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java.lang.Objectorg.biojava.bio.program.gff.GFFParser
Parse a stream of GFF text into a stream of records and comments.
Constructor Summary | |
GFFParser()
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Method Summary | |
protected GFFRecord |
createRecord(GFFDocumentHandler handler,
java.util.List aList,
java.lang.String rest,
java.lang.String comment)
Actually turns a list of tokens, some value string and a comment into a GFFRecord and informs handler. |
GFFErrorHandler |
getErrorHandler()
Find the error handler used by this parser. |
void |
parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler)
Informs handler of each line of gff read from bReader. |
void |
parse(java.io.BufferedReader bReader,
GFFDocumentHandler handler,
java.lang.String locator)
Informs handler of each line of GFF read from bReader |
protected java.util.Map |
parseAttribute(java.lang.String attValList)
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 |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public GFFParser()
Method Detail |
public void setErrorHandler(GFFErrorHandler errors)
public GFFErrorHandler getErrorHandler()
public void parse(java.io.BufferedReader bReader, GFFDocumentHandler handler) throws java.io.IOException, BioException, ParserException
bReader
- the BufferedReader to parsehandler
- the GFFDocumentHandler that will
listen for 'stuff'
- class="type">IOException if for any reason
bReader throws one
- class="type">BioException if
handler can not correct a parse error
java.io.IOException
BioException
ParserException
public void parse(java.io.BufferedReader bReader, GFFDocumentHandler handler, java.lang.String locator) throws java.io.IOException, BioException, ParserException
bReader
- the BufferedReader to parsehandler
- the GFFDocumentHandler that will
listen for 'stuff'
- class="type">IOException if for any reason
bReader throws one
- class="type">BioException if
handler can not correct a parse error
java.io.IOException
BioException
ParserException
protected GFFRecord createRecord(GFFDocumentHandler handler, java.util.List aList, java.lang.String rest, java.lang.String comment) throws BioException, ParserException, IgnoreRecordException
handler
- a GFFDocumentHandler to inform of
any parse errors, and the completed GFFRecordaList
- 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.
- class="type">BioException if handler
could not correct a parse error
BioException
ParserException
IgnoreRecordException
protected java.util.Map parseAttribute(java.lang.String attValList)
The resulting Map will have String keys, with List values. If there are no values associated with a key, then it will have an empty List, not null as its value.
attValList
- the String to parse
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