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This is an interface that provides a definition for any sequence parsers. It takes input and returns a sequence alignment object. Parsers may or may not have state attached to them. Furthermore they may be re-entered or alternatively they may not. You have been warned.
One thing which cannot be enforced in the interface is that every parser should have a default constructor (ie no arguments to the constructor). This is because the parsers are generated through Class.newInstance(). Created: Thu May 25 23:01:02 2000
Method Summary | |
String |
getDescription()
Returns the description of this alignment parser, and should be human readable/understandable. |
SequenceAlignment |
parse(Identifier ident,
Reader reader,
ParserExceptionHandler eh)
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SequenceAlignment |
parse(Reader reader,
ParserExceptionHandler eh)
This method returns a sequence alignment from a buffered reader input stream. |
Method Detail |
public SequenceAlignment parse(Identifier ident, Reader reader, ParserExceptionHandler eh) throws IOException
IOException
public SequenceAlignment parse(Reader reader, ParserExceptionHandler eh) throws IOException
reader
- the input streameh
- exception handler
IOException
public String getDescription()
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