// preserves original behaviour prior to version 2.3
}
- public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource)
- throws IOException
+ public FileFormatI identify(AlignmentFileReaderI file,
+ boolean closeSource) throws IOException
{
- FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());
+ FileParse fp = new FileParse(file.getInFile(),
+ file.getDataSourceType());
return identify(fp, closeSource);
}
break;
}
- if ((data.indexOf("//") == 0)
- || ((data.indexOf("!!") > -1) && (data.indexOf("!!") < data
- .indexOf("_MULTIPLE_ALIGNMENT "))))
+ if ((data.indexOf("//") == 0) || ((data.indexOf("!!") > -1) && (data
+ .indexOf("!!") < data.indexOf("_MULTIPLE_ALIGNMENT "))))
{
reply = FileFormat.MSF;
}
if (trimmedLength == 0)
{
- System.err
- .println("File Identification failed! - Empty file was read.");
+ System.err.println(
+ "File Identification failed! - Empty file was read.");
throw new FileFormatException("EMPTY DATA FILE");
}
System.out.println("File format identified as " + reply.toString());
type = ider.identify(args[i], DataSourceType.FILE);
} catch (FileFormatException e)
{
- System.err.println(String.format(
- "Error '%s' identifying file type for %s", args[i],
- e.getMessage()));
+ System.err.println(
+ String.format("Error '%s' identifying file type for %s",
+ args[i], e.getMessage()));
}
System.out.println("Type of " + args[i] + " is " + type);
}