X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=02e53ecf395534900bf2792fbccec1e51dfa3dd6;hb=bb1629fd423f5ce90ca1a951f10e9183fbbbc8d0;hp=60cce4647dfdf9b7666342ec41a89f18e5e33aa7;hpb=a4da7f0f52e97ebb3fb0c42d6ab3a71762c4b899;p=jalview.git
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 60cce46..02e53ec 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -64,6 +64,8 @@ import java.util.Vector;
import javax.swing.LookAndFeel;
import javax.swing.UIManager;
+import com.threerings.getdown.util.LaunchUtil;
+
import groovy.lang.Binding;
import groovy.util.GroovyScriptEngine;
@@ -122,8 +124,8 @@ public class Jalview
class FeatureFetcher
{
/*
- * TODO: generalise to track all jalview events to orchestrate batch
- * processing events.
+ * TODO: generalise to track all jalview events to orchestrate batch processing
+ * events.
*/
private int queued = 0;
@@ -181,7 +183,7 @@ public class Jalview
* main class for Jalview application
*
* @param args
- * open filename
+ * open filename
*/
public static void main(String[] args)
{
@@ -200,6 +202,8 @@ public class Jalview
System.out.println(System.getProperty("os.arch") + " "
+ System.getProperty("os.name") + " "
+ System.getProperty("os.version"));
+ // report Jalview version
+ Cache.loadBuildProperties(true);
ArgsParser aparser = new ArgsParser(args);
boolean headless = false;
@@ -304,8 +308,9 @@ public class Jalview
"Failed to set QuaQua look and feel: " + e.toString());
}
}
- if (lookAndFeel == null || !(lookAndFeel.getClass()
- .isAssignableFrom(UIManager.getLookAndFeel().getClass()))
+ if (lookAndFeel == null
+ || !(lookAndFeel.getClass().isAssignableFrom(
+ UIManager.getLookAndFeel().getClass()))
|| !UIManager.getLookAndFeel().getClass().toString()
.toLowerCase().contains("quaqua"))
{
@@ -323,10 +328,10 @@ public class Jalview
}
/*
- * configure 'full' SO model if preferences say to,
- * else use the default (SO Lite)
+ * configure 'full' SO model if preferences say to, else use the default (SO
+ * Lite)
*/
- if (Cache.getDefault("USE_FULL_SO", false))
+ if (Cache.getDefault("USE_FULL_SO", true))
{
SequenceOntologyFactory.setInstance(new SequenceOntology());
}
@@ -341,10 +346,12 @@ public class Jalview
JalviewTaskbar.setTaskbar(this);
} catch (Exception e)
{
- e.printStackTrace();
+ System.out.println("Cannot set Taskbar");
+ // e.printStackTrace();
} catch (Throwable t)
{
- t.printStackTrace();
+ System.out.println("Cannot set Taskbar");
+ // t.printStackTrace();
}
desktop.setVisible(true);
@@ -399,6 +406,25 @@ public class Jalview
BioJsHTMLOutput.updateBioJS();
}
+ // Move any new getdown-launcher-new.jar into place over old
+ // getdown-launcher.jar
+ String appdirString = System.getProperty("getdownappdir");
+ if (appdirString != null && appdirString.length() > 0)
+ {
+ final File appdir = new File(appdirString);
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ LaunchUtil.upgradeGetdown(
+ new File(appdir, "getdown-launcher-old.jar"),
+ new File(appdir, "getdown-launcher.jar"),
+ new File(appdir, "getdown-launcher-new.jar"));
+ }
+ }.start();
+ }
+
String file = null, data = null;
FileFormatI format = null;
DataSourceType protocol = null;
@@ -549,9 +575,8 @@ public class Jalview
{
data.replaceAll("%20", " ");
- ColourSchemeI cs = ColourSchemeProperty
- .getColourScheme(af.getViewport(),
- af.getViewport().getAlignment(), data);
+ ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+ af.getViewport(), af.getViewport().getAlignment(), data);
if (cs != null)
{
@@ -885,10 +910,10 @@ 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)
{
@@ -975,7 +1000,7 @@ public class Jalview
}
try
{
- Map vbinding = new HashMap<>();
+ Map vbinding = new HashMap<>();
vbinding.put("Jalview", this);
if (af != null)
{
@@ -1017,8 +1042,8 @@ 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()
{