Class EmblLikeFormat
- All Implemented Interfaces:
Serializable
,EventListener
,SequenceFormat
,ParseErrorListener
,ParseErrorSource
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.
- Since:
- 1.1
- Author:
- Thomas Down, Greg Cox, Keith James, Len Trigg, Lorna Morris
- See Also:
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated.protected static final String
Deprecated. -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
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.Deprecated.boolean
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
(String line, StreamParser parser) Deprecated.Dispatch symbol data from SQ-block line of an EMBL-like file.boolean
readSequence
(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, PrintStream os) Deprecated.writeSequence
writes a sequence to the specified PrintStream, using the default format.void
writeSequence
(Sequence seq, String format, PrintStream os) Deprecated.use writeSequence(Sequence seq, PrintStream os)
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Field Details
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DEFAULT
Deprecated.- See Also:
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ID_TAG
Deprecated.- See Also:
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SIZE_TAG
Deprecated.- See Also:
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STRAND_NUMBER_TAG
Deprecated.- See Also:
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TYPE_TAG
Deprecated.- See Also:
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CIRCULAR_TAG
Deprecated.- See Also:
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DIVISION_TAG
Deprecated.- See Also:
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DR_TAG
Deprecated.- See Also:
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ACCESSION_TAG
Deprecated.- See Also:
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VERSION_TAG
Deprecated.- See Also:
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DATE_TAG
Deprecated.- See Also:
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DEFINITION_TAG
Deprecated.- See Also:
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KEYWORDS_TAG
Deprecated.- See Also:
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SOURCE_TAG
Deprecated.- See Also:
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ORGANISM_TAG
Deprecated.- See Also:
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ORGANISM_XREF_TAG
Deprecated.- See Also:
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REFERENCE_TAG
Deprecated.- See Also:
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COORDINATE_TAG
Deprecated.- See Also:
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REF_ACCESSION_TAG
Deprecated.- See Also:
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AUTHORS_TAG
Deprecated.- See Also:
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REF_XREF_TAG
Deprecated.- See Also:
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TITLE_TAG
Deprecated.- See Also:
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JOURNAL_TAG
Deprecated.- See Also:
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COMMENT_TAG
Deprecated.- See Also:
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FEATURE_TAG
Deprecated.- See Also:
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SEPARATOR_TAG
Deprecated.- See Also:
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FEATURE_TABLE_TAG
Deprecated.- See Also:
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START_SEQUENCE_TAG
Deprecated.- See Also:
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END_SEQUENCE_TAG
Deprecated.- See Also:
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Constructor Details
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EmblLikeFormat
public EmblLikeFormat()Deprecated.
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Method Details
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setElideSymbols
Deprecated.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 theSeqIOListener
, 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.
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getElideSymbols
Deprecated.Return a flag indicating if symbol data will be skipped when parsing streams. -
readSequence
public boolean readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) throws IllegalSymbolException, IOException, ParseException Deprecated.Description copied from interface:SequenceFormat
Read a sequence and pass data on to a SeqIOListener.- Specified by:
readSequence
in interfaceSequenceFormat
- Parameters:
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.- Returns:
- a boolean indicating whether or not the stream contains any more sequences.
- Throws:
IllegalSymbolException
- if it is not possible to translate character data from the stream into valid BioJava symbols.IOException
- if an error occurs while reading from the stream.ParseException
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processSequenceLine
protected void processSequenceLine(String line, StreamParser parser) throws IllegalSymbolException, ParseException Deprecated.Dispatch symbol data from SQ-block line of an EMBL-like file.- Throws:
IllegalSymbolException
ParseException
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writeSequence
Deprecated.Description copied from interface:SequenceFormat
writeSequence
writes a sequence to the specified PrintStream, using the default format.- Specified by:
writeSequence
in interfaceSequenceFormat
- Parameters:
seq
- the sequence to write out.os
- the printstream to write to.- Throws:
IOException
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writeSequence
Deprecated.use writeSequence(Sequence seq, PrintStream os)writeSequence
writes a sequence to the specifiedPrintStream
, using the specified format.- Specified by:
writeSequence
in interfaceSequenceFormat
- Parameters:
seq
- aSequence
to write out.format
- aString
indicating which sub-format of those available from a particularSequenceFormat
implemention to use when writing.os
- aPrintStream
object.- Throws:
IOException
- if an error occurs.
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getDefaultFormat
Deprecated.getDefaultFormat
returns the String identifier for the default format written by aSequenceFormat
implementation.- Specified by:
getDefaultFormat
in interfaceSequenceFormat
- Returns:
- a
String
.
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BadLineParsed
Deprecated.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.
- Specified by:
BadLineParsed
in interfaceParseErrorListener
- Parameters:
theEvent
- The event that contains the bad line and token.
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addParseErrorListener
Deprecated.Adds a parse error listener to the list of listeners if it isn't already included.- Specified by:
addParseErrorListener
in interfaceParseErrorSource
- Parameters:
theListener
- Listener to be added.
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removeParseErrorListener
Deprecated.Removes a parse error listener from the list of listeners if it is included.- Specified by:
removeParseErrorListener
in interfaceParseErrorSource
- Parameters:
theListener
- Listener to be removed.
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notifyParseErrorEvent
Deprecated.Passes the event on to all the listeners registered for ParseErrorEvents.- Parameters:
theEvent
- The event to be handed to the listeners.
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