import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FileParse;
import jalview.io.IdentifyFile;
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.
rtn = true;
is.close();
}
- System.err.println("Resource '" + file + "' was "
+ jalview.bin.Console.errPrintln("Resource '" + file + "' was "
+ (rtn ? "" : "not") + " located by classloader.");
if (rtn)
{
} catch (Exception ex)
{
- System.out.println("Exception checking resources: " + file + " "
- + ex);
+ jalview.bin.Console.outPrintln(
+ "Exception checking resources: " + file + " " + ex);
}
if (file.indexOf("://") > -1)
{
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())
{
}
else
{
- System.out.println("Resource at " + file
+ jalview.bin.Console.outPrintln("Resource at " + file
+ " cannot be read with protocol==" + protocol);
return;
}
- FileFormatI format = FileFormat.valueOf(getParameter("format"));
+ FileFormatI format = FileFormats.getInstance()
+ .forName(getParameter("format"));
if (format == null)
{
format = new IdentifyFile().identify(file, protocol);
- System.out.println("Format is " + format);
+ jalview.bin.Console.outPrintln("Format is " + format);
}
else
{
- System.out.println("User specified Format is " + format);
+ jalview.bin.Console.outPrintln("User specified Format is " + format);
}
AlignmentI al = null;
try
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)
{
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.Fasta, al, false));
+ jalview.bin.Console.outPrintln(new AppletFormatAdapter()
+ .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();
}
}