git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' into patch/JAL-4110_stdout_for_tests
[jalview.git]
/
src
/
jalview
/
bin
/
JalviewLiteURLRetrieve.java
diff --git
a/src/jalview/bin/JalviewLiteURLRetrieve.java
b/src/jalview/bin/JalviewLiteURLRetrieve.java
index
f2ffda5
..
d38892a
100644
(file)
--- a/
src/jalview/bin/JalviewLiteURLRetrieve.java
+++ b/
src/jalview/bin/JalviewLiteURLRetrieve.java
@@
-64,7
+64,7
@@
public class JalviewLiteURLRetrieve extends Applet
DataSourceType protocol = null;
try
{
DataSourceType protocol = null;
try
{
- System.out.println("Loading thread started with:\n>>file\n" + file
+ jalview.bin.Console.outPrintln("Loading thread started with:\n>>file\n" + file
+ ">>endfile");
// This might throw a security exception in certain browsers
// Netscape Communicator for instance.
+ ">>endfile");
// This might throw a security exception in certain browsers
// Netscape Communicator for instance.
@@
-77,7
+77,7
@@
public class JalviewLiteURLRetrieve extends Applet
rtn = true;
is.close();
}
rtn = true;
is.close();
}
- System.err.println("Resource '" + file + "' was "
+ jalview.bin.Console.errPrintln("Resource '" + file + "' was "
+ (rtn ? "" : "not") + " located by classloader.");
if (rtn)
{
+ (rtn ? "" : "not") + " located by classloader.");
if (rtn)
{
@@
-86,7
+86,7
@@
public class JalviewLiteURLRetrieve extends Applet
} catch (Exception ex)
{
} catch (Exception ex)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"Exception checking resources: " + file + " " + ex);
}
if (file.indexOf("://") > -1)
"Exception checking resources: " + file + " " + ex);
}
if (file.indexOf("://") > -1)
@@
-99,7
+99,7
@@
public class JalviewLiteURLRetrieve extends Applet
protocol = DataSourceType.FILE;
}
protocol = DataSourceType.FILE;
}
- System.out.println("Trying to get contents of resource:");
+ jalview.bin.Console.outPrintln("Trying to get contents of resource:");
FileParse fp = new FileParse(file, protocol);
if (fp.isValid())
{
FileParse fp = new FileParse(file, protocol);
if (fp.isValid())
{
@@
-112,7
+112,7
@@
public class JalviewLiteURLRetrieve extends Applet
}
else
{
}
else
{
- System.out.println("Resource at " + file
+ jalview.bin.Console.outPrintln("Resource at " + file
+ " cannot be read with protocol==" + protocol);
return;
}
+ " cannot be read with protocol==" + protocol);
return;
}
@@
-121,11
+121,11
@@
public class JalviewLiteURLRetrieve extends Applet
if (format == null)
{
format = new IdentifyFile().identify(file, protocol);
if (format == null)
{
format = new IdentifyFile().identify(file, protocol);
- System.out.println("Format is " + format);
+ jalview.bin.Console.outPrintln("Format is " + format);
}
else
{
}
else
{
- System.out.println("User specified Format is " + format);
+ jalview.bin.Console.outPrintln("User specified Format is " + format);
}
AlignmentI al = null;
try
}
AlignmentI al = null;
try
@@
-133,17
+133,17
@@
public class JalviewLiteURLRetrieve extends Applet
al = new AppletFormatAdapter().readFile(file, protocol, format);
} catch (java.io.IOException ex)
{
al = new AppletFormatAdapter().readFile(file, protocol, format);
} catch (java.io.IOException ex)
{
- System.err.println("Failed to open the file.");
+ jalview.bin.Console.errPrintln("Failed to open the file.");
ex.printStackTrace();
}
if (al != null)
{
ex.printStackTrace();
}
if (al != null)
{
- System.out.println(new AppletFormatAdapter()
+ jalview.bin.Console.outPrintln(new AppletFormatAdapter()
.formatSequences(FileFormat.Fasta, al, false));
}
} catch (Exception e)
{
.formatSequences(FileFormat.Fasta, al, false));
}
} catch (Exception e)
{
- System.err.println("bailing out : Unexpected exception:");
+ jalview.bin.Console.errPrintln("bailing out : Unexpected exception:");
e.printStackTrace();
}
}
e.printStackTrace();
}
}