From 8ac246459db21ac8c6a07834b815261ee961fb9a Mon Sep 17 00:00:00 2001 From: soares Date: Wed, 22 Apr 2020 20:45:19 +0100 Subject: [PATCH] JAL-3608 saved in Eclipse with auto formatting --- src/jalview/bin/Jalview.java | 307 +++++++++++++++++++++--------------------- 1 file changed, 155 insertions(+), 152 deletions(-) diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index afe4055..5c026fd 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,27 +20,6 @@ */ package jalview.bin; -import jalview.ext.so.SequenceOntology; -import jalview.gui.AlignFrame; -import jalview.gui.Desktop; -import jalview.gui.PromptUserConfig; -import jalview.io.AppletFormatAdapter; -import jalview.io.BioJsHTMLOutput; -import jalview.io.DataSourceType; -import jalview.io.FileFormat; -import jalview.io.FileFormatException; -import jalview.io.FileFormatI; -import jalview.io.FileLoader; -import jalview.io.HtmlSvgOutput; -import jalview.io.IdentifyFile; -import jalview.io.NewickFile; -import jalview.io.gff.SequenceOntologyFactory; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemeProperty; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.ws.jws2.Jws2Discoverer; - import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -71,6 +50,26 @@ import com.threerings.getdown.util.LaunchUtil; import groovy.lang.Binding; import groovy.util.GroovyScriptEngine; +import jalview.ext.so.SequenceOntology; +import jalview.gui.AlignFrame; +import jalview.gui.Desktop; +import jalview.gui.PromptUserConfig; +import jalview.io.AppletFormatAdapter; +import jalview.io.BioJsHTMLOutput; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatException; +import jalview.io.FileFormatI; +import jalview.io.FileLoader; +import jalview.io.HtmlSvgOutput; +import jalview.io.IdentifyFile; +import jalview.io.NewickFile; +import jalview.io.gff.SequenceOntologyFactory; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.jws2.Jws2Discoverer; /** * Main class for Jalview Application
@@ -112,21 +111,21 @@ public class Jalview */ { // grab all the rights we can for the JVM - Policy.setPolicy(new Policy() - { - @Override - public PermissionCollection getPermissions(CodeSource codesource) - { - Permissions perms = new Permissions(); - perms.add(new AllPermission()); - return (perms); - } - - @Override - public void refresh() - { - } - }); + Policy.setPolicy(new Policy() + { + @Override + public PermissionCollection getPermissions(CodeSource codesource) + { + Permissions perms = new Permissions(); + perms.add(new AllPermission()); + return (perms); + } + + @Override + public void refresh() + { + } + }); } } @@ -198,27 +197,27 @@ public class Jalview * main class for Jalview application * * @param args - * open filename + * open filename */ public static void main(String[] args) { -// setLogging(); // BH - for event debugging in JavaScript + // setLogging(); // BH - for event debugging in JavaScript instance = new Jalview(); instance.doMain(args); -} + } - private static void logClass(String name) - { - // BH - for event debugging in JavaScript - ConsoleHandler consoleHandler = new ConsoleHandler(); - consoleHandler.setLevel(Level.ALL); - Logger logger = Logger.getLogger(name); - logger.setLevel(Level.ALL); - logger.addHandler(consoleHandler); + private static void logClass(String name) + { + // BH - for event debugging in JavaScript + ConsoleHandler consoleHandler = new ConsoleHandler(); + consoleHandler.setLevel(Level.ALL); + Logger logger = Logger.getLogger(name); + logger.setLevel(Level.ALL); + logger.addHandler(consoleHandler); } @SuppressWarnings("unused") - private static void setLogging() + private static void setLogging() { /** @@ -229,26 +228,23 @@ public class Jalview System.out.println("not in js"); } - // BH - for event debugging in JavaScript (Java mode only) + // BH - for event debugging in JavaScript (Java mode only) if (!Platform.isJS()) /** * Java only * * @j2sIgnore */ - { - Logger.getLogger("").setLevel(Level.ALL); - logClass("java.awt.EventDispatchThread"); - logClass("java.awt.EventQueue"); - logClass("java.awt.Component"); - logClass("java.awt.focus.Component"); - logClass("java.awt.focus.DefaultKeyboardFocusManager"); - } + { + Logger.getLogger("").setLevel(Level.ALL); + logClass("java.awt.EventDispatchThread"); + logClass("java.awt.EventQueue"); + logClass("java.awt.Component"); + logClass("java.awt.focus.Component"); + logClass("java.awt.focus.DefaultKeyboardFocusManager"); + } } - - - /** * @param args @@ -262,22 +258,24 @@ public class Jalview } System.out - .println("Java version: " - + System.getProperty("java.version")); + .println("Java version: " + System.getProperty("java.version")); System.out.println("Java Home: " + System.getProperty("java.home")); System.out.println(System.getProperty("os.arch") + " " + System.getProperty("os.name") + " " + System.getProperty("os.version")); String val = System.getProperty("sys.install4jVersion"); - if (val != null) { - System.out.println("Install4j version: " + val); + if (val != null) + { + System.out.println("Install4j version: " + val); } val = System.getProperty("installer_template_version"); - if (val != null) { + if (val != null) + { System.out.println("Install4j template version: " + val); } val = System.getProperty("launcher_version"); - if (val != null) { + if (val != null) + { System.out.println("Launcher version: " + val); } @@ -344,7 +342,7 @@ public class Jalview System.out.println("Executing setprop argument: " + defs); if (Platform.isJS()) { - Cache.setProperty(defs.substring(0,p), defs.substring(p+1)); + Cache.setProperty(defs.substring(0, p), defs.substring(p + 1)); } } defs = aparser.getValue("setprop"); @@ -370,37 +368,39 @@ public class Jalview desktop = null; // property laf = "crossplatform", "system" or "mac" - // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac, try Quaqua/Vaqua. - String laf = System.getProperty("laf","none"); + // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac, + // try Quaqua/Vaqua. + String laf = System.getProperty("laf", "none"); boolean lafSet = false; - switch(laf) { + switch (laf) + { case "crossplatform": lafSet = setCrossPlatformLookAndFeel(); if (!lafSet) { - System.err.println("Could not set requested laf="+laf); + 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); + 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); + System.err.println("Could not set requested laf=" + laf); } break; case "none": break; default: - System.err.println("Requested laf="+laf+" not implemented"); + System.err.println("Requested laf=" + laf + " not implemented"); } - if (! lafSet) + if (!lafSet) { setSystemLookAndFeel(); if (Platform.isAMacAndNotJS()) @@ -543,11 +543,11 @@ public class Jalview System.out.println("CMD [-open " + file + "] executed successfully!"); if (!Platform.isJS()) - /** - * ignore in JavaScript -- can't just file existence - could load it? - * - * @j2sIgnore - */ + /** + * ignore in JavaScript -- can't just file existence - could load it? + * + * @j2sIgnore + */ { if (!file.startsWith("http://") && !file.startsWith("https://")) // BH 2019 added https check for Java @@ -563,7 +563,7 @@ public class Jalview } } - protocol = AppletFormatAdapter.checkProtocol(file); + protocol = AppletFormatAdapter.checkProtocol(file); try { @@ -783,8 +783,7 @@ public class Jalview */ { file = Cache.getDefault("STARTUP_FILE", - Cache.getDefault("www.jalview.org", - "http://www.jalview.org") + 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")) @@ -848,74 +847,78 @@ public class Jalview } } - private static boolean setCrossPlatformLookAndFeel() { - boolean set = false; - try - { - UIManager.setLookAndFeel(UIManager.getCrossPlatformLookAndFeelClassName()); - set = true; - } catch (Exception ex) - { - System.err.println("Unexpected Look and Feel Exception"); - ex.printStackTrace(); - } - return set; + private static boolean setCrossPlatformLookAndFeel() + { + boolean set = false; + try + { + UIManager.setLookAndFeel( + UIManager.getCrossPlatformLookAndFeelClassName()); + set = true; + } catch (Exception ex) + { + System.err.println("Unexpected Look and Feel Exception"); + ex.printStackTrace(); + } + return set; } - private static boolean setSystemLookAndFeel() { - boolean set = false; - try - { - UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); - set = true; - } catch (Exception ex) - { - System.err.println("Unexpected Look and Feel Exception"); - ex.printStackTrace(); - } - return set; + private static boolean setSystemLookAndFeel() + { + boolean set = false; + try + { + UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName()); + set = true; + } catch (Exception ex) + { + System.err.println("Unexpected Look and Feel Exception"); + ex.printStackTrace(); + } + return set; } - - private static boolean setMacLookAndFeel() { - boolean set = false; - LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager - .getLookAndFeel(); - System.setProperty("com.apple.mrj.application.apple.menu.about.name", - "Jalview"); - System.setProperty("apple.laf.useScreenMenuBar", "true"); - if (lookAndFeel != null) - { - try - { - UIManager.setLookAndFeel(lookAndFeel); - set = true; - } catch (Throwable e) - { - System.err.println( - "Failed to set QuaQua look and feel: " + e.toString()); - } - } - if (lookAndFeel == null - || !(lookAndFeel.getClass().isAssignableFrom( - UIManager.getLookAndFeel().getClass())) - || !UIManager.getLookAndFeel().getClass().toString() - .toLowerCase().contains("quaqua")) - { - try - { - System.err.println( - "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976"); - UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel"); - set = true; - } catch (Throwable e) - { - System.err.println( - "Failed to reset look and feel: " + e.toString()); - } - } - return set; + + private static boolean setMacLookAndFeel() + { + boolean set = false; + LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager + .getLookAndFeel(); + System.setProperty("com.apple.mrj.application.apple.menu.about.name", + "Jalview"); + System.setProperty("apple.laf.useScreenMenuBar", "true"); + if (lookAndFeel != null) + { + try + { + UIManager.setLookAndFeel(lookAndFeel); + set = true; + } catch (Throwable e) + { + System.err.println( + "Failed to set QuaQua look and feel: " + e.toString()); + } + } + if (lookAndFeel == null + || !(lookAndFeel.getClass().isAssignableFrom( + UIManager.getLookAndFeel().getClass())) + || !UIManager.getLookAndFeel().getClass().toString() + .toLowerCase().contains("quaqua")) + { + try + { + System.err.println( + "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976"); + UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel"); + set = true; + } catch (Throwable e) + { + System.err + .println("Failed to reset look and feel: " + e.toString()); + } + } + return set; } - + private static void showUsage() { System.out.println( @@ -992,10 +995,10 @@ public class Jalview * Locate the given string as a file and pass it to the groovy interpreter. * * @param groovyscript - * the script to execute + * the script to execute * @param jalviewContext - * the Jalview Desktop object passed in to the groovy - * binding as the 'Jalview' object. + * the Jalview Desktop object passed in to the groovy binding as the + * 'Jalview' object. */ private void executeGroovyScript(String groovyscript, AlignFrame af) { @@ -1124,8 +1127,8 @@ public class Jalview } /** - * Quit method delegates to Desktop.quit - unless running in headless mode when - * it just ends the JVM + * Quit method delegates to Desktop.quit - unless running in headless mode + * when it just ends the JVM */ public void quit() { -- 1.7.10.2