*/
package jalview.bin;
+import java.awt.Color;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.security.Permissions;
import java.security.Policy;
import java.util.HashMap;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
import java.util.logging.ConsoleHandler;
import java.util.logging.Level;
import java.util.logging.Logger;
+import javax.swing.SwingUtilities;
import javax.swing.UIManager;
import javax.swing.UIManager.LookAndFeelInfo;
+import com.formdev.flatlaf.FlatLightLaf;
+import com.formdev.flatlaf.util.SystemInfo;
import com.threerings.getdown.util.LaunchUtil;
+//import edu.stanford.ejalbert.launching.IBrowserLaunching;
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
import jalview.ext.so.SequenceOntology;
import jalview.io.FileFormat;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.io.gff.SequenceOntologyFactory;
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;
static
{
Platform.getURLCommandArguments();
+ Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
+ Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
+ Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
+ Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
}
- // singleton instance of this class
-
+ /*
+ * singleton instance of this class
+ */
private static Jalview instance;
private Desktop desktop;
}
// anything else!
+ // allow https handshakes to download intermediate certs if necessary
+ System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
+
final String jabawsUrl = aparser.getValue("jabaws");
if (jabawsUrl != null)
{
"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");
}
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+
try
{
- Cache.initLogger();
+ Console.initLogger();
} catch (NoClassDefFoundError error)
{
error.printStackTrace();
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)
+ {
+ Console.info("Cannot set Taskbar");
+ Console.error(e.getMessage());
+ // e.printStackTrace();
} catch (Throwable t)
{
- System.out.println("Error setting Taskbar: " + t.getMessage());
+ Console.info("Cannot set Taskbar");
+ Console.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);
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
- Cache.log.debug("Starting questionnaire url at " + url);
+ Console.debug("Starting questionnaire url at " + url);
desktop.checkForQuestionnaire(url);
System.out.println("CMD questionnaire[-" + url
+ "] executed successfully!");
// String defurl =
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
- String defurl = "http://www.jalview.org/cgi-bin/questionnaire.pl";
- Cache.log.debug(
+ String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
+ Console.debug(
"Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
}
.println("CMD [-noquestionnaire] executed successfully!");
}
- if (!aparser.contains("nonews"))
+ if (!aparser.contains("nonews")
+ || Cache.getProperty("NONEWS") == null)
{
desktop.checkForNews();
}
- BioJsHTMLOutput.updateBioJS();
+ if (!aparser.contains("nohtmltemplates")
+ || Cache.getProperty("NOHTMLTEMPLATES") == null)
+ {
+ BioJsHTMLOutput.updateBioJS();
+ }
}
}
* @j2sIgnore
*/
{
- if (!file.startsWith("http://") && !file.startsWith("https://"))
- // BH 2019 added https check for Java
+ if (!HttpUtils.startsWithHttpOrHttps(file))
{
if (!(new File(file)).exists())
{
af.createEPS(outputFile);
continue;
}
-
- af.saveAlignment(file, format);
- if (af.isSaveAlignmentSuccessful())
+ FileFormatI outFormat = null;
+ try
{
- System.out.println("Written alignment in " + format
- + " format to " + file);
+ outFormat = FileFormats.getInstance().forName(outputFormat);
+ } catch (Exception formatP)
+ {
+ System.out.println("Couldn't parse " + outFormat
+ + " as a valid Jalview format string.");
}
- else
+ if (outFormat != null)
{
- System.out.println("Error writing file " + file + " in "
- + format + " format!!");
+ if (!outFormat.isWritable())
+ {
+ System.out.println(
+ "This version of Jalview does not support alignment export as "
+ + outputFormat);
+ }
+ else
+ {
+ af.saveAlignment(file, outFormat);
+ if (af.isSaveAlignmentSuccessful())
+ {
+ System.out.println("Written alignment in "
+ + outFormat.getName() + " format to " + file);
+ }
+ else
+ {
+ System.out.println("Error writing file " + file + " in "
+ + outFormat.getName() + " format!!");
+ }
+ }
}
}
*/
{
file = Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_7.jar");
- if (file.equals(
- "http://www.jalview.org/examples/exampleFile_2_3.jar"))
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp");
+ if (file.equals("http://www.jalview.org/examples/exampleFile_2_3.jar")
+ || file.equals(
+ "http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
+ file.replace("http:", "https:");
// hardwire upgrade of the startup file
- file.replace("_2_3.jar", "_2_7.jar");
+ file.replace("_2_3", "_2_7");
+ file.replace("2_7.jar", "2_7.jvp");
// and remove the stale setting
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 void setLookAndFeel()
+ {
+ // property laf = "crossplatform", "system", "gtk", "metal", "nimbus",
+ // "mac" or "flat"
+ // 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)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "system":
+ lafSet = setSystemLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "gtk":
+ lafSet = setGtkLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "metal":
+ lafSet = setMetalLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "nimbus":
+ lafSet = setNimbusLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "flat":
+ lafSet = setFlatLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "quaqua":
+ lafSet = setQuaquaLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "vaqua":
+ lafSet = setVaquaLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "mac":
+ lafSet = setMacLookAndFeel();
+ if (!lafSet)
+ {
+ Console.error("Could not set requested laf=" + laf);
+ }
+ break;
+ case "none":
+ break;
+ default:
+ Console.error("Requested laf=" + laf + " not implemented");
+ }
+ if (!lafSet)
+ {
+ setSystemLookAndFeel();
+ if (Platform.isLinux())
+ {
+ setMetalLookAndFeel();
+ }
+ if (Platform.isMac())
+ {
+ setMacLookAndFeel();
+ }
+ }
+ }
+
private static boolean setCrossPlatformLookAndFeel()
{
boolean set = false;
set = true;
} catch (Exception ex)
{
- System.err.println("Unexpected Look and Feel Exception");
- ex.printStackTrace();
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
set = true;
} catch (Exception ex)
{
- System.err.println("Unexpected Look and Feel Exception");
- ex.printStackTrace();
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
{
if (info.getName() != null && nameStartsWith
- ? info.getName().toLowerCase()
- .startsWith(name.toLowerCase())
- : info.getName().toLowerCase().equals(name.toLowerCase()))
+ ? info.getName().toLowerCase(Locale.ROOT)
+ .startsWith(name.toLowerCase(Locale.ROOT))
+ : info.getName().toLowerCase(Locale.ROOT)
+ .equals(name.toLowerCase(Locale.ROOT)))
{
className = info.getClassName();
break;
set = true;
} catch (Exception ex)
{
- System.err.println("Unexpected Look and Feel Exception");
- ex.printStackTrace();
+ Console.error("Unexpected Look and Feel Exception");
+ Console.error(ex.getMessage());
+ Console.debug(Cache.getStackTraceString(ex));
}
return set;
}
"javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
}
+ private static boolean setFlatLookAndFeel()
+ {
+ boolean set = setSpecificLookAndFeel("flatlaf light",
+ "com.formdev.flatlaf.FlatLightLaf", false);
+ if (set)
+ {
+ if (Platform.isMac())
+ {
+ System.setProperty("apple.laf.useScreenMenuBar", "true");
+ System.setProperty("apple.awt.application.name",
+ ChannelProperties.getProperty("app_name"));
+ System.setProperty("apple.awt.application.appearance", "system");
+ if (SystemInfo.isMacFullWindowContentSupported
+ && Desktop.desktop != null)
+ {
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.fullWindowContent", true);
+ Desktop.desktop.getRootPane()
+ .putClientProperty("apple.awt.transparentTitleBar", true);
+ }
+
+ SwingUtilities.invokeLater(() -> {
+ FlatLightLaf.setup();
+ });
+ }
+
+ UIManager.put("TabbedPane.showTabSeparators", true);
+ UIManager.put("TabbedPane.tabSeparatorsFullHeight", true);
+ UIManager.put("TabbedPane.tabsOverlapBorder", true);
+ // UIManager.put("TabbedPane.hasFullBorder", true);
+ UIManager.put("TabbedPane.tabLayoutPolicy", "scroll");
+ UIManager.put("TabbedPane.scrollButtonsPolicy", "asNeeded");
+ UIManager.put("TabbedPane.smoothScrolling", true);
+ UIManager.put("TabbedPane.tabWidthMode", "compact");
+ UIManager.put("TabbedPane.selectedBackground", Color.white);
+ }
+ return set;
+ }
+
private static boolean setQuaquaLookAndFeel()
{
return setSpecificLookAndFeel("quaqua",
{
boolean set = false;
System.setProperty("com.apple.mrj.application.apple.menu.about.name",
- "Jalview");
+ ChannelProperties.getProperty("app_name"));
System.setProperty("apple.laf.useScreenMenuBar", "true");
set = setQuaquaLookAndFeel();
if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
- .toLowerCase().contains("quaqua"))
+ .toLowerCase(Locale.ROOT).contains("quaqua"))
{
set = setVaquaLookAndFeel();
}
+ "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
+ "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
+ "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
- + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
+ + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+ + "\n~Read documentation in Application or visit https://www.jalview.org for description of Features and Annotations file~\n\n");
}
private static void startUsageStats(final Desktop desktop)
@Override
public void run()
{
- Cache.log.debug(
+ Console.debug(
"Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
- Cache.log.debug("Tracking enabled.");
+ Console.debug("Tracking enabled.");
}
}, new Runnable()
{
@Override
public void run()
{
- Cache.log.debug("Not enabling Google Tracking.");
+ Console.debug("Not enabling Google Tracking.");
}
}, null, true);
desktop.addDialogThread(prompter);
git://source.jalview.org / jalview.git / blobdiff