X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=357f0e43753a4375226ed55c0153ff6d32a60a43;hb=853cdaf827241e4bf51d9a1fef32a395cb72cf45;hp=fe48283085a702013fab5c85f74bf41535a7819b;hpb=9d2408483e451285fd555c3cd6e0273977acbaa7;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index fe48283..357f0e4 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -20,8 +20,6 @@ */ package jalview.bin; -import java.util.Locale; - import java.io.BufferedReader; import java.io.File; import java.io.FileOutputStream; @@ -39,6 +37,7 @@ import java.security.PermissionCollection; 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; @@ -96,6 +95,10 @@ public class Jalview 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"); } /* @@ -319,6 +322,9 @@ public class Jalview } // 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) { @@ -363,9 +369,10 @@ public class Jalview } System.setProperty("http.agent", "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); + try { - Cache.initLogger(); + Console.initLogger(); } catch (NoClassDefFoundError error) { error.printStackTrace(); @@ -399,13 +406,13 @@ public class Jalview JalviewTaskbar.setTaskbar(this); } catch (Exception e) { - Cache.log.info("Cannot set Taskbar"); - Cache.log.error(e.getMessage()); + Console.info("Cannot set Taskbar"); + Console.error(e.getMessage()); // e.printStackTrace(); } catch (Throwable t) { - Cache.log.info("Cannot set Taskbar"); - Cache.log.error(t.getMessage()); + Console.info("Cannot set Taskbar"); + Console.error(t.getMessage()); // t.printStackTrace(); } @@ -441,7 +448,7 @@ public class Jalview { // 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!"); @@ -456,7 +463,7 @@ public class Jalview // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; // // String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl"; - Cache.log.debug( + Console.debug( "Starting questionnaire with default url: " + defurl); desktop.checkForQuestionnaire(defurl); } @@ -468,12 +475,17 @@ public class Jalview .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(); + } } } @@ -784,12 +796,11 @@ public class Jalview * @j2sIgnore */ { - file = jalview.bin.Cache.getDefault("STARTUP_FILE", - jalview.bin.Cache.getDefault("www.jalview.org", - "https://www.jalview.org") + file = Cache.getDefault("STARTUP_FILE", + 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( + 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:"); @@ -872,62 +883,62 @@ public class Jalview lafSet = setCrossPlatformLookAndFeel(); if (!lafSet) { - Cache.log.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "system": lafSet = setSystemLookAndFeel(); if (!lafSet) { - Cache.log.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "gtk": lafSet = setGtkLookAndFeel(); if (!lafSet) { - Cache.log.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "metal": lafSet = setMetalLookAndFeel(); if (!lafSet) { - Cache.log.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "nimbus": lafSet = setNimbusLookAndFeel(); if (!lafSet) { - Cache.log.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "quaqua": lafSet = setQuaquaLookAndFeel(); if (!lafSet) { - Cache.log.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "vaqua": lafSet = setVaquaLookAndFeel(); if (!lafSet) { - Cache.log.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "mac": lafSet = setMacLookAndFeel(); if (!lafSet) { - Cache.log.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "none": break; default: - Cache.log.error("Requested laf=" + laf + " not implemented"); + Console.error("Requested laf=" + laf + " not implemented"); } if (!lafSet) { @@ -953,9 +964,9 @@ public class Jalview set = true; } catch (Exception ex) { - Cache.log.error("Unexpected Look and Feel Exception"); - Cache.log.error(ex.getMessage()); - Cache.log.debug(Cache.getStackTraceString(ex)); + Console.error("Unexpected Look and Feel Exception"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); } return set; } @@ -969,9 +980,9 @@ public class Jalview set = true; } catch (Exception ex) { - Cache.log.error("Unexpected Look and Feel Exception"); - Cache.log.error(ex.getMessage()); - Cache.log.debug(Cache.getStackTraceString(ex)); + Console.error("Unexpected Look and Feel Exception"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); } return set; } @@ -987,7 +998,8 @@ public class Jalview if (info.getName() != null && nameStartsWith ? info.getName().toLowerCase(Locale.ROOT) .startsWith(name.toLowerCase(Locale.ROOT)) - : info.getName().toLowerCase(Locale.ROOT).equals(name.toLowerCase(Locale.ROOT))) + : info.getName().toLowerCase(Locale.ROOT) + .equals(name.toLowerCase(Locale.ROOT))) { className = info.getClassName(); break; @@ -997,9 +1009,9 @@ public class Jalview set = true; } catch (Exception ex) { - Cache.log.error("Unexpected Look and Feel Exception"); - Cache.log.error(ex.getMessage()); - Cache.log.debug(Cache.getStackTraceString(ex)); + Console.error("Unexpected Look and Feel Exception"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); } return set; } @@ -1109,17 +1121,16 @@ public class Jalview @Override public void run() { - Cache.log.debug( - "Initialising googletracker for usage stats."); + 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);