println("Setting Test LaF to '${testLaf}'")
systemProperty "laf", testLaf
}
+ def testHiDPIScale = project.findProperty("test_HiDPIScale")
+ if (testHiDPIScale != null) {
+ println("Setting Test HiDPI Scale to '${testHiDPIScale}'")
+ systemProperty "sun.java2d.uiScale", testHiDPIScale
+ }
sourceCompatibility = compile_source_compatibility
targetCompatibility = compile_target_compatibility
jvmArgs += additional_compiler_args
-1.8.3-1.2.8_FJVL
+1.8.3-1.2.10_FJVL
-1.8.3-1.2.8_JVL
+1.8.3-1.2.10_JVL
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.8_FJVL</version>
+ <version>1.8.3-1.2.10_FJVL</version>
</parent>
<artifactId>getdown-ant</artifactId>
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.8_FJVL</version>
+ <version>1.8.3-1.2.10_FJVL</version>
</parent>
<artifactId>getdown-core</artifactId>
import java.lang.reflect.Method;
import java.net.MalformedURLException;
import java.net.Proxy;
+import java.net.SocketAddress;
+import java.net.InetSocketAddress;
import java.net.URI;
import java.net.URISyntaxException;
import java.net.URL;
}
// pass along our proxy settings
- String proxyHost;
- if ((proxyHost = System.getProperty("http.proxyHost")) != null) {
+ String proxyHost = System.getProperty("http.proxyHost");
+ String proxyPort = StringUtil.isBlank(System.getProperty("http.proxyPort")) ? "80" : System.getProperty("http.proxyPort");
+ if (StringUtil.isBlank(proxyHost) && ! proxy.equals(Proxy.NO_PROXY)) {
+ try {
+ SocketAddress a = proxy.address();
+ if (a != null && a instanceof InetSocketAddress) {
+ InetSocketAddress ia = (InetSocketAddress)a;
+ proxyHost = ia.getHostString();
+ proxyPort = String.valueOf(ia.getPort());
+ }
+ } catch (Exception e) {
+ log.error("Problem obtaining proxy settings from Proxy object");
+ e.printStackTrace();
+ }
+ }
+ if (proxyHost != null) {
+ log.info("Using proxy settings "+proxyHost+":"+proxyPort);
args.add("-Dhttp.proxyHost=" + proxyHost);
- args.add("-Dhttp.proxyPort=" + System.getProperty("http.proxyPort"));
+ args.add("-Dhttp.proxyPort=" + proxyPort);
args.add("-Dhttps.proxyHost=" + proxyHost);
- args.add("-Dhttps.proxyPort=" + System.getProperty("http.proxyPort"));
- }
+ args.add("-Dhttps.proxyPort=" + proxyPort);
+ } else {
+ log.info("Not setting proxy");
+ }
// add the marker indicating the app is running in getdown
args.add("-D" + Properties.GETDOWN + "=true");
+/*
+ * 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.lang.management.ManagementFactory;
package jalview.bin;
-import java.awt.Toolkit;
+import java.awt.HeadlessException;
public class HiDPISetting
{
- public static final int dpi;
+ private static final int hidpiThreshold = 160;
- public static final int scale;
+ private static final int hidpiMultiThreshold = 240;
- private static final int hidpi = 110;
+ private static final int bigScreenThreshold = 1400;
- private static final String scaleProperty = "sun.java2d.uiScale";
+ public static final String scalePropertyName = "sun.java2d.uiScale";
- private static final boolean isAMac = System.getProperty("os.name")
- .indexOf("Mac") > -1;
+ private static final boolean isLinux;
- private static final boolean isLinux = System.getProperty("os.name")
- .toLowerCase().indexOf("linux") > -1;
+ // private static final boolean isAMac;
- private static final boolean isWindows = System.getProperty("os.name")
- .toLowerCase().indexOf("windows") > -1;
+ // private static final boolean isWindows;
+
+ public static final String setHiDPIPropertyName = "setHiDPI";
+
+ public static final String setHiDPIScalePropertyName = "setHiDPIScale";
+
+ private static boolean setHiDPI = false;
+
+ private static int setHiDPIScale = 0;
+
+ public static int dpi = 0;
+
+ public static int mindimension = 0;
+
+ public static int width = 0;
+
+ public static int scale = 0;
+
+ private static boolean doneInit = false;
+
+ private static boolean allowScalePropertyArg = false;
+
+ private static ScreenInfo screenInfo = new ScreenInfo();
static
{
- dpi = Toolkit.getDefaultToolkit().getScreenResolution();
- scale = dpi / hidpi + 1;
- if (scale > 1 && isLinux)
+ String system = System.getProperty("os.name") == null ? null
+ : System.getProperty("os.name").toLowerCase();
+ if (system != null)
+ {
+ isLinux = system.indexOf("linux") > -1;
+ // isAMac = system.indexOf("mac") > -1;
+ // isWindows = system.indexOf("windows") > -1;
+ }
+ else
{
- System.out.println("DPI detected as " + dpi
- + ". Scaling factor set to " + scale + ".");
+ isLinux = false;
+ // isAMac = isWindows = false;
}
}
- public static String getScalePropertyArg()
+ private static void init()
{
- // HiDPI setting. Just looking at Linux to start with. Test with Windows.
- if (!isLinux)
+ if (doneInit)
{
- return null;
+ return;
}
- if (scale > 1)
+
+ // get and use command line property values first
+ String setHiDPIProperty = System.getProperty(setHiDPIPropertyName);
+ setHiDPI = setHiDPIProperty != null
+ && setHiDPIProperty.equalsIgnoreCase("true");
+
+ String setHiDPIScaleProperty = System
+ .getProperty(setHiDPIScalePropertyName);
+ if (setHiDPIScaleProperty != null)
+ {
+ try
+ {
+ setHiDPIScale = Integer.parseInt(setHiDPIScaleProperty);
+ } catch (NumberFormatException e)
+ {
+ System.err.println(setHiDPIScalePropertyName + " property give ("
+ + setHiDPIScaleProperty + ") but not parseable as integer");
+ }
+ }
+ if (setHiDPI && setHiDPIScale > 0)
+ {
+ setHiDPIScale(setHiDPIScale);
+ return;
+ }
+
+ // check to see if the scale property has already been set by something else
+ // (e.g. the OS)
+ String existingProperty = System.getProperty(scalePropertyName);
+ if (existingProperty != null)
+ {
+ try
+ {
+ int existingPropertyVal = Integer.parseInt(existingProperty);
+ System.out.println("Existing " + scalePropertyName + " is "
+ + existingPropertyVal);
+ if (existingPropertyVal > 1)
+ {
+ setHiDPIScale(existingPropertyVal);
+ return;
+ }
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Could not convert property " + scalePropertyName
+ + " vale '" + existingProperty + "' to number");
+ }
+ }
+
+ // Try and auto guess a good scale based on reported DPI (not trustworthy)
+ // and screen resolution (more trustworthy)
+
+ // get screen dpi
+ screenInfo = getScreenInfo();
+ try
+ {
+ dpi = screenInfo.getScreenResolution();
+ } catch (HeadlessException e)
+ {
+ System.err.println("Cannot get screen resolution: " + e.getMessage());
+ }
+
+ // try and get screen size height and width
+ try
+ {
+ int height = screenInfo.getScreenHeight();
+ int width = screenInfo.getScreenWidth();
+ // using mindimension in case of portrait screens
+ mindimension = Math.min(height, width);
+ } catch (HeadlessException e)
+ {
+ System.err.println(
+ "Cannot get screen size height and width:" + e.getMessage());
+ }
+
+ // attempt at a formula for scaling based on screen dpi and mindimension.
+ // scale will be an integer >=1. This formula is based on some testing and
+ // guesswork!
+
+ // scale based on reported dpi. if dpi>hidpiThreshold then scale=2+multiples
+ // of hidpiMultiThreshold (else scale=1)
+ // (e.g. dpi of 110 scales 1. dpi of 120 scales 2. dpi of 360 scales 3)
+ int dpiScale = (dpi - hidpiThreshold > 0)
+ ? 2 + ((dpi - hidpiThreshold) / hidpiMultiThreshold)
+ : 1;
+
+ int dimensionScale = 1 + (mindimension / bigScreenThreshold);
+
+ // choose larger of dimensionScale or dpiScale (most likely dimensionScale
+ // as dpiScale often misreported)
+ int autoScale = Math.max(dpiScale, dimensionScale);
+
+ // only make an automatic change if scale is changed and other conditions
+ // (OS is linux) apply, or if setHiDPI has been specified
+ if ((autoScale > 1 && isLinux) || setHiDPI)
+ {
+ setHiDPIScale(autoScale);
+ return;
+ }
+
+ // looks like we're not doing any scaling
+ doneInit = true;
+ }
+
+ public static void setHiDPIScale(int s)
+ {
+ scale = s;
+ allowScalePropertyArg = true;
+ doneInit = true;
+ }
+
+ public static String getScalePropertyArg(int s)
+ {
+ return "-D" + scalePropertyName + "=" + String.valueOf(s);
+ }
+
+ public static String getScalePropertyArg()
+ {
+ init();
+ // HiDPI setting. Just looking at Linux to start with. Test with Windows.
+ return allowScalePropertyArg ? getScalePropertyArg(scale) : null;
+ }
+
+ public static void clear()
+ {
+ setHiDPI = false;
+ setHiDPIScale = 0;
+ dpi = 0;
+ mindimension = 0;
+ width = 0;
+ scale = 0;
+ doneInit = false;
+ allowScalePropertyArg = false;
+ }
+
+ public static void setScreenInfo(ScreenInfo si)
+ {
+ screenInfo = si;
+ }
+
+ public static ScreenInfo getScreenInfo()
+ {
+ if (screenInfo == null)
{
- return "-D" + scaleProperty + "=" + scale;
+ screenInfo = new ScreenInfo();
}
- return null;
+ return screenInfo;
}
}
+/*
+ * 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;
/**
private static final long GIGABYTE = 1073741824; // 1GB
- public static final long LEAVE_FREE_MIN_MEMORY = GIGABYTE/2;
+ public static final long LEAVE_FREE_MIN_MEMORY = GIGABYTE / 2;
- public static final long APPLICATION_MIN_MEMORY = GIGABYTE/2;
+ public static final long APPLICATION_MIN_MEMORY = GIGABYTE / 2;
private static final long MAX_HEAPSIZE_GB_DEFAULT = 32;
* values: jvmmempc - the maximum percentage of total physical memory to
* allocate, and jvmmemmax - the maximum absolute amount of physical memory to
* allocate. These can be provided as arguments. If not provided as arguments
- * (or set as null) system properties will be used instead (if set). The memory
- * setting returned will be the lower of the two values. If either of the values
- * are not provided then defaults will be used (jvmmempc=90, jvmmemmax=32GB). If
- * total physical memory can't be ascertained when jvmmempc was set or neither
- * jvmmempc nor jvmmemmax were set, then jvmmemmax defaults to a much safer 8GB.
- * In this case explicitly setting jvmmemmax and not setting jvmmempc can set a
- * higher memory for Jalview. The calculation also tries to ensure 0.5GB memory
- * for the OS, but also tries to ensure at least 0.5GB memory for Jalview (which
- * takes priority over the OS) If there is less then 0.5GB of physical memory
- * then the total physical memory is used for Jalview.
+ * (or set as null) system properties will be used instead (if set). The
+ * memory setting returned will be the lower of the two values. If either of
+ * the values are not provided then defaults will be used (jvmmempc=90,
+ * jvmmemmax=32GB). If total physical memory can't be ascertained when
+ * jvmmempc was set or neither jvmmempc nor jvmmemmax were set, then jvmmemmax
+ * defaults to a much safer 8GB. In this case explicitly setting jvmmemmax and
+ * not setting jvmmempc can set a higher memory for Jalview. The calculation
+ * also tries to ensure 0.5GB memory for the OS, but also tries to ensure at
+ * least 0.5GB memory for Jalview (which takes priority over the OS) If there
+ * is less then 0.5GB of physical memory then the total physical memory is
+ * used for Jalview.
*
* @param jvmmemmaxarg
- * Maximum value of memory to set. This can be a numeric
- * string optionally followed by "b", "k", "m", "g", "t"
- * (case insensitive) to indicate bytes, kilobytes,
- * megabytes, gigabytes, terabytes respectively. If null a
- * default value of 32G will be used. If null and either
- * physical memory can't be determined then the default is
- * 8GB.
+ * Maximum value of memory to set. This can be a numeric string
+ * optionally followed by "b", "k", "m", "g", "t" (case insensitive)
+ * to indicate bytes, kilobytes, megabytes, gigabytes, terabytes
+ * respectively. If null a default value of 32G will be used. If null
+ * and either physical memory can't be determined then the default is
+ * 8GB.
* @param jvmmempcarg
- * Max percentage of physical memory to use. Defaults to
- * "90".
+ * Max percentage of physical memory to use. Defaults to "90".
*
* @return The amount of memory (in bytes) to allocate to Jalview
*/
{
memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
System.out.println("MemorySetting Property '"
- + MAX_HEAPSIZE_PROPERTY_NAME
- + "' ("
- + jvmmemmaxarg + "') badly formatted, using default ("
+ + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ + "') badly formatted, using default ("
+ MAX_HEAPSIZE_GB_DEFAULT + "g).");
}
if (Long.MAX_VALUE / memmax < multiplier)
{
memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println(
- "MemorySetting Property '" + MAX_HEAPSIZE_PROPERTY_NAME + "' ("
- + jvmmemmaxarg
- + ") too big, using default ("
- + MAX_HEAPSIZE_GB_DEFAULT + "g).");
+ System.out.println("MemorySetting Property '"
+ + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ + ") too big, using default (" + MAX_HEAPSIZE_GB_DEFAULT
+ + "g).");
}
else
{
if (memmax < APPLICATION_MIN_MEMORY)
{
memmax = APPLICATION_MIN_MEMORY;
- System.out.println(
- "MemorySetting Property '" + MAX_HEAPSIZE_PROPERTY_NAME + "' ("
- + jvmmemmaxarg
- + ") too small, using minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ System.out.println("MemorySetting Property '"
+ + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ + ") too small, using minimum (" + APPLICATION_MIN_MEMORY
+ + ").");
}
}
}
else
{
- System.out.println(
- "MemorySetting Property '"
- + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
- + "' should be in range 1..100. Using default "
- + percent + "%");
+ System.out.println("MemorySetting Property '"
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
+ + "' should be in range 1..100. Using default " + percent
+ + "%");
}
}
} catch (NumberFormatException e)
{
- System.out.println(
- "MemorySetting property '" + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
- + "' (" + jvmmempcarg + ") badly formatted");
+ System.out.println("MemorySetting property '"
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
+ + ") badly formatted");
}
// catch everything in case of no com.sun.management.OperatingSystemMXBean
else
{
System.out.println("MemorySetting Property '"
- + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
- + ") too small. Using minimum (" + APPLICATION_MIN_MEMORY
- + ").");
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ + jvmmempcarg + ") too small. Using minimum ("
+ + APPLICATION_MIN_MEMORY + ").");
}
mempc = APPLICATION_MIN_MEMORY;
}
// jvmmempc was set OR neither jvmmempc nor jvmmemmax were set), let's cap
// maxMemLong to 8GB
if (memoryPercentError && mempc == -1
- && !(jvmmempcarg == null && jvmmemmaxarg != null) // the same as (jvmmempcarg != null || (jvmmempcarg == null && jvmmemmaxarg
+ && !(jvmmempcarg == null && jvmmemmaxarg != null) // the same as
+ // (jvmmempcarg !=
+ // null ||
+ // (jvmmempcarg ==
+ // null &&
+ // jvmmemmaxarg
// == null))
&& memmax > NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE)
{
--- /dev/null
+package jalview.bin;
+
+import java.awt.Toolkit;
+
+public class ScreenInfo
+{
+ public int getScreenResolution()
+ {
+ return Toolkit.getDefaultToolkit().getScreenResolution();
+ }
+
+ public int getScreenHeight()
+ {
+ return (int) Toolkit.getDefaultToolkit().getScreenSize().getHeight();
+ }
+
+ public int getScreenWidth()
+ {
+ return (int) Toolkit.getDefaultToolkit().getScreenSize().getWidth();
+ }
+}
<parent>
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
- <version>1.8.3-1.2.8_FJVL</version>
+ <version>1.8.3-1.2.10_FJVL</version>
</parent>
<artifactId>getdown-launcher</artifactId>
if [ x$JVLVERSION != x ]; then
export VERSION=$JVLVERSION
else
- export VERSION=1.8.3-1.2.8_JVL
+ export VERSION=1.8.3-1.2.10_JVL
fi
if [ x${VERSION%_JVL} = x$VERSION ]; then
<groupId>com.threerings.getdown</groupId>
<artifactId>getdown</artifactId>
<packaging>pom</packaging>
- <version>1.8.3-1.2.8_FJVL</version>
+ <version>1.8.3-1.2.10_FJVL</version>
<name>getdown</name>
<description>An application installer and updater.</description>
browser application.
</p>
<p>
- <em>Proxy Server</em><br> If you normally use a proxy server
- for using the internet, you must tick the box "Use a Proxy
- Server" and enter the address and port details as necessary.
+ <em>Proxy Server</em><br>
+ There are three settings to choose from:<br>
+ <ul>
+ <li><em>No proxy servers</em> will configure Jalview to use a
+ direct internet connection.</li>
+ <li><em>System proxy servers</em> will configure Jalview to use
+ the proxy server passed to it by your system at startup.</li>
+ <li><em>Use these proxy servers:</em> allows you to set a custom
+ proxy server.</li>
+ </ul>
+ If you normally use a proxy server for using the internet, you must
+ choose one of <em>System proxy servers</em>, or if these have not been
+ passed correctly you should set your own proxy servers to use by selecting
+ <em>Use these proxy servers</em>.
+ You will then need to enter the host and port details as necessary.
Web Services will not work if you are using a proxy server and do
- not enter the settings here.
+ not choose the system proxy or enter your own settings here.<br>
+ There are separate host and port settings for HTTP and HTTPS proxies.
+ Often these are the same but you should enter the host and port into both
+ rows.<br>
+ You can also check the <em>Authentication required</em> box if your proxy
+ requires username and password authentication. You can enter both the
+ <em>Username</em> and <em>Password</em> but only the <em>Username</em> will
+ be stored in Jalview's preferences file, the password will only be stored
+ until the end of the current Jalview session.<br>
+ This means that if the proxy settings are still valid, Jalview will ask for
+ the password when it starts the next session.
</p>
<p>
<em>Usage statistics, Questionnaire and Version checks</em><br>
label.example_param = Example: {0}
label.select_file_format_before_saving = You must select a file format before saving!
label.file_format_not_specified = File format not specified
-label.couldnt_save_file = Couldn't save file: {0}
+label.couldnt_save_file = Couldn''t save file: {0}
label.error_saving_file = Error Saving File
label.remove_from_default_list = Remove from default list?
label.remove_user_defined_colour = Remove user defined colour
label.prot_alignment_colour = Protein Alignment Colour
label.nuc_alignment_colour = Nucleotide Alignment Colour
label.address = Address
+label.host = Host
label.port = Port
label.default_browser_unix = Default Browser (Unix)
label.send_usage_statistics = Send usage statistics
label.check_for_questionnaires = Check for questionnaires
label.check_for_latest_version = Check for latest version
label.url_linkfrom_sequence_id = URL link from Sequence ID
-label.use_proxy_server = Use a proxy server
+label.no_proxy = No proxy servers
+label.system_proxy = System proxy servers (http={0}; https={1})
+label.use_proxy_server = Use these proxy servers
+label.auth_required = Authentication required
+label.username = Username
+label.password = Password
+label.proxy_password_required = Proxy password required
+label.not_stored = not stored in Preferences file
label.rendering_style = {0} rendering style
label.append_start_end = Append /start-end (/15-380)
label.full_sequence_id = Full Sequence Id
label.details = Details
label.options = Options
label.parameters = Parameters
-label.proxy_server = Proxy Server
+label.proxy_servers = Proxy Servers
label.file_output = File Output
label.select_input_type = Select input type
label.set_options_for_type = Set options for type
label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Something possibly went wrong with the backups of this file.
label.backupfiles_confirm_save_new_saved_file_ok = The new saved file seems okay.
label.backupfiles_confirm_save_new_saved_file_not_ok = The new saved file might not be okay.
+label.continue_operation = Continue operation?
label.backups = Backups
label.backup = Backup
label.backup_files = Backup Files
label.no_features_to_sort_by = No features to sort by
label.ignore_hidden = Ignore hidden columns
label.ignore_hidden_tooltip = Ignore any characters in hidden columns when matching
+label.log_level = Log level
+label.log_level_tooltip = Temporarily set the log level for this console. The log level will revert to {0} when this Java console is closed.
+label.copy_to_clipboard = Copy to clipboard
+label.copy_to_clipboard_tooltip = Copy all of the log text in this console to the system clipboard
#label.scroll_highlighted_regions = Desplazarse hasta las regiones resaltadas
label.gap_symbol = Símbolo del hueco
label.address = Dirección
+label.host = Host
label.port = Puerto
label.default_browser_unix = Navegador por defecto (Unix)
label.send_usage_statistics = Enviar estadísticas de uso
label.check_for_questionnaires = Comprobar los cuestionarios
label.check_for_latest_version = Comprobar la última versión
label.url_linkfrom_sequence_id = URL del enlace del ID de la secuencia
-label.use_proxy_server = Utilizar un servidor proxy
+label.no_proxy = Sin servidores proxy
+label.system_proxy = Servidores proxy del sistema (http={0}; https={1})
+label.use_proxy_server = Utilizar estos servidores proxy
+label.auth_required = Autenticacion requerida
+label.username = Usario
+label.password = Contraseña
label.rendering_style = Estilo de visualización {0}
label.append_start_end = Añadir /inicio-fin (/15-380)
label.full_sequence_id = ID de la secuencia completo
label.details = Detalles
label.options = Opciones
label.parameters = Paramétros
-label.proxy_server = Servidor proxy
+label.proxy_servers = Servidores proxy
label.file_output = Fichero de salida
label.select_input_type = Seleccionar el tipo de entrada
label.set_options_for_type = Establecer opciones para el tipo
label.backupfiles_confirm_save_file_backupfiles_roll_wrong = Posiblemente algo está mal con los archivos de respaldos.
label.backupfiles_confirm_save_new_saved_file_ok = El nuevo archivo guardado parece estar bien.
label.backupfiles_confirm_save_new_saved_file_not_ok = El nuevo archivo guardado podría no estar bien.
+label.continue_operation = ¿Continuar operación?
label.backups = Respaldos
label.backup = Respaldo
label.backup_files = Archivos de respaldos
label.no_features_to_sort_by = No hay características para ordenar
label.ignore_hidden = Ignorar columnas ocultas
label.ignore_hidden_tooltip = Ignorar caracteres en columnas ocultas
+label.log_level = Nivel del registro
+label.log_level_tooltip = Establezca temporalmente el nivel de registro para esta consola. El nivel de registro volverá a {0} cuando se cierre esta consola de Java.
+label.copy_to_clipboard = Copiar en el portapapeles
+label.copy_to_clipboard_tooltip = Copie todo el texto de registro en esta consola al portapapeles del sistema
*/
package jalview.bin;
-import jalview.datamodel.PDBEntry;
-import jalview.gui.UserDefinedColours;
-import jalview.schemes.ColourSchemeLoader;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.UserColourScheme;
-import jalview.structure.StructureImportSettings;
-import jalview.urls.IdOrgSettings;
-import jalview.util.ColorUtils;
-import jalview.util.Platform;
-import jalview.ws.sifts.SiftsSettings;
-
import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.net.Authenticator;
+import java.net.PasswordAuthentication;
import java.net.URL;
import java.text.DateFormat;
import java.text.SimpleDateFormat;
+import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
import java.util.Enumeration;
import org.apache.log4j.Logger;
import org.apache.log4j.SimpleLayout;
+import jalview.datamodel.PDBEntry;
+import jalview.gui.Preferences;
+import jalview.gui.UserDefinedColours;
+import jalview.schemes.ColourSchemeLoader;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.urls.IdOrgSettings;
+import jalview.util.ColorUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.sifts.SiftsSettings;
+
/**
* Stores and retrieves Jalview Application Properties Lists and fields within
* list entries are separated by '|' symbols unless otherwise stated (|) clauses
*/
public static Logger log;
+ // save the proxy properties set at startup
+ public final static String[] startupProxyProperties = {
+ System.getProperty("http.proxyHost"),
+ System.getProperty("http.proxyPort"),
+ System.getProperty("https.proxyHost"),
+ System.getProperty("https.proxyPort"),
+ System.getProperty("http.proxyUser"),
+ System.getProperty("http.proxyPassword"),
+ System.getProperty("https.proxyUser"),
+ System.getProperty("https.proxyPassword"),
+ System.getProperty("http.nonProxyHosts") };
+
+ public final static String PROXYTYPE_NONE = "none";
+
+ // "false" and "true" for backward compatibility
+ public final static String PROXYTYPE_SYSTEM = "false";
+
+ public final static String PROXYTYPE_CUSTOM = "true";
+
+ // in-memory only storage of proxy password, safer to use char array
+ public static char[] proxyAuthPassword = null;
+
/** Jalview Properties */
public static Properties applicationProperties = new Properties()
{
// lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
// Level.INFO.toString())));
// we shouldn't need to do this
- org.apache.log4j.Logger.getRootLogger().setLevel(org.apache.log4j.Level.INFO);
+ org.apache.log4j.Logger.getRootLogger()
+ .setLevel(org.apache.log4j.Level.INFO);
jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
.getDefault("logs.Jalview.level", Level.INFO.toString())));
InputStream fis;
try
{
- fis = new java.net.URL(propertiesFile).openStream();
+ fis = new URL(propertiesFile).openStream();
System.out.println(
"Loading jalview properties from : " + propertiesFile);
System.out.println(
System.out.println("Error reading properties file: " + ex);
}
}
+
+ /* TO BE REPLACED WITH PROXY_TYPE SETTINGS
if (getDefault("USE_PROXY", false))
{
String proxyServer = getDefault("PROXY_SERVER", ""),
proxyPort = getDefault("PROXY_PORT", "8080");
+ }
+ */
- System.out.println("Using proxyServer: " + proxyServer
- + " proxyPort: " + proxyPort);
-
- System.setProperty("http.proxyHost", proxyServer);
- System.setProperty("http.proxyPort", proxyPort);
+ // PROXY TYPE settings (now three options "none", "false", "true", but using
+ // backward compatible strings)
+ String proxyType = getDefault("USE_PROXY", PROXYTYPE_SYSTEM);
+ // default to upgrading old settings
+ switch (proxyType)
+ {
+ case PROXYTYPE_NONE:
+ clearProxyProperties();
+ break;
+ case PROXYTYPE_SYSTEM: // use system settings
+ resetProxyProperties();
+ break;
+ case PROXYTYPE_CUSTOM: // use specified proxy settings
+ String httpHost = getDefault("PROXY_SERVER", "");
+ String httpPort = getDefault("PROXY_PORT", "8080");
+ String httpsHost = getDefault("PROXY_SERVER_HTTPS", httpHost);
+ String httpsPort = getDefault("PROXY_PORT_HTTPS", httpPort);
+ String httpUser = getDefault("PROXY_AUTH_USER", null);
+ // https.proxyUser and https.proxyPassword are not able to be
+ // independently set in Preferences yet (or http.nonProxyHosts)
+ String httpsUser = getDefault("PROXY_AUTH_USER_HTTPS", httpUser);
+ setProxyProperties(httpHost, httpPort, httpsHost, httpsPort, httpUser,
+ proxyAuthPassword, httpsUser, proxyAuthPassword, "localhost");
+ break;
+ default:
+ String message = "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ + proxyType;
+ Cache.warn(message);
}
// LOAD THE AUTHORS FROM THE authors.props file
}
if (authorDetails == null)
{
- applicationProperties.remove("AUTHORS");
- applicationProperties.remove("AUTHORFNAMES");
- applicationProperties.remove("YEAR");
+ applicationProperties.remove("AUTHORS");
+ applicationProperties.remove("AUTHORFNAMES");
+ applicationProperties.remove("YEAR");
}
loadBuildProperties(false);
String jnlpVersion = System.getProperty("jalview.version");
- // jnlpVersion will be null if a latest version check for the channel needs to
- // be done
+ // jnlpVersion will be null if a latest version check for the channel needs
+ // to be done
// Dont do this check if running in headless mode
if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
{
- new Thread()
+
+ class VersionChecker extends Thread
{
@Override
public void run()
setProperty("LATEST_VERSION", remoteVersion);
}
- }.start();
+ }
+
+ VersionChecker vc = new VersionChecker();
+ vc.start();
}
else
{
url = Cache.class.getResource(resourcePath).toString();
} catch (Exception ex)
{
- System.err.println("Failed to resolve resource " + resourcePath + ": "
- + ex.getMessage());
+ System.err.println("Failed to resolve resource " + resourcePath
+ + ": " + ex.getMessage());
}
}
else
new BuildDetails(codeVersion, null, codeInstallation);
if (printVersion && reportVersion)
{
- System.out
- .println("Jalview Version: " + codeVersion + codeInstallation);
+ System.out.println(
+ "Jalview Version: " + codeVersion + codeInstallation);
}
}
public static String getVersionDetailsForConsole()
{
StringBuilder sb = new StringBuilder();
- sb.append("Jalview Version: " + jalview.bin.Cache.getDefault("VERSION", "TEST"));
+ sb.append("Jalview Version: ");
+ sb.append(jalview.bin.Cache.getDefault("VERSION", "TEST"));
sb.append("\n");
- sb.append("Jalview Installation: "
- + jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
+ sb.append("Jalview Installation: ");
+ sb.append(jalview.bin.Cache.getDefault("INSTALLATION", "unknown"));
sb.append("\n");
- sb.append("Build Date: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
+ sb.append("Build Date: ");
+ sb.append(jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"));
sb.append("\n");
- sb.append("Java version: " + System.getProperty("java.version"));
+ sb.append("Java version: ");
+ sb.append(System.getProperty("java.version"));
sb.append("\n");
- sb.append(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version"));
+ sb.append(System.getProperty("os.arch"));
+ sb.append(" ");
+ sb.append(System.getProperty("os.name"));
+ sb.append(" ");
+ sb.append(System.getProperty("os.version"));
sb.append("\n");
appendIfNotNull(sb, "Install4j version: ",
System.getProperty("sys.install4jVersion"), "\n", null);
appendIfNotNull(sb, "Launcher version: ",
System.getProperty("launcher_version"), "\n", null);
LookAndFeel laf = UIManager.getLookAndFeel();
- String lafName = laf == null?"Not obtained":laf.getName();
- String lafClass = laf == null?"unknown":laf.getClass().getName();
- appendIfNotNull(sb, "LookAndFeel: ", lafName+" ("+lafClass+")", "\n", null);
- // Not displayed in release version ( determined by possible version number regex 9[9.]*9[.-_a9]* )
- if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$", jalview.bin.Cache.getDefault("VERSION", "TEST"))) {
+ String lafName = laf == null ? "Not obtained" : laf.getName();
+ String lafClass = laf == null ? "unknown" : laf.getClass().getName();
+ sb.append("LookAndFeel: ");
+ sb.append(lafName);
+ sb.append(" (");
+ sb.append(lafClass);
+ sb.append(")\n");
+ // Not displayed in release version ( determined by possible version number
+ // regex 9[9.]*9[.-_a9]* )
+ if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
+ jalview.bin.Cache.getDefault("VERSION", "TEST")))
+ {
appendIfNotNull(sb, "Getdown appdir: ",
System.getProperty("getdownappdir"), "\n", null);
appendIfNotNull(sb, "Java home: ", System.getProperty("java.home"),
// eg 'built from Source' or update channel
return jalview.bin.Cache.getDefault("INSTALLATION", "unknown");
}
-}
+
+ public static String getStackTraceString(Throwable t)
+ {
+ StringWriter sw = new StringWriter();
+ PrintWriter pw = new PrintWriter(sw);
+ t.printStackTrace(pw);
+ return sw.toString();
+ }
+
+ // proxy properties methods
+ public static void clearProxyProperties()
+ {
+ setProxyProperties(null, null, null, null, null, null, null, null,
+ null);
+ }
+
+ public static void resetProxyProperties()
+ {
+ setProxyProperties(startupProxyProperties[0], startupProxyProperties[1],
+ startupProxyProperties[2], startupProxyProperties[3],
+ startupProxyProperties[4],
+ startupProxyProperties[5] == null ? null
+ : startupProxyProperties[5].toCharArray(),
+ startupProxyProperties[6],
+ startupProxyProperties[7] == null ? null
+ : startupProxyProperties[7].toCharArray(),
+ startupProxyProperties[8]);
+ StringBuilder sb = new StringBuilder();
+ sb.append("Setting proxy properties to: http.proxyHost=")
+ .append(startupProxyProperties[0]).append(", http.proxyPort=")
+ .append(startupProxyProperties[1])
+ .append(startupProxyProperties[4] != null
+ && !startupProxyProperties[4].isEmpty()
+ ? " [" + startupProxyProperties[4] + "]"
+ : "")
+ .append(", https.proxyHost=").append(startupProxyProperties[2])
+ .append(", https.proxyPort=").append(startupProxyProperties[3])
+ .append(startupProxyProperties[6] != null
+ && !startupProxyProperties[6].isEmpty()
+ ? " [" + startupProxyProperties[6] + "]"
+ : "");
+
+ Cache.debug(sb.toString());
+ }
+
+ public static void setProxyPropertiesFromPreferences()
+ {
+ setProxyPropertiesFromPreferences(Cache.PROXYTYPE_SYSTEM);
+ }
+
+ public static void setProxyPropertiesFromPreferences(
+ String previousProxyType)
+ {
+ String proxyType = Cache.getDefault("USE_PROXY",
+ Cache.PROXYTYPE_SYSTEM);
+ if (previousProxyType != null
+ && !proxyType.equals(Cache.PROXYTYPE_CUSTOM) // always apply
+ // customProxy
+ && proxyType.equals(previousProxyType))
+ {
+ // no change
+ return;
+ }
+ switch (proxyType)
+ {
+ case Cache.PROXYTYPE_NONE:
+ if (!previousProxyType.equals(proxyType))
+ {
+ Cache.log.info("Setting no proxy settings");
+ Cache.setProxyProperties(null, null, null, null, null, null, null,
+ null, null);
+ }
+ break;
+ case Cache.PROXYTYPE_CUSTOM:
+ // always re-set a custom proxy -- it might have changed, particularly
+ // password
+ Cache.log.info("Setting custom proxy settings");
+ boolean proxyAuthSet = Cache.getDefault("PROXY_AUTH", false);
+ Cache.setProxyProperties(Cache.getDefault("PROXY_SERVER", null),
+ Cache.getDefault("PROXY_PORT", null),
+ Cache.getDefault("PROXY_SERVER_HTTPS", null),
+ Cache.getDefault("PROXY_PORT_HTTPS", null),
+ proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+ : null,
+ proxyAuthSet ? Cache.proxyAuthPassword : null,
+ proxyAuthSet ? Cache.getDefault("PROXY_AUTH_USERNAME", "")
+ : null,
+ proxyAuthSet ? Cache.proxyAuthPassword : null, "localhost");
+ break;
+ default: // system proxy settings by default
+ Cache.log.info("Setting system proxy settings");
+ Cache.resetProxyProperties();
+ }
+ }
+
+ public static void setProxyProperties(String httpHost, String httpPort,
+ String httpsHost, String httpsPort, String httpUser,
+ char[] httpPassword, String httpsUser, char[] httpsPassword,
+ String nonProxyHosts)
+ {
+ setOrClearSystemProperty("http.proxyHost", httpHost);
+ setOrClearSystemProperty("http.proxyPort", httpPort);
+ setOrClearSystemProperty("https.proxyHost", httpsHost);
+ setOrClearSystemProperty("https.proxyPort", httpsPort);
+ setOrClearSystemProperty("http.proxyUser", httpUser);
+ setOrClearSystemProperty("https.proxyUser", httpsUser);
+ // note: passwords for http.proxyPassword and https.proxyPassword are sent
+ // via the Authenticator, properties do not need to be set
+
+ // are we using a custom proxy (password prompt might be required)?
+ boolean customProxySet = getDefault("USE_PROXY", PROXYTYPE_SYSTEM)
+ .equals(PROXYTYPE_CUSTOM);
+
+ /*
+ * A bug in Java means the AuthCache does not get reset, so once it has working credentials,
+ * it never asks for more, so changing the Authenticator has no effect (as getPasswordAuthentication()
+ * is not re-called).
+ * This could lead to password leak to a hostile proxy server, so I'm putting in a hack to clear
+ * the AuthCache.
+ * see https://www.generacodice.com/en/articolo/154918/Reset-the-Authenticator-credentials
+ * ...
+ * Turns out this is only accessible in Java 8, and not in Java 9 onwards, so commenting out
+ */
+ /*
+ try
+ {
+ sun.net.www.protocol.http.AuthCacheValue
+ .setAuthCache(new sun.net.www.protocol.http.AuthCacheImpl());
+ } catch (Throwable t)
+ {
+ Cache.error(t.getMessage());
+ Cache.debug(getStackTraceString(t));
+ }
+ */
+
+ if (httpUser != null || httpsUser != null)
+ {
+ try
+ {
+ char[] displayHttpPw = new char[httpPassword == null ? 0
+ : httpPassword.length];
+ Arrays.fill(displayHttpPw, '*');
+ Cache.debug("CACHE Proxy: setting new Authenticator with httpUser='"
+ + httpUser + "' httpPassword='" + displayHttpPw + "'");
+ Authenticator.setDefault(new Authenticator()
+ {
+ @Override
+ protected PasswordAuthentication getPasswordAuthentication()
+ {
+ if (getRequestorType() == RequestorType.PROXY)
+ {
+ String protocol = getRequestingProtocol();
+ boolean needProxyPasswordSet = false;
+ 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("https")
+ && (httpsUser != null
+ && httpsUser.length() > 0
+ && (httpsPassword == null
+ || httpsPassword.length == 0))))
+ {
+ // open Preferences -> Connections
+ String message = MessageManager
+ .getString("label.proxy_password_required");
+ Preferences.openPreferences(Preferences.CONNECTIONS_TAB,
+ message);
+ Preferences.getInstance()
+ .proxyAuthPasswordCheckHighlight(true, true);
+ }
+ else
+ {
+ try
+ {
+ if (protocol.equalsIgnoreCase("http")
+ && getRequestingHost().equalsIgnoreCase(httpHost)
+ && getRequestingPort() == Integer
+ .valueOf(httpPort))
+ {
+ Cache.debug(
+ "AUTHENTICATOR returning PasswordAuthentication(\""
+ + httpUser + "\", '"
+ + new String(displayHttpPw) + "')");
+ return new PasswordAuthentication(httpUser,
+ httpPassword);
+ }
+ if (protocol.equalsIgnoreCase("https")
+ && getRequestingHost().equalsIgnoreCase(httpsHost)
+ && getRequestingPort() == Integer
+ .valueOf(httpsPort))
+ {
+ char[] displayHttpsPw = new char[httpPassword.length];
+ Arrays.fill(displayHttpsPw, '*');
+ Cache.debug(
+ "AUTHENTICATOR returning PasswordAuthentication(\""
+ + httpsUser + "\", '" + displayHttpsPw
+ + "'");
+ return new PasswordAuthentication(httpsUser,
+ httpsPassword);
+ }
+ } catch (NumberFormatException e)
+ {
+ Cache.error("Problem with proxy port values [http:"
+ + httpPort + ", https:" + httpsPort + "]");
+ }
+ Cache.debug(
+ "AUTHENTICATOR after trying to get PasswordAuthentication");
+ }
+ }
+ // non proxy request
+ Cache.debug("AUTHENTICATOR returning null");
+ return null;
+ }
+ });
+ // required to re-enable basic authentication (should be okay for a
+ // local proxy)
+ Cache.debug(
+ "AUTHENTICATOR setting property 'jdk.http.auth.tunneling.disabledSchemes' to \"\"");
+ System.setProperty("jdk.http.auth.tunneling.disabledSchemes", "");
+ } catch (SecurityException e)
+ {
+ Cache.error("Could not set default Authenticator");
+ Cache.debug(getStackTraceString(e));
+ }
+ }
+ else
+ {
+ // reset the Authenticator to protect http.proxyUser and
+ // http.proxyPassword Just In Case
+ /* as noted above, due to bug in java this doesn't work if the sun.net.www.protocol.http.AuthCache
+ * has working credentials. No workaround for Java 11.
+ */
+ Cache.debug("AUTHENTICATOR setting default Authenticator to null");
+ Authenticator.setDefault(null);
+ }
+
+ // nonProxyHosts not currently configurable in Preferences
+ Cache.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ + nonProxyHosts + "\"");
+ setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
+ }
+
+ public static void setOrClearSystemProperty(String key, char[] value)
+ {
+ setOrClearSystemProperty(key,
+ (value == null) ? null : new String(value));
+ }
+
+ public static void setOrClearSystemProperty(String key, String value)
+ {
+ if (key == null)
+ {
+ return;
+ }
+ if (value == null)
+ {
+ System.clearProperty(key);
+ }
+ else
+ {
+ System.setProperty(key, value);
+ }
+ }
+
+ public final static int TRACE = 10;
+
+ public final static int DEBUG = 20;
+
+ public final static int INFO = 30;
+
+ public final static int WARN = 40;
+
+ public final static int ERROR = 50;
+
+ public static boolean println(int level, String message)
+ {
+ if (Cache.log == null)
+ {
+ if (level >= WARN)
+ System.err.println(message);
+ else if (level >= INFO)
+ System.out.println(message);
+ // not printing debug or trace messages
+ return false;
+ }
+ if (level >= ERROR)
+ {
+ Cache.log.error(message);
+ }
+ else if (level >= WARN)
+ {
+ Cache.log.warn(message);
+ }
+ else if (level >= INFO)
+ {
+ Cache.log.info(message);
+ }
+ else if (level >= DEBUG)
+ {
+ Cache.log.debug(message);
+ }
+ else
+ {
+ Cache.log.trace(message);
+ }
+ return true;
+ }
+
+ public static void trace(String message)
+ {
+ println(TRACE, message);
+ }
+
+ public static void debug(String message)
+ {
+ println(DEBUG, message);
+ }
+
+ public static void info(String message)
+ {
+ println(INFO, message);
+ }
+
+ public static void warn(String message)
+ {
+ println(WARN, message);
+ }
+
+ public static void error(String message)
+ {
+ println(ERROR, message);
+ }
+}
\ No newline at end of file
package jalview.bin;
-import java.awt.Toolkit;
+import java.awt.HeadlessException;
public class HiDPISetting
{
- public static final int dpi;
+ private static final int hidpiThreshold = 160;
- public static final int scale;
+ private static final int hidpiMultiThreshold = 240;
- private static final int hidpi = 110;
+ private static final int bigScreenThreshold = 1400;
- private static final String scaleProperty = "sun.java2d.uiScale";
+ public static final String scalePropertyName = "sun.java2d.uiScale";
- private static final boolean isAMac = System.getProperty("os.name")
- .indexOf("Mac") > -1;
+ private static final boolean isLinux;
- private static final boolean isLinux = System.getProperty("os.name")
- .toLowerCase().indexOf("linux") > -1;
+ // private static final boolean isAMac;
- private static final boolean isWindows = System.getProperty("os.name")
- .toLowerCase().indexOf("windows") > -1;
+ // private static final boolean isWindows;
+
+ public static final String setHiDPIPropertyName = "setHiDPI";
+
+ public static final String setHiDPIScalePropertyName = "setHiDPIScale";
+
+ private static boolean setHiDPI = false;
+
+ private static int setHiDPIScale = 0;
+
+ public static int dpi = 0;
+
+ public static int mindimension = 0;
+
+ public static int width = 0;
+
+ public static int scale = 0;
+
+ private static boolean doneInit = false;
+
+ private static boolean allowScalePropertyArg = false;
+
+ private static ScreenInfo screenInfo = new ScreenInfo();
static
{
- dpi = Toolkit.getDefaultToolkit().getScreenResolution();
- scale = dpi / hidpi + 1;
- if (scale > 1 && isLinux)
+ String system = System.getProperty("os.name") == null ? null
+ : System.getProperty("os.name").toLowerCase();
+ if (system != null)
+ {
+ isLinux = system.indexOf("linux") > -1;
+ // isAMac = system.indexOf("mac") > -1;
+ // isWindows = system.indexOf("windows") > -1;
+ }
+ else
{
- System.out.println("DPI detected as " + dpi
- + ". Scaling factor set to " + scale + ".");
+ isLinux = false;
+ // isAMac = isWindows = false;
}
}
- public static String getScalePropertyArg()
+ private static void init()
{
- // HiDPI setting. Just looking at Linux to start with. Test with Windows.
- if (!isLinux)
+ if (doneInit)
{
- return null;
+ return;
}
- if (scale > 1)
+
+ // get and use command line property values first
+ String setHiDPIProperty = System.getProperty(setHiDPIPropertyName);
+ setHiDPI = setHiDPIProperty != null
+ && setHiDPIProperty.equalsIgnoreCase("true");
+
+ String setHiDPIScaleProperty = System
+ .getProperty(setHiDPIScalePropertyName);
+ if (setHiDPIScaleProperty != null)
+ {
+ try
+ {
+ setHiDPIScale = Integer.parseInt(setHiDPIScaleProperty);
+ } catch (NumberFormatException e)
+ {
+ System.err.println(setHiDPIScalePropertyName + " property give ("
+ + setHiDPIScaleProperty + ") but not parseable as integer");
+ }
+ }
+ if (setHiDPI && setHiDPIScale > 0)
+ {
+ setHiDPIScale(setHiDPIScale);
+ return;
+ }
+
+ // check to see if the scale property has already been set by something else
+ // (e.g. the OS)
+ String existingProperty = System.getProperty(scalePropertyName);
+ if (existingProperty != null)
+ {
+ try
+ {
+ int existingPropertyVal = Integer.parseInt(existingProperty);
+ System.out.println("Existing " + scalePropertyName + " is "
+ + existingPropertyVal);
+ if (existingPropertyVal > 1)
+ {
+ setHiDPIScale(existingPropertyVal);
+ return;
+ }
+ } catch (NumberFormatException e)
+ {
+ System.out.println("Could not convert property " + scalePropertyName
+ + " vale '" + existingProperty + "' to number");
+ }
+ }
+
+ // Try and auto guess a good scale based on reported DPI (not trustworthy)
+ // and screen resolution (more trustworthy)
+
+ // get screen dpi
+ screenInfo = getScreenInfo();
+ try
+ {
+ dpi = screenInfo.getScreenResolution();
+ } catch (HeadlessException e)
+ {
+ System.err.println("Cannot get screen resolution: " + e.getMessage());
+ }
+
+ // try and get screen size height and width
+ try
+ {
+ int height = screenInfo.getScreenHeight();
+ int width = screenInfo.getScreenWidth();
+ // using mindimension in case of portrait screens
+ mindimension = Math.min(height, width);
+ } catch (HeadlessException e)
+ {
+ System.err.println(
+ "Cannot get screen size height and width:" + e.getMessage());
+ }
+
+ // attempt at a formula for scaling based on screen dpi and mindimension.
+ // scale will be an integer >=1. This formula is based on some testing and
+ // guesswork!
+
+ // scale based on reported dpi. if dpi>hidpiThreshold then scale=2+multiples
+ // of hidpiMultiThreshold (else scale=1)
+ // (e.g. dpi of 110 scales 1. dpi of 120 scales 2. dpi of 360 scales 3)
+ int dpiScale = (dpi - hidpiThreshold > 0)
+ ? 2 + ((dpi - hidpiThreshold) / hidpiMultiThreshold)
+ : 1;
+
+ int dimensionScale = 1 + (mindimension / bigScreenThreshold);
+
+ // choose larger of dimensionScale or dpiScale (most likely dimensionScale
+ // as dpiScale often misreported)
+ int autoScale = Math.max(dpiScale, dimensionScale);
+
+ // only make an automatic change if scale is changed and other conditions
+ // (OS is linux) apply, or if setHiDPI has been specified
+ if ((autoScale > 1 && isLinux) || setHiDPI)
+ {
+ setHiDPIScale(autoScale);
+ return;
+ }
+
+ // looks like we're not doing any scaling
+ doneInit = true;
+ }
+
+ public static void setHiDPIScale(int s)
+ {
+ scale = s;
+ allowScalePropertyArg = true;
+ doneInit = true;
+ }
+
+ public static String getScalePropertyArg(int s)
+ {
+ return "-D" + scalePropertyName + "=" + String.valueOf(s);
+ }
+
+ public static String getScalePropertyArg()
+ {
+ init();
+ // HiDPI setting. Just looking at Linux to start with. Test with Windows.
+ return allowScalePropertyArg ? getScalePropertyArg(scale) : null;
+ }
+
+ public static void clear()
+ {
+ setHiDPI = false;
+ setHiDPIScale = 0;
+ dpi = 0;
+ mindimension = 0;
+ width = 0;
+ scale = 0;
+ doneInit = false;
+ allowScalePropertyArg = false;
+ }
+
+ public static void setScreenInfo(ScreenInfo si)
+ {
+ screenInfo = si;
+ }
+
+ public static ScreenInfo getScreenInfo()
+ {
+ if (screenInfo == null)
{
- return "-D" + scaleProperty + "=" + scale;
+ screenInfo = new ScreenInfo();
}
- return null;
+ return screenInfo;
}
}
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.util.ChannelProperties;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
Platform.getURLCommandArguments();
}
- // singleton instance of this class
-
+ /*
+ * singleton instance of this class
+ */
private static Jalview instance;
private Desktop desktop;
"Invalid jabaws parameter: " + jabawsUrl + " ignored");
}
}
-
}
+
String defs = aparser.getValue("setprop");
while (defs != null)
{
{
Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
}
+ // DISABLED FOR SECURITY REASONS
+ // TODO: add a property to allow properties to be overriden by cli args
+ // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
}
defs = aparser.getValue("setprop");
}
desktop = null;
- // property laf = "crossplatform", "system", "gtk", "metal" or "mac"
- // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
- // try Quaqua/Vaqua.
- String lafProp = System.getProperty("laf");
- String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
- String laf = "none";
- if (lafProp != null)
- {
- laf = lafProp;
- }
- else if (lafSetting != null)
- {
- laf = lafSetting;
- }
- boolean lafSet = false;
- switch (laf)
- {
- case "crossplatform":
- lafSet = setCrossPlatformLookAndFeel();
- if (!lafSet)
- {
- System.err.println("Could not set requested laf=" + laf);
- }
- break;
- case "system":
- lafSet = setSystemLookAndFeel();
- if (!lafSet)
- {
- System.err.println("Could not set requested laf=" + laf);
- }
- break;
- case "gtk":
- lafSet = setGtkLookAndFeel();
- {
- System.err.println("Could not set requested laf=" + laf);
- }
- break;
- case "metal":
- lafSet = setMetalLookAndFeel();
- {
- System.err.println("Could not set requested laf=" + laf);
- }
- break;
- case "nimbus":
- lafSet = setNimbusLookAndFeel();
- {
- System.err.println("Could not set requested laf=" + laf);
- }
- break;
- case "quaqua":
- lafSet = setQuaquaLookAndFeel();
- {
- System.err.println("Could not set requested laf=" + laf);
- }
- break;
- case "vaqua":
- lafSet = setVaquaLookAndFeel();
- {
- System.err.println("Could not set requested laf=" + laf);
- }
- break;
- case "mac":
- lafSet = setMacLookAndFeel();
- if (!lafSet)
- {
- System.err.println("Could not set requested laf=" + laf);
- }
- break;
- case "none":
- break;
- default:
- System.err.println("Requested laf=" + laf + " not implemented");
- }
- if (!lafSet)
- {
- setSystemLookAndFeel();
- if (Platform.isLinux() && !Platform.isJS())
- {
- setMetalLookAndFeel();
- }
- if (Platform.isAMacAndNotJS())
- {
- setMacLookAndFeel();
- }
- }
+ setLookAndFeel();
/*
* configure 'full' SO model if preferences say to, else use the default (full SO)
if (!headless)
{
-
+ Desktop.nosplash = aparser.contains("nosplash");
desktop = new Desktop();
desktop.setInBatchMode(true); // indicate we are starting up
try
{
JalviewTaskbar.setTaskbar(this);
+ } catch (Exception e)
+ {
+ Cache.log.info("Cannot set Taskbar");
+ Cache.log.error(e.getMessage());
+ // e.printStackTrace();
} catch (Throwable t)
{
- System.out.println("Error setting Taskbar: " + t.getMessage());
+ Cache.log.info("Cannot set Taskbar");
+ Cache.log.error(t.getMessage());
+ // t.printStackTrace();
}
+ // set Proxy settings before all the internet calls
+ Cache.setProxyPropertiesFromPreferences();
+
desktop.setVisible(true);
if (!Platform.isJS())
* @j2sIgnore
*/
{
- desktop.startServiceDiscovery();
+ if (!aparser.contains("nowebservicediscovery"))
+ {
+ desktop.startServiceDiscovery();
+ }
if (!aparser.contains("nousagestats"))
{
startUsageStats(desktop);
* @j2sIgnore
*/
{
- if (!file.startsWith("http://") && !file.startsWith("https://"))
- // BH 2019 added https check for Java
+ if (!HttpUtils.startsWithHttpOrHttps(file))
{
if (!(new File(file)).exists())
{
Cache.removeProperty("STARTUP_FILE");
}
- protocol = DataSourceType.FILE;
-
- if (file.indexOf("http:") > -1)
- {
- protocol = DataSourceType.URL;
- }
+ protocol = AppletFormatAdapter.checkProtocol(file);
if (file.endsWith(".jar"))
{
}
}
- private static boolean setCrossPlatformLookAndFeel()
+ private static void setLookAndFeel()
{
- return setGenericLookAndFeel(false);
+ // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
+ // "mac"
+ // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
+ // try Quaqua/Vaqua.
+ String lafProp = System.getProperty("laf");
+ String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
+ String laf = "none";
+ if (lafProp != null)
+ {
+ laf = lafProp;
+ }
+ else if (lafSetting != null)
+ {
+ laf = lafSetting;
+ }
+ boolean lafSet = false;
+ switch (laf)
+ {
+ case "crossplatform":
+ lafSet = setCrossPlatformLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "system":
+ lafSet = setSystemLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "gtk":
+ lafSet = setGtkLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "metal":
+ lafSet = setMetalLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "nimbus":
+ lafSet = setNimbusLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "quaqua":
+ lafSet = setQuaquaLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "vaqua":
+ lafSet = setVaquaLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "mac":
+ lafSet = setMacLookAndFeel();
+ if (!lafSet)
+ {
+ Cache.log.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "none":
+ break;
+ default:
+ Cache.log.error("Requested laf=" + laf + " not implemented");
+ }
+ if (!lafSet)
+ {
+ setSystemLookAndFeel();
+ if (Platform.isLinux())
+ {
+ setMetalLookAndFeel();
+ }
+ if (Platform.isMac())
+ {
+ setMacLookAndFeel();
+ }
+ }
}
- private static boolean setSystemLookAndFeel()
+ private static boolean setCrossPlatformLookAndFeel()
{
- return setGenericLookAndFeel(true);
+ boolean set = false;
+ try
+ {
+ UIManager.setLookAndFeel(
+ UIManager.getCrossPlatformLookAndFeelClassName());
+ set = true;
+ } catch (Exception ex)
+ {
+ Cache.log.error("Unexpected Look and Feel Exception");
+ Cache.log.error(ex.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(ex));
+ }
+ return set;
}
- private static boolean setGenericLookAndFeel(boolean system)
+ private static boolean setSystemLookAndFeel()
{
boolean set = false;
try
{
- UIManager.setLookAndFeel(
- system ? UIManager.getSystemLookAndFeelClassName()
- : UIManager.getCrossPlatformLookAndFeelClassName());
+ UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
set = true;
} catch (Exception ex)
{
- System.err.println("Unexpected Look and Feel Exception");
- ex.printStackTrace();
+ Cache.log.error("Unexpected Look and Feel Exception");
+ Cache.log.error(ex.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(ex));
}
return set;
}
set = true;
} catch (Exception ex)
{
- System.err.println("Unexpected Look and Feel Exception");
- ex.printStackTrace();
+ Cache.log.error("Unexpected Look and Feel Exception");
+ Cache.log.error(ex.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(ex));
}
return set;
}
String scalePropertyArg = HiDPISetting.getScalePropertyArg();
if (scalePropertyArg != null)
{
+ System.out.println("Running " + startClass + " with scale setting "
+ + scalePropertyArg);
command.add(scalePropertyArg);
}
"LAUNCHER COMMAND: " + String.join(" ", builder.command()));
}
System.out.println("Running " + startClass + " with "
- + (memSetting == null ? "no memory setting" : memSetting));
+ + (memSetting == null ? "no memory setting"
+ : ("memory setting " + memSetting)));
if (Boolean.parseBoolean(System.getProperty("launcherstop", "false")))
{
private static final long GIGABYTE = 1073741824; // 1GB
- public static final long LEAVE_FREE_MIN_MEMORY = GIGABYTE/2;
+ public static final long LEAVE_FREE_MIN_MEMORY = GIGABYTE / 2;
- public static final long APPLICATION_MIN_MEMORY = GIGABYTE/2;
+ public static final long APPLICATION_MIN_MEMORY = GIGABYTE / 2;
private static final long MAX_HEAPSIZE_GB_DEFAULT = 32;
* values: jvmmempc - the maximum percentage of total physical memory to
* allocate, and jvmmemmax - the maximum absolute amount of physical memory to
* allocate. These can be provided as arguments. If not provided as arguments
- * (or set as null) system properties will be used instead (if set). The memory
- * setting returned will be the lower of the two values. If either of the values
- * are not provided then defaults will be used (jvmmempc=90, jvmmemmax=32GB). If
- * total physical memory can't be ascertained when jvmmempc was set or neither
- * jvmmempc nor jvmmemmax were set, then jvmmemmax defaults to a much safer 8GB.
- * In this case explicitly setting jvmmemmax and not setting jvmmempc can set a
- * higher memory for Jalview. The calculation also tries to ensure 0.5GB memory
- * for the OS, but also tries to ensure at least 0.5GB memory for Jalview (which
- * takes priority over the OS) If there is less then 0.5GB of physical memory
- * then the total physical memory is used for Jalview.
+ * (or set as null) system properties will be used instead (if set). The
+ * memory setting returned will be the lower of the two values. If either of
+ * the values are not provided then defaults will be used (jvmmempc=90,
+ * jvmmemmax=32GB). If total physical memory can't be ascertained when
+ * jvmmempc was set or neither jvmmempc nor jvmmemmax were set, then jvmmemmax
+ * defaults to a much safer 8GB. In this case explicitly setting jvmmemmax and
+ * not setting jvmmempc can set a higher memory for Jalview. The calculation
+ * also tries to ensure 0.5GB memory for the OS, but also tries to ensure at
+ * least 0.5GB memory for Jalview (which takes priority over the OS) If there
+ * is less then 0.5GB of physical memory then the total physical memory is
+ * used for Jalview.
*
* @param jvmmemmaxarg
- * Maximum value of memory to set. This can be a numeric
- * string optionally followed by "b", "k", "m", "g", "t"
- * (case insensitive) to indicate bytes, kilobytes,
- * megabytes, gigabytes, terabytes respectively. If null a
- * default value of 32G will be used. If null and either
- * physical memory can't be determined then the default is
- * 8GB.
+ * Maximum value of memory to set. This can be a numeric string
+ * optionally followed by "b", "k", "m", "g", "t" (case insensitive)
+ * to indicate bytes, kilobytes, megabytes, gigabytes, terabytes
+ * respectively. If null a default value of 32G will be used. If null
+ * and either physical memory can't be determined then the default is
+ * 8GB.
* @param jvmmempcarg
- * Max percentage of physical memory to use. Defaults to
- * "90".
+ * Max percentage of physical memory to use. Defaults to "90".
*
* @return The amount of memory (in bytes) to allocate to Jalview
*/
{
memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
System.out.println("MemorySetting Property '"
- + MAX_HEAPSIZE_PROPERTY_NAME
- + "' ("
- + jvmmemmaxarg + "') badly formatted, using default ("
+ + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ + "') badly formatted, using default ("
+ MAX_HEAPSIZE_GB_DEFAULT + "g).");
}
if (Long.MAX_VALUE / memmax < multiplier)
{
memmax = MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE;
- System.out.println(
- "MemorySetting Property '" + MAX_HEAPSIZE_PROPERTY_NAME + "' ("
- + jvmmemmaxarg
- + ") too big, using default ("
- + MAX_HEAPSIZE_GB_DEFAULT + "g).");
+ System.out.println("MemorySetting Property '"
+ + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ + ") too big, using default (" + MAX_HEAPSIZE_GB_DEFAULT
+ + "g).");
}
else
{
if (memmax < APPLICATION_MIN_MEMORY)
{
memmax = APPLICATION_MIN_MEMORY;
- System.out.println(
- "MemorySetting Property '" + MAX_HEAPSIZE_PROPERTY_NAME + "' ("
- + jvmmemmaxarg
- + ") too small, using minimum ("
- + APPLICATION_MIN_MEMORY + ").");
+ System.out.println("MemorySetting Property '"
+ + MAX_HEAPSIZE_PROPERTY_NAME + "' (" + jvmmemmaxarg
+ + ") too small, using minimum (" + APPLICATION_MIN_MEMORY
+ + ").");
}
}
}
else
{
- System.out.println(
- "MemorySetting Property '"
- + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
- + "' should be in range 1..100. Using default "
- + percent + "%");
+ System.out.println("MemorySetting Property '"
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
+ + "' should be in range 1..100. Using default " + percent
+ + "%");
}
}
} catch (NumberFormatException e)
{
- System.out.println(
- "MemorySetting property '" + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME
- + "' (" + jvmmempcarg + ") badly formatted");
+ System.out.println("MemorySetting property '"
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
+ + ") badly formatted");
}
// catch everything in case of no com.sun.management.OperatingSystemMXBean
else
{
System.out.println("MemorySetting Property '"
- + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' (" + jvmmempcarg
- + ") too small. Using minimum (" + APPLICATION_MIN_MEMORY
- + ").");
+ + MAX_HEAPSIZE_PERCENT_PROPERTY_NAME + "' ("
+ + jvmmempcarg + ") too small. Using minimum ("
+ + APPLICATION_MIN_MEMORY + ").");
}
mempc = APPLICATION_MIN_MEMORY;
}
// jvmmempc was set OR neither jvmmempc nor jvmmemmax were set), let's cap
// maxMemLong to 8GB
if (memoryPercentError && mempc == -1
- && !(jvmmempcarg == null && jvmmemmaxarg != null) // the same as (jvmmempcarg != null || (jvmmempcarg == null && jvmmemmaxarg
+ && !(jvmmempcarg == null && jvmmemmaxarg != null) // the same as
+ // (jvmmempcarg !=
+ // null ||
+ // (jvmmempcarg ==
+ // null &&
+ // jvmmemmaxarg
// == null))
&& memmax > NOMEM_MAX_HEAPSIZE_GB_DEFAULT * GIGABYTE)
{
--- /dev/null
+package jalview.bin;
+
+import java.awt.Toolkit;
+
+public class ScreenInfo
+{
+ public int getScreenResolution()
+ {
+ return Toolkit.getDefaultToolkit().getScreenResolution();
+ }
+
+ public int getScreenHeight()
+ {
+ return (int) Toolkit.getDefaultToolkit().getScreenSize().getHeight();
+ }
+
+ public int getScreenWidth()
+ {
+ return (int) Toolkit.getDefaultToolkit().getScreenSize().getWidth();
+ }
+}
import java.beans.PropertyChangeEvent;
import java.io.File;
import java.io.FileWriter;
+import java.io.IOException;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.HttpUtils;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
*/
void init()
{
-// setBackground(Color.white); // BH 2019
-
+ // setBackground(Color.white); // BH 2019
+
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
Desktop.instance.closeAssociatedWindows();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
: DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
if (fileObject == null)
{
- DataSourceType protocol = (fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE);
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
+ fileName) ? DataSourceType.URL : DataSourceType.FILE;
newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
currentFileFormat);
}
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null || (currentFileFormat == null)
- || fileName.startsWith("http"))
+ || HttpUtils.startsWithHttpOrHttps(fileName))
{
saveAs_actionPerformed();
}
if (!lastSaveSuccessful)
{
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { lastFilenameSaved }),
- MessageManager.getString("label.error_saving_file"),
- JvOptionPane.WARNING_MESSAGE);
+ if (!Platform.isHeadless())
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }),
+ MessageManager.getString("label.error_saving_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ Cache.log.error(MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }));
+ }
}
else
{
String shortName = title;
if (shortName.indexOf(File.separatorChar) > -1)
{
- shortName = shortName.substring(
- shortName.lastIndexOf(File.separatorChar) + 1);
+ shortName = shortName
+ .substring(shortName.lastIndexOf(File.separatorChar) + 1);
}
- lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
-
+ lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
+ shortName);
+
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format }));
-
+ { file, format }));
+
return;
}
{
// create backupfiles object and get new temp filename destination
boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
+ BackupFiles backupfiles = null;
+ if (doBackup)
+ {
+ Cache.log.trace(
+ "ALIGNFRAME making backupfiles object for " + file);
+ backupfiles = new BackupFiles(file);
+ }
try
{
- String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
- PrintWriter out = new PrintWriter(
- new FileWriter(tempFilePath));
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath()
+ : file;
+ Cache.log.trace("ALIGNFRAME setting PrintWriter");
+ PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+
+ if (backupfiles != null)
+ {
+ Cache.log.trace("ALIGNFRAME about to write to temp file "
+ + backupfiles.getTempFilePath());
+ }
out.print(output);
+ Cache.log.trace("ALIGNFRAME about to close file");
out.close();
+ Cache.log.trace("ALIGNFRAME closed file");
AlignFrame.this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format.getName() }));
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format.getName() }));
lastSaveSuccessful = true;
+ } catch (IOException e)
+ {
+ lastSaveSuccessful = false;
+ Cache.log.error(
+ "ALIGNFRAME Something happened writing the temp file");
+ Cache.log.error(e.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(e));
} catch (Exception ex)
{
lastSaveSuccessful = false;
- ex.printStackTrace();
+ Cache.log.error(
+ "ALIGNFRAME Something unexpected happened writing the temp file");
+ Cache.log.error(ex.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(ex));
}
if (doBackup)
{
backupfiles.setWriteSuccess(lastSaveSuccessful);
+ Cache.log.debug("ALIGNFRAME writing temp file was "
+ + (lastSaveSuccessful ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
+ Cache.log.trace(
+ "ALIGNFRAME about to rollBackupsAndRenameTempFile");
lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ Cache.log.debug(
+ "ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ + (lastSaveSuccessful ? "" : "un")
+ + "successfully");
}
}
}
final JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- String tooltip = MessageManager.getString("label.load_jalview_annotations");
+ String tooltip = MessageManager
+ .getString("label.load_jalview_annotations");
chooser.setDialogTitle(tooltip);
chooser.setToolTipText(tooltip);
chooser.setResponseHandler(0, new Runnable()
}
/**
- * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode
+ * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
+ * or the sequence under cursor in keyboard mode
*
* @param up
* or down (if !up)
if (sg == null)
{
- if (viewport.cursorMode)
+ if (viewport.cursorMode)
{
sg = new SequenceGroup();
- sg.addSequence(viewport.getAlignment()
- .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
- } else {
+ sg.addSequence(viewport.getAlignment().getSequenceAt(
+ alignPanel.getSeqPanel().seqCanvas.cursorY), false);
+ }
+ else
+ {
return;
}
}
-
+
if (sg.getSize() < 1)
{
- return;
+ return;
}
-
+
// TODO: JAL-3733 - add an event to the undo buffer for this !
-
+
viewport.getAlignment().moveSelectedSequencesByOne(sg,
viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true, false);
return;
}
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
-
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
-
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
- {
- try
- {
- AlignFrame.this.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
- }};
+ Runnable okAction = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
+
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(),
+ sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
+
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ };
/*
* If the cut affects all sequences, prompt for confirmation
*/
- boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
+ boolean wholeHeight = sg.getSize() == viewport.getAlignment()
+ .getHeight();
boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
+ 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (wholeHeight && wholeWidth)
- {
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
- dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
- Object[] options = new Object[] { MessageManager.getString("action.ok"),
- MessageManager.getString("action.cancel") };
- dialog.showDialog(MessageManager.getString("warn.delete_all"),
- MessageManager.getString("label.delete_all"),
- JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
- options, options[0]);
- } else
- {
- okAction.run();
- }
+ if (wholeHeight && wholeWidth)
+ {
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+ Object[] options = new Object[] {
+ MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ dialog.showDialog(MessageManager.getString("warn.delete_all"),
+ MessageManager.getString("label.delete_all"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ }
+ else
+ {
+ okAction.run();
+ }
}
/**
column, viewport.getAlignment());
}
- setStatus(MessageManager
- .formatMessage("label.removed_columns", new String[]
+ setStatus(MessageManager.formatMessage("label.removed_columns",
+ new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
- setStatus(MessageManager
- .formatMessage("label.removed_empty_columns", new Object[]
+ setStatus(MessageManager.formatMessage("label.removed_empty_columns",
+ new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
if (viewport.getViewName() == null)
{
- viewport.setViewName(MessageManager
- .getString("label.view_name_original"));
+ viewport.setViewName(
+ MessageManager.getString("label.view_name_original"));
}
/*
JLabel textLabel = new JLabel();
textLabel.setText(content);
textLabel.setBackground(Color.WHITE);
-
+
pane = new JPanel(new BorderLayout());
((JPanel) pane).setOpaque(true);
pane.setBackground(Color.WHITE);
* otherwise set the chosen colour scheme (or null for 'None')
*/
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
- viewport,
- viewport.getAlignment(), viewport.getHiddenRepSequences());
+ viewport, viewport.getAlignment(),
+ viewport.getHiddenRepSequences());
changeColour(cs);
}
Enumeration<String> labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
- addSortByAnnotScoreMenuItem(sortByAnnotScore,
- labels.nextElement());
+ addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- chooser.setResponseHandler(0,new Runnable()
+ chooser.setResponseHandler(0, new Runnable()
{
@Override
public void run()
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = secstrpr
- .get(i);
+ final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
int p = secstrmenu.getItemCount();
if (protocol == DataSourceType.FILE)
{
File fl;
- if (file instanceof File) {
+ if (file instanceof File)
+ {
fl = (File) file;
Platform.cacheFileData(fl);
- } else {
+ }
+ else
+ {
fl = new File(fileName);
}
pdbfn = fl.getName();
}
private Rectangle lastFeatureSettingsBounds = null;
+
@Override
public void setFeatureSettingsGeometry(Rectangle bounds)
{
*/
package jalview.gui;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
+import java.awt.Color;
import java.awt.Dimension;
import java.awt.GraphicsEnvironment;
+import java.awt.GridBagConstraints;
+import java.awt.GridBagLayout;
import java.awt.Rectangle;
import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.StringSelection;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.awt.event.WindowListener;
import java.io.PrintStream;
import javax.swing.JButton;
+import javax.swing.JComboBox;
import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
+import org.apache.log4j.Level;
import org.apache.log4j.SimpleLayout;
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
/**
* Simple Jalview Java Console. Version 1 - allows viewing of console output
* after desktop is created. Acquired with thanks from RJHM's site
private int MIN_HEIGHT = 250;
+ private JComboBox<Level> logLevelCombo = new JComboBox<Level>();
+
+ protected Level startingLogLevel = Level.INFO;
+
public Console()
{
// create all components and add them
// textArea = cpt.getTextArea();
textArea = new JTextArea();
textArea.setEditable(false);
- JButton button = new JButton(MessageManager.getString("action.clear"));
+ JButton clearButton = new JButton(
+ MessageManager.getString("action.clear"));
+ JButton copyToClipboardButton = new JButton(
+ MessageManager.getString("label.copy_to_clipboard"));
+ copyToClipboardButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ copyConsoleTextToClipboard();
+ }
+ });
+ copyToClipboardButton.addMouseListener(new MouseAdapter()
+ {
+ private Color bg = textArea.getBackground();
+
+ private Color fg = textArea.getForeground();
+
+ public void mousePressed(MouseEvent e)
+ {
+ textArea.setBackground(textArea.getSelectionColor());
+ textArea.setForeground(textArea.getSelectedTextColor());
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ textArea.setBackground(bg);
+ textArea.setForeground(fg);
+ }
+
+ });
+ copyToClipboardButton.setToolTipText(
+ MessageManager.getString("label.copy_to_clipboard_tooltip"));
+
+ JLabel logLevelLabel = new JLabel(
+ MessageManager.getString("label.log_level") + ":");
+
+ // logLevelCombo.addItem(Level.ALL);
+ logLevelCombo.addItem(Level.TRACE);
+ logLevelCombo.addItem(Level.DEBUG);
+ logLevelCombo.addItem(Level.INFO);
+ logLevelCombo.addItem(Level.WARN);
+ // logLevelCombo.addItem(Level.ERROR);
+ // logLevelCombo.addItem(Level.FATAL);
+ // logLevelCombo.addItem(Level.OFF);
+ // set startingLogLevel
+ startingLogLevel = Cache.log == null ? Level.INFO
+ : Cache.log.getLevel();
+ setChosenLogLevelCombo();
+ logLevelCombo.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if (Cache.log != null)
+ {
+ Cache.log.setLevel((Level) logLevelCombo.getSelectedItem());
+ }
+ }
+
+ });
// frame = cpt;
frame.getContentPane().setLayout(new BorderLayout());
frame.getContentPane().add(new JScrollPane(textArea),
BorderLayout.CENTER);
- frame.getContentPane().add(button, BorderLayout.SOUTH);
+ JPanel southPanel = new JPanel();
+ southPanel.setLayout(new GridBagLayout());
+
+ JPanel logLevelPanel = new JPanel();
+ logLevelPanel.setAlignmentX(JPanel.LEFT_ALIGNMENT);
+ logLevelPanel.add(logLevelLabel);
+ logLevelPanel.add(logLevelCombo);
+ String logLevelTooltip = MessageManager.formatMessage(
+ "label.log_level_tooltip", startingLogLevel.toString());
+ logLevelLabel.setToolTipText(logLevelTooltip);
+ logLevelCombo.setToolTipText(logLevelTooltip);
+
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.gridx = 0;
+ gbc.gridy = 0;
+ gbc.gridwidth = 1;
+ gbc.gridheight = 1;
+ gbc.weightx = 0.1;
+ southPanel.add(logLevelPanel, gbc);
+
+ gbc.gridx++;
+ gbc.weightx = 0.8;
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ southPanel.add(clearButton, gbc);
+
+ gbc.gridx++;
+ gbc.weightx = 0.1;
+ gbc.fill = GridBagConstraints.NONE;
+ southPanel.add(copyToClipboardButton, gbc);
+
+ southPanel.setVisible(true);
+ frame.getContentPane().add(southPanel, BorderLayout.SOUTH);
frame.setVisible(visible);
updateConsole = visible;
frame.addWindowListener(this);
- button.addActionListener(this);
+ clearButton.addActionListener(this);
+
if (redirect)
{
redirectStreams();
textAppender.start();
}
+ private void setChosenLogLevelCombo()
+ {
+ setChosenLogLevelCombo(startingLogLevel);
+ }
+
+ private void setChosenLogLevelCombo(Level setLogLevel)
+ {
+ logLevelCombo.setSelectedItem(setLogLevel);
+ if (!logLevelCombo.getSelectedItem().equals(setLogLevel))
+ {
+ // setLogLevel not (yet) in list
+ if (setLogLevel != null && setLogLevel instanceof Level)
+ {
+ // add new item to list (might be set via .jalview_properties)
+ boolean added = false;
+ for (int i = 0; i < logLevelCombo.getItemCount(); i++)
+ {
+ Level l = (Level) logLevelCombo.getItemAt(i);
+ if (l.isGreaterOrEqual(setLogLevel))
+ {
+ logLevelCombo.insertItemAt(setLogLevel, i);
+ added = true;
+ break;
+ }
+ }
+ if (!added) // lower priority than others or some confusion -- add to
+ // end of list
+ {
+ logLevelCombo.addItem(setLogLevel);
+ }
+ logLevelCombo.setSelectedItem(setLogLevel);
+ }
+ else
+ {
+ logLevelCombo.setSelectedItem(Level.INFO);
+ }
+ }
+ }
+
+ private void copyConsoleTextToClipboard()
+ {
+ String consoleText = textArea.getText();
+ StringSelection consoleTextSelection = new StringSelection(consoleText);
+ Clipboard cb = Toolkit.getDefaultToolkit().getSystemClipboard();
+ cb.setContents(consoleTextSelection, null);
+ }
+
PipedOutputStream pout = null, perr = null;
public void redirectStreams()
frame.setVisible(selected);
if (selected == true)
{
+ setChosenLogLevelCombo();
redirectStreams();
updateConsole = true;
frame.toFront();
}
else
{
+ // reset log level to what it was before
+ if (Cache.log != null)
+ {
+ Cache.log.setLevel(startingLogLevel);
+ }
+
unredirectStreams();
updateConsole = false;
}
import java.awt.Dimension;
import java.awt.FontMetrics;
import java.awt.Graphics;
+import java.awt.Graphics2D;
import java.awt.GridLayout;
import java.awt.Point;
import java.awt.Rectangle;
import java.awt.event.MouseEvent;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.awt.geom.AffineTransform;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.File;
private JalviewChangeSupport changeSupport = new JalviewChangeSupport();
+ public static boolean nosplash = false;
+
/**
* news reader - null if it was never started.
*/
checkURLLinks();
// Spawn a thread that shows the splashscreen
-
- SwingUtilities.invokeLater(new Runnable()
+ if (!nosplash)
{
- @Override
- public void run()
+ SwingUtilities.invokeLater(new Runnable()
{
- new SplashScreen(true);
- }
- });
+ @Override
+ public void run()
+ {
+ new SplashScreen(true);
+ }
+ });
+ }
// Thread off a new instance of the file chooser - this reduces the time
// it
}
});
desktop.addMouseListener(ma);
-
}
/**
@Override
protected void preferences_actionPerformed(ActionEvent e)
{
- new Preferences();
+ Preferences.openPreferences();
}
/**
10, getHeight() - fm.getHeight());
}
}
+
+ // output debug scale message. Important for jalview.bin.HiDPISettingTest2
+ Desktop.debugScaleMessage(Desktop.getDesktop().getGraphics());
}
}
}
return result;
}
+
+ public static final String debugScaleMessage = "Desktop graphics transform scale=";
+
+ private static boolean debugScaleMessageDone = false;
+
+ public static void debugScaleMessage(Graphics g)
+ {
+ if (debugScaleMessageDone)
+ {
+ return;
+ }
+ // output used by tests to check HiDPI scaling settings in action
+ try
+ {
+ Graphics2D gg = (Graphics2D) g;
+ if (gg != null)
+ {
+ AffineTransform t = gg.getTransform();
+ double scaleX = t.getScaleX();
+ double scaleY = t.getScaleY();
+ Cache.debug(debugScaleMessage + scaleX + " (X)");
+ Cache.debug(debugScaleMessage + scaleY + " (Y)");
+ debugScaleMessageDone = true;
+ }
+ else
+ {
+ Cache.debug("Desktop graphics null");
+ }
+ } catch (Exception e)
+ {
+ Cache.debug(Cache.getStackTraceString(e));
+ }
+ }
}
* @author $author$
* @version $Revision$
*/
+/*
+ * for merge with Jalview-JS
+ public class Preferences extends GPreferences implements ApplicationSingletonI
+ */
public class Preferences extends GPreferences
{
public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
private static final int MAX_FONT_SIZE = 30;
+ private String previousProxyType;
+
+ private static Preferences INSTANCE = null; // add "final"
+
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
private OptionsParam textOpt = new OptionsParam(
MessageManager.getString("action.text"), "Text");
+ // get singleton Preferences instance
+ public static Preferences getInstance()
+ {
+ if (INSTANCE == null || INSTANCE.frame == null
+ || INSTANCE.frame.isClosed())
+ {
+ INSTANCE = new Preferences();
+ }
+ return INSTANCE;
+
+ /*
+ * Replace code with the following for Jalvew-JS
+ Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
+ if (INSTANCE == null || INSTANCE.frame == null
+ || INSTANCE.frame.isClosed())
+ {
+ ApplicationSingletonProvider.remove(Preferences.class);
+ INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
+ }
+ return INSTANCE;
+ */
+ }
+
+ public static void openPreferences()
+ {
+ openPreferences(0, null);
+ }
+
+ public static void openPreferences(int selectTab, String message)
+ {
+ Preferences p = getInstance();
+ p.selectTab(selectTab);
+ p.setMessage(message);
+ p.frame.show();
+ p.frame.moveToFront();
+ p.frame.grabFocus();
+ }
+
/**
* Creates a new Preferences object.
*/
- public Preferences()
+ private Preferences()
{
super();
frame = new JInternalFrame();
/*
* Set overview panel defaults
*/
- gapColour.setBackground(
- Cache.getDefaultColour(GAP_COLOUR,
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
- hiddenColour.setBackground(
- Cache.getDefaultColour(HIDDEN_COLOUR,
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+ gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+ hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
+ jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
gapLabel.setEnabled(!useLegacyGap.isSelected());
gapColour.setEnabled(!useLegacyGap.isSelected());
* set choice of structure viewer, and path if saved as a preference;
* default to Jmol (first choice) if an unexpected value is found
*/
- String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
+ String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
+ ViewerType.JMOL.name());
structViewer.setSelectedItem(viewerType);
String viewerPath = "";
ViewerType type = null;
{
if (validateViewerPath())
{
- Cache.setProperty(structViewer.getSelectedItem()
- .equals(ViewerType.CHIMERAX.name())
- ? CHIMERAX_PATH
- : CHIMERA_PATH, structureViewerPath.getText());
+ Cache.setProperty(
+ structViewer.getSelectedItem().equals(
+ ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH
+ : CHIMERA_PATH,
+ structureViewerPath.getText());
}
}
});
}
}
- useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
- useProxy_actionPerformed(); // make sure useProxy is correctly initialised
- proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
- proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+ String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
+ previousProxyType = proxyTypeString;
+ switch (proxyTypeString)
+ {
+ case Cache.PROXYTYPE_NONE:
+ proxyType.setSelected(noProxy.getModel(), true);
+ break;
+ case Cache.PROXYTYPE_SYSTEM:
+ proxyType.setSelected(systemProxy.getModel(), true);
+ break;
+ case Cache.PROXYTYPE_CUSTOM:
+ proxyType.setSelected(customProxy.getModel(), true);
+ break;
+ default:
+ Cache.log.warn(
+ "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ + proxyTypeString);
+ }
+ proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
+ proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
+ proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
+ proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
+ proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
+ proxyAuthUsernameTB
+ .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
+ // we are not storing or retrieving proxy password from .jalview_properties
+ proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
+ : new String(Cache.proxyAuthPassword));
+ setCustomProxyEnabled();
+ applyProxyButtonEnabled(false);
defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
annotations_actionPerformed(null); // update the display of the annotation
// settings
-
-
+
/*
* Set Backups tab defaults
*/
comboBox.addItem(promptEachTimeOpt);
comboBox.addItem(lineArtOpt);
comboBox.addItem(textOpt);
-
+
/*
* JalviewJS doesn't support Lineart so force it to Text
*/
return;
}
+ /*
+ * Set proxy settings first (to be before web services refresh)
+ */
+ saveProxySettings();
+
/*
* Save Visual settings
*/
Boolean.toString(structFromPdb.isSelected()));
String viewer = structViewer.getSelectedItem().toString();
String viewerPath = structureViewerPath.getText();
- Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
- viewer);
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
if (viewer.equals(ViewerType.CHIMERA.name()))
{
Cache.setOrRemove(CHIMERA_PATH, viewerPath);
/*
* Save Connections settings
*/
+ // Proxy settings set first (to catch web services)
+
Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
jalview.util.BrowserLauncher.resetBrowser();
Cache.applicationProperties.setProperty("DEFAULT_URL",
sequenceUrlLinks.getPrimaryUrlId());
- Cache.applicationProperties.setProperty("USE_PROXY",
- Boolean.toString(useProxy.isSelected()));
-
- Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
-
- Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
-
- if (useProxy.isSelected())
- {
- System.setProperty("http.proxyHost", proxyServerTB.getText());
- System.setProperty("http.proxyPort", proxyPortTB.getText());
- }
- else
- {
- System.setProperty("http.proxyHost", "");
- System.setProperty("http.proxyPort", "");
- }
Cache.setProperty("VERSION_CHECK",
Boolean.toString(versioncheck.isSelected()));
if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
Boolean.toString(enableBackupFiles.isSelected()));
int preset = getComboIntStringKey(backupfilesPresetsCombo);
- Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+ Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
+ Integer.toString(preset));
if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
{
BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
- Cache.applicationProperties
- .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
- customBFPE.toString());
+ Cache.applicationProperties.setProperty(
+ BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
}
BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
}
}
+ public void saveProxySettings()
+ {
+ String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
+ : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
+ : Cache.PROXYTYPE_SYSTEM;
+ Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
+ Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
+ Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
+ Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
+ Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
+ Cache.setOrRemove("PROXY_AUTH",
+ Boolean.toString(proxyAuth.isSelected()));
+ Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
+ Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
+ Cache.setProxyPropertiesFromPreferences(previousProxyType);
+ if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
+ || !newProxyType.equals(previousProxyType))
+ {
+ // force a re-lookup of ws if proxytype is custom or has changed
+ wsPrefs.update++;
+ }
+ previousProxyType = newProxyType;
+ }
+
/**
* Do any necessary validation before saving settings. Return focus to the
* first tab which fails validation.
if (!useLegacyGap.isSelected())
{
JalviewColourChooser.showColourChooser(this,
- MessageManager.getString("label.select_gap_colour"),
- gap);
+ MessageManager.getString("label.select_gap_colour"), gap);
}
}
public void hiddenColour_actionPerformed(JPanel hidden)
{
JalviewColourChooser.showColourChooser(this,
- MessageManager.getString("label.select_hidden_colour"),
- hidden);
+ MessageManager.getString("label.select_hidden_colour"), hidden);
}
@Override
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.jbgui.GWsPreferences;
-import jalview.util.MessageManager;
-import jalview.ws.jws2.Jws2Discoverer;
-import jalview.ws.rest.RestServiceDescription;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.util.Vector;
import javax.swing.JLabel;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JTable;
import javax.swing.JTextField;
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableCellRenderer;
+import jalview.bin.Cache;
+import jalview.jbgui.GWsPreferences;
+import jalview.util.MessageManager;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.rest.RestServiceDescription;
+
public class WsPreferences extends GWsPreferences
{
/**
* state counters for ensuring that updates only happen if config has changed.
*/
- private long update = 0, lastrefresh = 0;
+ protected long update = 0;
+
+ private long lastrefresh = 0;
/*
* (non-Javadoc)
*/
package jalview.io;
-import jalview.bin.Cache;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
import java.io.File;
import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.TreeMap;
+import jalview.bin.Cache;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
/*
* BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
* User configurable options are:
private static final SimpleDateFormat sdf = new SimpleDateFormat(
"yyyy-MM-dd HH:mm:ss");
+ private static final String newTempFileSuffix = "_newfile";
+
+ private static final String oldTempFileSuffix = "_oldfile_tobedeleted";
+
public BackupFiles(String filename)
{
this(new File(filename));
{
classInit();
this.file = file;
- BackupFilesPresetEntry bfpe = BackupFilesPresetEntry.getSavedBackupEntry();
+ BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+ .getSavedBackupEntry();
this.suffix = bfpe.suffix;
this.noMax = bfpe.keepAll;
this.max = bfpe.rollMax;
{
String tempfilename = file.getName();
File tempdir = file.getParentFile();
- temp = File.createTempFile(tempfilename, TEMP_FILE_EXT + "_newfile",
- tempdir);
+ Cache.trace(
+ "BACKUPFILES [file!=null] attempting to create temp file for "
+ + tempfilename + " in dir " + tempdir);
+ temp = File.createTempFile(tempfilename,
+ TEMP_FILE_EXT + newTempFileSuffix, tempdir);
+ Cache.debug(
+ "BACKUPFILES using temp file " + temp.getAbsolutePath());
}
else
{
+ Cache.trace(
+ "BACKUPFILES [file==null] attempting to create default temp file "
+ + DEFAULT_TEMP_FILE + " with extension "
+ + TEMP_FILE_EXT);
temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
}
} catch (IOException e)
{
- System.out.println(
- "Could not create temp file to save into (IOException)");
+ Cache.error("Could not create temp file to save to (IOException)");
+ Cache.error(e.getMessage());
+ Cache.debug(Cache.getStackTraceString(e));
} catch (Exception e)
{
- System.out.println("Exception ctreating temp file for saving");
+ Cache.error("Exception creating temp file for saving");
+ Cache.debug(Cache.getStackTraceString(e));
}
this.setTempFile(temp);
}
public static void classInit()
{
- setEnabled(Cache.getDefault(ENABLED, !Platform.isJS()));
+ Cache.initLogger();
+ Cache.trace("BACKUPFILES classInit");
+ boolean e = Cache.getDefault(ENABLED, !Platform.isJS());
+ setEnabled(e);
+ Cache.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
.getSavedBackupEntry();
+ Cache.trace("BACKUPFILES preset scheme " + bfpe.toString());
setConfirmDelete(bfpe.confirmDelete);
+ Cache.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
}
public static void setEnabled(boolean flag)
path = this.getTempFile().getCanonicalPath();
} catch (IOException e)
{
- System.out.println(
- "IOException when getting Canonical Path of temp file '"
- + this.getTempFile().getName() + "'");
+ Cache.error("IOException when getting Canonical Path of temp file '"
+ + this.getTempFile().getName() + "'");
+ Cache.debug(Cache.getStackTraceString(e));
}
return path;
}
public boolean renameTempFile()
{
- return tempFile.renameTo(file);
+ return moveFileToFile(tempFile, file);
}
// roll the backupfiles
|| suffix.length() == 0)
{
// nothing to do
+ Cache.debug("BACKUPFILES rollBackupFiles nothing to do." + ", "
+ + "filename: " + (file != null ? file.getName() : "null")
+ + ", " + "file exists: " + file.exists() + ", " + "enabled: "
+ + enabled + ", " + "max: " + max + ", " + "suffix: '" + suffix
+ + "'");
return true;
}
+ Cache.trace("BACKUPFILES rollBackupFiles starting");
+
String dir = "";
File dirFile;
try
{
dirFile = file.getParentFile();
dir = dirFile.getCanonicalPath();
+ Cache.trace("BACKUPFILES dir: " + dir);
} catch (Exception e)
{
- System.out.println(
- "Could not get canonical path for file '" + file + "'");
+ Cache.error("Could not get canonical path for file '" + file + "'");
+ Cache.error(e.getMessage());
+ Cache.debug(Cache.getStackTraceString(e));
return false;
}
String filename = file.getName();
String basename = filename;
+ Cache.trace("BACKUPFILES filename is " + filename);
boolean ret = true;
// Create/move backups up one
File[] backupFiles = dirFile.listFiles(bff);
int nextIndexNum = 0;
+ Cache.trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
if (backupFiles.length == 0)
{
// No other backup files. Just need to move existing file to backupfile_1
+ Cache.trace(
+ "BACKUPFILES no existing backup files, setting index to 1");
nextIndexNum = 1;
}
else
if (reverseOrder)
{
// backup style numbering
-
+ Cache.trace("BACKUPFILES rolling files in reverse order");
int tempMax = noMax ? -1 : max;
// noMax == true means no limits
tempMax = i;
}
}
-
+
File previousFile = null;
File fileToBeDeleted = null;
for (int n = tempMax; n > 0; n--)
// no "oldest" file to delete
previousFile = backupfile_n;
fileToBeDeleted = null;
+ Cache.trace("BACKUPFILES No oldest file to delete");
continue;
}
File replacementFile = backupfile_n;
long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
long replacementFileLMT = replacementFile.lastModified();
+ Cache.trace("BACKUPFILES fileToBeDeleted is "
+ + fileToBeDeleted.getAbsolutePath());
+ Cache.trace("BACKUPFILES replacementFile is "
+ + backupfile_n.getAbsolutePath());
try
{
File oldestTempFile = nextTempFile(fileToBeDeleted.getName(),
dirFile);
-
+
if (fileToBeDeletedLMT > replacementFileLMT)
{
String fileToBeDeletedLMTString = sdf
.format(fileToBeDeletedLMT);
String replacementFileLMTString = sdf
.format(replacementFileLMT);
- System.out.println("WARNING! I am set to delete backupfile "
+ Cache.warn("WARNING! I am set to delete backupfile "
+ fileToBeDeleted.getName()
+ " has modification time "
+ fileToBeDeletedLMTString
boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, true);
+ Cache.trace("BACKUPFILES " + (delete ? "confirmed" : "not")
+ + " deleting file "
+ + fileToBeDeleted.getAbsolutePath()
+ + " which is newer than "
+ + replacementFile.getAbsolutePath());
if (delete)
{
}
else
{
- fileToBeDeleted.renameTo(oldestTempFile);
+ Cache.debug("BACKUPFILES moving "
+ + fileToBeDeleted.getAbsolutePath() + " to "
+ + oldestTempFile.getAbsolutePath());
+ moveFileToFile(fileToBeDeleted, oldestTempFile);
}
}
else
{
- fileToBeDeleted.renameTo(oldestTempFile);
+ Cache.debug("BACKUPFILES going to move "
+ + fileToBeDeleted.getAbsolutePath() + " to "
+ + oldestTempFile.getAbsolutePath());
+ moveFileToFile(fileToBeDeleted, oldestTempFile);
addDeleteFile(oldestTempFile);
}
} catch (Exception e)
{
- System.out.println(
+ Cache.error(
"Error occurred, probably making new temp file for '"
+ fileToBeDeleted.getName() + "'");
- e.printStackTrace();
+ Cache.error(Cache.getStackTraceString(e));
}
// reset
{
if (previousFile != null)
{
- ret = ret && backupfile_n.renameTo(previousFile);
+ // using boolean '&' instead of '&&' as don't want moveFileToFile
+ // attempt to be conditional (short-circuit)
+ ret = ret & moveFileToFile(backupfile_n, previousFile);
}
}
// index to use for the latest backup
nextIndexNum = 1;
}
- else
+ else // not reverse numbering
{
// version style numbering (with earliest file deletion if max files
// reached)
bfTreeMap.values().toArray(backupFiles);
+ StringBuilder bfsb = new StringBuilder();
+ for (int i = 0; i < backupFiles.length; i++)
+ {
+ if (bfsb.length() > 0)
+ {
+ bfsb.append(", ");
+ }
+ bfsb.append(backupFiles[i].getName());
+ }
+ Cache.trace("BACKUPFILES backupFiles: " + bfsb.toString());
// noMax == true means keep all backup files
if ((!noMax) && bfTreeMap.size() >= max)
{
+ Cache.trace("BACKUPFILES noMax: " + noMax + ", " + "max: " + max
+ + ", " + "bfTreeMap.size(): " + bfTreeMap.size());
// need to delete some files to keep number of backups to designated
- // max
- int numToDelete = bfTreeMap.size() - max + 1;
+ // max.
+ // Note that if the suffix is not numbered then do not delete any
+ // backup files later or we'll delete the new backup file (there can
+ // be only one).
+ int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
+ ? bfTreeMap.size() - max + 1
+ : 0;
+ Cache.trace("BACKUPFILES numToDelete: " + numToDelete);
// the "replacement" file is the latest backup file being kept (it's
// not replacing though)
File replacementFile = numToDelete < backupFiles.length
File fileToBeDeleted = backupFiles[i];
boolean delete = true;
+ Cache.trace("BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
+
boolean newer = false;
if (replacementFile != null)
{
String replacementFileLMTString = sdf
.format(replacementFileLMT);
- System.out
- .println("WARNING! I am set to delete backupfile '"
- + fileToBeDeleted.getName()
- + "' has modification time "
+ Cache.warn("WARNING! I am set to delete backupfile '"
+ + fileToBeDeleted.getName()
+ + "' has modification time "
+ fileToBeDeletedLMTString
- + " which is newer than the oldest backupfile being kept '"
+ + " which is newer than the oldest backupfile being kept '"
+ replacementFile.getName()
- + "' with modification time "
+ + "' with modification time "
+ replacementFileLMTString);
delete = confirmNewerDeleteFile(fileToBeDeleted,
{
// User has confirmed delete -- no need to add it to the list
fileToBeDeleted.delete();
+ Cache.debug("BACKUPFILES deleting fileToBeDeleted: "
+ + fileToBeDeleted);
delete = false;
}
else
{
// keeping file, nothing to do!
+ Cache.debug("BACKUPFILES keeping fileToBeDeleted: "
+ + fileToBeDeleted);
}
}
}
if (delete)
{
addDeleteFile(fileToBeDeleted);
+ Cache.debug("BACKUPFILES addDeleteFile(fileToBeDeleted): "
+ + fileToBeDeleted);
}
}
String latestBackupFilename = dir + File.separatorChar
+ BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
suffix, digits);
- ret |= file.renameTo(new File(latestBackupFilename));
-
+ Cache.trace("BACKUPFILES Moving old file [" + file
+ + "] to latestBackupFilename [" + latestBackupFilename + "]");
+ // using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
+ // be conditional (short-circuit)
+ ret = ret & moveFileToFile(file, new File(latestBackupFilename));
+ Cache.debug("BACKUPFILES moving " + file + " to " + latestBackupFilename
+ + " was " + (ret ? "" : "NOT ") + "successful");
if (tidyUp)
{
+ Cache.debug("BACKUPFILES tidying up files");
tidyUpFiles();
}
saveFile = nextTempFile(ftbd.getName(), ftbd.getParentFile());
} catch (Exception e)
{
- System.out.println(
+ Cache.error(
"Error when confirming to keep backup file newer than other backup files.");
e.printStackTrace();
}
"label.newerdelete_replacement_line", new String[]
{ ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
rfSize }));
+ // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted and
+ // replaced by apparently older file \n''{1}''\t(modified {3}, size
+ // {5}).""
messageSB.append("\n\n");
messageSB.append(MessageManager.formatMessage(
"label.confirm_deletion_or_rename", new String[]
{ ftbd.getName(), saveFile.getName() }));
+ // "Confirm deletion of ''{0}'' or rename to ''{1}''?"
String[] options = new String[] {
MessageManager.getString("label.delete"),
MessageManager.getString("label.rename") };
- confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager.getString("label.backupfiles_confirm_delete"),
- JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
- null, options, options[0]);
+ confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+ : JvOptionPane.showOptionDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_delete"),
+ // "Confirm delete"
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.WARNING_MESSAGE, null, options,
+ options[0]);
}
else
{
.formatMessage("label.newerdelete_line", new String[]
{ ftbd.getName(), rf.getName(), ftbdLMT, rfLMT, ftbdSize,
rfSize }));
+ // "Backup file\n''{0}''\t(modified {2}, size {4})\nis to be deleted but
+ // is newer than the oldest remaining backup file \n''{1}''\t(modified
+ // {3}, size {5})."
messageSB.append("\n\n");
messageSB.append(MessageManager
.formatMessage("label.confirm_deletion", new String[]
{ ftbd.getName() }));
+ // "Confirm deletion of ''{0}''?"
String[] options = new String[] {
MessageManager.getString("label.delete"),
MessageManager.getString("label.keep") };
- confirmButton = JvOptionPane.showOptionDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager.getString("label.backupfiles_confirm_delete"),
- JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
- null, options, options[0]);
+ confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+ : JvOptionPane.showOptionDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_delete"),
+ // "Confirm delete"
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.WARNING_MESSAGE, null, options,
+ options[0]);
}
-
// return should be TRUE if file is to be deleted
return (confirmButton == JvOptionPane.YES_OPTION);
}
messageSB = new StringBuilder();
messageSB.append(MessageManager
.getString("label.backupfiles_confirm_delete_old_files"));
+ // "Delete the following older backup files? (see the Backups tab in
+ // Preferences for more options)"
for (int i = 0; i < deleteFiles.size(); i++)
{
File df = deleteFiles.get(i);
new String[]
{ sdf.format(df.lastModified()),
Long.toString(df.length()) }));
+ // "(modified {0}, size {1})"
}
- int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager
- .getString("label.backupfiles_confirm_delete"),
- JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+ int confirmButton = Platform.isHeadless() ? JvOptionPane.YES_OPTION
+ : JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_delete"),
+ // "Confirm delete"
+ JvOptionPane.YES_NO_OPTION,
+ JvOptionPane.WARNING_MESSAGE);
doDelete = (confirmButton == JvOptionPane.YES_OPTION);
}
for (int i = 0; i < deleteFiles.size(); i++)
{
File fileToDelete = deleteFiles.get(i);
+ Cache.trace("BACKUPFILES about to delete fileToDelete:"
+ + fileToDelete);
fileToDelete.delete();
- System.out.println("DELETING '" + fileToDelete.getName() + "'");
+ Cache.warn("deleted '" + fileToDelete.getName() + "'");
}
}
}
private TreeMap<Integer, File> sortBackupFilesAsTreeMap(
- File[] backupFiles,
- String basename)
+ File[] backupFiles, String basename)
{
// sort the backup files (based on integer found in the suffix) using a
// precomputed Hashmap for speed
boolean rename = false;
if (write)
{
- roll = this.rollBackupFiles(false);
+ roll = this.rollBackupFiles(false); // tidyUpFiles at the end
rename = this.renameTempFile();
}
if (!okay)
{
StringBuilder messageSB = new StringBuilder();
- messageSB.append(MessageManager.getString( "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+ messageSB.append(MessageManager.getString(
+ "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
+ // "Something possibly went wrong with the backups of this file."
if (rename)
{
if (messageSB.length() > 0)
}
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_new_saved_file_ok"));
+ // "The new saved file seems okay."
}
else
{
}
messageSB.append(MessageManager.getString(
"label.backupfiles_confirm_save_new_saved_file_not_ok"));
+ // "The new saved file might not be okay."
}
-
- int confirmButton = JvOptionPane.showConfirmDialog(Desktop.desktop,
- messageSB.toString(),
- MessageManager
- .getString("label.backupfiles_confirm_save_file"),
- JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
+ if (messageSB.length() > 0)
+ {
+ messageSB.append("\n");
+ }
+ messageSB
+ .append(MessageManager.getString("label.continue_operation"));
+
+ int confirmButton = Platform.isHeadless() ? JvOptionPane.OK_OPTION
+ : JvOptionPane.showConfirmDialog(Desktop.desktop,
+ messageSB.toString(),
+ MessageManager.getString(
+ "label.backupfiles_confirm_save_file"),
+ // "Confirm save file"
+ JvOptionPane.OK_OPTION, JvOptionPane.WARNING_MESSAGE);
okay = confirmButton == JvOptionPane.OK_OPTION;
}
if (okay)
dirFile = file.getParentFile();
} catch (Exception e)
{
- System.out.println(
- "Could not get canonical path for file '" + file + "'");
+ Cache.error("Could not get canonical path for file '" + file + "'");
return new TreeMap<>();
}
int pos = deleteFiles.indexOf(fileToBeDeleted);
if (pos > -1)
{
+ Cache.debug("BACKUPFILES not adding file "
+ + fileToBeDeleted.getAbsolutePath()
+ + " to the delete list (already at index" + pos + ")");
return true;
}
else
{
+ Cache.debug("BACKUPFILES adding file "
+ + fileToBeDeleted.getAbsolutePath() + " to the delete list");
deleteFiles.add(fileToBeDeleted);
}
return ret;
}
+ public static boolean moveFileToFile(File oldFile, File newFile)
+ {
+ Cache.initLogger();
+ boolean ret = false;
+ Path oldPath = Paths.get(oldFile.getAbsolutePath());
+ Path newPath = Paths.get(newFile.getAbsolutePath());
+ try
+ {
+ // delete destination file - not usually necessary but Just In Case...
+ Cache.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
+ newFile.delete();
+ Cache.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() + " to "
+ + newFile.getAbsolutePath());
+ Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
+ ret = true;
+ Cache.trace("BACKUPFILES move seems to have succeeded");
+ } catch (IOException e)
+ {
+ Cache.warn("Could not move file '" + oldPath.toString() + "' to '"
+ + newPath.toString() + "'");
+ Cache.error(e.getMessage());
+ Cache.debug(Cache.getStackTraceString(e));
+ ret = false;
+ } catch (Exception e)
+ {
+ Cache.error(e.getMessage());
+ Cache.debug(Cache.getStackTraceString(e));
+ ret = false;
+ }
+ return ret;
+ }
}
*/
package jalview.io;
-import jalview.bin.Cache;
-import jalview.util.MessageManager;
-
import java.util.HashMap;
import java.util.Map;
import java.util.StringTokenizer;
+import jalview.bin.Cache;
+import jalview.util.MessageManager;
+
public class BackupFilesPresetEntry
{
import javax.swing.JFileChooser;
import javax.swing.JLabel;
import javax.swing.JPanel;
+import javax.swing.JPasswordField;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSpinner;
import javax.swing.border.TitledBorder;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
import javax.swing.table.TableCellEditor;
import javax.swing.table.TableCellRenderer;
/*
* Connections tab components
*/
+ protected JPanel connectTab;
+
protected JTable linkUrlTable = new JTable();
protected JButton editLink = new JButton();
protected JButton userOnly = new JButton();
+ protected JLabel httpLabel = new JLabel();
+
+ protected JLabel httpsLabel = new JLabel();
+
protected JLabel portLabel = new JLabel();
protected JLabel serverLabel = new JLabel();
- protected JTextField proxyServerTB = new JTextField();
+ protected JLabel portLabel2 = new JLabel();
+
+ protected JLabel serverLabel2 = new JLabel();
+
+ protected JLabel proxyAuthUsernameLabel = new JLabel();
+
+ protected JLabel proxyAuthPasswordLabel = new JLabel();
+
+ protected JLabel passwordNotStoredLabel = new JLabel();
+
+ protected JTextField proxyServerHttpTB = new JTextField();
+
+ protected JTextField proxyPortHttpTB = new JTextField();
- protected JTextField proxyPortTB = new JTextField();
+ protected JTextField proxyServerHttpsTB = new JTextField();
+
+ protected JTextField proxyPortHttpsTB = new JTextField();
+
+ protected JCheckBox proxyAuth = new JCheckBox();
+
+ protected JTextField proxyAuthUsernameTB = new JTextField();
+
+ protected JPasswordField proxyAuthPasswordPB = new JPasswordField();
protected JTextField defaultBrowser = new JTextField();
- protected JCheckBox useProxy = new JCheckBox();
+ protected ButtonGroup proxyType = new ButtonGroup();
+
+ protected JRadioButton noProxy = new JRadioButton();
+
+ protected JRadioButton systemProxy = new JRadioButton();
+
+ protected JRadioButton customProxy = new JRadioButton();
+
+ protected JButton applyProxyButton = new JButton();
protected JCheckBox usagestats = new JCheckBox();
protected JTextArea backupfilesExampleLabel = new JTextArea();
+ private final JTabbedPane tabbedPane = new JTabbedPane();
+
+ private JLabel messageLabel = new JLabel("", JLabel.CENTER);
+
/**
* Creates a new GPreferences object.
*/
*/
private void jbInit() throws Exception
{
- final JTabbedPane tabbedPane = new JTabbedPane();
+ // final JTabbedPane tabbedPane = new JTabbedPane();
this.setLayout(new BorderLayout());
+
+ // message label at top
+ this.add(messageLabel, BorderLayout.NORTH);
+
JPanel okCancelPanel = initOkCancelPanel();
this.add(tabbedPane, BorderLayout.CENTER);
this.add(okCancelPanel, BorderLayout.SOUTH);
tabbedPane.add(initConnectionsTab(),
MessageManager.getString("label.connections"));
- if (!Platform.isJS())
- {
- tabbedPane.add(initBackupsTab(),
- MessageManager.getString("label.backups"));
- }
+ if (!Platform.isJS())
+ {
+ tabbedPane.add(initBackupsTab(),
+ MessageManager.getString("label.backups"));
+ }
tabbedPane.add(initLinksTab(),
MessageManager.getString("label.urllinks"));
/*
* Handler to validate a tab before leaving it - currently only for
* Structure.
+ * Adding a clearMessage() so messages are cleared when changing tabs.
*/
tabbedPane.addChangeListener(new ChangeListener()
{
}
}
lastTab = tabbedPane.getSelectedComponent();
+
+ clearMessage();
}
});
}
+ public void setMessage(String message)
+ {
+ if (message != null)
+ {
+ messageLabel.setText(message);
+ messageLabel.setFont(LABEL_FONT_BOLD);
+ messageLabel.setForeground(Color.RED.darker());
+ messageLabel.revalidate();
+ messageLabel.repaint();
+ }
+ // note message not cleared if message is null. call clearMessage()
+ // directly.
+ this.revalidate();
+ this.repaint();
+ }
+
+ public void clearMessage()
+ {
+ // only repaint if message exists
+ if (messageLabel.getText() != null
+ && messageLabel.getText().length() > 0)
+ {
+ messageLabel.setText("");
+ messageLabel.revalidate();
+ messageLabel.repaint();
+ this.revalidate();
+ this.repaint();
+ }
+ }
+
+ public final static int CONNECTIONS_TAB = 5;
+
+ public void selectTab(int selectTab)
+ {
+ // select a given tab - currently only for Connections
+ switch (selectTab)
+ {
+ case CONNECTIONS_TAB:
+ tabbedPane.setSelectedComponent(connectTab);
+ break;
+ default:
+ }
+ }
+
/**
* Initialises the Editing tabbed panel.
*
*/
private JPanel initConnectionsTab()
{
- JPanel connectTab = new JPanel();
+ connectTab = new JPanel();
connectTab.setLayout(new GridBagLayout());
// Label for browser text box
private JPanel initConnTabProxyPanel()
{
// Label for server text box
- serverLabel.setText(MessageManager.getString("label.address"));
+ serverLabel.setText(MessageManager.getString("label.host") + ": ");
serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
serverLabel.setFont(LABEL_FONT);
+ serverLabel2.setText(MessageManager.getString("label.host") + ": ");
+ serverLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
+ serverLabel2.setFont(LABEL_FONT);
// Proxy server and port text boxes
- proxyServerTB.setFont(LABEL_FONT);
- proxyPortTB.setFont(LABEL_FONT);
+ proxyServerHttpTB.setFont(LABEL_FONT);
+ proxyServerHttpTB.setColumns(40);
+ proxyPortHttpTB.setFont(LABEL_FONT);
+ proxyPortHttpTB.setColumns(4);
+ proxyServerHttpsTB.setFont(LABEL_FONT);
+ proxyServerHttpsTB.setColumns(40);
+ proxyPortHttpsTB.setFont(LABEL_FONT);
+ proxyPortHttpsTB.setColumns(4);
+ proxyAuthUsernameTB.setFont(LABEL_FONT);
+ proxyAuthUsernameTB.setColumns(30);
+
+ // check for any change to enable applyProxyButton
+ DocumentListener d = new DocumentListener()
+ {
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ applyProxyButtonEnabled(true);
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ applyProxyButtonEnabled(true);
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ applyProxyButtonEnabled(true);
+ }
+ };
+ proxyServerHttpTB.getDocument().addDocumentListener(d);
+ proxyPortHttpTB.getDocument().addDocumentListener(d);
+ proxyServerHttpsTB.getDocument().addDocumentListener(d);
+ proxyPortHttpsTB.getDocument().addDocumentListener(d);
+ proxyAuthUsernameTB.getDocument().addDocumentListener(d);
+ proxyAuthPasswordPB.setFont(LABEL_FONT);
+ proxyAuthPasswordPB.setColumns(30);
+ proxyAuthPasswordPB.getDocument()
+ .addDocumentListener(new DocumentListener()
+ {
+ @Override
+ public void changedUpdate(DocumentEvent e)
+ {
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
+ }
+
+ @Override
+ public void insertUpdate(DocumentEvent e)
+ {
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
+ }
+
+ @Override
+ public void removeUpdate(DocumentEvent e)
+ {
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
+ }
+
+ });
// Label for Port text box
portLabel.setFont(LABEL_FONT);
portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
- portLabel.setText(MessageManager.getString("label.port"));
-
- // Use proxy server checkbox
- useProxy.setFont(LABEL_FONT);
- useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
- useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
- useProxy.setText(MessageManager.getString("label.use_proxy_server"));
- useProxy.addActionListener(new ActionListener()
+ portLabel.setText(MessageManager.getString("label.port") + ": ");
+ portLabel2.setFont(LABEL_FONT);
+ portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
+ portLabel2.setText(MessageManager.getString("label.port") + ": ");
+
+ httpLabel.setText("HTTP");
+ httpLabel.setFont(LABEL_FONT_BOLD);
+ httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
+ httpsLabel.setText("HTTPS");
+ httpsLabel.setFont(LABEL_FONT_BOLD);
+ httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
+
+ proxyAuthUsernameLabel
+ .setText(MessageManager.getString("label.username") + ": ");
+ proxyAuthUsernameLabel.setFont(LABEL_FONT);
+ proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ proxyAuthPasswordLabel
+ .setText(MessageManager.getString("label.password") + ": ");
+ proxyAuthPasswordLabel.setFont(LABEL_FONT);
+ proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+ passwordNotStoredLabel.setText(
+ "(" + MessageManager.getString("label.not_stored") + ")");
+ passwordNotStoredLabel.setFont(LABEL_FONT_ITALIC);
+ passwordNotStoredLabel.setHorizontalAlignment(SwingConstants.LEFT);
+
+ // Proxy type radio buttons
+ noProxy.setFont(LABEL_FONT);
+ noProxy.setHorizontalAlignment(SwingConstants.LEFT);
+ noProxy.setText(MessageManager.getString("label.no_proxy"));
+ systemProxy.setFont(LABEL_FONT);
+ systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
+ systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
+ displayUserHostPort(Cache.startupProxyProperties[4],
+ Cache.startupProxyProperties[0],
+ Cache.startupProxyProperties[1]),
+ displayUserHostPort(Cache.startupProxyProperties[6],
+ Cache.startupProxyProperties[2],
+ Cache.startupProxyProperties[3])));
+ customProxy.setFont(LABEL_FONT);
+ customProxy.setHorizontalAlignment(SwingConstants.LEFT);
+ customProxy.setText(
+ MessageManager.getString("label.use_proxy_server") + ":");
+ ActionListener al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ proxyType_actionPerformed();
+ }
+ };
+ noProxy.addActionListener(al);
+ systemProxy.addActionListener(al);
+ customProxy.addActionListener(al);
+ proxyType.add(noProxy);
+ proxyType.add(systemProxy);
+ proxyType.add(customProxy);
+
+ proxyAuth.setFont(LABEL_FONT);
+ proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
+ proxyAuth.setText(MessageManager.getString("label.auth_required"));
+ proxyAuth.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- useProxy_actionPerformed();
+ proxyAuth_actionPerformed();
}
});
+ setCustomProxyEnabled();
+
// Make proxy server panel
JPanel proxyPanel = new JPanel();
TitledBorder titledBorder1 = new TitledBorder(
- MessageManager.getString("label.proxy_server"));
+ MessageManager.getString("label.proxy_servers"));
proxyPanel.setBorder(titledBorder1);
proxyPanel.setLayout(new GridBagLayout());
- proxyPanel.add(serverLabel,
- new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(0, 2, 2, 0), 5, 0));
- proxyPanel.add(portLabel,
- new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(0, 0, 2, 0), 11, 0));
- proxyPanel.add(useProxy,
- new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.NONE,
- new Insets(0, 2, 5, 185), 2, -4));
- proxyPanel.add(proxyPortTB,
- new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 2, 2), 54, 1));
- proxyPanel.add(proxyServerTB,
- new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
- GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
- new Insets(0, 2, 2, 0), 263, 1));
+ GridBagConstraints gbc = new GridBagConstraints();
+ gbc.fill = GridBagConstraints.HORIZONTAL;
+ gbc.weightx = 1.0;
+
+ GridBagConstraints c = new GridBagConstraints();
+ // Proxy type radio buttons (3)
+ JPanel ptPanel = new JPanel();
+ ptPanel.setLayout(new GridBagLayout());
+ c.weightx = 1.0;
+ c.gridy = 0;
+ c.gridx = 0;
+ c.gridwidth = 1;
+ c.fill = GridBagConstraints.HORIZONTAL;
+ ptPanel.add(noProxy, c);
+ c.gridy++;
+ ptPanel.add(systemProxy, c);
+ c.gridy++;
+ ptPanel.add(customProxy, c);
+
+ gbc.gridy = 0;
+ proxyPanel.add(ptPanel, gbc);
+
+ // host and port text boxes
+ JPanel hpPanel = new JPanel();
+ hpPanel.setLayout(new GridBagLayout());
+ // HTTP host port row
+ c.gridy = 0;
+ c.gridx = 0;
+
+ c.weightx = 0.1;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(httpLabel, c);
+
+ c.gridx++;
+ c.weightx = 0.1;
+ c.anchor = GridBagConstraints.LINE_END;
+ hpPanel.add(serverLabel, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(proxyServerHttpTB, c);
+
+ c.gridx++;
+ c.weightx = 0.1;
+ c.anchor = GridBagConstraints.LINE_END;
+ hpPanel.add(portLabel, c);
+
+ c.gridx++;
+ c.weightx = 0.2;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(proxyPortHttpTB, c);
+
+ // HTTPS host port row
+ c.gridy++;
+ c.gridx = 0;
+ c.gridwidth = 1;
+
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(httpsLabel, c);
+
+ c.gridx++;
+ c.anchor = GridBagConstraints.LINE_END;
+ hpPanel.add(serverLabel2, c);
+
+ c.gridx++;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(proxyServerHttpsTB, c);
+
+ c.gridx++;
+ c.anchor = GridBagConstraints.LINE_END;
+ hpPanel.add(portLabel2, c);
+
+ c.gridx++;
+ c.anchor = GridBagConstraints.LINE_START;
+ hpPanel.add(proxyPortHttpsTB, c);
+
+ gbc.gridy++;
+ proxyPanel.add(hpPanel, gbc);
+
+ // Require authentication checkbox
+ gbc.gridy++;
+ proxyPanel.add(proxyAuth, gbc);
+
+ // username and password
+ JPanel upPanel = new JPanel();
+ upPanel.setLayout(new GridBagLayout());
+ // username row
+ c.gridy = 0;
+ c.gridx = 0;
+ c.gridwidth = 1;
+ c.weightx = 0.4;
+ c.anchor = GridBagConstraints.LINE_END;
+ upPanel.add(proxyAuthUsernameLabel, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.anchor = GridBagConstraints.LINE_START;
+ upPanel.add(proxyAuthUsernameTB, c);
+
+ // password row
+ c.gridy++;
+ c.gridx = 0;
+ c.weightx = 0.4;
+ c.anchor = GridBagConstraints.LINE_END;
+ upPanel.add(proxyAuthPasswordLabel, c);
+
+ c.gridx++;
+ c.weightx = 1.0;
+ c.anchor = GridBagConstraints.LINE_START;
+ upPanel.add(proxyAuthPasswordPB, c);
+
+ c.gridx++;
+ c.weightx = 0.4;
+ c.anchor = GridBagConstraints.LINE_START;
+ upPanel.add(passwordNotStoredLabel, c);
+
+ gbc.gridy++;
+ proxyPanel.add(upPanel, gbc);
+
+ applyProxyButton.setText(MessageManager.getString("action.apply"));
+ applyProxyButton.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ saveProxySettings();
+ applyProxyButton.setEnabled(false);
+ }
+ });
+ gbc.gridy++;
+ gbc.fill = GridBagConstraints.NONE;
+ gbc.anchor = GridBagConstraints.LINE_END;
+ proxyPanel.add(applyProxyButton, gbc);
return proxyPanel;
}
+ public void proxyAuthPasswordCheckHighlight(boolean enabled)
+ {
+ proxyAuthPasswordCheckHighlight(enabled, false);
+ }
+
+ public void proxyAuthPasswordCheckHighlight(boolean enabled,
+ boolean grabFocus)
+ {
+ if (enabled && proxyType.isSelected(customProxy.getModel())
+ && proxyAuth.isSelected()
+ && !proxyAuthUsernameTB.getText().isEmpty()
+ && proxyAuthPasswordPB.getDocument().getLength() == 0)
+ {
+ if (grabFocus)
+ proxyAuthPasswordPB.grabFocus();
+ proxyAuthPasswordPB.setBackground(Color.PINK);
+ }
+ else
+ {
+ proxyAuthPasswordPB.setBackground(Color.WHITE);
+ }
+ }
+
+ public void applyProxyButtonEnabled(boolean enabled)
+ {
+ applyProxyButton.setEnabled(enabled);
+ }
+
+ public void saveProxySettings()
+ {
+ // overridden in Preferences
+ }
+
+ private String displayUserHostPort(String user, String host, String port)
+ {
+ boolean hostBlank = (host == null || host.isEmpty());
+ boolean portBlank = (port == null || port.isEmpty());
+ if (hostBlank && portBlank)
+ {
+ return MessageManager.getString("label.none");
+ }
+
+ StringBuilder sb = new StringBuilder();
+ if (user != null)
+ {
+ sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
+ : user);
+ sb.append("@");
+ }
+ sb.append(hostBlank ? "" : host);
+ if (!portBlank)
+ {
+ sb.append(":");
+ sb.append(port);
+ }
+ return sb.toString();
+ }
+
/**
* Initialises the checkboxes in the Connections tab
*/
ypos += lineSpacing;
structureViewerPathLabel = new JLabel();
- structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, 11));
+ structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0,
+ // 11));
structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
structureViewerPathLabel.setText(MessageManager
.formatMessage("label.viewer_path", "Chimera(X)"));
- structureViewerPathLabel.setBounds(new Rectangle(10, ypos, 170, height));
+ structureViewerPathLabel
+ .setBounds(new Rectangle(10, ypos, 170, height));
structureViewerPathLabel.setEnabled(false);
structureTab.add(structureViewerPathLabel);
/*
* hide Chimera options in JalviewJS
*/
- if (Platform.isJS())
+ if (Platform.isJS())
{
structureViewerPathLabel.setVisible(false);
structureViewerPath.setVisible(false);
viewerLabel.setVisible(false);
structViewer.setVisible(false);
}
-
+
return structureTab;
}
visualTab.add(fontNameCB);
visualTab.add(fontSizeCB);
visualTab.add(fontStyleCB);
-
+
if (Platform.isJS())
{
startupCheckbox.setVisible(false);
startupFileTextfield.setVisible(false);
}
-
+
return visualTab;
}
{
BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
.getSavedBackupEntry();
- enableBackupFiles
- .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
+ enableBackupFiles.setSelected(
+ Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
.createBackupFilesPresetEntry(Cache
}
});
-
// enable checkbox 1 col
gbc.gridwidth = 1;
gbc.gridheight = 1;
presetsComboLabel = new JLabel(title + ":");
presetsPanel.add(presetsComboLabel, gbc);
- List<Object> entries = Arrays
- .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+ List<Object> entries = Arrays.asList(
+ (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
List<String> tooltips = Arrays.asList(
BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
{
if (customiseCheckbox.isSelected())
{
- // got here by clicking on customiseCheckbox so don't change the values
+ // got here by clicking on customiseCheckbox so don't change the
+ // values
backupfilesCustomOptionsSetEnabled();
}
else
private JPanel initBackupsTabFilenameExamplesPanel()
{
- String title = MessageManager
- .getString("label.scheme_examples");
+ String title = MessageManager.getString("label.scheme_examples");
TitledBorder tb = new TitledBorder(title);
exampleFilesPanel.setBorder(tb);
exampleFilesPanel.setLayout(new GridBagLayout());
-
backupfilesExampleLabel.setEditable(false);
backupfilesExampleLabel
.setBackground(exampleFilesPanel.getBackground());
}
protected void setComboIntStringKey(
- JComboBox<Object> backupfilesPresetsCombo2,
- int key)
+ JComboBox<Object> backupfilesPresetsCombo2, int key)
{
for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
{
JPanel jp = new JPanel();
jp.setLayout(new FlowLayout());
- oldBackupFilesLabel
- .setText(MessageManager
- .getString("label.autodelete_old_backup_files"));
+ oldBackupFilesLabel.setText(
+ MessageManager.getString("label.autodelete_old_backup_files"));
oldBackupFilesLabel.setFont(LABEL_FONT);
oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
jp.add(oldBackupFilesLabel);
}
- // add some extra empty lines to pad out the example files box. ugh, please tell
+ // add some extra empty lines to pad out the example files box. ugh, please
+ // tell
// me how to do this better
int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
if (remainingLines > 0)
private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
{
boolean enabled = tryEnabled && enableBackupFiles.isSelected()
- && customiseCheckbox.isSelected()
- && suffixTemplate.getText()
+ && customiseCheckbox.isSelected() && suffixTemplate.getText()
.indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
keepfilesPanel.setEnabled(enabled);
backupfilesKeepAll.setEnabled(enabled);
}
- public void useProxy_actionPerformed()
+ public void setProxyAuthEnabled()
+ {
+ boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
+ proxyAuthUsernameLabel.setEnabled(enabled);
+ proxyAuthPasswordLabel.setEnabled(enabled);
+ passwordNotStoredLabel.setEnabled(enabled);
+ proxyAuthUsernameTB.setEnabled(enabled);
+ proxyAuthPasswordPB.setEnabled(enabled);
+ }
+
+ public void setCustomProxyEnabled()
{
- boolean enabled = useProxy.isSelected();
+ boolean enabled = customProxy.isSelected();
portLabel.setEnabled(enabled);
serverLabel.setEnabled(enabled);
- proxyServerTB.setEnabled(enabled);
- proxyPortTB.setEnabled(enabled);
+ portLabel2.setEnabled(enabled);
+ serverLabel2.setEnabled(enabled);
+ httpLabel.setEnabled(enabled);
+ httpsLabel.setEnabled(enabled);
+ proxyServerHttpTB.setEnabled(enabled);
+ proxyPortHttpTB.setEnabled(enabled);
+ proxyServerHttpsTB.setEnabled(enabled);
+ proxyPortHttpsTB.setEnabled(enabled);
+ proxyAuth.setEnabled(enabled);
+ setProxyAuthEnabled();
+ }
+
+ public void proxyType_actionPerformed()
+ {
+ setCustomProxyEnabled();
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
+ }
+
+ public void proxyAuth_actionPerformed()
+ {
+ setProxyAuthEnabled();
+ proxyAuthPasswordCheckHighlight(true);
+ applyProxyButtonEnabled(true);
}
/**
}
}
-
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.Format;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.StringUtils;
// create backupfiles object and get new temp filename destination
boolean doBackup = BackupFiles.getEnabled();
BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
- FileOutputStream fos = new FileOutputStream(doBackup ?
- backupfiles.getTempFilePath() : jarFile);
+ FileOutputStream fos = new FileOutputStream(
+ doBackup ? backupfiles.getTempFilePath() : jarFile);
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
else
{
vamsasSeq = createVamsasSequence(id, jds);
-// vamsasSet.addSequence(vamsasSeq);
+ // vamsasSet.addSequence(vamsasSeq);
vamsasSet.getSequence().add(vamsasSeq);
vamsasSetIds.put(id, vamsasSeq);
seqRefIds.put(id, jds);
if (frames[f] instanceof StructureViewerBase)
{
StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
- matchedFile = saveStructureViewer(ap, jds, pdb, entry, viewIds,
- matchedFile, viewFrame);
+ matchedFile = saveStructureViewer(ap, jds, pdb, entry,
+ viewIds, matchedFile, viewFrame);
/*
* Only store each structure viewer's state once in the project
* jar. First time through only (storeDS==false)
}
else
{
- Cache.log.error("Failed to save viewer state for "
- +
- viewerType);
+ Cache.log.error(
+ "Failed to save viewer state for " + viewerType);
}
}
}
if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(
- setUserColourScheme(colourScheme, userColours,
- object));
+ jGroup.setColour(setUserColourScheme(colourScheme,
+ userColours, object));
}
else
{
}
}
- //jms.setJGroup(groups);
+ // jms.setJGroup(groups);
Object group;
for (JGroup grp : groups)
{
* save any filter for the feature type
*/
FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
- if (filter != null) {
- Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
+ if (filter != null)
+ {
+ Iterator<FeatureMatcherI> filters = filter.getMatchers()
+ .iterator();
FeatureMatcherI firstFilter = filters.next();
- setting.setMatcherSet(Jalview2XML.marshalFilter(
- firstFilter, filters, filter.isAnded()));
+ setting.setMatcherSet(Jalview2XML.marshalFilter(firstFilter,
+ filters, filter.isAnded()));
}
/*
setting.setDisplay(
av.getFeaturesDisplayed().isVisible(featureType));
- float rorder = fr
- .getOrder(featureType);
+ float rorder = fr.getOrder(featureType);
if (rorder > -1)
{
setting.setOrder(rorder);
Group g = new Group();
g.setName(grp);
g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
- .booleanValue());
+ .booleanValue());
// fs.addGroup(g);
fs.getGroup().add(g);
groupsAdded.addElement(grp);
{
if (calcIdParam.getVersion().equals("1.0"))
{
- final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
+ final String[] calcIds = calcIdParam.getServiceURL()
+ .toArray(new String[0]);
Jws2Instance service = Jws2Discoverer.getDiscoverer()
.getPreferredServiceFor(calcIds);
if (service != null)
}
if (ref.hasMap())
{
- Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
- jds, recurse);
+ Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds,
+ recurse);
dbref.setMapping(mp);
}
vamsasSeq.getDBRef().add(dbref);
return id;
}
- jalview.schemes.UserColourScheme getUserColourScheme(
- JalviewModel jm, String id)
+ jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
+ String id)
{
List<UserColours> uc = jm.getUserColours();
UserColours colours = null;
-/*
+ /*
for (int i = 0; i < uc.length; i++)
{
if (uc[i].getId().equals(id))
break;
}
}
-*/
+ */
for (UserColours c : uc)
{
if (c.getId().equals(id))
newColours = new java.awt.Color[23];
for (int i = 0; i < 23; i++)
{
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour().get(i + 24)
- .getRGB(),
- 16));
+ newColours[i] = new java.awt.Color(
+ Integer.parseInt(colours.getUserColourScheme().getColour()
+ .get(i + 24).getRGB(), 16));
}
ucs.setLowerCaseColours(newColours);
}
return af;
}
- @SuppressWarnings("unused")
- private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
+ @SuppressWarnings("unused")
+ private jarInputStreamProvider createjarInputStreamProvider(
+ final Object ofile) throws MalformedURLException
+ {
- // BH 2018 allow for bytes already attached to File object
- try {
- String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+ // BH 2018 allow for bytes already attached to File object
+ try
+ {
+ String file = (ofile instanceof File
+ ? ((File) ofile).getCanonicalPath()
+ : ofile.toString());
byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
: null;
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (file.startsWith("http://")) {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider() {
-
- @Override
- public JarInputStream getJarInputStream() throws IOException {
- if (bytes != null) {
-// System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
- return new JarInputStream(new ByteArrayInputStream(bytes));
- }
- if (_url != null) {
-// System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
- return new JarInputStream(_url.openStream());
- } else {
-// System.out.println("Jalview2XML: opening file jarInputStream for " + file);
- return new JarInputStream(new FileInputStream(file));
- }
- }
-
- @Override
- public String getFilename() {
- return file;
- }
- };
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
+ URL url = null;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded.clear();
+ frefedSequence = null;
+
+ if (HttpUtils.startsWithHttpOrHttps(file))
+ {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider()
+ {
+
+ @Override
+ public JarInputStream getJarInputStream() throws IOException
+ {
+ if (bytes != null)
+ {
+ // System.out.println("Jalview2XML: opening byte jarInputStream for
+ // bytes.length=" + bytes.length);
+ return new JarInputStream(new ByteArrayInputStream(bytes));
+ }
+ if (_url != null)
+ {
+ // System.out.println("Jalview2XML: opening url jarInputStream for "
+ // + _url);
+ return new JarInputStream(_url.openStream());
+ }
+ else
+ {
+ // System.out.println("Jalview2XML: opening file jarInputStream for
+ // " + file);
+ return new JarInputStream(new FileInputStream(file));
+ }
+ }
+
+ @Override
+ public String getFilename()
+ {
+ return file;
+ }
+ };
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ return null;
+ }
+ }
/**
* Recover jalview session from a jalview project archive. Caller may
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(jin);
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- JAXBElement<JalviewModel> jbe = um
- .unmarshal(streamReader, JalviewModel.class);
+ JAXBElement<JalviewModel> jbe = um.unmarshal(streamReader,
+ JalviewModel.class);
JalviewModel object = jbe.getValue();
if (true) // !skipViewport(object))
AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
- SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+ SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
+ .get(0);
List<Sequence> vamsasSeqs = vamsasSet.getSequence();
// JalviewModelSequence jms = object.getJalviewModelSequence();
if (tmpSeq.getStart() != jseq.getStart()
|| tmpSeq.getEnd() != jseq.getEnd())
{
- System.err.println(
- String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
- tmpSeq.getName(), tmpSeq.getStart(),
- tmpSeq.getEnd(), jseq.getStart(),
- jseq.getEnd()));
+ System.err.println(String.format(
+ "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+ tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
+ jseq.getStart(), jseq.getEnd()));
}
}
else
else
{
// defer to later
- frefedSequence.add(
- newAlcodMapRef(map.getDnasq(), cf, mapping));
+ frefedSequence
+ .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
}
}
}
jaa.setCalcId(annotation.getCalcId());
if (annotation.getProperty().size() > 0)
{
- for (Annotation.Property prop : annotation
- .getProperty())
+ for (Annotation.Property prop : annotation.getProperty())
{
jaa.setProperty(prop.getName(), prop.getValue());
}
sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
// attributes with a default in the schema are never null
- sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
- sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
- sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
+ sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
+ sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
+ sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
if (jGroup.getConsThreshold() != null
&& jGroup.getConsThreshold().intValue() != 0)
if (addAnnotSchemeGroup)
{
// reconstruct the annotation colourscheme
- sg.setColourScheme(constructAnnotationColour(
- jGroup.getAnnotationColours(), null, al, jalviewModel, false));
+ sg.setColourScheme(
+ constructAnnotationColour(jGroup.getAnnotationColours(),
+ null, al, jalviewModel, false));
}
}
}
* @param av
* @param ap
*/
- protected void loadTrees(JalviewModel jm, Viewport view,
- AlignFrame af, AlignViewport av, AlignmentPanel ap)
+ protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
+ AlignViewport av, AlignmentPanel ap)
{
// TODO result of automated refactoring - are all these parameters needed?
try
for (int s = 0; s < structureStateCount; s++)
{
// check to see if we haven't already created this structure view
- final StructureState structureState = pdbid
- .getStructureState().get(s);
+ final StructureState structureState = pdbid.getStructureState()
+ .get(s);
String sviewid = (structureState.getViewId() == null) ? null
: structureState.getViewId() + uniqueSetSuffix;
jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
colourByViewer &= structureState.isColourByJmol();
jmoldat.setColourByViewer(colourByViewer);
- if (jmoldat.getStateData().length() < structureState
- .getValue()/*Content()*/.length())
+ if (jmoldat.getStateData().length() < structureState.getValue()
+ /*Content()*/.length())
{
jmoldat.setStateData(structureState.getValue());// Content());
}
} catch (IllegalArgumentException | NullPointerException e)
{
// TODO JAL-3619 show error dialog / offer an alternative viewer
- Cache.log.error(
- "Invalid structure viewer type: " + type);
+ Cache.log.error("Invalid structure viewer type: " + type);
}
}
}
AlignFrame loadViewport(String file, List<JSeq> JSEQ,
- List<SequenceI> hiddenSeqs, AlignmentI al,
- JalviewModel jm, Viewport view, String uniqueSeqSetId,
- String viewId, List<JvAnnotRow> autoAlan)
+ List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+ Viewport view, String uniqueSeqSetId, String viewId,
+ List<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, safeInt(view.getWidth()),
- safeInt(view.getHeight()), uniqueSeqSetId, viewId)
-// {
-//
-// @Override
-// protected void processKeyEvent(java.awt.event.KeyEvent e) {
-// System.out.println("Jalview2XML AF " + e);
-// super.processKeyEvent(e);
-//
-// }
-//
-// }
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId)
+ // {
+ //
+ // @Override
+ // protected void processKeyEvent(java.awt.event.KeyEvent e) {
+ // System.out.println("Jalview2XML AF " + e);
+ // super.processKeyEvent(e);
+ //
+ // }
+ //
+ // }
;
af.setFileName(file, FileFormat.Jalview);
viewport.setColourText(safeBoolean(view.isShowColourText()));
- viewport
- .setConservationSelected(
- safeBoolean(view.isConservationSelected()));
+ viewport.setConservationSelected(
+ safeBoolean(view.isConservationSelected()));
viewport.setIncrement(safeInt(view.getConsThreshold()));
viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
af.changeColour(cs);
viewport.setColourAppliesToAllGroups(true);
- viewport
- .setShowSequenceFeatures(
- safeBoolean(view.isShowSequenceFeatures()));
+ viewport.setShowSequenceFeatures(
+ safeBoolean(view.isShowSequenceFeatures()));
viewport.setCentreColumnLabels(view.isCentreColumnLabels());
viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
.getFeatureRenderer();
FeaturesDisplayed fdi;
viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
- String[] renderOrder = new String[jm.getFeatureSettings()
- .getSetting().size()];
+ String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+ .size()];
Map<String, FeatureColourI> featureColours = new Hashtable<>();
Map<String, Float> featureOrder = new Hashtable<>();
- for (int fs = 0; fs < jm.getFeatureSettings()
- .getSetting().size(); fs++)
+ for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+ .size(); fs++)
{
Setting setting = jm.getFeatureSettings().getSetting().get(fs);
String featureType = setting.getType();
.getMatcherSet();
if (filters != null)
{
- FeatureMatcherSetI filter = Jalview2XML
- .parseFilter(featureType, filters);
+ FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+ filters);
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
FeatureColourI gc = new FeatureColour(maxColour, minColour,
- maxColour,
- noValueColour, min, max);
+ maxColour, noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
gc.setAttributeName(setting.getAttributeName().toArray(
}
else
{
- featureColours.put(featureType,
- new FeatureColour(maxColour));
+ featureColours.put(featureType, new FeatureColour(maxColour));
}
renderOrder[fs] = featureType;
if (setting.getOrder() != null)
}
}
}
+
/**
*
* @param vamsasSeq
* @param af
* @param jprovider
*/
- protected void createStructureViewer(
- ViewerType viewerType, final Entry<String, StructureViewerModel> viewerData,
+ protected void createStructureViewer(ViewerType viewerType,
+ final Entry<String, StructureViewerModel> viewerData,
AlignFrame af, jarInputStreamProvider jprovider)
{
final StructureViewerModel viewerModel = viewerData.getValue();
{
String viewerJarEntryName = getViewerJarEntryName(
viewerModel.getViewId());
- sessionFilePath = copyJarEntry(jprovider,
- viewerJarEntryName,
+ sessionFilePath = copyJarEntry(jprovider, viewerJarEntryName,
"viewerSession", ".tmp");
}
final String sessionPath = sessionFilePath;
addNewStructureViewer(sview);
} catch (OutOfMemoryError ex)
{
- new OOMWarning("Restoring structure view for "
- + viewerType,
+ new OOMWarning("Restoring structure view for " + viewerType,
(OutOfMemoryError) ex.getCause());
if (sview != null && sview.isVisible())
{
String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
filedat = oldFiles.get(new File(reformatedOldFilename));
}
- rewritten
- .append(Platform.escapeBackslashes(filedat.getFilePath()));
+ rewritten.append(Platform.escapeBackslashes(filedat.getFilePath()));
rewritten.append("\"");
cp = ecp + 1; // advance beyond last \" and set cursor so we can
// look for next file statement.
* @param fcol
* @return
*/
- public static Colour marshalColour(
- String featureType, FeatureColourI fcol)
+ public static Colour marshalColour(String featureType,
+ FeatureColourI fcol)
{
Colour col = new Colour();
if (fcol.isSimpleColour())
boolean and)
{
jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
-
+
if (filters.hasNext())
{
/*
}
result.setMatchCondition(matcherModel);
}
-
+
return result;
}
* @param matcherSetModel
* @return
*/
- public static FeatureMatcherSetI parseFilter(
- String featureType,
+ public static FeatureMatcherSetI parseFilter(String featureType,
jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
{
FeatureMatcherSetI result = new FeatureMatcherSet();
featureType, e.getMessage()));
// return as much as was parsed up to the error
}
-
+
return result;
}
* @throws IllegalStateException
* if AND and OR conditions are mixed
*/
- protected static void parseFilterConditions(
- FeatureMatcherSetI matcherSet,
+ protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
boolean and)
{
else if (filterBy == FilterBy.BY_SCORE)
{
matchCondition = FeatureMatcher.byScore(cond, pattern);
-
+
}
else if (filterBy == FilterBy.BY_ATTRIBUTE)
{
matchCondition = FeatureMatcher.byAttribute(cond, pattern,
attNames);
}
-
+
/*
* note this throws IllegalStateException if AND-ing to a
* previously OR-ed compound condition, or vice versa
public static FeatureColourI parseColour(Colour colourModel)
{
FeatureColourI colour = null;
-
+
if (colourModel.getMax() != null)
{
Color mincol = null;
Color maxcol = null;
Color noValueColour = null;
-
+
try
{
mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
{
Cache.log.warn("Couldn't parse out graduated feature color.", e);
}
-
+
NoValueColour noCol = colourModel.getNoValueColour();
if (noCol == NoValueColour.MIN)
{
{
noValueColour = maxcol;
}
-
+
colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
colour = new FeatureColour(color);
}
-
+
return colour;
}
}
return false;
}
+ public static boolean startsWithHttpOrHttps(String file)
+ {
+ return file.startsWith("http://") || file.startsWith("https://");
+ }
+
}
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
+import jalview.io.BackupFiles;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
private enum CoordinateSys
{
UNIPROT("UniProt"), PDB("PDBresnum"), PDBe("PDBe");
+
private String name;
private CoordinateSys(String name)
{
NAME_SEC_STRUCTURE("nameSecondaryStructure"),
CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation");
+
private String code;
private ResidueDetailType(String code)
SiftsSettings.getCacheThresholdInDays()))
{
File oldSiftsFile = new File(siftsFileName + "_old");
- siftsFile.renameTo(oldSiftsFile);
+ BackupFiles.moveFileToFile(siftsFile, oldSiftsFile);
try
{
siftsFile = downloadSiftsFile(pdbId.toLowerCase());
} catch (IOException e)
{
e.printStackTrace();
- oldSiftsFile.renameTo(siftsFile);
+ BackupFiles.moveFileToFile(oldSiftsFile, siftsFile);
return new File(siftsFileName);
}
}
}
String siftFile = pdbId + ".xml.gz";
String siftsFileFTPURL = SIFTS_FTP_BASE_URL + siftFile;
-
+
/*
* Download the file from URL to either
* Java: directory of cached downloaded SIFTS files
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
InputStream inputStream = conn.getInputStream();
- FileOutputStream outputStream = new FileOutputStream(
- downloadTo);
+ FileOutputStream outputStream = new FileOutputStream(downloadTo);
byte[] buffer = new byte[BUFFER_SIZE];
int bytesRead = -1;
while ((bytesRead = inputStream.read(buffer)) != -1)
SequenceI seq, java.io.PrintStream os) throws SiftsException
{
List<Integer> omitNonObserved = new ArrayList<>();
- int nonObservedShiftIndex = 0,pdbeNonObserved=0;
+ int nonObservedShiftIndex = 0, pdbeNonObserved = 0;
// System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
List<Segment> segments = entity.getSegment();
SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
- omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
+ omitNonObserved, nonObservedShiftIndex, pdbeNonObserved);
processSegments(segments, shp);
try
{
{
throw new SiftsException("SIFTS mapping failed");
}
- // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys
+ // also construct a mapping object between the seq-coord sys and the PDB
+ // seq's coord sys
Integer[] keys = mapping.keySet().toArray(new Integer[0]);
Arrays.sort(keys);
seqStart = keys[0];
seqEnd = keys[keys.length - 1];
- List<int[]> from=new ArrayList<>(),to=new ArrayList<>();
- int[]_cfrom=null,_cto=null;
+ List<int[]> from = new ArrayList<>(), to = new ArrayList<>();
+ int[] _cfrom = null, _cto = null;
String matchedSeq = originalSeq;
- if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1
+ if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb
+ // sequence that starts <-1
{
- for (int seqps:keys)
+ for (int seqps : keys)
{
int pdbpos = mapping.get(seqps)[PDBE_POS];
if (pdbpos == UNASSIGNED)
// not correct - pdbpos might be -1, but leave it for now
continue;
}
- if (_cfrom==null || seqps!=_cfrom[1]+1)
+ if (_cfrom == null || seqps != _cfrom[1] + 1)
{
- _cfrom = new int[] { seqps,seqps};
+ _cfrom = new int[] { seqps, seqps };
from.add(_cfrom);
_cto = null; // discontinuity
- } else {
- _cfrom[1]= seqps;
}
- if (_cto==null || pdbpos!=1+_cto[1])
+ else
+ {
+ _cfrom[1] = seqps;
+ }
+ if (_cto == null || pdbpos != 1 + _cto[1])
{
- _cto = new int[] { pdbpos,pdbpos};
+ _cto = new int[] { pdbpos, pdbpos };
to.add(_cto);
- } else {
+ }
+ else
+ {
_cto[1] = pdbpos;
}
}
;
seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
- 1,
- 1);
+ 1, 1);
pdbStart = mapping.get(seqStart)[PDB_RES_POS];
pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
int orignalSeqStart = seq.getStart();
}
// if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
// true
- // numbering
- // is
- // not
- // up
- // to
- // seq.getEnd()
+ // numbering
+ // is
+ // not
+ // up
+ // to
+ // seq.getEnd()
{
int resNum = (pdbRefDb == null)
{
return pdbeNonObserved;
}
+
public SequenceI getSeq()
{
return seq;
--- /dev/null
+package jalview.bin;
+
+import static org.testng.Assert.assertEquals;
+
+import org.mockito.Mockito;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
+/*
+ * Testing a HiDPI display is difficult without running in a HiDPI display.
+ * The gathering of screen size and resolution performed by jalview.bin.HiDPISetting
+ * is now farmed out into a separate class jalview.bin.ScreenInfo so it can be more
+ * easily Mocked in tests.
+ * Two sets of tests are performed.
+ * 1) testLinuxScalePropertyToActualTransform() sets the property that HiDPISetting
+ * uses (via jalview.bin.Launcher or getdown) to scale up Jalview, and then looks at
+ * the alignment panel graphics2d transform to see if it's been scaled by the same
+ * amount (in this case 4 -- unlikely to happen by accident!).
+ * 2) testHiDPISettingInit() which tests the calculation that HiDPISetting uses to
+ * decide from apparent screen information (mocked using Mockito in the tests) what
+ * scaling factor to set (it doesn't actually set it, just suggests it to
+ * jalview.bin.Launcher)
+ */
+public class HiDPISettingTest1
+{
+
+ AlignFrame af = null;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ Cache.loadProperties("test/jalview/bin/hidpiTestProps.jvprops");
+ Jalview.main(
+ new String[]
+ { "-nosplash", "-nonews", "-noquestionnaire",
+ "-nowebservicediscovery" });
+
+ af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+ DataSourceType.FILE);
+
+ /*
+ * wait for Consensus thread to complete
+ */
+ do
+ {
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
+ {
+ }
+ } while (af.getViewport().getCalcManager().isWorking());
+ }
+
+ @AfterClass(alwaysRun = true)
+ public void tearDown()
+ {
+ Desktop.instance.closeAll_actionPerformed(null);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testHiDPISettingInit()
+ {
+ String scalePropertyName = "sun.java2d.uiScale";
+ // ensure scale property is cleared (otherwise it will be re-used)
+ System.clearProperty(HiDPISetting.scalePropertyName);
+
+ { // keep the mock under lock
+ // Ancient monitor -- no property change set
+ setMockScreen(1024, 768, 72);
+ assertEquals(HiDPISetting.getScalePropertyArg(), null);
+
+ // Old monitor -- no property change set
+ setMockScreen(1200, 800, 96);
+ assertEquals(HiDPISetting.getScalePropertyArg(), null);
+
+ // HD screen -- no property change set
+ setMockScreen(1920, 1080, 96);
+ assertEquals(HiDPISetting.getScalePropertyArg(), null);
+
+ // 4K screen -- scale by 2
+ setMockScreen(3180, 2160, 80);
+ assertEquals(HiDPISetting.getScalePropertyArg(),
+ "-D" + scalePropertyName + "=2");
+
+ // 4K screen with high dpi -- scale by 3
+ setMockScreen(3180, 2160, 450);
+ assertEquals(HiDPISetting.getScalePropertyArg(),
+ "-D" + scalePropertyName + "=3");
+
+ // stupidly big screen -- scale by 8
+ setMockScreen(19200, 10800, 72);
+ assertEquals(HiDPISetting.getScalePropertyArg(),
+ "-D" + scalePropertyName + "=8");
+ }
+ }
+
+ private void setMockScreen(int width, int height, int dpi)
+ {
+ HiDPISetting.clear();
+ ScreenInfo mockScreenInfo = Mockito.spy(HiDPISetting.getScreenInfo());
+ Mockito.doReturn(height).when(mockScreenInfo).getScreenHeight();
+ Mockito.doReturn(width).when(mockScreenInfo).getScreenWidth();
+ Mockito.doReturn(dpi).when(mockScreenInfo).getScreenResolution();
+ HiDPISetting.setScreenInfo(mockScreenInfo);
+ }
+}
--- /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 static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.concurrent.TimeUnit;
+
+import org.testng.Assert;
+import org.testng.SkipException;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import io.github.classgraph.ClassGraph;
+import io.github.classgraph.ScanResult;
+import jalview.gui.Desktop;
+import jalview.util.Platform;
+
+public class HiDPISettingTest2
+{
+ private static final int TIMEOUT = 10;
+
+ private static class Worker extends Thread
+ {
+ private final Process process;
+
+ private BufferedReader outputReader;
+
+ private BufferedReader errorReader;
+
+ private boolean exited;
+
+ private Worker(Process process)
+ {
+ this.process = process;
+ }
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ exited = process.waitFor(TIMEOUT, TimeUnit.SECONDS);
+ } catch (InterruptedException ignore)
+ {
+ return;
+ }
+ this.interrupt();
+ this.process.destroy();
+ }
+
+ public BufferedReader getOutputReader()
+ {
+ return outputReader;
+ }
+
+ public void setOutputReader(BufferedReader outputReader)
+ {
+ this.outputReader = outputReader;
+ }
+
+ public BufferedReader getErrorReader()
+ {
+ return errorReader;
+ }
+
+ public void setErrorReader(BufferedReader errorReader)
+ {
+ this.errorReader = errorReader;
+ }
+ }
+
+ private static ClassGraph scanner = null;
+
+ private static String classpath = null;
+
+ private static String java_exe = null;
+
+ public synchronized static String getClassPath()
+ {
+ if (scanner == null)
+ {
+ scanner = new ClassGraph();
+ ScanResult scan = scanner.scan();
+ classpath = scan.getClasspath();
+ java_exe = System.getProperty("java.home") + File.separator + "bin"
+ + File.separator + "java";
+
+ }
+ while (classpath == null)
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException x)
+ {
+
+ }
+ }
+ return classpath;
+ }
+
+ private Worker getJalviewDesktopRunner(String jvmArgs, String appArgs)
+ {
+ String classpath = getClassPath();
+ String cmd = java_exe + " " + " -classpath " + classpath + " " + jvmArgs
+ + " jalview.bin.Jalview " + " "
+ + "-props test/jalview/bin/hidpiTestProps.jvprops " + appArgs;
+ Process proc = null;
+ Worker worker = null;
+ try
+ {
+ proc = Runtime.getRuntime().exec(cmd);
+ } catch (Throwable e)
+ {
+ e.printStackTrace();
+ }
+ if (proc != null)
+ {
+ BufferedReader outputReader = new BufferedReader(
+ new InputStreamReader(proc.getInputStream()));
+ BufferedReader errorReader = new BufferedReader(
+ new InputStreamReader(proc.getErrorStream()));
+ worker = new Worker(proc);
+ worker.start();
+ worker.setOutputReader(outputReader);
+ worker.setErrorReader(errorReader);
+ }
+ return worker;
+ }
+
+ @BeforeTest(alwaysRun = true)
+ public void initialize()
+ {
+ new HiDPISettingTest2();
+ }
+
+ @Test(groups = { "Functional" }, dataProvider = "hidpiScaleArguments")
+ public void testHiDPISettings(int scale)
+ {
+ if (Platform.isLinux())
+ {
+ throw new SkipException(
+ "Not linux platform, not testing actual scaling with "
+ + HiDPISetting.scalePropertyName);
+ }
+
+ String jvmArgs = HiDPISetting.getScalePropertyArg(scale);
+
+ String appArgs = " -open examples/uniref50.fa -nosplash -nonews -noquestionnaire -nousagestats -nowebservicediscovery";
+
+ Worker worker = getJalviewDesktopRunner(jvmArgs, appArgs);
+ assertNotNull(worker, "worker is null");
+
+ String ln = null;
+ int count = 0;
+ boolean scaleFound = false;
+ try
+ {
+ while ((ln = worker.getErrorReader().readLine()) != null)
+ {
+ if (++count > 100)
+ {
+ break;
+ }
+ if (ln.contains(Desktop.debugScaleMessage))
+ {
+ String number = ln.substring(ln.indexOf(Desktop.debugScaleMessage)
+ + Desktop.debugScaleMessage.length());
+ number = number.substring(0, number.indexOf(' '));
+ try
+ {
+ double d = Double.valueOf(number);
+
+ assertEquals(d, scale * 1.0);
+ scaleFound = true;
+ } catch (NumberFormatException e)
+ {
+ e.printStackTrace();
+ Assert.fail(
+ "Debug scale message line '" + ln + "' gives number '"
+ + number + "' which could not be parsed");
+ }
+ break;
+ }
+ }
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ if (worker != null && worker.exited == false)
+ {
+ worker.interrupt();
+ worker.process.destroy();
+ }
+ if (!scaleFound)
+ {
+ Assert.fail("Did not find Debug scale message line '"
+ + Desktop.debugScaleMessage + "'");
+ }
+ }
+
+ @DataProvider(name = "hidpiScaleArguments")
+ public static Object[][] getHiDPIScaleArguments()
+ {
+ return new Object[][] { { 1 }, { 2 }, { 4 }, { 10 } };
+ }
+}
--- /dev/null
+#---JalviewX Properties File---
+# HiDPI screen
+SCREENGEOMETRY_WIDTH=3840
+SCREENGEOMETRY_HEIGHT=2160
+SCREEN_WIDTH=3000
+SCREEN_HEIGHT=2000
+USAGESTATS=false
+STARTUP_FILE=examples/uniref50.fa
+SHOW_STARTUP_FILE=false
+FONT_STYLE=plain
+FONT_SIZE=10
+ANTI_ALIAS=false
+SHOW_JAVA_CONSOLE=false
+DAS_REGISTRY_URL=http\://www.ebi.ac.uk/das-srv/registry/das/
+logs.Jalview.level=DEBUG
git://source.jalview.org / jalview.git / commitdiff