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java.lang.Objectorg.biojava.bio.program.gff3.GFF3Parser
public class GFF3Parser
Parse a stream of GFF text into a stream of records and comments.
Developed from GFFParser
.
Constructor Summary | |
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GFF3Parser()
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Method Summary | |
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protected GFF3Record |
createRecord(GFF3DocumentHandler handler,
List aList,
String rest,
String comment,
Ontology ontology,
Ontology fallBack)
Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler. |
GFFErrorHandler |
getErrorHandler()
Find the error handler used by this parser. |
void |
parse(BufferedReader bReader,
GFF3DocumentHandler handler,
Ontology ontology)
Informs handler of each line of gff read from bReader. |
void |
parse(BufferedReader bReader,
GFF3DocumentHandler handler,
Ontology ontology,
String locator)
Informs handler of each line of GFF read from bReader |
protected void |
parseAttribute(String attValList,
Annotation anno,
Ontology onto,
Ontology fallBack)
Parse attValList into a Map of attributes and value lists. |
void |
setErrorHandler(GFFErrorHandler errors)
Set the error handler used by this parser. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public GFF3Parser()
Method Detail |
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public void setErrorHandler(GFFErrorHandler errors)
public GFFErrorHandler getErrorHandler()
public void parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology) throws IOException, BioException, ParserException
bReader
- the BufferedReader to parsehandler
- the GFF3DocumentHandler that will
listen for 'stuff'ontology
- an Ontology that all terms should come from
- class="type">IOException if for any reason
bReader throws one
- class="type">BioException if
handler can not correct a parse error
IOException
BioException
ParserException
public void parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology, String locator) throws IOException, BioException, ParserException
bReader
- the BufferedReader to parsehandler
- the GFF3DocumentHandler that will
listen for 'stuff'ontology
- an Ontology that all terms should come from
- class="type">IOException if for any reason
bReader throws one
- class="type">BioException if
handler can not correct a parse error
IOException
BioException
ParserException
protected GFF3Record createRecord(GFF3DocumentHandler handler, List aList, String rest, String comment, Ontology ontology, Ontology fallBack) throws BioException, ParserException, IgnoreRecordException
handler
- a GFF3DocumentHandler to inform of
any parse errors, and the completed GFF3RecordaList
- a List containing the 8 mandatory GFF columnsrest
- a String representing the unparsed
attribute-value text, or null if there is nonecomment
- a String containing the comment (without the
leading '#
' character.ontology
- the Ontology to resolve Terms in
- class="type">BioException if handler
could not correct a parse error
BioException
ParserException
IgnoreRecordException
protected void parseAttribute(String attValList, Annotation anno, Ontology onto, Ontology fallBack) throws ChangeVetoException
Populates an Annotation instance with Ontology Term keys and string/list values.
attValList
- the String to parse
ChangeVetoException
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