X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbin%2FJalview.java;h=4fc7714126eaae3e09d4ec25e8b754907add335f;hb=6003472b3bf23fb34988fb45bef9dc78e0fd5bbd;hp=920c86ddbebf52875cfaea79389d2c0028c364f4;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 920c86d..4fc7714 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -49,6 +49,7 @@ import javax.swing.UIManager.LookAndFeelInfo; 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; @@ -69,6 +70,7 @@ import jalview.io.NewickFile; import jalview.io.gff.SequenceOntologyFactory; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; +import jalview.util.BrowserLauncher; import jalview.util.ChannelProperties; import jalview.util.HttpUtils; import jalview.util.MessageManager; @@ -95,6 +97,10 @@ 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"); } /* @@ -284,17 +290,6 @@ public class Jalview System.out.println("Launcher version: " + val); } - try - { - Cache.initLogger(); - } catch (NoClassDefFoundError error) - { - error.printStackTrace(); - System.out.println("\nEssential logging libraries not found." - + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview"); - System.exit(0); - } - // report Jalview version Cache.loadBuildProperties(true); @@ -377,6 +372,17 @@ public class Jalview System.setProperty("http.agent", "Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown")); + try + { + Console.initLogger(); + } catch (NoClassDefFoundError error) + { + error.printStackTrace(); + System.out.println("\nEssential logging libraries not found." + + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview"); + System.exit(0); + } + desktop = null; setLookAndFeel(); @@ -402,13 +408,13 @@ public class Jalview JalviewTaskbar.setTaskbar(this); } catch (Exception e) { - Cache.info("Cannot set Taskbar"); - Cache.error(e.getMessage()); + Console.info("Cannot set Taskbar"); + Console.error(e.getMessage()); // e.printStackTrace(); } catch (Throwable t) { - Cache.info("Cannot set Taskbar"); - Cache.error(t.getMessage()); + Console.info("Cannot set Taskbar"); + Console.error(t.getMessage()); // t.printStackTrace(); } @@ -444,7 +450,7 @@ public class Jalview { // Start the desktop questionnaire prompter with the specified // questionnaire - Cache.debug("Starting questionnaire url at " + url); + Console.debug("Starting questionnaire url at " + url); desktop.checkForQuestionnaire(url); System.out.println("CMD questionnaire[-" + url + "] executed successfully!"); @@ -459,7 +465,7 @@ public class Jalview // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl"; // // String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl"; - Cache.debug( + Console.debug( "Starting questionnaire with default url: " + defurl); desktop.checkForQuestionnaire(defurl); } @@ -471,12 +477,17 @@ 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(); + } } } @@ -499,6 +510,15 @@ public class Jalview }.start(); } + // set default browser + String defaultBrowser = Cache.getProperty("DEFAULT_BROWSER"); + if (defaultBrowser != null) + { + System.setProperty(BrowserLauncher.getBrowserSystemProperty(), + defaultBrowser); + BrowserLauncher.resetBrowser(); + } // don't clearProperty if DEFAULT_BROWSER is null, might be set by user + String file = null, data = null; FileFormatI format = null; DataSourceType protocol = null; @@ -874,62 +894,62 @@ public class Jalview lafSet = setCrossPlatformLookAndFeel(); if (!lafSet) { - Cache.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "system": lafSet = setSystemLookAndFeel(); if (!lafSet) { - Cache.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "gtk": lafSet = setGtkLookAndFeel(); if (!lafSet) { - Cache.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "metal": lafSet = setMetalLookAndFeel(); if (!lafSet) { - Cache.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "nimbus": lafSet = setNimbusLookAndFeel(); if (!lafSet) { - Cache.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "quaqua": lafSet = setQuaquaLookAndFeel(); if (!lafSet) { - Cache.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "vaqua": lafSet = setVaquaLookAndFeel(); if (!lafSet) { - Cache.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "mac": lafSet = setMacLookAndFeel(); if (!lafSet) { - Cache.error("Could not set requested laf=" + laf); + Console.error("Could not set requested laf=" + laf); } break; case "none": break; default: - Cache.error("Requested laf=" + laf + " not implemented"); + Console.error("Requested laf=" + laf + " not implemented"); } if (!lafSet) { @@ -955,9 +975,9 @@ public class Jalview set = true; } catch (Exception ex) { - Cache.error("Unexpected Look and Feel Exception"); - Cache.error(ex.getMessage()); - Cache.debug(Cache.getStackTraceString(ex)); + Console.error("Unexpected Look and Feel Exception"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); } return set; } @@ -971,9 +991,9 @@ public class Jalview set = true; } catch (Exception ex) { - Cache.error("Unexpected Look and Feel Exception"); - Cache.error(ex.getMessage()); - Cache.debug(Cache.getStackTraceString(ex)); + Console.error("Unexpected Look and Feel Exception"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); } return set; } @@ -1000,9 +1020,9 @@ public class Jalview set = true; } catch (Exception ex) { - Cache.error("Unexpected Look and Feel Exception"); - Cache.error(ex.getMessage()); - Cache.debug(Cache.getStackTraceString(ex)); + Console.error("Unexpected Look and Feel Exception"); + Console.error(ex.getMessage()); + Console.debug(Cache.getStackTraceString(ex)); } return set; } @@ -1112,16 +1132,17 @@ public class Jalview @Override public void run() { - Cache.debug("Initialising googletracker for usage stats."); + Console.debug( + "Initialising googletracker for usage stats."); Cache.initGoogleTracker(); - Cache.debug("Tracking enabled."); + Console.debug("Tracking enabled."); } }, new Runnable() { @Override public void run() { - Cache.debug("Not enabling Google Tracking."); + Console.debug("Not enabling Google Tracking."); } }, null, true); desktop.addDialogThread(prompter);