&1 >/dev/null; then
+ COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
+fi
+JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dgetdownappdir=${APPDIR}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.script=${SCRIPT}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
+
+JAVAEXT=""
+# WINDOWS ONLY in Cygwin or Windows Subsystem for Linux (WSL)
+# change paths for Cygwin or WSL
if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
- if [ "$(uname -o)" = "Cygwin" ]; then
+ if [ "$(uname -o)" = "Cygwin" ]; then # Cygwin
# CYGWIN
CLASSPATH=$(cygpath -pw "${CLASSPATH}")
# now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
ARGS=( "${ARGS[@]}" "${ARG}" )
fi
done
- elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
+ elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then # WSL
# WSL
CLASSPATH=""
for JARPATH in "${JARPATHS[@]}"; do
ARGS=( "${ARGS[@]}" "${ARG}" )
fi
done
- JAVA="${JAVA}.exe"
- SYSJAVA="java.exe"
+ JAVAEXT=".exe"
+ JAVA="${JAVA}${JAVAEXT}"
+ SYSJAVA="java${JAVAEXT}"
fi
fi
-# get console width -- three ways to try, just in case
-if command -v tput 2>&1 >/dev/null; then
- COLUMNS=$(tput cols) 2>/dev/null
-elif command -v stty 2>&1 >/dev/null; then
- COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
-elif command -v resize 2>&1 >/dev/null; then
- COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
+# look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
+if [ ! -z "${JAVABIN}" -a -e "${JAVABIN}/${NAME}${JAVAEXT}" ]; then
+ JAVA="${JAVABIN}/${NAME}${JAVAEXT}"
fi
-JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
-JVMARGS=( "${JVMARGS[@]}" "-Dgetdownappdir=${APPDIR}" )
-
-# Is there a bundled Java? If not just try one in the PATH (do need .exe in WSL)
-if [ \! -e "${JAVA}" ]; then
- JAVA=$SYSJAVA
- echo "Cannot find bundled java, using system ${JAVA} and hoping for the best!" >&2
+# If not just try one in the PATH (we need .exe in WSL, added above)
+if [ -z "${JAVABIN}" -o ! -e "${JAVA}" ]; then
+ JAVA="${SYSJAVA}"
+ echo "Cannot find bundled ${JAVA}, using system ${SYSJAVA} and hoping for the best!" >&2
fi
+# This is just needed for display purposes
function quotearray() {
QUOTEDVALS=""
for VAL in "${@}"; do
- if [ \! "$QUOTEDVALS" = "" ]; then
+ if [ ! "$QUOTEDVALS" = "" ]; then
QUOTEDVALS="${QUOTEDVALS} "
fi
QUOTEDVALS="${QUOTEDVALS}\"${VAL}\""
echo $QUOTEDVALS
}
+# for the debug command display
JVMARGSSTR=$(quotearray "${JVMARGS[@]}")
ARGSSTR=$(quotearray "${ARGS[@]}")
if [ "${DEBUG}" = 1 ]; then
- echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${CLASSPATH}"\" jalview.bin.Launcher ${ARGSSTR}
+ echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${CLASSPATH}"\" \""${CLASS}"\" ${ARGSSTR} >&2
fi
-"${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" jalview.bin.Launcher "${ARGS[@]}"
+"${JAVA}" "${JVMARGS[@]}" -cp "${CLASSPATH}" "${CLASS}" "${ARGS[@]}"
--- /dev/null
+#!/usr/bin/env pwsh
+
+$OTHERSCRIPT = "__OTHERSCRIPT__"
+
+# actual path of this script (which should be the getdown appdir/bin). Follow all symlinks. Like GNU readlink -f
+function Readlink-f {
+ Param(
+ [Parameter(mandatory=$true, ValueFromPipeline=$true)]$Link,
+ [Parameter()]$iteration_count = 1
+ )
+ if ( $iteration_count -ge 100 ) {
+ Write-Error "Readlink-f iterated 100 times"
+ return $Link
+ }
+ if ( $Link -eq "" -or $Link -eq $null ) {
+ return $null
+ }
+ $path_components = @()
+ $dir = Get-Item $Link
+ while ( $dir -ne $null ) {
+ while ( $dir.Target -ne $null ) {
+ # [System.IO.Path]::Combine caters for a multitude of sins that it's almost impossible to deal with with Join-Path
+ $dir = Get-Item ([System.IO.Path]::GetFullPath( [System.IO.Path]::Combine( (Split-Path $dir -Parent), $dir.Target )))
+ }
+ $parent = Split-Path -Path $dir -Parent
+ $path_components = @( (Split-Path -Path $dir -Leaf) ) + $path_components
+ $dir = Readlink-f $parent ($iteration_count + 1)
+ }
+ $real = Get-Item "/"
+ foreach ( $component in $path_components) {
+ # [System.IO.Path]::Combine caters for a multitude of sins that it's almost impossible to deal with with Join-Path
+ $real = Get-Item ([System.IO.Path]::GetFullPath( [System.IO.Path]::Combine( $real, $component )))
+ }
+ $real
+}
+
+$CMDPATH = ( Get-Item $MyInvocation.MyCommand.Path )
+$SCRIPTPATH = Readlink-f -Link $CMDPATH
+$SCRIPTBIN = Split-Path -Path $SCRIPTPATH -Parent
+$SCRIPT = Join-Path $SCRIPTBIN -ChildPath $OTHERSCRIPT
+
+if ( $args.Count -eq 0 ) {
+ & $SCRIPT
+} else {
+ if ($args.Contains("--debug")) {
+ Write-Host "Running: $SCRIPT $args"
+ }
+ & $SCRIPT @args
+}
--- /dev/null
+#!/usr/bin/env pwsh
+
+# setup for powershell version < 6.0
+[bool] $myIsWindows = 0
+[bool] $myIsMacOS = 0
+if ( $IsWindows -eq $null ) {
+ # for powershell version < 6.0 let's assume Windows
+ $myIsWindows = 1
+ $myIsMacOS = 0
+} else {
+ $myIsWindows = $IsWindows
+ $myIsMacOS = $IsMacOS
+}
+
+$USAGE = "Please use either --installation or --userspace."
+
+[bool] $debug = 0
+[bool] $userspace = 0
+[bool] $installation = 0
+Switch ($args) {
+ "--debug" {
+ $debug = 1
+ Continue
+ }
+ "--installation" {
+ $installation = 1
+ Continue
+ }
+ "--userspace" {
+ $userspace = 1
+ Continue
+ }
+ Default {
+ throw "Unknown option '$_'. ${USAGE}."
+ }
+}
+
+if ( -not ( $userspace -or -$installation ) ) {
+ Write-Output "${USAGE}."
+ Exit
+}
+
+# actual path of this script (which should be the getdown appdir/bin). Follow all symlinks. Like GNU readlink -f
+function Readlink-f {
+ Param(
+ [Parameter(mandatory=$true, ValueFromPipeline=$true)]$Link,
+ [Parameter()]$iteration_count = 1
+ )
+ if ( $iteration_count -ge 100 ) {
+ Write-Error "Readlink-f iterated 100 times"
+ return $Link
+ }
+ if ( $Link -eq "" -or $Link -eq $null ) {
+ return $null
+ }
+ $path_components = @()
+ $dir = Get-Item $Link
+ while ( $dir -ne $null ) {
+ while ( $dir.Target -ne $null ) {
+ # [System.IO.Path]::Combine caters for a multitude of sins that it's almost impossible to deal with with Join-Path
+ $dir = Get-Item ([System.IO.Path]::GetFullPath( [System.IO.Path]::Combine( (Split-Path $dir -Parent), $dir.Target )))
+ }
+ $parent = Split-Path -Path $dir -Parent
+ $path_components = @( (Split-Path -Path $dir -Leaf) ) + $path_components
+ $dir = Readlink-f $parent ($iteration_count + 1)
+ }
+ $real = Get-Item "/"
+ foreach ( $component in $path_components) {
+ # [System.IO.Path]::Combine caters for a multitude of sins that it's almost impossible to deal with with Join-Path
+ $real = Get-Item ([System.IO.Path]::GetFullPath( [System.IO.Path]::Combine( $real, $component )))
+ }
+ $real
+}
+
+# Avert problem with unix version of powershell and tell user the reason (Windows must always have .ps1 extension)
+if ( $MyInvocation.MyCommand.Path -eq $null ) {
+ throw "Script or link to script must have extension .ps1"
+}
+
+# args for the JVM
+$JVMARGS = @()
+
+$CMDPATH = ( Get-Item $MyInvocation.MyCommand.Path )
+$SCRIPTPATH = Readlink-f -Link $CMDPATH
+$SCRIPT = $SCRIPTPATH
+$DIR = Split-Path -Path $SCRIPTPATH -Parent
+$APPDIR = If ( ( Split-Path -Path $DIR -Leaf ) -eq "bin" ) { Split-Path -Path $DIR -Parent } Else { $DIR }
+$JAVAEXE = If ( $myIsWindows ) { "java.exe" } Else { "java" }
+if ( $myIsMacOS ) {
+ $JAVABIN = Join-Path -Path $APPDIR -ChildPath "jre/Contents/Home/bin"
+ $APPFOLDER = ( $APPDIR -Replace "\.app.*", "" ) + ".app"
+ $VMOPTIONS = Join-Path -Path $APPFOLDER -ChildPath "Contents/vmoptions.txt"
+} else {
+ $JAVABIN = Join-Path -Path $APPDIR -ChildPath "jre" | Join-Path -ChildPath "bin"
+ $APPFOLDER = $APPDIR
+ $VMOPTIONS = Join-Path -Path $APPDIR -ChildPath "jalviewg.vmoptions"
+}
+$JAVA = Join-Path -Path $JAVABIN -ChildPath $JAVAEXE
+
+$JVMARGS += "-Djava.awt.headless=true"
+if ( $myIsMacOS ) {
+ $JVMARGS += "-Dapple.awt.UIElement=true"
+}
+
+$GETDOWNLAUNCHERJAR = Join-Path -Path $APPDIR -ChildPath "getdown-launcher.jar"
+$GETDOWNCOREJAR = Join-Path -Path $APPDIR -ChildPath "resource" | Join-Path -ChildPath "getdown-core.jar"
+$CHANNELPROPS = Join-Path -Path $APPDIR -ChildPath "channel.props"
+$NAME = ( Select-String -Path "${CHANNELPROPS}" -Pattern "^app_name=(.*)$" ).Matches.Groups[1].Value
+$US_NAME = $NAME -Replace " ", "_"
+
+# getdown-launcher classpath
+if ( Test-Path -Path $GETDOWNLAUNCHERJAR ) {
+ $GDL_CLASSPATH = "${GETDOWNLAUNCHERJAR}"
+} else {
+ throw "Cannot find ${GETDOWNLAUNCHERJAR} to run update"
+}
+
+# getdown-core classpath
+if ( Test-Path -Path $GETDOWNCOREJAR ) {
+ $GDC_CLASSPATH = "${GETDOWNCOREJAR}"
+} else {
+ throw "Cannot find ${GETDOWNCOREJAR} to run update"
+}
+
+# USER space update
+if ( $userspace ) {
+ if ( Test-Path -Path $VMOPTIONS ) {
+ $LINENUM = 0
+ $lines = Get-Content -Path $VMOPTIONS
+ foreach ( $line in $lines ) {
+ # remove comments
+ $line -Replace "#.*", "" | Out-Null
+ # remove leading and trailing whitespace
+ $line -Replace "(^\s+|\s+$)", "" | Out-Null
+ $LINENUM++
+
+ if ( $line -Match "^-Dsetuserappdirpath=" ) {
+ $JVMARGS += $line
+ }
+ if ( $line -Match "^-Dnouserdefaultappdir=" ) {
+ $NOUSERUPDATEVALUE = ( $line -Replace ".*=", "" ).ToLower()
+ if ( $NOUSERUPDATEVALUE -eq "true" ) {
+ throw "Cannot perform manual user-space update when user-space updates are disabled.`nSee line ${LINENUM} (${line}) in file '${VMOPTIONS}'."
+ }
+ $JVMARGS += $line
+ }
+ }
+ } else {
+ echo "Could not find VMOPTIONS file '${VMOPTIONS}'"
+ }
+ $JVMARGS += "-Duserdefaultappdir=true"
+ $JVMARGS += "-Dnouserdefaultappdir=false"
+}
+
+# INSTALLATION update
+if ( $installation ) {
+ $JVMARGS += "-Duserdefaultappdir=false"
+ $JVMARGS += "-Dnouserdefaultappdir=true"
+ $JVMARGS += "-Dlauncher.appdir=${APPDIR}"
+ $JVMARGS += "-Dappdir=${APPDIR}"
+}
+
+# setting the appdir arg[0] and appid arg[1] to blank values
+# so appDir is determined by EnvConfig.getUserAppdir() or appdir property
+# and appId is passed as system property appid
+$GDL_ARGS = @( "", "" )
+
+# both USER and INSTALLATION updates
+$JVMARGS += "-Dinstaller.appdir=${APPDIR}"
+$JVMARGS += "-Dinstaller.application_folder=${US_NAME}"
+$JVMARGS += "-Dlauncher.script=${SCRIPT}"
+$JVMARGS += "-Dlauncher.update=true"
+$JVMARGS += "-Dchannel.app_name=${NAME}"
+$JVMARGS += "-Dappid=jalview"
+
+# IMPORTANT! tell getdown to update jalview withouth launching
+$JVMARGS += "-Dsilent=true"
+
+# add these Just In Case although jalview shouldn't be launched due to -Dsilent=true
+$GDL_ARGS += ( "--headless", "--quit", "--nojavaconsole", "--nosplash", "--nonews" )
+
+# look for bundled JRE. Might not be there if unix installer used in which case just invoke "java"
+if ( -not ( Test-Path -Path $JAVA ) ) {
+ Write-Host "Cannot find bundled ${JAVA}. Using system ${JAVAEXE} and hoping for the best!"
+ $JAVA = $JAVAEXE
+}
+
+# we should always have at least one JVMARGS and GDL_ARGS so this is okay
+$myJvmArgsString = '"' + $($JVMARGS -join '" "') + '"'
+$myGdlArgsString = '"' + $($GDL_ARGS -join '" "') + '"'
+
+# quote the args and the command (in case of spaces) with escape chars (`) and precede with & to indicate a command not string
+$COMMAND = "& `"${JAVA}`" ${myJvmArgsString} -cp `"${GDL_CLASSPATH}`" com.threerings.getdown.launcher.GetdownApp ${myGdlArgsString}"
+if ( $debug ) {
+ Write-Output "Shell running: ${COMMAND}"
+}
+Invoke-Expression -Command $COMMAND
+
+# move updated getdown-launcher.jar into place
+$COMMAND = "& `"${JAVA}`" ${myJvmArgsString} -cp `"${GDC_CLASSPATH}`" jalview.bin.GetdownLauncherUpdate"
+if ( $debug ) {
+ Write-Output "Shell running: ${COMMAND}"
+}
+Invoke-Expression -Command $COMMAND
--- /dev/null
+#!/usr/bin/env bash
+
+declare -a ARGS=("${@}")
+
+ISMACOS=0
+if [ "$( uname -s )" = "Darwin" ]; then
+ ISMACOS=1
+fi
+
+USAGE="Please use either --installation or --userspace"
+
+DEBUG=0
+USERSPACE=0
+INSTALLATION=0
+DISABLEROOTCHECK=0
+for RAWARG in "${@}"; do
+ ARG="${RAWARG%%=*}"
+ case "${ARG}" in
+ --debug)
+ DEBUG=1
+ ;;
+ --installation)
+ INSTALLATION=1
+ ;;
+ --userspace)
+ USERSPACE=1
+ ;;
+ --norootcheck)
+ DISABLEROOTCHECK=1
+ ;;
+ *)
+ echo "Unknown option '${ARG}'. ${USAGE}." >&2
+ exit 2
+ esac
+done
+
+if [ "${USERSPACE}${INSTALLATION}" = "00" ]; then
+ echo "${USAGE}."
+ exit
+fi
+
+# this whole next part is because there's no readlink -f in Darwin
+function readlinkf() {
+ FINDFILE="$1"
+ FILE="${FINDFILE}"
+ PREVFILE=""
+ C=0
+ MAX=100 # just in case we end up in a loop
+ FOUND=0
+ while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
+ PREVFILE="${FILE}"
+ FILE="$(readlink "${FILE}")"
+ if [ -z "${FILE}" ]; then
+ # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
+ FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
+ FOUND=1
+ elif [ "${FILE#/}" = "${FILE}" ]; then
+ # FILE is not an absolute path link, we need to add the relative path to the previous dir
+ FILE="$(dirname "${PREVFILE}")/${FILE}"
+ fi
+ C=$((C+1))
+ done
+ if [ "${FOUND}" -ne 1 ]; then
+ echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
+ exit 1
+ fi
+ echo "${FILE}"
+}
+
+# args for the JVM
+declare -a JVMARGS=()
+
+# set vars for being inside the macos App Bundle
+if [ "${ISMACOS}" = 1 ]; then
+# MACOS ONLY
+ SCRIPT="$(readlinkf "$0")"
+ DIR="$(dirname "${SCRIPT}")"
+ APPDIR="${DIR%/bin}"
+ JAVABIN="${APPDIR}/jre/Contents/Home/bin"
+ # e.g. APPFOLDER=/Applications/Jalview.app
+ APPFOLDER="${APPDIR%%.app/*}.app"
+ VMOPTIONS="${APPFOLDER}/Contents/vmoptions.txt"
+else
+# NOT MACOS
+ SCRIPT="$(readlink -f "$0")"
+ DIR="$(dirname "${SCRIPT}")"
+ APPDIR="${DIR%/bin}"
+ JAVABIN="${APPDIR}/jre/bin"
+ # e.g. APPFOLDER=/opt/jalview
+ APPFOLDER="${APPDIR}"
+ VMOPTIONS="${APPDIR}/jalviewg.vmoptions"
+fi
+JAVA="${JAVABIN}/java"
+
+# headless java arguments
+JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
+if [ "${ISMACOS}" = 1 ]; then
+ JVMARGS=( "${JVMARGS[@]}" "-Dapple.awt.UIElement=true" )
+fi
+
+SYSJAVA=java
+GETDOWNLAUNCHERJAR="${APPDIR}/getdown-launcher.jar"
+GETDOWNCOREJAR="${APPDIR}/resource/getdown-core.jar"
+CHANNELPROPS="${APPDIR}/channel.props"
+NAME="$( grep app_name= "${CHANNELPROPS}" | cut -d= -f2 )"
+US_NAME="${NAME// /_}"
+
+GDL_CLASSPATH=""
+GDC_CLASSPATH=""
+# save an array of JAR paths in case we're in WSL (see later)
+declare -a GDL_JARPATHS=()
+declare -a GDC_JARPATHS=()
+declare -a GDL_ARGS=()
+
+# getdown-launcher classpath
+if [ -e "${GETDOWNLAUNCHERJAR}" ]; then
+ GDL_CLASSPATH="${GETDOWNLAUNCHERJAR}"
+ GDL_JARPATHS=( "${GDL_JARPATHS[@]}" "${GETDOWNLAUNCHERJAR}" )
+else
+ echo "Cannot find ${GETDOWNLAUNCHERJAR} to run update" >&2
+ exit 3
+fi
+
+# getdown-core classpath
+if [ -e "${GETDOWNCOREJAR}" ]; then
+ GDC_CLASSPATH="${GETDOWNCOREJAR}"
+ GDC_JARPATHS=( "${GDC_JARPATHS[@]}" "${GETDOWNCOREJAR}" )
+else
+ echo "Cannot find $( basename "${GETDOWNCOREJAR}" ) to run update" >&2
+ exit 4
+fi
+
+# USER space update
+if [ "${USERSPACE}" = 1 ]; then
+ if [ -e "${VMOPTIONS}" ]; then
+ LINENUM=0
+ while IFS= read -r line; do
+ # remove comments
+ line=${line%%#*}
+ # remove leading and trailing whitespace
+ line="${line%"${line##*[![:space:]]}"}"
+ line="${line#"${line%%[![:space:]]*}"}"
+ LINENUM=$((LINENUM+1))
+
+ # add settings for user appdir
+ if [ "${line}" != "${line#-Dsetuserappdirpath=}" ]; then # starts with -Dsetuserappdirpath=
+ JVMARGS=( "${JVMARGS[@]}" "${line}" )
+ fi
+ if [ "${line}" != "${line#-Dnouserdefaultappdir=}" ]; then # starts with -Dnouserdefaultappdir=
+ # don't perform user update if user updates are disabled
+ NOUSERUPDATEVALUE="$(echo "${line#-Dnouserdefaultappdir=}" | tr '[:upper:]' '[:lower:]')"
+ if [ "${NOUSERUPDATEVALUE}" = "true" ]; then
+ echo "Cannot perform manual user-space update when user-space updates are disabled." >&2
+ echo "See line ${LINENUM} (${line}) in file '${VMOPTIONS}'." >&2
+ exit 5
+ fi
+ JVMARGS=( "${JVMARGS[@]}" "${line}" )
+ fi
+ done < "${VMOPTIONS}"
+ fi
+ JVMARGS=( "${JVMARGS[@]}" "-Duserdefaultappdir=true" )
+ JVMARGS=( "${JVMARGS[@]}" "-Dnouserdefaultappdir=false" )
+fi
+
+# INSTALLATION update
+if [ "${INSTALLATION}" = 1 ]; then
+ # root permissions check
+ if [ "${DISABLEROOTCHECK}" != 1 -a "${EUID}" != 0 ]; then
+ echo "--installation updates should be run with root permissions, or disable this root check with --norootcheck" >&2
+ exit 6
+ fi
+ JVMARGS=( "${JVMARGS[@]}" "-Duserdefaultappdir=false" )
+ JVMARGS=( "${JVMARGS[@]}" "-Dnouserdefaultappdir=true" )
+ JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.appdir=${APPDIR}" )
+ JVMARGS=( "${JVMARGS[@]}" "-Dappdir=${APPDIR}" )
+fi
+
+# setting the appdir arg[0] and appid arg[1] to blank values
+# so appDir is determined by EnvConfig.getUserAppdir() or appdir property
+# and appId is passed as system property appid
+GDL_ARGS=( "" "" )
+
+# both USER and INSTALLATION updates
+JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.appdir=${APPDIR}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dinstaller.application_folder=${US_NAME}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.script=${SCRIPT}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dlauncher.update=true" )
+JVMARGS=( "${JVMARGS[@]}" "-Dchannel.app_name=${NAME}" )
+JVMARGS=( "${JVMARGS[@]}" "-Dappid=jalview" )
+
+# IMPORTANT! tell getdown to update jalview withouth launching
+JVMARGS=( "${JVMARGS[@]}" "-Dsilent=true" )
+
+# add these Just In Case although jalview shouldn't be launched due to -Dsilent=true
+GDL_ARGS=( "${GDL_ARGS[@]}" "--headless" "--quit" "--nojavaconsole" "--nosplash" "--nonews" )
+
+# WINDOWS ONLY in Cygwin or Windows Subsystem for Linux (WSL)
+# change paths for Cygwin or WSL
+if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
+ if [ "$(uname -o)" = "Cygwin" ]; then
+ # CYGWIN
+ GDL_CLASSPATH=$(cygpath -pw "${GDL_CLASSPATH}")
+ GDC_CLASSPATH=$(cygpath -pw "${GDC_CLASSPATH}")
+ elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
+ # WSL
+ GDL_CLASSPATH=""
+ for JARPATH in "${GDL_JARPATHS[@]}"; do
+ [ -n "${GDL_CLASSPATH}" ] && GDL_CLASSPATH="${GDL_CLASSPATH};"
+ GDL_CLASSPATH="${GDL_CLASSPATH}$(wslpath -aw "${JARPATH}")"
+ done
+ GDC_CLASSPATH=""
+ for JARPATH in "${GDC_JARPATHS[@]}"; do
+ [ -n "${GDC_CLASSPATH}" ] && GDC_CLASSPATH="${GDC_CLASSPATH};"
+ GDC_CLASSPATH="${GDC_CLASSPATH}$(wslpath -aw "${JARPATH}")"
+ done
+ JAVA="${JAVA}.exe"
+ SYSJAVA="java.exe"
+ fi
+fi
+
+# Is there a bundled Java? If not just try one in the PATH (we need .exe in WSL, added above)
+if [ \! -e "${JAVA}" ]; then
+ JAVA=$SYSJAVA
+ echo "Cannot find bundled ${JAVA}, using system ${SYSJAVA} and hoping for the best!" >&2
+fi
+
+# This is just needed for display purposes
+function quotearray() {
+ QUOTEDVALS=""
+ for VAL in "${@}"; do
+ if [ \! "$QUOTEDVALS" = "" ]; then
+ QUOTEDVALS="${QUOTEDVALS} "
+ fi
+ QUOTEDVALS="${QUOTEDVALS}\"${VAL}\""
+ done
+ echo $QUOTEDVALS
+}
+
+JVMARGSSTR=$(quotearray "${JVMARGS[@]}")
+ARGSSTR=$(quotearray "${GDL_ARGS[@]}")
+
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${GDL_CLASSPATH}"\" com.threerings.getdown.launcher.GetdownApp ${ARGSSTR} >&2
+fi
+
+"${JAVA}" "${JVMARGS[@]}" -cp "${GDL_CLASSPATH}" com.threerings.getdown.launcher.GetdownApp "${GDL_ARGS[@]}"
+
+# move updated getdown-launcher.jar into place
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: \""${JAVA}"\" ${JVMARGSSTR} -cp \""${GDC_CLASSPATH}"\" jalview.bin.GetdownLauncherUpdate >&2
+fi
+
+"${JAVA}" "${JVMARGS[@]}" -cp "${GDC_CLASSPATH}" jalview.bin.GetdownLauncherUpdate
--- /dev/null
+# Enter one VM parameter per line
+# For example, to adjust the maximum memory usage to 512 MB, uncomment the following line:
+# -Xmx512m
+# To include another file, uncomment the following line:
+# -include-options [path to other .vmoption file]
+
+# Jalview specific options below
+
+# Jalview options added by __INSTALLERFILENAME__ at __INSTALLDATETIME__
+#
+# Uncomment the following line to disable user-space updates
+#-Dnouserdefaultappdir=true
+#
+# Uncomment the below line to set a custom path for user-space updates -- use with caution.
+# A leading ~/ or %h anywhere will be substituted with the user's home path, and %u by the username.
+# If not set, the default is ${installer:userDefaultAppdirBase} for ${installer:osName}
+#-Dsetuserappdirpath=/tmp/jalview/%u
+#
+# Uncomment the following line to also disable all updates
+#-Dsilent=noupdate
+
<!-- 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">
+ <action name="Jalview (.jvp) message" id="10000" customizedId="FA_MESSAGE-Jalview" 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>
</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">
+ <action name="Jalview (.jvp) progress bar 0" id="10001" customizedId="FA_PROGRESSBAR-Jalview" 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">
+ <action name="Jalview (.jvp) file association" id="10002" customizedId="FA_FILEASSOCIATION-Jalview-true" 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>
<!-- 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">
+ <action name="Jalview Launch (.jvl) message" id="10003" customizedId="FA_MESSAGE-Jalview Launch" 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>
</serializedBean>
</action>
- <action name="Jalview Launch (.jvl) progress bar 3" id="10004" customizedId="Jalview Launch-jvl-10004-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Launch (.jvl) progress bar 3" id="10004" customizedId="FA_PROGRESSBAR-Jalview Launch" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="3" />
</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">
+ <action name="Jalview Launch (.jvl) file association" id="10005" customizedId="FA_FILEASSOCIATION-Jalview Launch-true" 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>
<!-- 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">
+ <action name="CIF (.cif) message" id="10006" customizedId="FA_MESSAGE-CIF" 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>
</serializedBean>
</action>
- <action name="CIF (.cif) progress bar 7" id="10007" customizedId="CIF-cif-10007-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="CIF (.cif) progress bar 7" id="10007" customizedId="FA_PROGRESSBAR-CIF" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="7" />
</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">
+ <action name="CIF (.cif) file association" id="10008" customizedId="FA_FILEASSOCIATION-CIF-false" 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>
<!-- 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">
+ <action name="mmCIF (.mcif, .mmcif) message" id="10009" customizedId="FA_MESSAGE-mmCIF" 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>
</serializedBean>
</action>
- <action name="mmCIF (.mcif, .mmcif) progress bar 11" id="10010" customizedId="mmCIF-mcif,mmcif-10010-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="mmCIF (.mcif, .mmcif) progress bar 11" id="10010" customizedId="FA_PROGRESSBAR-mmCIF" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="11" />
</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">
+ <action name="mmCIF (.mcif, .mmcif) file association" id="10011" customizedId="FA_FILEASSOCIATION-mmCIF-false" 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>
<!-- 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">
+ <action name="PDB (.ent, .pdb) message" id="10012" customizedId="FA_MESSAGE-PDB" 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>
</serializedBean>
</action>
- <action name="PDB (.ent, .pdb) progress bar 15" id="10013" customizedId="PDB-ent,pdb-10013-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PDB (.ent, .pdb) progress bar 15" id="10013" customizedId="FA_PROGRESSBAR-PDB" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="15" />
</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">
+ <action name="PDB (.ent, .pdb) file association" id="10014" customizedId="FA_FILEASSOCIATION-PDB-false" 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>
<!-- 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">
+ <action name="AMSA (.amsa) message" id="10015" customizedId="FA_MESSAGE-AMSA" 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>
</serializedBean>
</action>
- <action name="AMSA (.amsa) progress bar 19" id="10016" customizedId="AMSA-amsa-10016-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="AMSA (.amsa) progress bar 19" id="10016" customizedId="FA_PROGRESSBAR-AMSA" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="19" />
</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">
+ <action name="AMSA (.amsa) file association" id="10017" customizedId="FA_FILEASSOCIATION-AMSA-true" 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>
<!-- 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">
+ <action name="Jalview Annotations (.annotations, .jvannotations) message" id="10018" customizedId="FA_MESSAGE-Jalview Annotations" 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>
</serializedBean>
</action>
- <action name="Jalview Annotations (.annotations, .jvannotations) progress bar 23" id="10019" customizedId="Jalview Annotations-annotations,jvannotations-10019-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Annotations (.annotations, .jvannotations) progress bar 23" id="10019" customizedId="FA_PROGRESSBAR-Jalview Annotations" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="23" />
</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">
+ <action name="Jalview Annotations (.annotations, .jvannotations) file association" id="10020" customizedId="FA_FILEASSOCIATION-Jalview Annotations-true" 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>
<!-- 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">
+ <action name="BioJSON (.biojson) message" id="10021" customizedId="FA_MESSAGE-BioJSON" 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>
</serializedBean>
</action>
- <action name="BioJSON (.biojson) progress bar 26" id="10022" customizedId="BioJSON-biojson-10022-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="BioJSON (.biojson) progress bar 26" id="10022" customizedId="FA_PROGRESSBAR-BioJSON" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="26" />
</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">
+ <action name="BioJSON (.biojson) file association" id="10023" customizedId="FA_FILEASSOCIATION-BioJSON-true" 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>
<!-- 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">
+ <action name="BLC (.blc) message" id="10024" customizedId="FA_MESSAGE-BLC" 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>
</serializedBean>
</action>
- <action name="BLC (.blc) progress bar 30" id="10025" customizedId="BLC-blc-10025-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="BLC (.blc) progress bar 30" id="10025" customizedId="FA_PROGRESSBAR-BLC" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="30" />
</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">
+ <action name="BLC (.blc) file association" id="10026" customizedId="FA_FILEASSOCIATION-BLC-true" 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>
<!-- 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">
+ <action name="Clustal (.aln) message" id="10027" customizedId="FA_MESSAGE-Clustal" 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>
</serializedBean>
</action>
- <action name="Clustal (.aln) progress bar 34" id="10028" customizedId="Clustal-aln-10028-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Clustal (.aln) progress bar 34" id="10028" customizedId="FA_PROGRESSBAR-Clustal" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="34" />
</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">
+ <action name="Clustal (.aln) file association" id="10029" customizedId="FA_FILEASSOCIATION-Clustal-true" 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>
<!-- END -->
<!-- Fasta (.fa, .fasta) BEGIN -->
- <action name="Fasta (.fa, .fasta) message" id="10030" customizedId="Fasta-fa,fasta-10030-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Fasta (.fa, .fasta) message" id="10030" customizedId="FA_MESSAGE-Fasta" 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>
</serializedBean>
</action>
- <action name="Fasta (.fa, .fasta) progress bar 38" id="10031" customizedId="Fasta-fa,fasta-10031-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Fasta (.fa, .fasta) progress bar 38" id="10031" customizedId="FA_PROGRESSBAR-Fasta" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="38" />
</serializedBean>
</action>
- <action name="Fasta (.fa, .fasta) file association" id="10032" customizedId="Fasta-fa,fasta-10032-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fa,fasta file association">
+ <action name="Fasta (.fa, .fasta) file association" id="10032" customizedId="FA_FILEASSOCIATION-Fasta-true" 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>
<!-- END -->
<!-- Jalview Features (.features, .jvfeatures) BEGIN -->
- <action name="Jalview Features (.features, .jvfeatures) message" id="10033" customizedId="Jalview Features-features,jvfeatures-10033-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Features (.features, .jvfeatures) message" id="10033" customizedId="FA_MESSAGE-Jalview Features" 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>
</serializedBean>
</action>
- <action name="Jalview Features (.features, .jvfeatures) progress bar 42" id="10034" customizedId="Jalview Features-features,jvfeatures-10034-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Features (.features, .jvfeatures) progress bar 42" id="10034" customizedId="FA_PROGRESSBAR-Jalview Features" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="42" />
</serializedBean>
</action>
- <action name="Jalview Features (.features, .jvfeatures) file association" id="10035" customizedId="Jalview Features-features,jvfeatures-10035-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .features,jvfeatures file association">
+ <action name="Jalview Features (.features, .jvfeatures) file association" id="10035" customizedId="FA_FILEASSOCIATION-Jalview Features-true" 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>
<!-- END -->
<!-- Jalview Feature Settings File (.fc) BEGIN -->
- <action name="Jalview Feature Settings File (.fc) message" id="10036" customizedId="Jalview Feature Settings File-fc-10036-message" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Feature Settings File (.fc) message" id="10036" customizedId="FA_MESSAGE-Jalview Feature Settings File" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="detailMessage" type="string">Jalview Feature Settings File (.fc)</property>
<property name="statusMessage" type="string">Creating file associations...</property>
</serializedBean>
</action>
- <action name="Jalview Feature Settings File (.fc) progress bar 46" id="10037" customizedId="Jalview Feature Settings File-fc-10037-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Jalview Feature Settings File (.fc) progress bar 46" id="10037" customizedId="FA_PROGRESSBAR-Jalview Feature Settings File" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="46" />
</serializedBean>
</action>
- <action name="Jalview Feature Settings File (.fc) file association" id="10038" customizedId="Jalview Feature Settings File-fc-10038-fileassociation" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fc file association">
+ <action name="Jalview Feature Settings File (.fc) file association" id="10038" customizedId="FA_FILEASSOCIATION-Jalview Feature Settings File-true" beanClass="com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make .fc file association">
<serializedBean>
<property name="description" type="string">Jalview Feature Settings File File</property>
<property name="extension" type="string">fc</property>
<!-- 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">
+ <action name="GenBank Flatfile (.gb, .gbk) message" id="10039" customizedId="FA_MESSAGE-GenBank Flatfile" 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>
</serializedBean>
</action>
- <action name="GenBank Flatfile (.gb, .gbk) progress bar 50" id="10040" customizedId="GenBank Flatfile-gb,gbk-10040-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="GenBank Flatfile (.gb, .gbk) progress bar 50" id="10040" customizedId="FA_PROGRESSBAR-GenBank Flatfile" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="50" />
</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">
+ <action name="GenBank Flatfile (.gb, .gbk) file association" id="10041" customizedId="FA_FILEASSOCIATION-GenBank Flatfile-true" 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>
<!-- 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">
+ <action name="Generic Features Format v2 (.gff2) message" id="10042" customizedId="FA_MESSAGE-Generic Features Format v2" 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>
</serializedBean>
</action>
- <action name="Generic Features Format v2 (.gff2) progress bar 53" id="10043" customizedId="Generic Features Format v2-gff2-10043-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Generic Features Format v2 (.gff2) progress bar 53" id="10043" customizedId="FA_PROGRESSBAR-Generic Features Format v2" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="53" />
</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">
+ <action name="Generic Features Format v2 (.gff2) file association" id="10044" customizedId="FA_FILEASSOCIATION-Generic Features Format v2-true" 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>
<!-- 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">
+ <action name="Generic Features Format v3 (.gff3) message" id="10045" customizedId="FA_MESSAGE-Generic Features Format v3" 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>
</serializedBean>
</action>
- <action name="Generic Features Format v3 (.gff3) progress bar 57" id="10046" customizedId="Generic Features Format v3-gff3-10046-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Generic Features Format v3 (.gff3) progress bar 57" id="10046" customizedId="FA_PROGRESSBAR-Generic Features Format v3" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="57" />
</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">
+ <action name="Generic Features Format v3 (.gff3) file association" id="10047" customizedId="FA_FILEASSOCIATION-Generic Features Format v3-true" 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>
<!-- 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">
+ <action name="JnetFile (.concise, .jnet) message" id="10048" customizedId="FA_MESSAGE-JnetFile" 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>
</serializedBean>
</action>
- <action name="JnetFile (.concise, .jnet) progress bar 61" id="10049" customizedId="JnetFile-concise,jnet-10049-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="JnetFile (.concise, .jnet) progress bar 61" id="10049" customizedId="FA_PROGRESSBAR-JnetFile" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="61" />
</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">
+ <action name="JnetFile (.concise, .jnet) file association" id="10050" customizedId="FA_FILEASSOCIATION-JnetFile-true" 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>
<!-- 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">
+ <action name="MSF (.msf) message" id="10051" customizedId="FA_MESSAGE-MSF" 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>
</serializedBean>
</action>
- <action name="MSF (.msf) progress bar 65" id="10052" customizedId="MSF-msf-10052-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="MSF (.msf) progress bar 65" id="10052" customizedId="FA_PROGRESSBAR-MSF" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="65" />
</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">
+ <action name="MSF (.msf) file association" id="10053" customizedId="FA_FILEASSOCIATION-MSF-true" 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>
<!-- 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">
+ <action name="PFAM (.pfam) message" id="10054" customizedId="FA_MESSAGE-PFAM" 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>
</serializedBean>
</action>
- <action name="PFAM (.pfam) progress bar 69" id="10055" customizedId="PFAM-pfam-10055-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PFAM (.pfam) progress bar 69" id="10055" customizedId="FA_PROGRESSBAR-PFAM" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="69" />
</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">
+ <action name="PFAM (.pfam) file association" id="10056" customizedId="FA_FILEASSOCIATION-PFAM-true" 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>
<!-- 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">
+ <action name="PHYLIP (.phy) message" id="10057" customizedId="FA_MESSAGE-PHYLIP" 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>
</serializedBean>
</action>
- <action name="PHYLIP (.phy) progress bar 73" id="10058" customizedId="PHYLIP-phy-10058-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PHYLIP (.phy) progress bar 73" id="10058" customizedId="FA_PROGRESSBAR-PHYLIP" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="73" />
</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">
+ <action name="PHYLIP (.phy) file association" id="10059" customizedId="FA_FILEASSOCIATION-PHYLIP-true" 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>
<!-- 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">
+ <action name="PileUp (.pileup) message" id="10060" customizedId="FA_MESSAGE-PileUp" 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>
</serializedBean>
</action>
- <action name="PileUp (.pileup) progress bar 76" id="10061" customizedId="PileUp-pileup-10061-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PileUp (.pileup) progress bar 76" id="10061" customizedId="FA_PROGRESSBAR-PileUp" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="76" />
</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">
+ <action name="PileUp (.pileup) file association" id="10062" customizedId="FA_FILEASSOCIATION-PileUp-true" 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>
<!-- 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">
+ <action name="PIR (.pir) message" id="10063" customizedId="FA_MESSAGE-PIR" 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>
</serializedBean>
</action>
- <action name="PIR (.pir) progress bar 80" id="10064" customizedId="PIR-pir-10064-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="PIR (.pir) progress bar 80" id="10064" customizedId="FA_PROGRESSBAR-PIR" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="80" />
</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">
+ <action name="PIR (.pir) file association" id="10065" customizedId="FA_FILEASSOCIATION-PIR-true" 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>
<!-- 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">
+ <action name="RNAML (.rnaml) message" id="10066" customizedId="FA_MESSAGE-RNAML" 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>
</serializedBean>
</action>
- <action name="RNAML (.rnaml) progress bar 84" id="10067" customizedId="RNAML-rnaml-10067-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="RNAML (.rnaml) progress bar 84" id="10067" customizedId="FA_PROGRESSBAR-RNAML" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="84" />
</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">
+ <action name="RNAML (.rnaml) file association" id="10068" customizedId="FA_FILEASSOCIATION-RNAML-true" 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>
<!-- 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">
+ <action name="Substitution Matrix (.mat) message" id="10069" customizedId="FA_MESSAGE-Substitution Matrix" 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>
</serializedBean>
</action>
- <action name="Substitution Matrix (.mat) progress bar 88" id="10070" customizedId="Substitution Matrix-mat-10070-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Substitution Matrix (.mat) progress bar 88" id="10070" customizedId="FA_PROGRESSBAR-Substitution Matrix" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="88" />
</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">
+ <action name="Substitution Matrix (.mat) file association" id="10071" customizedId="FA_FILEASSOCIATION-Substitution Matrix-true" 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>
<!-- 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">
+ <action name="Stockholm (.stk, .sto) message" id="10072" customizedId="FA_MESSAGE-Stockholm" 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>
</serializedBean>
</action>
- <action name="Stockholm (.stk, .sto) progress bar 92" id="10073" customizedId="Stockholm-stk,sto-10073-progressbar" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <action name="Stockholm (.stk, .sto) progress bar 92" id="10073" customizedId="FA_PROGRESSBAR-Stockholm" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
<property name="percentValue" type="int" value="92" />
</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">
+ <action name="Stockholm (.stk, .sto) file association" id="10074" customizedId="FA_FILEASSOCIATION-Stockholm-true" 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>
<!-- $$NAME$$ ($$DISPLAYEXTENSION$$) 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">
+ <action name="$$NAME$$ ($$DISPLAYEXTENSION$$) message" id="$$ID$$" customizedId="FA_MESSAGE-$$NAME$$" 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>
</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">
+ <action name="$$NAME$$ ($$DISPLAYEXTENSION$$) progress bar $$PROGRESSPERCENT$$" id="$$ID1$$" customizedId="FA_PROGRESSBAR-$$NAME$$" 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">
+ <action name="$$NAME$$ ($$DISPLAYEXTENSION$$) file association" id="$$ID2$$" customizedId="FA_FILEASSOCIATION-$$NAME$$-$$PRIMARY$$" 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>
<?xml version="1.0" encoding="UTF-8"?>
<install4j version="10.0.8" 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="${compiler:JAVA_MAX_VERSION}" allowBetaVM="true" jdkMode="jdk" jdkName="JDK 11.0">
+ <directoryPresets config="." />
+ <application name="${compiler:JALVIEW_APPLICATION_NAME}" applicationId="${compiler:WINDOWS_APPLICATION_ID}" mediaDir="${compiler:JALVIEW_DIR}/${compiler:BUILD_DIR}" lzmaCompression="true" shortName="${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 />
<variable name="MACOSARCHIVE_VOLUMEICON" />
<variable name="WRAPPER_LINK" value="jalview" />
<variable name="BASH_WRAPPER_SCRIPT" value="jalview.sh" />
+ <variable name="POWERSHELL_WRAPPER_SCRIPT" value="jalview.ps1" />
+ <variable name="BASH_UPDATE_SCRIPT" value="update.sh" />
+ <variable name="POWERSHELL_UPDATE_SCRIPT" value="update.ps1" />
<variable name="WRAPPER_SCRIPT_BIN_DIR" value="bin" />
<variable name="MACOSARCHIVE_X64_NAME" value="Install Jalview (Intel)" />
<variable name="MACOSARCHIVE_AARCH64_NAME" value="Install Jalview (Apple Silicon)" />
<variable name="WINDOWS_ICONS_FILE" value="jalview_logo.ico" />
<variable name="PNG_ICON_FILE" value="jalview_logo.png" />
<variable name="BACKGROUND" value="utils/channels/release/images/jalview_logo_background_fade-640x480.png" />
- <variable name="BATCH_WRAPPER_SCRIPT" value="jalview.bat" />
- <variable name="POWERSHELL_WRAPPER_SCRIPT" value="jalview.ps1" />
- <variable name="WIZARD_WIDTH" value="640" description="Default/initial width of installer wizard window. Linux media types adapt this.
NOT USED" />
- <variable name="WIZARD_HEIGHT" value="480" description="Default/initial width of installer wizard window. Linux media types adapt this.
NOT USED" />
+ <variable name="WIZARD_WIDTH" value="960" description="Default/initial width of installer wizard window. Linux media types adapt this.
NOT USED" />
+ <variable name="WIZARD_HEIGHT" value="720" description="Default/initial width of installer wizard window. Linux media types adapt this.
NOT USED" />
<variable name="MACOSARCHIVE_X64_DMG_FILENAME" value="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-x64-java_${compiler:JAVA_INTEGER_VERSION}" />
<variable name="MACOSARCHIVE_AARCH64_DMG_FILENAME" value="${compiler:APPLICATION_FOLDER}-${compiler:JALVIEW_VERSION}-${compiler:sys.platform}-aarch64-java_${compiler:JAVA_INTEGER_VERSION}" />
- <variable name="INSTALLER_ICON" value="jalview_installer.png" />
- <variable name="INSTALLER_MAC_ICON" value="jalview_installer.icns" />
- <variable name="INSTALLER_WINDOWS_ICON" value="jalview_installer.ico" />
+ <variable name="INSTALLER_ICON" value="jalview_installer.png" description="An icon with installation arrow.
NOT USED" />
+ <variable name="INSTALLER_MAC_ICON" value="jalview_installer.icns" description="An icon with installation arrow.
NOT USED" />
+ <variable name="INSTALLER_WINDOWS_ICON" value="jalview_installer.ico" description="An icon with installation arrow.
NOT USED" />
+ <variable name="TITLE_ICON" value="jalview_logo-64.png" description="Icon sized for the installer wizard title bar" />
<variable name="LOG_FILE" value=".jalview.log" />
</variables>
<codeSigning macEnabled="true" macPkcs12File="${compiler:OSX_KEYSTORE}" macNotarize="true" appleId="${compiler:OSX_APPLEID}">
<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">
+ <component name="jalview_getdown" id="1031" changeable="false" hidden="true">
<include>
<entry filesetId="734" />
</include>
</files>
<launchers>
<launcher name="Jalview User Launcher" id="2823" customizedId="JALVIEW" menuName="${compiler:JALVIEW_APPLICATION_NAME}" icnsFile="${compiler:JALVIEW_DIR}/${compiler:ICONS_DIR}/${compiler:MAC_ICONS_FILE}" customMacBundleIdentifier="true" macBundleIdentifier="${compiler:BUNDLE_ID}" fileset="734" addMacApplicationCategory="true" macApplicationCategory="public.app-category.education" useCustomMacosExecutableName="true" customMacosExecutableName="${compiler:JALVIEW_APPLICATION_NAME}">
- <executable name="${compiler:EXECUTABLE_NAME}" iconSet="true" iconFile="${compiler:JALVIEW_DIR}/${compiler:ICONS_DIR}/${compiler:WINDOWS_ICONS_FILE}" stderrFile="~/.${compiler:LOG_FILE}" redirectStdout="true" stdoutFile="~/.${compiler:LOG_FILE}" executableMode="gui" changeWorkingDirectory="false" singleInstance="true" executionLevel="highestAvailable" checkConsoleParameter="true">
+ <executable name="${compiler:EXECUTABLE_NAME}" iconSet="true" iconFile="${compiler:JALVIEW_DIR}/${compiler:ICONS_DIR}/${compiler:WINDOWS_ICONS_FILE}" stderrFile="~/.${compiler:LOG_FILE}" redirectStdout="true" stdoutFile="~/.${compiler:LOG_FILE}" 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">
# To include another file, uncomment the following line:
# -include-options [path to other .vmoption file]
-# Uncomment these two lines to disable user-space automatic updates.
-#-Dnouserdefaultappdir=true
-#-Dsilent=noupdate</content>
+# Jalview specific options below</content>
</vmOptionsFile>
<infoPlist>${compiler:file("${compiler:INFO_PLIST_FILE_ASSOCIATIONS_FILE}")}</infoPlist>
<iconImageFiles>
</launcher>
</launchers>
<installerGui autoUpdateDescriptorUrl="https://www.jalview.org/install4j/updates.xml">
+ <staticMembers>/*
+
+import java.beans.BeanInfo;
+import java.beans.Introspector;
+import java.beans.PropertyDescriptor;
+import java.beans.IntrospectionException;
+import java.lang.reflect.Method;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Array;
+
+ public static String printDataType(Object o) {
+ return printDataType("", o);
+ }
+
+ public static String printDataType(String prefix, Object o) {
+ return printDataType(prefix, o, 1);
+ }
+ public static String printDataType(String prefix, Object o, int iter) {
+ StringBuilder stringRep = new StringBuilder();
+
+ try {
+ if (o != null) {
+ Class objectType = o.getClass();
+ if (objectType.isPrimitive() ||
+ objectType.equals(String.class) ||
+ objectType.equals(Date.class)) {
+ stringRep.append(prefix + " (" + objectType.getSimpleName() +
+ ") = " + o.toString() + "\n");
+ } else if (objectType.isArray()) {
+ if (Array.getLength(o) == 0) {
+ stringRep.append(prefix + " = empty array\n");
+ }
+ if (objectType.getComponentType().isPrimitive() ||
+ objectType.getComponentType().equals(String.class) ||
+ objectType.getComponentType().equals(Date.class)) {
+ for (int i = 0; i < Array.getLength(o); i++) {
+ stringRep.append(prefix + "[" + i + "] = " +
+ Array.get(o, i).toString() + "\n");
+ }
+ } else {
+ for (int i = 0; i < Array.getLength(o); i++) {
+ stringRep.append(printDataType(prefix + "[" + i + "]",
+ Array.get(o, i), iter + 1));
+ }
+ }
+ } else if (o instanceof Iterable) {
+ int i = 0;
+ Iterator it = ((Iterable) o).iterator();
+ if (!it.hasNext()) {
+ stringRep.append(prefix + " = empty set\n");
+ }
+ while (it.hasNext()) {
+ stringRep.append(printDataType(prefix + "[" + i++ + "]",
+ it.next(), iter + 1));
+ }
+ } else if (o instanceof Map) {
+ Set<Object> keys = ((Map) o).keySet();
+ if (keys.isEmpty()) {
+ stringRep.append(prefix + " = empty map\n");
+ }
+ for (Object key : keys) {
+ stringRep.append(printDataType(prefix + "[" + key.toString() + "]",
+ ((Map) o).get(key), iter + 1));
+ }
+ } else if (o instanceof Class) {
+ // Do nothing otherwise the stack blows up
+ } else {
+ Method[] methods = objectType.getMethods();
+
+ for (Method method : methods) {
+ if (method.getName().startsWith("get") &&
+ method.getParameterCount() == 0) {
+ String propertyName = method.getName().substring(3,4).toLowerCase() +
+ method.getName().substring(4);
+ Object value = method.invoke(o, new Object[] {} );
+ // value.getClass().isPrimitive returns false, even if
+ // method.getReturnType().isPrimitive returns true
+ if (method.getReturnType().isPrimitive()) {
+ stringRep.append(prefix + "." + propertyName + " (" +
+ method.getReturnType().getSimpleName() + ") = " +
+ value.toString() + "\n");
+ } else {
+ if (iter < 10) {
+ stringRep.append(printDataType(prefix + "." + propertyName, value, iter + 1));
+ } else {
+ stringRep.append("...");
+ }
+ }
+ } else if (method.getName().startsWith("is") &&
+ method.getParameterCount() == 0 &&
+ method.getReturnType().equals(boolean.class)) {
+ String propertyName = method.getName().substring(2,3).toLowerCase() +
+ method.getName().substring(3);
+ stringRep.append(prefix + "." + propertyName + " (boolean) = " +
+ (method.invoke(o, new Object[] {}).equals(true) ? "true" : "false") + "\n");
+ }
+ }
+ }
+ } else {
+ return prefix + " = null\n";
+ }
+ } catch (Exception e) {
+ //e.printStackTrace();
+ //return e.toString();
+ stringRep.append("Exception("+e.getMessage()+")");
+ }
+
+ return stringRep.toString();
+ }
+
+*/
+
+public static String getOsAppDataPath(Context context) {
+ Map<String, String> osAppDataPathMap = new HashMap<>();
+ osAppDataPathMap.put("macos", "Library/Application Support/Jalview-Desktop");
+ osAppDataPathMap.put("linux", ".local/share/jalview-desktop");
+ osAppDataPathMap.put("windows", "AppData\\Local\\Jalview-Desktop");
+ osAppDataPathMap.put("other", ".jalview-desktop");
+ String appDataPath;
+ String append;
+ if (Util.isMacOS()) {
+ appDataPath = osAppDataPathMap.get("macos");
+ append = context.getCompilerVariable("JALVIEW_APPLICATION_NAME");
+ } else if (Util.isWindows()) {
+ appDataPath = osAppDataPathMap.get("windows");
+ append = context.getCompilerVariable("APPLICATION_FOLDER");
+ } else if (Util.isLinux()) {
+ appDataPath = osAppDataPathMap.get("linux");
+ append = context.getCompilerVariable("APPLICATION_FOLDER").toLowerCase(Locale.ROOT);
+ } else {
+ appDataPath = osAppDataPathMap.get("other");
+ append = context.getCompilerVariable("APPLICATION_FOLDER").toLowerCase(Locale.ROOT);
+ }
+ return "~" + File.separator + appDataPath + File.separator + append;
+}
+
+// methods used in advanced options form validation
+public static void validateUserSpaceAdvancedOptionsForm(FormEnvironment formEnvironment) {
+ FormComponent fc_advancedOptions = formEnvironment.getFormComponentById("US_ADVANCED_OPTIONS");
+ FormComponent fc_notUsed = formEnvironment.getFormComponentById("US_NOT_USED");
+ FormComponent fc_userUpdates = formEnvironment.getFormComponentById("US_ALLOW_USER_APPDIR_UPDATES");
+ FormComponent fc_warning = formEnvironment.getFormComponentById("US_NO_UPDATES_WARNING");
+ LayoutGroup lg_advancedOptions = formEnvironment.getLayoutGroupById("US_ADVANCED_OPTIONS_GROUP");
+
+ // get boolean status of "Enable advanced options" checkbox
+ JCheckBox jcb_advancedOptions = (JCheckBox) fc_advancedOptions.getConfigurationObject();
+ boolean advancedOptions = jcb_advancedOptions.isSelected();
+
+ // set visibility of Advanced options layout group
+ lg_advancedOptions.setVisible(advancedOptions);
+ fc_notUsed.setVisible(!advancedOptions);
+
+ if (!advancedOptions) {
+ return;
+ }
+
+ JCheckBox jcb_userUpdates = (JCheckBox) fc_userUpdates.getConfigurationObject();
+ boolean userUpdates = fc_userUpdates.isEnabled() && jcb_userUpdates.isSelected();
+
+ boolean showWarning = advancedOptions && (!userUpdates);
+
+ fc_warning.setVisible(showWarning);
+}
+
+public static void validateSystemSpaceAdvancedOptionsForm(Context context, FormEnvironment formEnvironment) {
+ validateSystemSpaceAdvancedOptionsForm(context, formEnvironment, true);
+}
+
+public static boolean validateSystemSpaceAdvancedOptionsForm(Context context, FormEnvironment formEnvironment, boolean ret) {
+ FormComponent fc_advancedOptions = formEnvironment.getFormComponentById("SS_ADVANCED_OPTIONS");
+ FormComponent fc_notUsed = formEnvironment.getFormComponentById("SS_NOT_USED");
+ FormComponent fc_userUpdates = formEnvironment.getFormComponentById("SS_ALLOW_USER_APPDIR_UPDATES");
+ FormComponent fc_installerUpdates = formEnvironment.getFormComponentById("SS_ALLOW_INSTALLER_APPDIR_UPDATES");
+ FormComponent fc_allowUserAppdirPath = formEnvironment.getFormComponentById("SS_ALLOW_USER_APPDIR_PATH");
+ FormComponent fc_userAppdirPath = formEnvironment.getFormComponentById("SS_USER_APPDIR_PATH");
+ LayoutGroup lg_advancedGroup = formEnvironment.getLayoutGroupById("SS_ADVANCED_OPTIONS_GROUP");
+ LayoutGroup lg_setUserAppdirPath = formEnvironment.getLayoutGroupById("SS_SET_USER_APPDIR_PATH");
+
+
+
+ // get boolean status of "Enable advanced options" checkbox
+ JCheckBox jcb_advancedOptions = (JCheckBox) fc_advancedOptions.getConfigurationObject();
+ boolean advancedOptions = jcb_advancedOptions.isSelected();
+
+ // set visibility of Advanced options layout group
+ lg_advancedGroup.setVisible(advancedOptions);
+ fc_notUsed.setVisible(!advancedOptions);
+
+ if (!advancedOptions) {
+ return ret;
+ }
+
+
+
+ // get boolean status of "Allow user-space updates" checkbox
+ JCheckBox jcb_user = (JCheckBox) fc_userUpdates.getConfigurationObject();
+ boolean userUpdates = jcb_user.isSelected();
+
+ // set enabled of customised user appdir path group
+ lg_setUserAppdirPath.setEnabled(advancedOptions && userUpdates);
+
+ // set enabled of allow installation updates checkbox
+ fc_installerUpdates.setEnabled(advancedOptions && !userUpdates);
+
+
+
+ // get boolean status of "Customise the user-space path" checkbox
+ JCheckBox jcb_allowUserAppdirPath = (JCheckBox) fc_allowUserAppdirPath.getConfigurationObject();
+ boolean allowUserAppdirPath = jcb_allowUserAppdirPath.isSelected();
+
+ // set enabled of userAppdirPath text field
+ fc_userAppdirPath.setEnabled(advancedOptions && allowUserAppdirPath && fc_allowUserAppdirPath.isEnabled());
+
+ // get String value of userAppdirPath text field
+ JTextField jtf_userAppdirPath = (JTextField) fc_userAppdirPath.getConfigurationObject();
+ String userAppdirPath = jtf_userAppdirPath.getText();
+
+
+
+ // get boolean status of "Allow installation updates" checkbox
+ JCheckBox jcb_installer = (JCheckBox) fc_installerUpdates.getConfigurationObject();
+ boolean installerUpdates = jcb_installer.isSelected();
+
+
+
+ // should we show the No updates warning?
+ boolean showNoUpdatesWarning = advancedOptions && !(userUpdates || installerUpdates);
+ FormComponent fc_noUpdatesWarning = formEnvironment.getFormComponentById("SS_NO_UPDATES_WARNING");
+ fc_noUpdatesWarning.setVisible(advancedOptions && showNoUpdatesWarning);
+
+
+
+ // should we show the invalid user-space path warning?
+ showInvalidUserAppdirPathWarning(context, formEnvironment);
+
+
+
+ // set whether "Set defaults" button should be enabled
+ FormComponent fc_setDefaults = formEnvironment.getFormComponentById("SS_SET_DEFAULTS");
+ JButton jb_setDefaults = (JButton) fc_setDefaults.getConfigurationObject();
+ boolean enableSetDefaults = !( userUpdates && !allowUserAppdirPath && userAppdirPath.length() == 0 && !installerUpdates );
+ jb_setDefaults.setEnabled(enableSetDefaults);
+
+
+
+ return ret;
+}
+
+public static boolean isUserAppdirPathValid(Context context) { // this is only valid when form is updated
+ return isUserAppdirPathValid(context, (String) context.getVariable("userAppdirPath"));
+}
+
+public static boolean isUserAppdirPathValid(Context context, FormComponent fc_userAppdirPath) {
+ // get String value of userAppdirPath text field
+ JTextField jtf_userAppdirPath = (JTextField) fc_userAppdirPath.getConfigurationObject();
+ String userAppdirPath = jtf_userAppdirPath.getText();
+ return isUserAppdirPathValid(context, userAppdirPath);
+}
+
+public static boolean isUserAppdirPathValid(Context context, String userAppdirPath) {
+ if (userAppdirPath == null || userAppdirPath.length() == 0) {
+ return true; // null will be switched to default
+ }
+
+ boolean u = userAppdirPath.contains("%u");
+ boolean h = userAppdirPath.contains("%h");
+ boolean t = userAppdirPath.startsWith("~" + (String)context.getVariable("sys.fileSeparator"));
+
+ return u || h || t;
+}
+
+public static void showInvalidUserAppdirPathWarning(Context context, FormEnvironment formEnvironment) {
+ FormComponent fc_advancedOptions = formEnvironment.getFormComponentById("SS_ADVANCED_OPTIONS");
+ FormComponent fc_userUpdates = formEnvironment.getFormComponentById("SS_ALLOW_USER_APPDIR_UPDATES");
+ FormComponent fc_allowUserAppdirPath = formEnvironment.getFormComponentById("SS_ALLOW_USER_APPDIR_PATH");
+ FormComponent fc_userAppdirPath = formEnvironment.getFormComponentById("SS_USER_APPDIR_PATH");
+ FormComponent fc_invalidPathWarning = formEnvironment.getFormComponentById("SS_INVALID_USER_APPDIR_PATH_WARNING");
+
+ // get boolean status of "Allow user-space updates" checkbox
+ boolean advancedOptions = ((JCheckBox) fc_advancedOptions.getConfigurationObject()).isSelected();
+
+ // get boolean status of "Allow user-space updates" checkbox
+ boolean userUpdates = ((JCheckBox) fc_userUpdates.getConfigurationObject()).isSelected();
+
+ // get boolean status of "Customise the user-space path" checkbox
+ boolean allowUserAppdirPath = ((JCheckBox) fc_allowUserAppdirPath.getConfigurationObject()).isSelected();
+
+ // show/hide warning
+ boolean showInvalidPathWarning = advancedOptions && userUpdates && allowUserAppdirPath && !isUserAppdirPathValid(context, fc_userAppdirPath);
+ fc_invalidPathWarning.setVisible(showInvalidPathWarning);
+}
+
+// methods to get installer.appdir hash
+protected static final String XLATE = "0123456789abcdef";
+
+public static String hexlate (byte[] bytes, int count)
+{
+ if (bytes == null) {
+ return "";
+ }
+
+ count = Math.min(count, bytes.length);
+ char[] chars = new char[count*2];
+
+ for (int i = 0; i < count; i++) {
+ int val = bytes[i];
+ if (val < 0) {
+ val += 256;
+ }
+ chars[2*i] = XLATE.charAt(val/16);
+ chars[2*i+1] = XLATE.charAt(val%16);
+ }
+
+ return new String(chars);
+}
+
+public static String hexlate (byte[] bytes)
+{
+ return (bytes == null) ? "" : hexlate(bytes, bytes.length);
+}
+
+public static final String getFullPathToDirectoryHash(String install_app_dir)
+{
+ java.security.MessageDigest md;
+ try {
+ md = java.security.MessageDigest.getInstance("SHA-256");
+ } catch (java.security.NoSuchAlgorithmException nsae) {
+ throw new RuntimeException("JVM does not support SHA-256. Gurp!");
+ }
+ byte[] contents = install_app_dir.getBytes(java.nio.charset.StandardCharsets.UTF_8);
+ String hash = hexlate(md.digest(contents));
+ return hash.substring(0,8);
+}
+
+public static final String getCanonicalFullPathToDirectoryHash(String installerAppdir) {
+ try {
+ return getFullPathToDirectoryHash(new File(installerAppdir).getCanonicalPath());
+ }catch (IOException ioex) {
+ System.err.println("Unable to resolve '"+installerAppdir+"' as a proper path on this system.\nNot generating an installer appdir hash");
+ return "";
+ }
+}
+</staticMembers>
<applications>
- <application id="installer" beanClass="com.install4j.runtime.beans.applications.InstallerApplication" actionElevationType="elevated" styleId="35" customIcnsFile="${compiler:JALVIEW_DIR}/${compiler:INSTALLER_MAC_ICON}" customIcoFile="${compiler:JALVIEW_DIR}/${compiler:INSTALLER_WINDOWS_ICON}">
+ <application id="installer" beanClass="com.install4j.runtime.beans.applications.InstallerApplication" actionElevationType="elevated" styleId="35" customIcnsFile="${compiler:JALVIEW_DIR}/${compiler:ICONS_DIR}/${compiler:MAC_ICONS_FILE}" customIcoFile="${compiler:JALVIEW_DIR}/${compiler:ICONS_DIR}/${compiler:WINDOWS_ICONS_FILE}">
<serializedBean>
- <property name="frameHeight" type="int" value="684" />
- <property name="frameWidth" type="int" value="912" />
+ <property name="frameHeight" type="int" value="720" />
+ <property name="frameWidth" type="int" value="960" />
<property name="useCustomIcon" type="boolean" value="true" />
</serializedBean>
<styleOverrides>
</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">
+ <formComponent name="Watermark" id="352" beanClass="com.install4j.runtime.beans.formcomponents.SeparatorComponent" insetTop="0" insetLeft="5" insetBottom="0" useExternalParametrization="true" externalParametrizationName="Custom watermark" externalParametrizationMode="include">
<serializedBean>
<property name="enabledTitleText" type="boolean" value="false" />
</serializedBean>
<property name="imageEdgeBorderWidth" type="int" value="2" />
<property name="imageFile">
<object class="com.install4j.api.beans.ExternalFile">
- <string>${compiler:JALVIEW_DIR}/${compiler:INSTALLER_ICON}</string>
+ <string>${compiler:JALVIEW_DIR}/${compiler:TITLE_ICON}</string>
</object>
</property>
<property name="imageInsets">
<serializedBean>
<property name="script">
<object class="com.install4j.api.beans.ScriptProperty">
- <property name="value" type="string">Util.isLinux() || Util.isUnixInstaller()</property>
+ <property name="value" type="string">Util.isLinux() || Util.isUnixInstaller() || ( Util.isMacosInstaller() && context.getBooleanVariable("isAdmin") )</property>
</object>
</property>
<property name="variableName" type="string">makeSymbolicLink</property>
</action>
<action name="BOTHSPACE: Set unixBinDir (Linux or Unix)" id="2845" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
<serializedBean>
+ <property name="responseFileVariable" type="boolean" value="true" />
<property name="script">
<object class="com.install4j.api.beans.ScriptProperty">
<property name="value" type="string">ArrayList<String> tryPaths = new ArrayList<> ();
</property>
<property name="variableName" type="string">unixBinDir</property>
</serializedBean>
- <condition>context.getBooleanVariable("makeSymbolicLink")</condition>
+ <condition>if (!context.getBooleanVariable("makeSymbolicLink")) {
+ return false;
+}
+String unixBinDir = (String) context.getVariable("unixBinDir");
+if (unixBinDir != null && unixBinDir.length() > 0) {
+ if (unixBinDir.startsWith("~/")) {
+ unixBinDir = (String)context.getVariable("sys.userHome") + unixBinDir.substring(1);
+ context.setVariable("unixBinDir", unixBinDir);
+ }
+ return false;
+}
+return true;</condition>
</action>
- <action name="USERSPACE: Set macWrapperLinkLocation (macOS)" id="2745" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <action name="USERSPACE: Set MacOSDir (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;
+String MacOSDir = null;
if (i > -1) {
- wrapperLink = javaHome.substring(0, i) + appName + File.separator + "Contents" + File.separator + "MacOS" + File.separator + ((String)context.getCompilerVariable("WRAPPER_LINK"));
+ MacOSDir = javaHome.substring(0, i) + appName + File.separator + "Contents" + File.separator + "MacOS";
}
-return wrapperLink;
+return MacOSDir;
</property>
</object>
</property>
- <property name="variableName" type="string">macWrapperLinkLocation</property>
+ <property name="variableName" type="string">MacOSDir</property>
</serializedBean>
<condition>Util.isMacOS() && !context.getBooleanVariable("isAdmin") // Admin on macOS will add path to /etc/paths.d in Create File action</condition>
</action>
+ <action name="BOTHSPACE: Set advancedOptions" id="3040" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="onlyIfUndefined" type="boolean" value="true" />
+ <property name="responseFileVariable" type="boolean" value="true" />
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">Boolean.FALSE</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">advancedOptions</property>
+ </serializedBean>
+ </action>
+ <action name="BOTHSPACE: Set allowUserDefaultAppdirUpdates" id="2976" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="onlyIfUndefined" type="boolean" value="true" />
+ <property name="responseFileVariable" type="boolean" value="true" />
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">Boolean.TRUE</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">allowUserDefaultAppdirUpdates</property>
+ </serializedBean>
+ </action>
+ <action name="BOTHSPACE: Set allowSetUserAppdirPath" id="3039" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="onlyIfUndefined" type="boolean" value="true" />
+ <property name="responseFileVariable" type="boolean" value="true" />
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">Boolean.FALSE</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">allowSetUserAppdirPath</property>
+ </serializedBean>
+ </action>
+ <action name="BOTHSPACE: Set userAppdirPath" id="3038" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="onlyIfUndefined" type="boolean" value="true" />
+ <property name="responseFileVariable" type="boolean" value="true" />
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">""</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">userAppdirPath</property>
+ </serializedBean>
+ </action>
+ <action name="BOTHSPACE: Set allowInstallerAppdirUpdates" id="2977" beanClass="com.install4j.runtime.beans.actions.control.SetVariableAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="onlyIfUndefined" type="boolean" value="true" />
+ <property name="responseFileVariable" type="boolean" value="true" />
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">Boolean.FALSE</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">allowInstallerAppdirUpdates</property>
+ </serializedBean>
+ </action>
+ <action name="BOTHSPACE: Set userDefaultAppdirBase for tooltip explanation" id="2981" 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">getOsAppDataPath(context)</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">userDefaultAppdirBase</property>
+ </serializedBean>
+ </action>
+ <action name="BOTHSPACE: Set osName variable for tooltip explanation" id="2982" 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">if (Util.isWindows()) {
+ return "Windows";
+} else if (Util.isMacOS()) {
+ return "macOS";
+} else if (Util.isLinux()) {
+ return "Linux";
+}
+return context.getCompilerVariable("sys.platform");</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">osName</property>
+ </serializedBean>
+ </action>
+ <action name="CONSOLE: Set consoleDisableUserAppdir" id="3075" 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">Boolean.FALSE</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">consoleDisableUserAppdir</property>
+ </serializedBean>
+ </action>
+ <action name="CONSOLE: Set consoleDisableAllUpdates" id="3076" 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">Boolean.FALSE</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">consoleDisableAllUpdates</property>
+ </serializedBean>
+ </action>
+ <action name="CONSOLE: Set consoleAllowUserAppdirPath" id="3077" 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">Boolean.FALSE</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">consoleAllowUserAppdirPath</property>
+ </serializedBean>
+ </action>
+ <action name="Extra Command Line Options" id="3074" beanClass="com.install4j.runtime.beans.actions.control.RunScriptAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">String[] args = context.getExtraCommandLineArguments();
+
+for (int i = 0; i < args.length; i++) {
+ String arg = args[i];
+ switch(arg) {
+ case "-a":
+ if (args.length - 1 < i + 1) {
+ System.out.println("Option " + arg + " requires a value. Ignoring.");
+ }
+ context.setInstallationDirectory(new File(args[i + 1]));
+ i++;
+ break;
+ case "-u":
+ if (args.length - 1 < i + 1) {
+ System.out.println("Option " + arg + " requires a value. Ignoring.");
+ }
+ context.setVariable("userAppdirPath", args[i + 1]);
+ context.setVariable("consoleAllowUserAppdirPath", true);
+ i++;
+ break;
+ case "-U":
+ context.setVariable("consoleDisableUserAppdir", true);
+ break;
+ case "-S":
+ context.setVariable("consoleDisableAllUpdates", true);
+ break;
+ default:
+ System.out.println("Option " + arg + " not recognised. Ignoring.");
+ break;
+ }
+}
+
+return true;</property>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>context.isConsole() || context.isUnattended()</condition>
+ </action>
+ <action name="Set sys.fileAssociation.launchers correctly" id="3080" beanClass="com.install4j.runtime.beans.actions.control.RunScriptAction" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="script">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">String[] extensions = (String[]) context.getVariable("sys.fileAssociation.extensions");
+if (extensions == null) {
+ return false;
+}
+int num = extensions.length;
+String[] launchers = new String[num];
+for (int i = 0; i < num; i++) {
+ launchers[i] = "JALVIEW";
+}
+context.setVariable("sys.fileAssociation.launchers", launchers);
+return true;</property>
+ </object>
+ </property>
+ </serializedBean>
+ </action>
</actions>
</screen>
</startup>
<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">
+ <property name="excludedVariables" type="array" elementType="string" length="5">
<element index="0">sys.installationDir</element>
+ <element index="1">sys.adminRights$Boolean</element>
+ <element index="2">sys.adminRightsUiRootUnix$Boolean</element>
+ <element index="3">sys.component.1031$Boolean</element>
+ <element index="4">sys.fileAssociation.launchers$StringArray</element>
</property>
</serializedBean>
<condition>context.getBooleanVariable("sys.confirmedUpdateInstallation")</condition>
</action>
</actions>
<formComponents>
+ <formComponent name="Administrator mode label" id="3028" beanClass="com.install4j.runtime.beans.formcomponents.MultilineHtmlLabelComponent" insetBottom="16">
+ <serializedBean>
+ <property name="labelHtml" type="string"><strong>Administrator mode</strong></property>
+ </serializedBean>
+ <visibilityScript>context.getBooleanVariable("isAdmin")</visibilityScript>
+ </formComponent>
<formComponent id="3" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent">
<serializedBean>
<property name="labelText" type="string">${form:welcomeMessage}</property>
</formComponent>
</formComponents>
</screen>
- <screen id="8" beanClass="com.install4j.runtime.beans.screens.InstallationDirectoryScreen" rollbackBarrierExitCode="0">
+ <screen id="8" customizedId="LOCATION_SCREEN" beanClass="com.install4j.runtime.beans.screens.InstallationDirectoryScreen" rollbackBarrierExitCode="0">
<condition>!context.getBooleanVariable("sys.confirmedUpdateInstallation")</condition>
<actions>
<action id="11" beanClass="com.install4j.runtime.beans.actions.misc.LoadResponseFileAction" rollbackBarrierExitCode="0" multiExec="true">
<serializedBean>
- <property name="excludedVariables" type="array" elementType="string" length="1">
+ <property name="excludedVariables" type="array" elementType="string" length="5">
<element index="0">sys.installationDir</element>
+ <element index="1">sys.adminRights$Boolean</element>
+ <element index="2">sys.adminRightsUiRootUnix$Boolean</element>
+ <element index="3">sys.component.1031$Boolean</element>
+ <element index="4">sys.fileAssociation.launchers$StringArray</element>
</property>
</serializedBean>
<condition>context.getVariable("sys.responseFile") == null</condition>
</action>
</actions>
<formComponents>
+ <formComponent name="Administrator mode label" id="3057" beanClass="com.install4j.runtime.beans.formcomponents.MultilineHtmlLabelComponent" insetBottom="16">
+ <serializedBean>
+ <property name="labelHtml" type="string"><strong>Administrator mode</strong></property>
+ </serializedBean>
+ <visibilityScript>context.getBooleanVariable("isAdmin")</visibilityScript>
+ </formComponent>
<formComponent id="9" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetBottom="25">
<serializedBean>
<property name="labelText" type="string">${i18n:SelectDirLabel(${compiler:sys.fullName})}</property>
</screen>
<screen id="1692" beanClass="com.install4j.runtime.beans.screens.FileAssociationsScreen" rollbackBarrierExitCode="0">
<formComponents>
+ <formComponent name="Administrator mode label" id="3058" beanClass="com.install4j.runtime.beans.formcomponents.MultilineHtmlLabelComponent" insetBottom="16">
+ <serializedBean>
+ <property name="labelHtml" type="string"><strong>Administrator mode</strong></property>
+ </serializedBean>
+ <visibilityScript>context.getBooleanVariable("isAdmin")</visibilityScript>
+ </formComponent>
<formComponent id="1693" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent">
<serializedBean>
<property name="labelText" type="string">${i18n:SelectAssociationsLabel}</property>
</serializedBean>
</formComponent>
- <formComponent id="1694" beanClass="com.install4j.runtime.beans.formcomponents.FileAssociationsComponent" useExternalParametrization="true" externalParametrizationName="File Associations" externalParametrizationMode="include">
+ <formComponent id="3069" beanClass="com.install4j.runtime.beans.formcomponents.ButtonComponent" enabled="false" commentSet="true" comment="This button is desirable but not working.
The best that can be done is

Screen s = formEnvironment.getScreen();
context.gotoScreen(s);

but this adds extra "File Association" screens into the "Back" history (but not the "Next" stack).">
+ <serializedBean>
+ <property name="actionScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">Screen s = formEnvironment.getScreen();
+
+FormComponent fc = formEnvironment.getFormComponentById("FILE_ASSOCIATIONS_SELECTOR");
+com.install4j.api.actions.Action a0 = context.getActionById("FA_FILEASSOCIATION-CIF-false");
+Screen s2 = context.getScreenById("EXTENSIONS_REPLACED_BY_GRADLE_PARENT_GROUP");
+
+for (com.install4j.api.actions.Action a : context.getActions(s2)) {
+ String aid = context.getId(a);
+ if (aid.startsWith("FA_FILEASSOCIATION-")) {
+ com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction aa = (com.install4j.runtime.beans.actions.desktop.CreateFileAssociationAction) a;
+ boolean set = aid.endsWith("-true");
+ boolean got = aa.isSelected();
+ aa.setSelected(set);
+ System.err.println("Setting '"+aid+"' from "+got+" to "+set);
+ }
+}
+
+context.gotoScreen(s);
+//formEnvironment.reinitializeFormComponents();</property>
+ </object>
+ </property>
+ <property name="buttonText" type="string">Reset</property>
+ </serializedBean>
+ </formComponent>
+ <formComponent id="1694" customizedId="FILE_ASSOCIATIONS_SELECTOR" 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>
+ <propertyName>showSelectionButtons</propertyName>
</externalParametrizationPropertyNames>
</formComponent>
</formComponents>
</screen>
<screen name="USERSPACE: Additional checkboxes" id="2893" beanClass="com.install4j.runtime.beans.screens.FormScreen" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="subTitle" type="string">User account</property>
+ <property name="subTitle" type="string">Additional tasks for user installation (${installer:sys.userName})</property>
<property name="title" type="string">${i18n:WizardSelectTasks}</property>
</serializedBean>
<condition>!context.getBooleanVariable("isAdmin")</condition>
|| Util.isUnixInstaller()
|| (
( Util.isMacOS() && !Util.hasFullAdminRights() ) // Admin on macOS will add path to /etc/paths.d
- && context.getVariable("macWrapperLinkLocation") != null
+ && context.getVariable("MacOSDir") != null
)
)</visibilityScript>
</formComponent>
+ <formComponent id="2983" beanClass="com.install4j.runtime.beans.formcomponents.SpacerComponent" />
+ <formComponent name="Enable ADVANCED OPTIONS" id="3006" customizedId="US_ADVANCED_OPTIONS" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">Enable advanced options for user installation</property>
+ <property name="coupledComponentIds">
+ <add type="string">2980</add>
+ <add type="string">3014</add>
+ <add type="string">2975</add>
+ <add type="string">2989</add>
+ </property>
+ <property name="selectionScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">validateUserSpaceAdvancedOptionsForm(formEnvironment)</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">advancedOptions</property>
+ </serializedBean>
+ </formComponent>
+ <formComponent name="Advanced options not used label" id="3036" customizedId="US_NOT_USED" beanClass="com.install4j.runtime.beans.formcomponents.LabelComponent" insetLeft="20">
+ <serializedBean>
+ <property name="labelColor">
+ <object class="java.awt.Color">
+ <int>128</int>
+ <int>128</int>
+ <int>128</int>
+ <int>255</int>
+ </object>
+ </property>
+ <property name="labelFontSizePercent" type="int" value="80" />
+ <property name="labelFontType" type="enum" class="com.install4j.runtime.beans.formcomponents.FontType" value="DERIVED" />
+ <property name="labelText" type="string">Advanced options will not be used</property>
+ </serializedBean>
+ <visibilityScript>!context.getBooleanVariable("advancedOptions")
+</visibilityScript>
+ </formComponent>
+ <group name="Advanced options (outer) group" id="3035" customizedId="US_ADVANCED_OPTIONS_GROUP" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup">
+ <serializedBean>
+ <property name="visibilityScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">FormComponent fc_advancedOptions = formEnvironment.getFormComponentById("US_ADVANCED_OPTIONS");
+
+JCheckBox jcb_advancedOptions = (JCheckBox) fc_advancedOptions.getConfigurationObject();
+boolean advancedOptions = jcb_advancedOptions.isSelected();
+
+return advancedOptions;</property>
+ </object>
+ </property>
+ </serializedBean>
+ <beans>
+ <group name="Advanced options (boxed) group" id="3034" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup">
+ <serializedBean>
+ <property name="borderSides">
+ <object class="com.install4j.runtime.beans.formcomponents.BorderSides">
+ <property name="bottom" type="boolean" value="true" />
+ <property name="left" type="boolean" value="true" />
+ <property name="right" type="boolean" value="true" />
+ <property name="top" type="boolean" value="true" />
+ </object>
+ </property>
+ <property name="insets">
+ <object class="java.awt.Insets">
+ <int>4</int>
+ <int>4</int>
+ <int>4</int>
+ <int>4</int>
+ </object>
+ </property>
+ </serializedBean>
+ <beans>
+ <formComponent name="Strongly recommended text" id="2980" customizedId="US_LABEL" beanClass="com.install4j.runtime.beans.formcomponents.MultilineHtmlLabelComponent" insetLeft="16">
+ <serializedBean>
+ <property name="labelHtml" type="string"><html>The following option is <strong>strongly recommended</strong>
+to be left as default unless there is a particular
+reason to change it.</html></property>
+ </serializedBean>
+ </formComponent>
+ <formComponent id="3014" customizedId="US_VSPACE" beanClass="com.install4j.runtime.beans.formcomponents.SpacerComponent" insetLeft="16" />
+ <formComponent name="BOTHSPACE: Allow automatic updates in user's home directory" id="2975" customizedId="US_ALLOW_USER_APPDIR_UPDATES" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent" insetLeft="16">
+ <serializedBean>
+ <property name="checkboxText" type="string">Allow user-space updates for ${compiler:JALVIEW_APPLICATION_NAME} components</property>
+ <property name="helpText" type="string"><html>This option allows updates to ${compiler:JALVIEW_APPLICATION_NAME}
+<br>
+components to be automatically downloaded
+<br>
+under the user's home space, separately from
+<br>
+the installation location.
+<br>
+<strong>This option is strongly recommended.</strong>
+<br>
+<br>
+On ${installer:osName}, user updates will be installed under
+<br>
+<pre>${installer:userDefaultAppdirBase}</pre>
+</html></property>
+ <property name="initiallySelected" type="boolean" value="true" />
+ <property name="selectionScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">validateUserSpaceAdvancedOptionsForm(formEnvironment)</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">allowUserDefaultAppdirUpdates</property>
+ </serializedBean>
+ </formComponent>
+ <formComponent name="BOTHSPACE: No updates warning" id="2989" customizedId="US_NO_UPDATES_WARNING" beanClass="com.install4j.runtime.beans.formcomponents.LabelComponent" insetLeft="16">
+ <serializedBean>
+ <property name="labelIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/warning.png</string>
+ </object>
+ </property>
+ <property name="labelText" type="string">No automatic updates will occur when Jalview is launched</property>
+ </serializedBean>
+ <visibilityScript>!( context.getBooleanVariable("allowUserDefaultAppdirUpdates") || context.getBooleanVariable("allowInstallerAppdirUpdates") )</visibilityScript>
+ </formComponent>
+ </beans>
+ </group>
+ </beans>
+ </group>
</formComponents>
</screen>
<screen name="SYSTEMSPACE: Additional checkboxes" id="2903" beanClass="com.install4j.runtime.beans.screens.FormScreen" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="subTitle" type="string">System</property>
+ <property name="subTitle" type="string">Additional tasks for administrator installation</property>
<property name="title" type="string">${i18n:WizardSelectTasks}</property>
</serializedBean>
<condition>context.getBooleanVariable("isAdmin")</condition>
<formComponents>
+ <formComponent name="Administrator mode label" id="3059" beanClass="com.install4j.runtime.beans.formcomponents.MultilineHtmlLabelComponent" insetBottom="16">
+ <serializedBean>
+ <property name="labelHtml" type="string"><strong>Administrator mode</strong></property>
+ </serializedBean>
+ <visibilityScript>context.getBooleanVariable("isAdmin")</visibilityScript>
+ </formComponent>
<formComponent id="2904" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetBottom="10">
<serializedBean>
<property name="labelText" type="string">${i18n:SelectTasksLabel2(${compiler:JALVIEW_APPLICATION_NAME})}</property>
|| Util.isUnixInstaller()
|| (
( Util.isMacOS() && !Util.hasFullAdminRights() ) // Admin on macOS will add path to /etc/paths.d
- && context.getVariable("macWrapperLinkLocation") != null
+ && context.getVariable("MacOSDir") != null
)
)
</visibilityScript>
</formComponent>
+ <formComponent id="2984" beanClass="com.install4j.runtime.beans.formcomponents.SpacerComponent" />
+ <formComponent name="Enable ADVANCED OPTIONS" id="3007" customizedId="SS_ADVANCED_OPTIONS" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">Enable advanced options for system installation</property>
+ <property name="coupledComponentIds">
+ <add type="string">3030</add>
+ <add type="string">2985</add>
+ <add type="string">3013</add>
+ <add type="string">2986</add>
+ <add type="string">2974</add>
+ <add type="string">2988</add>
+ </property>
+ <property name="selectionScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">validateSystemSpaceAdvancedOptionsForm(context, formEnvironment)</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">advancedOptions</property>
+ </serializedBean>
+ </formComponent>
+ <formComponent name="Advanced options not used label" id="3032" customizedId="SS_NOT_USED" beanClass="com.install4j.runtime.beans.formcomponents.LabelComponent" insetLeft="20">
+ <serializedBean>
+ <property name="labelColor">
+ <object class="java.awt.Color">
+ <int>128</int>
+ <int>128</int>
+ <int>128</int>
+ <int>255</int>
+ </object>
+ </property>
+ <property name="labelFontSizePercent" type="int" value="80" />
+ <property name="labelFontType" type="enum" class="com.install4j.runtime.beans.formcomponents.FontType" value="DERIVED" />
+ <property name="labelText" type="string">Advanced options will not be used</property>
+ </serializedBean>
+ <visibilityScript>!context.getBooleanVariable("advancedOptions")
+</visibilityScript>
+ </formComponent>
+ <group name="Advanced options (outer) group" id="3033" customizedId="SS_ADVANCED_OPTIONS_GROUP" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup">
+ <serializedBean>
+ <property name="visibilityScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">context.getBooleanVariable("advancedOptions")
+</property>
+ </object>
+ </property>
+ </serializedBean>
+ <beans>
+ <group name="Advanced options (boxed) group" id="3030" beanClass="com.install4j.runtime.beans.groups.VerticalFormComponentGroup">
+ <serializedBean>
+ <property name="borderSides">
+ <object class="com.install4j.runtime.beans.formcomponents.BorderSides">
+ <property name="bottom" type="boolean" value="true" />
+ <property name="left" type="boolean" value="true" />
+ <property name="right" type="boolean" value="true" />
+ <property name="top" type="boolean" value="true" />
+ </object>
+ </property>
+ <property name="insets">
+ <object class="java.awt.Insets">
+ <int>4</int>
+ <int>4</int>
+ <int>4</int>
+ <int>4</int>
+ </object>
+ </property>
+ <property name="visibilityScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string" />
+ </object>
+ </property>
+ </serializedBean>
+ <beans>
+ <formComponent name="Strongly recommended text" id="2985" customizedId="SS_LABEL" beanClass="com.install4j.runtime.beans.formcomponents.MultilineHtmlLabelComponent" insetLeft="16">
+ <serializedBean>
+ <property name="labelHtml" type="string"><html>The following options are <strong>strongly recommended</strong> to be left as default unless there is a particular reason to change them.</html></property>
+ </serializedBean>
+ </formComponent>
+ <formComponent id="3013" customizedId="SS_VSPACE" beanClass="com.install4j.runtime.beans.formcomponents.SpacerComponent" insetLeft="16" />
+ <formComponent name="BOTHSPACE: Allow automatic updates in user's home directory" id="2986" customizedId="SS_ALLOW_USER_APPDIR_UPDATES" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent" insetLeft="16">
+ <serializedBean>
+ <property name="checkboxText" type="string">Allow user-space updates for ${compiler:JALVIEW_APPLICATION_NAME} components</property>
+ <property name="coupledComponentIds">
+ <add type="string">3021</add>
+ </property>
+ <property name="helpText" type="string"><html>This option allows updates to ${compiler:JALVIEW_APPLICATION_NAME}
+<br>
+components to be automatically downloaded
+<br>
+under the user's home space, separately from
+<br>
+the installation location.
+<br>
+<strong>This option is strongly recommended.</strong>
+<br>
+<br>
+On ${installer:osName}, user updates will be installed under
+<pre>${installer:userDefaultAppdirBase}</pre>
+unless customised below.
+</html></property>
+ <property name="selectionScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">validateSystemSpaceAdvancedOptionsForm(context, formEnvironment)</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">allowUserDefaultAppdirUpdates</property>
+ </serializedBean>
+ </formComponent>
+ <group name="SYSTEMSPACE: Customise user appDir path" id="3021" customizedId="SS_SET_USER_APPDIR_PATH" beanClass="com.install4j.runtime.beans.groups.HorizontalFormComponentGroup">
+ <serializedBean>
+ <property name="insets">
+ <object class="java.awt.Insets">
+ <int>0</int>
+ <int>32</int>
+ <int>0</int>
+ <int>0</int>
+ </object>
+ </property>
+ <property name="visibilityScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string" />
+ </object>
+ </property>
+ </serializedBean>
+ <beans>
+ <formComponent name="SYSTEMSPACE: Allow setting userAppdirPath" id="3022" customizedId="SS_ALLOW_USER_APPDIR_PATH" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent">
+ <serializedBean>
+ <property name="checkboxText" type="string">Customise the user-space path</property>
+ <property name="selectionScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">validateSystemSpaceAdvancedOptionsForm(context, formEnvironment)</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">allowSetUserAppdirPath</property>
+ </serializedBean>
+ <initScript>component.setEnabled( context.getBooleanVariable("allowUserDefaultAppdirUpdates") )</initScript>
+ </formComponent>
+ <formComponent name="SYSTEMSPACE: Set userAppdirPath" id="3024" customizedId="SS_USER_APPDIR_PATH" beanClass="com.install4j.runtime.beans.formcomponents.TextfieldComponent">
+ <serializedBean>
+ <property name="helpText" type="string"><html>The base path where individual users' updates
+<br>
+will be stored.
+<br>
+<strong>Only change this option if you need to!</strong>
+<br>
+The following substitutions will be made:
+<table>
+<tr><td>%u</td><td>The user's username</td></tr>
+<tr><td>%h</td><td>The user's home directory path</td></tr>
+<tr><td>~${installer:sys.fileSeparator}</td><td>(at start) The user's home directory path${installer:sys.fileSeparator}</td></tr>
+</table>
+At least one of the above substitutions should be
+<br>
+used, e.g. <tt>/tmp/${compiler:UNIX_APPLICATION_FOLDER}/%u/app</tt>
+<br>
+The default value on ${installer:osName} is
+<br>
+<pre>${installer:userDefaultAppdirBase}</pre>
+</html></property>
+ <property name="inputVerifier">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">validateSystemSpaceAdvancedOptionsForm(context, formEnvironment, true)</property>
+ </object>
+ </property>
+ <property name="keyListener">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">showInvalidUserAppdirPathWarning(context, formEnvironment)
+</property>
+ </object>
+ </property>
+ <property name="keyValidator">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string" />
+ </object>
+ </property>
+ <property name="variableName" type="string">userAppdirPath</property>
+ </serializedBean>
+ <initScript>component.setEnabled( context.getBooleanVariable("allowUserDefaultAppdirUpdates") && context.getBooleanVariable("allowSetUserAppdirPath") );
+</initScript>
+ </formComponent>
+ </beans>
+ </group>
+ <formComponent name="SYSTEMSPACE: Allow automatic updates in the installation directory" id="2974" customizedId="SS_ALLOW_INSTALLER_APPDIR_UPDATES" beanClass="com.install4j.runtime.beans.formcomponents.CheckboxComponent" insetLeft="16">
+ <serializedBean>
+ <property name="checkboxText" type="string">Allow installation updates for ${compiler:JALVIEW_APPLICATION_NAME} components</property>
+ <property name="helpText" type="string"><html>This option allows updates to ${compiler:JALVIEW_APPLICATION_NAME}
+<br>
+components to be automatically downloaded
+<br>
+into the installation location.
+<br>
+If you are installing into a system location,
+<br>
+a non-administrator user may have problems
+<br>
+launching ${compiler:JALVIEW_APPLICATION_NAME}.
+<br>
+<strong>
+It is strongly recommended to use the
+<br>
+user-space updates option above.
+</strong>
+<br>
+<br>
+Installation updates will be installed into
+<br>
+<pre>${installer:sys.contentDir}</pre>
+</html></property>
+ <property name="selectionScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">validateSystemSpaceAdvancedOptionsForm(context, formEnvironment)</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">allowInstallerAppdirUpdates</property>
+ </serializedBean>
+ <initScript>component.setEnabled( !context.getBooleanVariable("allowUserDefaultAppdirUpdates") )</initScript>
+ </formComponent>
+ <formComponent name="Set defaults" id="3029" customizedId="SS_SET_DEFAULTS" beanClass="com.install4j.runtime.beans.formcomponents.ButtonComponent" insetTop="8" insetLeft="16">
+ <serializedBean>
+ <property name="actionScript">
+ <object class="com.install4j.api.beans.ScriptProperty">
+ <property name="value" type="string">FormComponent fc_userUpdates = formEnvironment.getFormComponentById("SS_ALLOW_USER_APPDIR_UPDATES");
+FormComponent fc_installerUpdates = formEnvironment.getFormComponentById("SS_ALLOW_INSTALLER_APPDIR_UPDATES");
+FormComponent fc_allowUserAppdirPath = formEnvironment.getFormComponentById("SS_ALLOW_USER_APPDIR_PATH");
+FormComponent fc_userAppdirPath = formEnvironment.getFormComponentById("SS_USER_APPDIR_PATH");
+
+// set defaults
+((JCheckBox) fc_userUpdates.getConfigurationObject()).setSelected(true);
+((JCheckBox) fc_allowUserAppdirPath.getConfigurationObject()).setSelected(false);
+((JTextField) fc_userAppdirPath.getConfigurationObject()).setText("");
+((JCheckBox) fc_installerUpdates.getConfigurationObject()).setSelected(false);
+
+// revalidate
+validateSystemSpaceAdvancedOptionsForm(context, formEnvironment);
+</property>
+ </object>
+ </property>
+ <property name="buttonText" type="string">Reset advanced options to defaults</property>
+ </serializedBean>
+ <initScript>FormComponent fc_advancedOptions = formEnvironment.getFormComponentById("SS_ADVANCED_OPTIONS");
+FormComponent fc_userUpdates = formEnvironment.getFormComponentById("SS_ALLOW_USER_APPDIR_UPDATES");
+FormComponent fc_userAppdirPath = formEnvironment.getFormComponentById("SS_USER_APPDIR_PATH");
+FormComponent fc_installerUpdates = formEnvironment.getFormComponentById("SS_ALLOW_INSTALLER_APPDIR_UPDATES");
+FormComponent fc_allowUserAppdirPath = formEnvironment.getFormComponentById("SS_ALLOW_USER_APPDIR_PATH");
+
+JCheckBox jcb_user = (JCheckBox) fc_userUpdates.getConfigurationObject();
+boolean userUpdates = jcb_user.isSelected();
+
+JCheckBox jcb_allowUserAppdirPath = (JCheckBox) fc_allowUserAppdirPath.getConfigurationObject();
+boolean allowUserAppdirPath = jcb_allowUserAppdirPath.isSelected();
+
+JTextField jtf_userAppdirPath = (JTextField) fc_userAppdirPath.getConfigurationObject();
+String userAppdirPath = jtf_userAppdirPath.getText();
+
+JCheckBox jcb_installer = (JCheckBox) fc_installerUpdates.getConfigurationObject();
+boolean installerUpdates = jcb_installer.isSelected();
+
+
+// set whether "Set defaults" button should be enabled
+boolean enableSetDefaults = !( userUpdates && !allowUserAppdirPath && userAppdirPath.length() == 0 && !installerUpdates );
+component.setEnabled(enableSetDefaults);</initScript>
+ </formComponent>
+ <formComponent name="BOTHSPACE: No updates warning" id="2988" customizedId="SS_NO_UPDATES_WARNING" beanClass="com.install4j.runtime.beans.formcomponents.LabelComponent" insetLeft="16">
+ <serializedBean>
+ <property name="labelIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/warning.png</string>
+ </object>
+ </property>
+ <property name="labelText" type="string">No automatic updates will occur when ${compiler:JALVIEW_APPLICATION_NAME} is launched</property>
+ </serializedBean>
+ <visibilityScript>!( context.getBooleanVariable("allowUserDefaultAppdirUpdates") || context.getBooleanVariable("allowInstallerAppdirUpdates") )</visibilityScript>
+ </formComponent>
+ <formComponent name="SYSTEMSPACE: Invalid user-space path warning" id="3027" customizedId="SS_INVALID_USER_APPDIR_PATH_WARNING" beanClass="com.install4j.runtime.beans.formcomponents.LabelComponent" insetLeft="16">
+ <serializedBean>
+ <property name="labelIconFile">
+ <object class="com.install4j.api.beans.ExternalFile">
+ <string>${compiler:JALVIEW_DIR}/${compiler:INSTALL4J_UTILS_DIR}/warning.png</string>
+ </object>
+ </property>
+ <property name="labelText" type="string">The user-space path should contain one of "~${installer:sys.fileSeparator}" (at the start), "%u" or "%h"</property>
+ </serializedBean>
+ <visibilityScript>String userAppdirPath = (String) context.getVariable("userAppdirPath");
+
+if (userAppdirPath == null) {
+ return false;
+}
+
+boolean u = userAppdirPath.contains("%u");
+boolean h = userAppdirPath.contains("%h");
+boolean t = userAppdirPath.startsWith("~" + (String)context.getVariable("sys.fileSeparator"));
+
+boolean showInvalidPathWarning = !( userAppdirPath.length() == 0 || u || h || t );
+
+return context.getBooleanVariable("allowUserDefaultAppdirUpdates") && context.getBooleanVariable("allowSetUserAppdirPath") && showInvalidPathWarning;</visibilityScript>
+ </formComponent>
+ </beans>
+ </group>
+ </beans>
+ </group>
</formComponents>
</screen>
- <screen id="15" beanClass="com.install4j.runtime.beans.screens.InstallationScreen" rollbackBarrier="true" rollbackBarrierExitCode="0">
+ <screen id="15" customizedId="INSTALLATION" beanClass="com.install4j.runtime.beans.screens.InstallationScreen" rollbackBarrier="true" rollbackBarrierExitCode="0">
<actions>
<action id="17" beanClass="com.install4j.runtime.beans.actions.InstallFilesAction" rollbackBarrierExitCode="0" failureStrategy="quit" errorMessage="${i18n:FileCorrupted}" />
<action name="Create program group (RELEASE)" id="18" customizedId="PROGRAM_GROUP_RELEASE" beanClass="com.install4j.runtime.beans.actions.desktop.CreateProgramGroupAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<property name="itemName" type="string">${compiler:sys.fullName} ${compiler:sys.version}</property>
</serializedBean>
</action>
- <group name="File Associations" id="2251" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
+ <group name="File Associations" id="2251" customizedId="FA_SCREEN" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
<beans>
<action id="2253" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
</action>
<action id="2541" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
- <property name="percentValue" type="int" value="100" />
+ <property name="percentValue" type="int" value="99" />
</serializedBean>
</action>
</beans>
</group>
+ <action id="3017" beanClass="com.install4j.runtime.beans.actions.control.SetMessageAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="statusMessage" type="string">${i18n:FinishedHeadingLabel(${compiler:JALVIEW_APPLICATION_NAME})}</property>
+ <property name="useDetail" type="boolean" value="true" />
+ <property name="useStatus" type="boolean" value="true" />
+ </serializedBean>
+ </action>
+ <action id="3018" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="progressChangeType" type="enum" class="com.install4j.runtime.beans.actions.control.ProgressChangeType" value="SET_INDETERMINATE" />
+ </serializedBean>
+ </action>
<group name="Register URL Handlers" id="2957" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
<beans>
<action id="2350" beanClass="com.install4j.runtime.beans.actions.desktop.UrlHandlerAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
</property>
</serializedBean>
<beans>
- <action name="USERSPACE: Create start menu item" id="2916" beanClass="com.install4j.runtime.beans.actions.desktop.CreateStartMenuEntryAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <action name="USERSPACE: Create Start Menu item" id="2916" beanClass="com.install4j.runtime.beans.actions.desktop.CreateStartMenuEntryAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
<property name="allUsers" type="boolean" value="false" />
<property name="categories" type="string">${compiler:APPLICATION_CATEGORIES}</property>
</object>
</property>
</serializedBean>
- <condition>!Util.hasFullAdminRights() && !context.getBooleanVariable("sys.programGroupDisabled")</condition>
+ <condition>!context.getBooleanVariable("sys.programGroupDisabled")</condition>
</action>
<action name="USERSPACE: Add a desktop link" id="2917" beanClass="com.install4j.runtime.beans.actions.desktop.CreateDesktopLinkAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not make desktop link">
<serializedBean>
</object>
</property>
</serializedBean>
- <condition>!Util.hasFullAdminRights() && context.getBooleanVariable("createDesktopLinkAction")</condition>
+ <condition>context.getBooleanVariable("createDesktopLinkAction")</condition>
</action>
<action name="USERSPACE: Add an executable to the dock (macOS)" id="2918" beanClass="com.install4j.runtime.beans.actions.desktop.AddToDockAction" actionElevationType="none" rollbackBarrierExitCode="0">
<serializedBean>
</object>
</property>
</serializedBean>
- <condition>!Util.hasFullAdminRights()
-&&
-context.getBooleanVariable("addToDockAction")</condition>
+ <condition>context.getBooleanVariable("addToDockAction")</condition>
</action>
<action name="USERSPACE: Add Jalview bin to the user's path (Windows)" id="2919" beanClass="com.install4j.runtime.beans.actions.misc.ModifyEnvironmentVariableAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not add "${installer:sys.contentDir}\${compiler:WRAPPER_SCRIPT_BIN_DIR}" to the Path environment variable">
<serializedBean>
<property name="value" type="string">${installer:sys.contentDir}\${compiler:WRAPPER_SCRIPT_BIN_DIR}</property>
<property name="variableName" type="string">Path</property>
</serializedBean>
- <condition>!Util.hasFullAdminRights() && context.getBooleanVariable("appendToPathAction")</condition>
+ <condition>context.getBooleanVariable("appendToPathAction")</condition>
</action>
- <action name="USERSPACE: Create macOS symbolic link to jalview in user's local bin" id="2920" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixBinDir}">
+ <action name="USERSPACE: Create macOS symbolic link to jalview.sh" id="2920" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:MacOSDir}">
<serializedBean>
<property name="file">
<object class="java.io.File">
- <string>${installer:macWrapperLinkLocation}</string>
+ <string>../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_WRAPPER_SCRIPT}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${installer:MacOSDir}/${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>Util.isMacOS() &&
+(
+ context.getBooleanVariable("makeSymbolicLinkAction")
+ && context.getVariable("unixBinDir") != null
+ && context.getVariable("MacOSDir") != null
+)</condition>
+ </action>
+ <action name="USERSPACE: Create macOS symbolic link to update.sh" id="3052" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:MacOSDir}">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_UPDATE_SCRIPT}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${installer:MacOSDir}/update_${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>Util.isMacOS() &&
+(
+ context.getBooleanVariable("makeSymbolicLinkAction")
+ && context.getVariable("unixBinDir") != null
+ && context.getVariable("MacOSDir") != null
+)</condition>
+ </action>
+ <action name="USERSPACE: Create macOS symbolic link to jalview in user's local bin" id="3048" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixBinDir}">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${installer:MacOSDir}/${compiler:WRAPPER_LINK}</string>
</object>
</property>
<property name="linkFile">
</object>
</property>
</serializedBean>
- <condition>Util.isMacOS() && !Util.hasFullAdminRights() // Admin on macOS will add path to /etc/paths.d
-&&
+ <condition>Util.isMacOS() &&
(
context.getBooleanVariable("makeSymbolicLinkAction")
&& context.getVariable("unixBinDir") != null
- && context.getVariable("macWrapperLinkLocation") != null
+ && context.getVariable("MacOSDir") != null
+)</condition>
+ </action>
+ <action name="USERSPACE: Create macOS symbolic link to jalview_update in user's local bin" id="3049" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixBinDir}">
+ <serializedBean>
+ <property name="file">
+ <object class="java.io.File">
+ <string>${installer:MacOSDir}/update_${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ <property name="linkFile">
+ <object class="java.io.File">
+ <string>${installer:unixBinDir}/update_${compiler:WRAPPER_LINK}</string>
+ </object>
+ </property>
+ </serializedBean>
+ <condition>Util.isMacOS() &&
+(
+ context.getBooleanVariable("makeSymbolicLinkAction")
+ && context.getVariable("unixBinDir") != null
+ && context.getVariable("MacOSDir") != null
)</condition>
</action>
</beans>
</property>
</serializedBean>
<beans>
- <action name="SYSTEMSPACE: Create start menu item" id="2950" beanClass="com.install4j.runtime.beans.actions.desktop.CreateStartMenuEntryAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <action name="SYSTEMSPACE: Create Start Menu item" id="2950" beanClass="com.install4j.runtime.beans.actions.desktop.CreateStartMenuEntryAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
<property name="categories" type="string">${compiler:APPLICATION_CATEGORIES}</property>
<property name="entryName" type="string">${compiler:JALVIEW_APPLICATION_NAME}</property>
</serializedBean>
<condition>context.getBooleanVariable("createDesktopLinkAction")</condition>
</action>
- <action name="SYSTEMSPACE: Add Jalview bin to the user's path (Windows)" id="2952" beanClass="com.install4j.runtime.beans.actions.misc.ModifyEnvironmentVariableAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not add "${installer:sys.contentDir}\${compiler:WRAPPER_SCRIPT_BIN_DIR}" to the Path environment variable">
+ <action name="SYSTEMSPACE: Add Jalview bin to the system path (Windows)" id="2952" beanClass="com.install4j.runtime.beans.actions.misc.ModifyEnvironmentVariableAction" actionElevationType="elevated" rollbackBarrierExitCode="0" errorMessage="Could not add "${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="userSpecific" type="boolean" value="false" />
</serializedBean>
<condition>context.getBooleanVariable("appendToPathAction")</condition>
</action>
+ <action name="SYSTEMSPACE: Set installationAppdirHash" id="3041" 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 dir = (String)context.getVariable("sys.installationDir");
+String hash = getCanonicalFullPathToDirectoryHash(dir);
+return (Object) hash;
+</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">installationAppdirHash</property>
+ </serializedBean>
+ </action>
<action name="SYSTEMSPACE: macOS /etc/paths.d entry" id="2953" beanClass="com.install4j.runtime.beans.actions.text.WriteTextFileAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
<serializedBean>
<property name="file">
<object class="java.io.File">
- <string>/etc/paths.d/${compiler:APPLICATION_FOLDER}</string>
+ <string>/etc/paths.d/${compiler:APPLICATION_FOLDER}-${installer:installationAppdirHash}</string>
</object>
</property>
- <property name="text" type="string">/Applications/${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS</property>
+ <property name="text" type="string">${installer:sys.installationDir}/${installer:sys.contentDir}/${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS</property>
</serializedBean>
<condition>Util.isMacOS()</condition>
</action>
</group>
<group name="BOTHSPACE: Actions" id="2956" beanClass="com.install4j.runtime.beans.groups.ActionGroup" actionElevationType="elevated">
<beans>
- <action name="BOTHSPACE: Create Linux/Unix user symbolic link to jalview.sh in system bin" id="2955" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixBinDir}">
+ <action name="BOTHSPACE: Create Linux/Unix user symbolic link to jalview.sh in system/user bin" id="2955" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make a ${compiler:WRAPPER_LINK} symbolic link in ~/${installer:unixBinDir}">
<serializedBean>
<property name="file">
<object class="java.io.File">
</action>
</beans>
</group>
+ <group name="USER/SYSTEMSPACE: VMOPTIONS Getdown update properties" id="3000" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
+ <beans>
+ <action name="Set disableUserDefaultAppdirUpdates" id="3011" 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">boolean advanced = context.getBooleanVariable("advancedOptions");
+boolean allowUser = context.getBooleanVariable("allowUserDefaultAppdirUpdates");
+boolean consoleDisableUserAppdir = context.getBooleanVariable("consoleDisableUserAppdir");
+if (consoleDisableUserAppdir) {
+ return true;
+}
+return advanced ? !allowUser : false;</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">disableUserDefaultAppdirUpdates</property>
+ </serializedBean>
+ </action>
+ <action name="Set setUserAppdirPath" id="3025" 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">boolean advanced = context.getBooleanVariable("advancedOptions");
+boolean allowUser = context.getBooleanVariable("allowUserDefaultAppdirUpdates");
+boolean allowSetUserAppdirPath = context.getBooleanVariable("allowSetUserAppdirPath");
+String userAppdirPath = (String)context.getVariable("userAppdirPath");
+boolean saneValue = userAppdirPath != null && userAppdirPath.length() > 0;
+boolean consoleAllowUserAppdirPath = context.getBooleanVariable("consoleAllowUserAppdirPath");
+if (consoleAllowUserAppdirPath && saneValue) {
+ return userAppdirPath;
+}
+return advanced && allowUser && allowSetUserAppdirPath && saneValue ? userAppdirPath : null;</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">setUserAppdirPath</property>
+ </serializedBean>
+ </action>
+ <action name="Set disableUpdates" id="3012" 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">boolean advanced = context.getBooleanVariable("advancedOptions");
+boolean allowUser = context.getBooleanVariable("allowUserDefaultAppdirUpdates");
+boolean allowInstaller = context.getBooleanVariable("allowInstallerAppdirUpdates");
+boolean consoleDisableAllUpdates = context.getBooleanVariable("consoleDisableAllUpdates");
+if (consoleDisableAllUpdates) {
+ return true;
+}
+return advanced ? !( allowUser || allowInstaller ) : false;</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">disableUpdates</property>
+ </serializedBean>
+ </action>
+ <action name="Set installerFilename" id="3043" 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 file = (String)context.getVariable("sys.mediaFile");
+int i = file.lastIndexOf(File.separator);
+return file.substring(i+1);</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">installerFilename</property>
+ </serializedBean>
+ </action>
+ <action name="Set installDateTime" id="3044" 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 date = (String)context.getVariable("sys.date");
+String time = (String)context.getVariable("sys.time");
+StringBuilder sb = new StringBuilder();
+sb.append(date.substring(0,4));
+sb.append("-");
+sb.append(date.substring(4,6));
+sb.append("-");
+sb.append(date.substring(6,8));
+sb.append(" ");
+sb.append(time.substring(0,2));
+sb.append(":");
+sb.append(time.substring(2,4));
+sb.append(":");
+sb.append(time.substring(4,6));
+return sb.toString();
+</property>
+ </object>
+ </property>
+ <property name="variableName" type="string">installDateTime</property>
+ </serializedBean>
+ </action>
+ <action name="Initial comment" id="3010" beanClass="com.install4j.runtime.beans.actions.misc.AddVmOptionsAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">2823</property>
+ <property name="vmOptions" type="array" elementType="string" length="1">
+ <element index="0"># Jalview options added by ${installer:installerFilename} at ${installer:installDateTime}</element>
+ </property>
+ </serializedBean>
+ </action>
+ <action name="Allow user-space updates" id="2996" beanClass="com.install4j.runtime.beans.actions.misc.AddVmOptionsAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">2823</property>
+ <property name="vmOptions" type="array" elementType="string" length="3">
+ <element index="0"># </element>
+ <element index="1"># Uncomment the following line to disable user-space updates</element>
+ <element index="2">#-Dnouserdefaultappdir=true</element>
+ </property>
+ </serializedBean>
+ <condition>!context.getBooleanVariable("disableUserDefaultAppdirUpdates")</condition>
+ </action>
+ <action name="Disable user-space updates" id="2997" beanClass="com.install4j.runtime.beans.actions.misc.AddVmOptionsAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">2823</property>
+ <property name="vmOptions" type="array" elementType="string" length="3">
+ <element index="0"># </element>
+ <element index="1"># Comment out the following line to allow user-space updates</element>
+ <element index="2">-Dnouserdefaultappdir=true</element>
+ </property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("disableUserDefaultAppdirUpdates")</condition>
+ </action>
+ <action name="Set setUserAppdirPath property" id="3026" beanClass="com.install4j.runtime.beans.actions.misc.AddVmOptionsAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">2823</property>
+ <property name="vmOptions" type="array" elementType="string" length="5">
+ <element index="0"># </element>
+ <element index="1"># The below line sets a custom path for user-space updates -- use with caution.</element>
+ <element index="2"># A leading ~/ or %h anywhere will be substituted with the user's home path, and %u by the username.</element>
+ <element index="3"># If unset, the default is ${installer:userDefaultAppdirBase} for ${installer:osName}</element>
+ <element index="4">-Dsetuserappdirpath=${installer:setUserAppdirPath}</element>
+ </property>
+ </serializedBean>
+ <condition>(String)context.getVariable("setUserAppdirPath") != null</condition>
+ </action>
+ <action name="Don't set setUserAppdirPath property" id="3037" beanClass="com.install4j.runtime.beans.actions.misc.AddVmOptionsAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">2823</property>
+ <property name="vmOptions" type="array" elementType="string" length="5">
+ <element index="0"># </element>
+ <element index="1"># Uncomment the below line to set a custom path for user-space updates -- use with caution.</element>
+ <element index="2"># A leading ~/ or %h anywhere will be substituted with the user's home path, and %u by the username.</element>
+ <element index="3"># If not set, the default is ${installer:userDefaultAppdirBase} for ${installer:osName}</element>
+ <element index="4">#-Dsetuserappdirpath=/tmp/jalview/%u</element>
+ </property>
+ </serializedBean>
+ <condition>(String)context.getVariable("setUserAppdirPath") == null</condition>
+ </action>
+ <action name="Allow updates" id="2998" beanClass="com.install4j.runtime.beans.actions.misc.AddVmOptionsAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">2823</property>
+ <property name="vmOptions" type="array" elementType="string" length="3">
+ <element index="0"># </element>
+ <element index="1"># Uncomment the following line to also disable all updates</element>
+ <element index="2">#-Dsilent=noupdate </element>
+ </property>
+ </serializedBean>
+ <condition>!context.getBooleanVariable("disableUpdates")</condition>
+ </action>
+ <action name="Disable updates" id="2999" beanClass="com.install4j.runtime.beans.actions.misc.AddVmOptionsAction" actionElevationType="elevated" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="launcherId" type="string">2823</property>
+ <property name="vmOptions" type="array" elementType="string" length="3">
+ <element index="0"># </element>
+ <element index="1"># Comment out the following line to enable updates</element>
+ <element index="2">-Dsilent=noupdate</element>
+ </property>
+ </serializedBean>
+ <condition>context.getBooleanVariable("disableUpdates")</condition>
+ </action>
+ </beans>
+ </group>
<group name="Java bin symlinks" id="2944" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
<beans>
<action name="macOS/Linux Jalview->java symlink" id="2942" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make symlink to wrapper script">
</property>
<property name="removeOnUninstall" type="boolean" value="false" />
</serializedBean>
- <condition>Util.isLinux() || Util.isMacOS()</condition>
+ <condition>Util.isLinux() || ( Util.isMacOS() && !Util.isUnixInstaller() )</condition>
</action>
<action name="macOS/Linux Jalview Appname->java symlink" id="2943" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make symlink to wrapper script">
<serializedBean>
</property>
<property name="removeOnUninstall" type="boolean" value="false" />
</serializedBean>
- <condition>(Util.isLinux() || Util.isMacOS())
+ <condition>( Util.isLinux() || ( Util.isMacOS() && !Util.isUnixInstaller() ) )
&& !((String)context.getCompilerVariable("JALVIEW_APPLICATION_NAME")).equals((String)context.getCompilerVariable("JALVIEW_NAME"))</condition>
</action>
</beans>
</group>
<group name="Jalview bin symlink" id="2946" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
<beans>
- <action name="Linux/Unix Jalview bin dir symlink" id="2945" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make symlink to wrapper script">
+ <action name="Linux/Unix jalview.sh bin dir symlink" id="2945" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make symlink to wrapper script">
<serializedBean>
<property name="file">
<object class="java.io.File">
</serializedBean>
<condition>Util.isLinux() || Util.isUnixInstaller() || Util.isMacOS()</condition>
</action>
- </beans>
- </group>
- <group name="Windows scripts" id="2949" beanClass="com.install4j.runtime.beans.groups.ActionGroup">
- <beans>
- <action name="Windows copy BAT file" id="2947" beanClass="com.install4j.runtime.beans.actions.files.CopyFileAction" rollbackBarrierExitCode="0">
+ <action name="Linux/Unix update.sh bin dir symlink" id="3079" beanClass="com.install4j.runtime.beans.actions.files.CreateSymlinkAction" rollbackBarrierExitCode="0" errorMessage="Could not make symlink to wrapper script">
<serializedBean>
- <property name="destinationFile">
+ <property name="file">
<object class="java.io.File">
- <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:WRAPPER_LINK}.bat</string>
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_UPDATE_SCRIPT}</string>
</object>
</property>
- <property name="files" type="array" class="java.io.File" length="1">
- <element index="0">
- <object class="java.io.File">
- <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BATCH_WRAPPER_SCRIPT}</string>
- </object>
- </element>
- </property>
- </serializedBean>
- <condition>Util.isWindows() && !(((String)context.getCompilerVariable("WRAPPER_LINK")+".bat").equals((String)context.getCompilerVariable("BATCH_WRAPPER_SCRIPT")))</condition>
- </action>
- <action name="Windows copy PS1 file" id="2948" beanClass="com.install4j.runtime.beans.actions.files.CopyFileAction" rollbackBarrierExitCode="0">
- <serializedBean>
- <property name="destinationFile">
+ <property name="linkFile">
<object class="java.io.File">
- <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:WRAPPER_LINK}.ps1</string>
+ <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:WRAPPER_LINK}_update</string>
</object>
</property>
- <property name="files" type="array" class="java.io.File" length="1">
- <element index="0">
- <object class="java.io.File">
- <string>${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:POWERSHELL_WRAPPER_SCRIPT}</string>
- </object>
- </element>
- </property>
</serializedBean>
- <condition>Util.isWindows() && !(((String)context.getCompilerVariable("WRAPPER_LINK")+".ps1").equals((String)context.getCompilerVariable("POWERSHELL_WRAPPER_SCRIPT")))</condition>
+ <condition>Util.isLinux() || Util.isUnixInstaller() || Util.isMacOS()</condition>
</action>
</beans>
</group>
+ <action id="3020" beanClass="com.install4j.runtime.beans.actions.control.SetProgressAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="percentValue" type="int" value="100" />
+ </serializedBean>
+ </action>
+ <action id="3065" beanClass="com.install4j.runtime.beans.actions.control.SleepAction" actionElevationType="none" rollbackBarrierExitCode="0">
+ <serializedBean>
+ <property name="sleepTimeMs" type="int" value="250" />
+ </serializedBean>
+ </action>
</actions>
<formComponents>
+ <formComponent name="Administrator mode label" id="3061" beanClass="com.install4j.runtime.beans.formcomponents.MultilineHtmlLabelComponent" insetBottom="16">
+ <serializedBean>
+ <property name="labelHtml" type="string"><strong>Administrator mode</strong></property>
+ </serializedBean>
+ <visibilityScript>context.getBooleanVariable("isAdmin")</visibilityScript>
+ </formComponent>
<formComponent id="16" beanClass="com.install4j.runtime.beans.formcomponents.ProgressComponent">
<serializedBean>
<property name="initialStatusMessage" type="string">${i18n:WizardPreparing}</property>
</screen>
<screen id="20" beanClass="com.install4j.runtime.beans.screens.FinishedScreen" rollbackBarrierExitCode="0" finishScreen="true">
<formComponents>
+ <formComponent name="Administrator mode label" id="3060" beanClass="com.install4j.runtime.beans.formcomponents.MultilineHtmlLabelComponent" insetBottom="16">
+ <serializedBean>
+ <property name="labelHtml" type="string"><strong>Administrator mode</strong></property>
+ </serializedBean>
+ <visibilityScript>context.getBooleanVariable("isAdmin")</visibilityScript>
+ </formComponent>
<formComponent id="21" beanClass="com.install4j.runtime.beans.formcomponents.MultilineLabelComponent" insetBottom="10">
<serializedBean>
<property name="labelText" type="string">${form:finishedMessage}</property>
( Util.isLinux()
|| Util.isUnixInstaller()
|| ( Util.isMacOS()
- && context.getVariable("macWrapperLinkLocation") != null
+ && context.getVariable("MacOSDir") != null
)
)
&& context.getVariable("unixBinDir") != null</visibilityScript>
</serializedBean>
<beans>
<formComponent id="38" beanClass="com.install4j.runtime.beans.styles.ContentComponent" insetTop="10" insetLeft="20" insetBottom="10" insetRight="20" />
- <formComponent name="Watermark" id="39" beanClass="com.install4j.runtime.beans.formcomponents.SeparatorComponent" insetTop="0" insetLeft="5" insetBottom="0" useExternalParametrization="true" externalParametrizationName="${compiler:JALVIEW_APPLICATION_NAME}" externalParametrizationMode="include">
+ <formComponent name="Watermark" id="39" beanClass="com.install4j.runtime.beans.formcomponents.SeparatorComponent" insetTop="0" insetLeft="5" insetBottom="0" useExternalParametrization="true" externalParametrizationMode="include">
<serializedBean>
<property name="enabledTitleText" type="boolean" value="false" />
</serializedBean>
<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}" />
+ <symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/${compiler:WRAPPER_LINK}_update" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_UPDATE_SCRIPT}" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/app/jre/Contents/Home/bin/${compiler:JALVIEW_APPLICATION_NAME}" target="java" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/app/jre/Contents/Home/bin/${compiler:JALVIEW_NAME}" target="java" />
<file name=".VolumeIcon.icns" file="${compiler:JALVIEW_DIR}/${compiler:MACOSARCHIVE_VOLUMEICON}" />
+ <file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/vmoptions.txt" file="${compiler:JALVIEW_DIR}/${compiler:BUILD_DIR}/tmp/default.vmoptions.X64" />
+ <file name=".jalview/build_properties" file="${compiler:JALVIEW_DIR}/build/resources/resources_build/.build_properties" />
+ <file name=".jalview/channel.props" file="${compiler:JALVIEW_DIR}/build/resources/resources_build/channel.props" />
</topLevelFiles>
</macosArchive>
<macosArchive name="macOS (Apple Silicon) Disk Image" id="2796" customizedId="MACOS-AARCH64-DMG" mediaFileName="${compiler:MACOSARCHIVE_AARCH64_DMG_FILENAME}" volumeName="${compiler:MACOSARCHIVE_AARCH64_NAME}" architecture="aarch64" launcherId="2823" setupAppId="2746">
<file name="${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}/${compiler:BASH_WRAPPER_SCRIPT}" />
+ <symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/MacOS/${compiler:WRAPPER_LINK}_update" target="../Resources/app/${compiler:WRAPPER_SCRIPT_BIN_DIR}/${compiler:BASH_UPDATE_SCRIPT}" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/app/jre/Contents/Home/bin/${compiler:JALVIEW_APPLICATION_NAME}" target="java" />
<symlink name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/Resources/app/jre/Contents/Home/bin/${compiler:JALVIEW_NAME}" target="java" />
<file name=".VolumeIcon.icns" file="${compiler:JALVIEW_DIR}/${compiler:MACOSARCHIVE_VOLUMEICON}" />
+ <file name="${compiler:JALVIEW_APPLICATION_NAME}.app/Contents/vmoptions.txt" file="${compiler:JALVIEW_DIR}/${compiler:BUILD_DIR}/tmp/default.vmoptions.AARCH64" />
+ <file name=".jalview/build_properties" file="${compiler:JALVIEW_DIR}/build/resources/resources_build/.build_properties" />
+ <file name=".jalview/channel.props" file="${compiler:JALVIEW_DIR}/build/resources/resources_build/channel.props" />
</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}">
</exclude>
<variables>
<variable name="variable" value="720" />
- <variable name="WIZARD_HEIGHT" value="540" />
+ <variable name="WIZARD_HEIGHT" value="800" />
</variables>
<jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_X64_JAVA_VM_TGZ}" manualJreEntry="true" />
</unixInstaller>
</exclude>
<variables>
<variable name="variable" value="720" />
- <variable name="WIZARD_HEIGHT" value="540" />
+ <variable name="WIZARD_HEIGHT" value="800" />
</variables>
<jreBundle jreBundleSource="preCreated" includedJre="${compiler:LINUX_AARCH64_JAVA_VM_TGZ}" manualJreEntry="true" />
</unixInstaller>
<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 buildAll="false">
+ <mediaSet refId="3042" />
</buildIds>
</install4j>
--- /dev/null
+#!/usr/bin/env bash
+
+usage() {
+ echo "Usage: $( basename $0 ) [-h] [ [-d] [-m arch] [-c channel] | [-i filename] ] [-a folder] [-u] [-U] [-S] [-P] [-R]"
+ echo ""
+ echo " This script downloads and installs Jalview in macOS, or installs from a previously downloaded Jalview DMG file."
+ echo " One of -d or -i should be specified, whichever comes last is used."
+ echo " Default behaviour with -d is to download the latest release version of Jalview for your architecture and install"
+ echo " the .app in /Applications with user-space updates enabled."
+ echo " These can be adjusted with the following options."
+ echo ""
+ echo " -h Show help"
+ echo " -d Download the latest DMG for the channel"
+ echo " -m arch (with -d) Download specific JVM architecture. Should be one of 'arm64' or 'x86_64' (defaults to \`uname -m\`)"
+ echo " -c channel (with -d) Download from channel. Should be one of 'release', 'test-release', 'develop' (defaults to 'release')."
+ echo " -i filename Use filename as DMG image file instead of downloading."
+ echo " -a folder Install the application .app bundle in folder (default '/Applications')."
+ echo " -v Verbose output."
+ echo " -y Assume 'yes' to confirmation."
+ echo " -q No output other than errors. Assumes -y."
+ echo ""
+ echo " Advanced options:"
+ echo ""
+ echo " -u template Use template for user-space updates path (defaults to '~/Library/Application Support/Jalview-Desktop')."
+ echo " template should contain one of: a leading '~/', '%u' (user's username) or '%h' (user's home path)."
+ echo " -U Disable user-space updates (updates will be attempted in the installation folder)."
+ echo " -S Disable all user-space and installation updates."
+ echo " -P Do not add the jalview command-line path to /etc/paths.d."
+ echo " -R Do not perform the check for root privileges."
+ echo " -t tmpdir Use tmpdir for installation files (defaults to /tmp)"
+}
+
+# check OS
+UOS="$(uname -s)"
+if [ "$UOS" != "Darwin" ]; then
+ echo "This install script is for macOS."
+ echo "Jalview can be installed on other OSes using the installers found at"
+ echo "https://www.jalview.org/download/"
+ exit 1
+fi
+
+# set defaults
+DOWNLOAD=0
+UARCH=$(uname -m)
+CHANNEL="release"
+DMGFILE=""
+INSTALLERNAME="$(basename $0)"
+APPLICATIONFOLDER="/Applications"
+VERBOSE=0
+YES=0
+QUIET=0
+USERAPPDIRTEMPLATE=""
+DISABLEUSERAPPDIR=0
+DISABLEALLUPDATES=0
+DISABLEGLOBALPATH=0
+DISABLEROOTCHECK=0
+USETEMPDIR=""
+TMP="/tmp"
+
+CURLOPT=""
+RSYNCOPT=""
+DITTOOPT=""
+HDIUTILOPT="-quiet"
+
+# set options
+while getopts "hdi:a:vyqu:c:USPR" opt; do
+ case ${opt} in
+ h)
+ usage
+ exit 0
+ ;;
+ d)
+ DOWNLOAD=1
+ ;;
+ m)
+ UARCH="${OPTARG}"
+ ;;
+ c)
+ CHANNEL="${OPTARG}"
+ ;;
+ i)
+ DMGFILE="${OPTARG}"
+ DOWNLOAD=0
+ ;;
+ a)
+ APPLICATIONFOLDER="${OPTARG}"
+ ;;
+ v)
+ VERBOSE=1
+ CURLOPT="-v"
+ RSYNCOPT="-v"
+ DITTOOPT="-V"
+ HDIUTILOPT="-verbose"
+ ;;
+ y)
+ YES=1
+ ;;
+ q)
+ QUIET=1
+ CURLOPT="-s"
+ RSYNCOPT="-q"
+ HDIUTILOPT="-quiet"
+ YES=1
+ ;;
+ u)
+ USERAPPDIRTEMPLATE="${OPTARG}"
+ ;;
+ U)
+ DISABLEUSERAPPDIR=1
+ ;;
+ S)
+ DISABLEALLUPDATES=1
+ ;;
+ P)
+ DISABLEGLOBALPATH=1
+ ;;
+ R)
+ DISABLEROOTCHECK=1
+ ;;
+ t)
+ TMP="${OPTARG}"
+ ;;
+ *)
+ echo "Unrecognised option. Run with -h for help."
+ exit 2
+ ;;
+ esac
+done
+
+myecho() {
+ if [ "${QUIET}" != 1 ]; then
+ echo "* $1"
+ fi
+}
+
+# no -d or -i arguments
+if [ "${DOWNLOAD}" = 0 -a -z "${DMGFILE}" ]; then
+ echo "Please use one of -d or -i options"
+ echo ""
+ usage
+ exit 0
+fi
+
+# root permissions check
+if [ "${DISABLEROOTCHECK}" != 1 -a "${EUID}" != 0 ]; then
+ echo "This script should be run with root permissions, or disable this root check with -R."
+ exit 5
+fi
+
+# check channel
+if [ ! -z "$DMGFILE" -a -e "$DMGFILE" ]; then
+ myecho "Using DMG file '${DMGFILE}'"
+ CHANNEL="dmg"
+else
+ case "$CHANNEL" in
+ release|test-release|develop)
+ myecho "Using channel ${CHANNEL}"
+ ;;
+ *)
+ echo "-c channel must be one of 'release', 'test-release' or 'develop'"
+ exit 3
+ ;;
+ esac
+fi
+
+# convert uarch to jarch
+case $UARCH in
+ x86_64)
+ JARCH=x64
+ ;;
+ arm64)
+ JARCH=aarch64
+ ;;
+ *)
+ echo "Unknown architecture '$UARCH'. Exiting."
+ exit 4;
+ ;;
+esac
+
+# dir for downloads and volume mount
+TEMPDIR=$(mktemp -d -p "${TMP}" -t "${INSTALLERNAME%.sh}_${CHANNEL}")
+if [ "${DOWNLOAD}" = 1 ]; then
+ myecho "Using directory '${TEMPDIR}' to download and mount disk image"
+else
+ myecho "Using directory '${TEMPDIR}' to mount disk image"
+fi
+FILEBASE="${TEMPDIR}/jalview-${CHANNEL}-latest-macos-${JARCH}"
+VOLUMEDIR="${FILEBASE}.vol"
+
+# Confirmation of what's about to happen
+if [ "${YES}" != 1 ]; then
+ if [ "${DOWNLOAD}" = 1 ]; then
+ myecho "This script will download Jalview from the '${CHANNEL}' channel and install it into the '${APPLICATIONFOLDER}' folder."
+ else
+ myecho "This script will install Jalview from the '${DMGFILE}' disk image file into the '${APPLICATIONFOLDER}' folder."
+ fi
+
+ read -r -p "Continue? [y/N] " response
+ case $(echo "${response}" | tr '[:upper:]' '[:lower:]') in
+ yes|y)
+ myecho "Excellent! Continuing."
+ ;;
+ *)
+ echo "Aborting due to negative confirmation." && exit
+ ;;
+ esac
+fi
+
+if [ "${DOWNLOAD}" = 1 ]; then
+ DMGFILE="${FILEBASE}.dmg"
+ SHA256=""
+
+ URL="https://www.jalview.org/downloads/${CHANNEL}/installer/macos-${JARCH}"
+
+ myecho "Downloading '${URL}' to '${DMGFILE}'"
+ curl ${CURLOPT} -f -L -o "${DMGFILE}" "${URL}"
+ [ $? != 0 ] && echo "Could not download '$URL' to '$DMGFILE'" && exit 6
+ SHA256=$( curl ${CURLOPT} -f -s -L "${URL}.sha256" )
+ [ $? != 0 ] && echo "Could not download '$URL.sha256'" && exit 7
+
+ CHECK=$( shasum -a 256 "${DMGFILE}" | cut -d" " -f1 )
+ if [ "${CHECK}" = "${SHA256}" ]; then
+ myecho "Downloaded file '$DMGFILE' checksum matches downloaded checksum '$SHA256'"
+ else
+ echo "Downloaded file '$DMGFILE' checksum does not match downloaded checksum '$SHA256'"
+ exit 8
+ fi
+fi
+
+# mount the DMG image
+myecho "Mounting disk image '${DMGFILE}' on '${VOLUMEDIR}'"
+hdiutil attach ${HDIUTILOPT} -mountpoint "${VOLUMEDIR}" "${DMGFILE}"
+[ $? != 0 ] && echo "Could not mount '${DMGFILE}' on mount point '${VOLUMEDIR}'" && exit 9
+
+myecho "MOUNTED"
+
+# difficult to use a wildcard for a non-user-readable folder without inserting sudo directly into the command
+# i.e. what I really want to do here is
+# APP=$( sudo sh -c "ls -1d ${VOLUMEDIR}/Jalview*.app" | head -1 )
+# but don't want to put sudo in the script because of the -R option. We'll loop through instead.
+VOLUMEFILES=$( ls -1 ${VOLUMEDIR} )
+while IFS= read -r VOLUMEFILE; do
+ FILE=$( basename "${VOLUMEFILE}" )
+ if [ "$FILE" != "${FILE#Jalview}" -a "$FILE" != "${FILE%.app}" ]; then
+ APP="$FILE"
+ break
+ fi
+done <<< "$VOLUMEFILES"
+[ -z "$APP" ] && echo "Could not find Jalview\*.app in the volume '${VOLUMEDIR}'" && exit 10
+
+APPNAME=$( basename "$APP" )
+myecho "Found application '${APP}'"
+
+# ensure no trailing slash on APPNAME or APPLICATIONFOLDER (important for rsync)
+while [ "${APPLICATIONFOLDER}" != "${APPLICATIONFOLDER%/}" -a "${APPLICATIONFOLDER}" != "/" ]; do
+ myecho "Removing trailing slash from APPLICATIONFOLDER='${APPLICATIONFOLDER}'"
+ APPLICATIONFOLDER="${APPLICATIONFOLDER%/}"
+done
+while [ "${APPNAME}" != "${APPNAME%/}" ]; do
+ myecho "Removing trailing slash from APPNAME='${APPNAME}'"
+ APPNAME=${APPNAME%/}
+done
+[ -z "$APPNAME" -o "${APPNAME%.app}" = "$APPNAME" ] && echo "Could not find suitable Jalview\*.app in the volume '${VOLUMEDIR}'" && exit 11
+
+## rsync .app from mounted volume to application folder
+#myecho "Rsyncing '${VOLUMEDIR}/${APPNAME}' to '${APPLICATIONFOLDER}/${APPNAME}'"
+#rsync ${RSYNCOPT} -ah --delete "${VOLUMEDIR}/${APPNAME}" "${APPLICATIONFOLDER}/"
+#[ $? != 0 ] && echo "Possible problem when rsyncing '${APP}' to '${APPLICATIONFOLDER}'" && exit 12
+#myecho "Finished rsync"
+
+# using ditto
+APPPATH="${APPLICATIONFOLDER}/${APPNAME}"
+OLDAPPPATH="${APPPATH}.old"
+myecho "Copying '${VOLUMEDIR}/${APPNAME}' to '${APPPATH}'"
+if [ -e "$APPPATH" ]; then
+ if [ -e "$OLDAPPPATH" ]; then
+ rm -Rf "$OLDAPPPATH"
+ fi
+ mv "$APPPATH" "$OLDAPPPATH"
+fi
+ditto ${DITTOOPT} "${VOLUMEDIR}/${APPNAME}" "$APPPATH" && [ -e "$OLDAPPPATH" ] && rm -Rf "$OLDAPPPATH"
+myecho "Finished copying '${APPNAME}'"
+
+EXIT=0
+declare -a WARNINGS=()
+addwarning() {
+ local W=$1
+ local N=$2
+ myecho "${W}"
+ WARNINGS=( "${WARNINGS[@]}" "${W}" )
+ # exit with the first warning value
+ [ "${EXIT}" = 0 ] && EXIT=$N
+}
+
+# unmount the DMG image
+myecho "Unmounting '${VOLUMEDIR}'"
+hdiutil detach ${HDIUTILOPT} "${VOLUMEDIR}" || addwarning "Possible problem when unmounting/deleting '${VOLUMEDIR}'. I'm continuing the install but you should look at it later." 13
+
+# delete the image file and temp dir
+if [ "${DOWNLOAD}" = 1 ]; then
+ myecho "Deleting downloaded disk image file '${DMGFILE}'"
+ rm "${DMGFILE}"
+fi
+myecho "Removing temporary directory '${TEMPDIR}'"
+rmdir "${TEMPDIR}"
+
+VMOPTIONS="${APPLICATIONFOLDER}/${APPNAME}/Contents/vmoptions.txt"
+
+VMOPTIONS_START=""
+if [ -e "${VMOPTIONS}" ]; then
+ while IFS= read -r line; do
+ VMOPTIONS_START="${VMOPTIONS_START}${line}"$'\n'
+ if [ "${line}" != "${line/Jalview/}" ]; then # i.e. $line contains "Jalview"
+ break
+ fi
+ done < "${VMOPTIONS}"
+fi
+
+LONGHASH=$( printf %s "${APPLICATIONFOLDER}/${APPNAME}/Contents/Resources/app" | shasum -a 256 -b )
+HASH=${LONGHASH:0:8}
+NAME=${APPNAME%.app}
+
+myecho "Writing vmoptions files '${VMOPTIONS}'"
+VMOPTIONS_COMMENT=$( cat << EOM
+# Jalview options added by $( basename $0 ) at $( date +"%F %T")
+EOM
+)
+
+# -Dnouserdefaultappdir=false
+if [ "${DISABLEUSERAPPDIR}" = 1 ]; then
+ myecho "- User-space updates DISABLED"
+ VMOPTIONS_USERAPPDIR=$( cat << EOM
+#
+# Comment out the following line to allow user-space updates
+-Dnouserdefaultappdir=true
+EOM
+)
+else
+ myecho "- User-space updates enabled"
+ VMOPTIONS_USERAPPDIR=$( cat << EOM
+#
+# Uncomment the following line to disable user-space updates
+#-Dnouserdefaultappdir=true
+EOM
+)
+fi
+
+# -Dsetuserappdirpath
+if [ -z "${USERAPPDIRTEMPLATE}" ]; then
+ myecho "- Default user-space updates path (~/Library/Application Support/Jalview-Desktop/${NAME}/${HASH})"
+ VMOPTIONS_USERAPPDIRPATH=$( cat << EOM
+#
+# Uncomment the below line to set a custom path for user-space updates -- use with caution.
+# A leading ~/ or %h anywhere will be substituted with the user's home path, and %u by the username.
+# If not set, the default is ~/Library/Application Support/Jalview-Desktop for macOS
+#-Dsetuserappdirpath=/tmp/jalview/%u
+EOM
+)
+else
+ myecho "- CUSTOMISED user-space updates path (${USERAPPDIRTEMPLATE})"
+ VMOPTIONS_USERAPPDIRPATH=$( cat << EOM
+#
+# The below line sets a custom path for user-space updates -- use with caution.
+# A leading ~/ or %h anywhere will be substituted with the user's home path, and %u by the username.
+# If unset, the default is ~/Library/Application Support/Jalview-Desktop for macOS
+-Dsetuserappdirpath=${USERAPPDIRTEMPLATE}
+EOM
+)
+fi
+
+# -Dsilent=noupdate
+if [ "${DISABLEALLUPDATES}" = 1 ]; then
+ myecho "- All automatic updates DISABLED"
+ VMOPTIONS_UPDATES=$( cat << EOM
+#
+# Comment out the following line to enable updates
+-Dsilent=noupdate
+EOM
+)
+else
+ if [ "${DISABLEUSERAPPDIR}" = 1 ]; then
+ myecho "- Automatic updates enabled IN INSTALLATION"
+ else
+ myecho "- Automatic updates enabled in user-space"
+ fi
+ VMOPTIONS_UPDATES=$( cat << EOM
+#
+# Uncomment the following line to also disable all updates
+#-Dsilent=noupdate
+EOM
+)
+fi
+
+printf "%s\n%s\n%s\n%s\n%s\n" "${VMOPTIONS_START}" "${VMOPTIONS_COMMENT}" "${VMOPTIONS_USERAPPDIR}" "${VMOPTIONS_USERAPPDIRPATH}" "${VMOPTIONS_UPDATES}" > "${VMOPTIONS}" || addwarning "Possible problem adding options to '${VMOPTIONS}'" 14
+
+# set a global path in /etc/paths.d
+if [ "${DISABLEGLOBALPATH}" != 1 ]; then
+ US_NAME="${NAME// /_}"
+ PATHFILE="/etc/paths.d/${US_NAME}-${HASH}"
+ myecho "Writing global PATH to '${PATHFILE}'"
+ echo "${APPLICATIONFOLDER}/${APPNAME}/Contents/MacOS" > "${PATHFILE}" || addwarning "Possible problem writing path file '${PATHFILE}'" 15
+fi
+
+# show accumulated warnings
+if [ "${#WARNINGS[@]}" != 0 ]; then
+ myecho "-----------------"
+ myecho "Installation complete."
+ myecho "Warnings summary:"
+ myecho "$( printf -- '- %s\n' "${WARNINGS[@]}" )"
+else
+ myecho "Successful installation!"
+fi
+
+exit $EXIT
--- /dev/null
+#!/bin/bash
+
+if [[ "$GITDIR" == "" ]]; then
+ GITDIR=~/uod-development/jalview-builds/git/jalview
+fi;
+
+if [[ "$DEVELOPERID" == "" ]]; then
+ DEVELOPERID="Developer ID"
+fi;
+
+if [[ "$TMPDMG" == "" ]]; then
+ TMPDMG="signingDMG"
+fi;
+
+echo APPNAME $APPNAME like Jalview Test
+echo doing ARCH $ARCH
+echo using entitlements from $GITDIR
+echo using key $DEVELOPERID
+
+FAPPNAME="${APPNAME/ /\\ }"
+FAPPNAMEESC="${APPNAME/ /\\\\\\ }"
+FWAPP="${APPNAME/ [A-Za-z]*/}"
+ARCHNAME="${APPNAME// /_}-${APPVER//\./_}-macos-$ARCH-java_$JVER"
+DMGNAME="${APPNAME/ /_}-${APPVER//\./_}-macos-$ARCH-java_$JVER.dmg"
+VOLNAME="${APPNAME// /_}\\ Installer\\ \\(${APPVER//\./_}\\ $ARCH\\ $JVER\\)"
+VLNAME="${APPNAME// /_} Installer (${APPVER//\./_} $ARCH $JVER)"
+BORINGVLNAME="${APPNAME} Installer"
+
+
+
+echo "will mount $DMGNAME as $VOLNAME"
+if [[ -d $TMPDMG ]]; then
+ echo "'$TMPDMG' is in the way. Please delete it or set TMPDMG"
+ exit 1;
+fi
+
+if [[ -f $DMGNAME ]]; then
+ hdiutil attach $DMGNAME
+ ditto /Volumes/${FWAPP}* $TMPDMG
+ hdiutil eject /Volumes/${FWAPP}*
+ mkdir -p unsigned
+ mv -v $DMGNAME unsigned/
+ echo Moved $DMGNAME to unsigned/$DMGNAME
+ codesign --remove-signature --force --deep -vvvv -s "Developer ID" --options runtime --entitlements $GITDIR/utils/osx_signing/entitlements.txt $TMPDMG/${FWAPP}*.app/Contents/Resources/app/jre/Contents/MacOS/libjli.dylib
+
+ codesign --verify --deep -v ./$TMPDMG/${FWAPP}*.app/Contents/Resources/app/jre/Contents/MacOS/libjli.dylib
+
+ codesign --remove-signature --force --deep -vvvv -s "Developer ID" --options runtime --entitlements $GITDIR/utils/osx_signing/entitlements.txt $TMPDMG/${FWAPP}*.app/Contents/MacOS/JavaApplicationStub
+
+ hdiutil create -megabytes 260 -srcfolder ./$TMPDMG -volname "$BORINGVLNAME" $ARCHNAME.dmg
+
+ codesign --force --deep -vvvv -s "Developer ID" --options runtime --entitlements $GITDIR/utils/osx_signing/entitlements.txt $ARCHNAME.dmg
+
+ codesign --deep -vvvv $ARCHNAME.dmg
+
+ rm -Rf $TMPDMG
+else
+ echo Can\'t find $DMGNAME - dit you set APPNAME APPVER ARCH and JVER correctly ?
+fi
+
--- /dev/null
+#!/bin/bash
+
+if [[ "$GITDIR" == "" ]]; then
+ GITDIR=~/uod-development/jalview-builds/git/jalview
+fi;
+
+
+if [[ "$DEVELOPERID" == "" ]]; then
+ DEVELOPERID="Developer ID"
+fi;
+
+if [[ "$TMPDMG" == "" ]]; then
+ TMPDMG="staplingDMG"
+fi;
+
+
+echo APPNAME $APPNAME like Jalview Test
+echo doing ARCH $ARCH
+echo using entitlements from $GITDIR
+
+FAPPNAME="${APPNAME/ /\\ }"
+FAPPNAMEESC="${APPNAME/ /\\\\\\ }"
+FWAPP="${APPNAME/ [A-Za-z]*/}"
+ARCHNAME="${APPNAME// /_}-${APPVER//\./_}-macos-$ARCH-java_$JVER"
+DMGNAME="${APPNAME/ /_}-${APPVER//\./_}-macos-$ARCH-java_$JVER.dmg"
+VOLNAME="${APPNAME// /_}\\ Installer\\ \\(${APPVER//\./_}\\ $ARCH\\ $JVER\\)"
+VLNAME="${APPNAME// /_} Installer (${APPVER//\./_} $ARCH $JVER)"
+BORINGVLNAME="${APPNAME} Installer"
+echo "will mount $DMGNAME as $VOLNAME"
+
+if [[ -d $TMPDMG ]]; then
+ echo "'$TMPDMG' is in the way. Please delete it or set TMPDMG"
+ exit 1;
+fi
+
+if [[ -f $DMGNAME ]]; then
+ hdiutil attach $DMGNAME
+ ditto /Volumes/${FWAPP}* $TMPDMG
+ hdiutil eject /Volumes/${FWAPP}*
+ xcrun stapler staple $TMPDMG/${FWAPP}*.app
+ mkdir -p stapled
+ hdiutil create -megabytes 240 -srcfolder $TMPDMG -volname "$BORINGVLNAME" stapled/$DMGNAME
+ codesign --force --deep -vvvv -s "$DEVELOPERID" --options runtime --entitlements ${GITDIR}/utils/osx_signing/entitlements.txt stapled/$DMGNAME
+ codesign --deep -vvvv stapled/$DMGNAME
+ echo "Stapled DMG is in stapled/$DMGNAME"
+ rm -Rf $TMPDMG
+else
+ echo Can\'t find $DMGNAME - dit you set APPNAME APPVER ARCH and JVER correctly ?
+fi
+
git://source.jalview.org / jalview.git / commitdiff
