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JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console
[jalview.git]
/
src
/
jalview
/
bin
/
Jalview.java
diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
fe48283
..
0c11808
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-20,8
+20,6
@@
*/
package jalview.bin;
*/
package jalview.bin;
-import java.util.Locale;
-
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
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.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.Map;
import java.util.Vector;
import java.util.logging.ConsoleHandler;
@@
-319,6
+318,9
@@
public class Jalview
}
// anything else!
}
// 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)
{
final String jabawsUrl = aparser.getValue("jabaws");
if (jabawsUrl != null)
{
@@
-363,9
+365,10
@@
public class Jalview
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
}
System.setProperty("http.agent",
"Jalview Desktop/" + Cache.getDefault("VERSION", "Unknown"));
+
try
{
try
{
- Cache.initLogger();
+ Console.initLogger();
} catch (NoClassDefFoundError error)
{
error.printStackTrace();
} catch (NoClassDefFoundError error)
{
error.printStackTrace();
@@
-399,13
+402,13
@@
public class Jalview
JalviewTaskbar.setTaskbar(this);
} catch (Exception e)
{
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)
{
// 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();
}
// t.printStackTrace();
}
@@
-441,7
+444,7
@@
public class Jalview
{
// Start the desktop questionnaire prompter with the specified
// questionnaire
{
// 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!");
desktop.checkForQuestionnaire(url);
System.out.println("CMD questionnaire[-" + url
+ "] executed successfully!");
@@
-456,7
+459,7
@@
public class Jalview
// "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
// //
String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
// "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);
}
"Starting questionnaire with default url: " + defurl);
desktop.checkForQuestionnaire(defurl);
}
@@
-784,12
+787,11
@@
public class Jalview
* @j2sIgnore
*/
{
* @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");
+ "/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:");
"http://www.jalview.org/examples/exampleFile_2_7.jar"))
{
file.replace("http:", "https:");
@@
-872,62
+874,62
@@
public class Jalview
lafSet = setCrossPlatformLookAndFeel();
if (!lafSet)
{
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)
{
}
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)
{
}
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)
{
}
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)
{
}
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)
{
}
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)
{
}
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)
{
}
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:
}
break;
case "none":
break;
default:
- Cache.log.error("Requested laf=" + laf + " not implemented");
+ Console.error("Requested laf=" + laf + " not implemented");
}
if (!lafSet)
{
}
if (!lafSet)
{
@@
-953,9
+955,9
@@
public class Jalview
set = true;
} catch (Exception ex)
{
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;
}
}
return set;
}
@@
-969,9
+971,9
@@
public class Jalview
set = true;
} catch (Exception ex)
{
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;
}
}
return set;
}
@@
-987,7
+989,8
@@
public class Jalview
if (info.getName() != null && nameStartsWith
? info.getName().toLowerCase(Locale.ROOT)
.startsWith(name.toLowerCase(Locale.ROOT))
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;
{
className = info.getClassName();
break;
@@
-997,9
+1000,9
@@
public class Jalview
set = true;
} catch (Exception ex)
{
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;
}
}
return set;
}
@@
-1109,17
+1112,16
@@
public class Jalview
@Override
public void run()
{
@Override
public void run()
{
- Cache.log.debug(
- "Initialising googletracker for usage stats.");
+ Console.debug("Initialising googletracker for usage stats.");
Cache.initGoogleTracker();
Cache.initGoogleTracker();
- Cache.log.debug("Tracking enabled.");
+ Console.debug("Tracking enabled.");
}
}, new Runnable()
{
@Override
public void run()
{
}
}, new Runnable()
{
@Override
public void run()
{
- Cache.log.debug("Not enabling Google Tracking.");
+ Console.debug("Not enabling Google Tracking.");
}
}, null, true);
desktop.addDialogThread(prompter);
}
}, null, true);
desktop.addDialogThread(prompter);