public class EmblLikeFormat extends java.lang.Object implements SequenceFormat, java.io.Serializable, ParseErrorSource, ParseErrorListener
Format processor for handling EMBL records and similar files. This takes a very simple approach: all `normal' attribute lines are passed to the listener as a tag (first two characters) and a value (the rest of the line from the 6th character onwards). Any data between the special `SQ' line and the "//" entry terminator is passed as a SymbolReader.
This low-level format processor should normally be used in conjunction with one or more `filter' objects, such as EmblProcessor.
Many ideas borrowed from the old EmblFormat processor by Thomas Down and Thad Welch.
Modifier and Type | Field and Description |
---|---|
protected static java.lang.String |
ACCESSION_TAG
Deprecated.
|
protected static java.lang.String |
AUTHORS_TAG
Deprecated.
|
protected static java.lang.String |
CIRCULAR_TAG
Deprecated.
|
protected static java.lang.String |
COMMENT_TAG
Deprecated.
|
protected static java.lang.String |
COORDINATE_TAG
Deprecated.
|
protected static java.lang.String |
DATE_TAG
Deprecated.
|
static java.lang.String |
DEFAULT
Deprecated.
|
protected static java.lang.String |
DEFINITION_TAG
Deprecated.
|
protected static java.lang.String |
DIVISION_TAG
Deprecated.
|
protected static java.lang.String |
DR_TAG
Deprecated.
|
protected static java.lang.String |
END_SEQUENCE_TAG
Deprecated.
|
protected static java.lang.String |
FEATURE_TABLE_TAG
Deprecated.
|
protected static java.lang.String |
FEATURE_TAG
Deprecated.
|
protected static java.lang.String |
ID_TAG
Deprecated.
|
protected static java.lang.String |
JOURNAL_TAG
Deprecated.
|
protected static java.lang.String |
KEYWORDS_TAG
Deprecated.
|
protected static java.lang.String |
ORGANISM_TAG
Deprecated.
|
protected static java.lang.String |
ORGANISM_XREF_TAG
Deprecated.
|
protected static java.lang.String |
REF_ACCESSION_TAG
Deprecated.
|
protected static java.lang.String |
REF_XREF_TAG
Deprecated.
|
protected static java.lang.String |
REFERENCE_TAG
Deprecated.
|
protected static java.lang.String |
SEPARATOR_TAG
Deprecated.
|
protected static java.lang.String |
SIZE_TAG
Deprecated.
|
protected static java.lang.String |
SOURCE_TAG
Deprecated.
|
protected static java.lang.String |
START_SEQUENCE_TAG
Deprecated.
|
protected static java.lang.String |
STRAND_NUMBER_TAG
Deprecated.
|
protected static java.lang.String |
TITLE_TAG
Deprecated.
|
protected static java.lang.String |
TYPE_TAG
Deprecated.
|
protected static java.lang.String |
VERSION_TAG
Deprecated.
|
Constructor and Description |
---|
EmblLikeFormat()
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
void |
addParseErrorListener(ParseErrorListener theListener)
Deprecated.
Adds a parse error listener to the list of listeners if it isn't already
included.
|
void |
BadLineParsed(ParseErrorEvent theEvent)
Deprecated.
This method determines the behaviour when a bad line is processed.
|
java.lang.String |
getDefaultFormat()
Deprecated.
|
boolean |
getElideSymbols()
Deprecated.
Return a flag indicating if symbol data will be skipped
when parsing streams.
|
protected void |
notifyParseErrorEvent(ParseErrorEvent theEvent)
Deprecated.
Passes the event on to all the listeners registered for ParseErrorEvents.
|
protected void |
processSequenceLine(java.lang.String line,
StreamParser parser)
Deprecated.
Dispatch symbol data from SQ-block line of an EMBL-like file.
|
boolean |
readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Deprecated.
Read a sequence and pass data on to a SeqIOListener.
|
void |
removeParseErrorListener(ParseErrorListener theListener)
Deprecated.
Removes a parse error listener from the list of listeners if it is
included.
|
void |
setElideSymbols(boolean b)
Deprecated.
Specifies whether the symbols (SQ) part of the entry should
be ignored.
|
void |
writeSequence(Sequence seq,
java.io.PrintStream os)
Deprecated.
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
writeSequence(Sequence seq,
java.lang.String format,
java.io.PrintStream os)
Deprecated.
use writeSequence(Sequence seq, PrintStream os)
|
public static final java.lang.String DEFAULT
protected static final java.lang.String ID_TAG
protected static final java.lang.String SIZE_TAG
protected static final java.lang.String STRAND_NUMBER_TAG
protected static final java.lang.String TYPE_TAG
protected static final java.lang.String CIRCULAR_TAG
protected static final java.lang.String DIVISION_TAG
protected static final java.lang.String DR_TAG
protected static final java.lang.String ACCESSION_TAG
protected static final java.lang.String VERSION_TAG
protected static final java.lang.String DATE_TAG
protected static final java.lang.String DEFINITION_TAG
protected static final java.lang.String KEYWORDS_TAG
protected static final java.lang.String SOURCE_TAG
protected static final java.lang.String ORGANISM_TAG
protected static final java.lang.String ORGANISM_XREF_TAG
protected static final java.lang.String REFERENCE_TAG
protected static final java.lang.String COORDINATE_TAG
protected static final java.lang.String REF_ACCESSION_TAG
protected static final java.lang.String AUTHORS_TAG
protected static final java.lang.String REF_XREF_TAG
protected static final java.lang.String TITLE_TAG
protected static final java.lang.String JOURNAL_TAG
protected static final java.lang.String COMMENT_TAG
protected static final java.lang.String FEATURE_TAG
protected static final java.lang.String SEPARATOR_TAG
protected static final java.lang.String FEATURE_TABLE_TAG
protected static final java.lang.String START_SEQUENCE_TAG
protected static final java.lang.String END_SEQUENCE_TAG
public void setElideSymbols(boolean b)
Specifies whether the symbols (SQ) part of the entry should
be ignored. If this property is set to true
, the
parser will never call addSymbols on the
SeqIOListener
, but parsing will be faster if
you're only interested in header information.
This property also allows the header to be parsed for files which have invalid sequence data.
public boolean getElideSymbols()
public boolean readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) throws IllegalSymbolException, java.io.IOException, ParseException
SequenceFormat
readSequence
in interface SequenceFormat
reader
- The stream of data to parse.symParser
- A SymbolParser defining a mapping from
character data to Symbols.listener
- A listener to notify when data is extracted
from the stream.IllegalSymbolException
- if it is not possible to
translate character data from the stream into valid BioJava
symbols.java.io.IOException
- if an error occurs while reading from the
stream.ParseException
protected void processSequenceLine(java.lang.String line, StreamParser parser) throws IllegalSymbolException, ParseException
IllegalSymbolException
ParseException
public void writeSequence(Sequence seq, java.io.PrintStream os) throws java.io.IOException
SequenceFormat
writeSequence
writes a sequence to the specified
PrintStream, using the default format.writeSequence
in interface SequenceFormat
seq
- the sequence to write out.os
- the printstream to write to.java.io.IOException
public void writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os) throws java.io.IOException
writeSequence
writes a sequence to the specified
PrintStream
, using the specified format.writeSequence
in interface SequenceFormat
seq
- a Sequence
to write out.format
- a String
indicating which sub-format
of those available from a particular
SequenceFormat
implemention to use when
writing.os
- a PrintStream
object.java.io.IOException
- if an error occurs.public java.lang.String getDefaultFormat()
getDefaultFormat
returns the String identifier for
the default format written by a SequenceFormat
implementation.getDefaultFormat
in interface SequenceFormat
String
.public void BadLineParsed(ParseErrorEvent theEvent)
This method determines the behaviour when a bad line is processed. Some options are to log the error, throw an exception, ignore it completely, or pass the event through.
This method should be overwritten when different behavior is desired.
BadLineParsed
in interface ParseErrorListener
theEvent
- The event that contains the bad line and token.public void addParseErrorListener(ParseErrorListener theListener)
addParseErrorListener
in interface ParseErrorSource
theListener
- Listener to be added.public void removeParseErrorListener(ParseErrorListener theListener)
removeParseErrorListener
in interface ParseErrorSource
theListener
- Listener to be removed.protected void notifyParseErrorEvent(ParseErrorEvent theEvent)
theEvent
- The event to be handed to the listeners.