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added description of alignment quality scores and separated
[jalview.git]
/
src
/
jalview
/
bin
/
Cache.java
diff --git
a/src/jalview/bin/Cache.java
b/src/jalview/bin/Cache.java
index
0013c63
..
9702a92
100755
(executable)
--- a/
src/jalview/bin/Cache.java
+++ b/
src/jalview/bin/Cache.java
@@
-22,7
+22,6
@@
import java.io.*;
\r
import java.util.*;
\r
\r
\r
import java.util.*;
\r
\r
-import java.net.*;
\r
import org.apache.log4j.Logger;
\r
import org.apache.log4j.SimpleLayout;
\r
import org.apache.log4j.Level;
\r
import org.apache.log4j.Logger;
\r
import org.apache.log4j.SimpleLayout;
\r
import org.apache.log4j.Level;
\r
@@
-73,7
+72,6
@@
public class Cache
jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
\r
"logs.Jalview.level",
\r
Level.INFO.toString())));
\r
jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
\r
"logs.Jalview.level",
\r
Level.INFO.toString())));
\r
-
\r
ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
\r
"System.err");
\r
ap.setName("JalviewLogger");
\r
ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
\r
"System.err");
\r
ap.setName("JalviewLogger");
\r
@@
-81,6
+79,8
@@
public class Cache
laxis.addAppender(ap);
\r
lcastor.addAppender(ap);
\r
jalview.bin.Cache.log.addAppender(ap);
\r
laxis.addAppender(ap);
\r
lcastor.addAppender(ap);
\r
jalview.bin.Cache.log.addAppender(ap);
\r
+ // Tell the user that debug is enabled
\r
+ jalview.bin.Cache.log.debug("Jalview Debugging Output Follows.");
\r
}
\r
catch (Exception ex)
\r
{
\r
}
\r
catch (Exception ex)
\r
{
\r
@@
-156,6
+156,7
@@
public class Cache
\r
System.out.println("Jalview Version: "+codeVersion);
\r
\r
\r
System.out.println("Jalview Version: "+codeVersion);
\r
\r
+
\r
// jnlpVersion will be null if we're using InstallAnywhere
\r
// Dont do this check if running in headless mode
\r
if(jnlpVersion==null && (
\r
// jnlpVersion will be null if we're using InstallAnywhere
\r
// Dont do this check if running in headless mode
\r
if(jnlpVersion==null && (
\r
@@
-163,7
+164,6
@@
public class Cache
|| System.getProperty("java.awt.headless").equals("false")))
\r
{
\r
\r
|| System.getProperty("java.awt.headless").equals("false")))
\r
{
\r
\r
-
\r
class VersionChecker
\r
extends Thread
\r
{
\r
class VersionChecker
\r
extends Thread
\r
{
\r
@@
-203,7
+203,10
@@
public class Cache
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
- setProperty("LATEST_VERSION", jnlpVersion);
\r
+ if(jnlpVersion!=null)
\r
+ setProperty("LATEST_VERSION", jnlpVersion);
\r
+ else
\r
+ applicationProperties.remove("LATEST_VERSION");
\r
}
\r
\r
setProperty("VERSION", codeVersion);
\r
}
\r
\r
setProperty("VERSION", codeVersion);
\r