Package org.biojavax.bio.seq.io
Interface RichSequenceFormat
- All Superinterfaces:
SequenceFormat
- All Known Implementing Classes:
EMBLFormat
,EMBLxmlFormat
,FastaFormat
,GenbankFormat
,INSDseqFormat
,RichSequenceFormat.BasicFormat
,RichSequenceFormat.HeaderlessFormat
,UniProtFormat
,UniProtXMLFormat
Allows a file format to be read/written as RichSequences.
- Since:
- 1.5
- Author:
- Richard Holland
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Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic class
Provides a basic format with simple things like line-widths precoded.static class
Provides the basic implementation required for simple header/footer-less files such as Genbank. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Informs the writer that we want to start writing.boolean
canRead
(BufferedInputStream stream) Check to see if a given stream is in our format.boolean
Check to see if a given file is in our format.void
Informs the writer that are done writing.boolean
Is the format going to emit events when comments data or remarks from bibliographic references are read?boolean
Is the format going to emit events when feature data is read?boolean
Is the format going to emit events when bibliographic reference data is read?boolean
Is the format going to emit events when sequence data is read?int
Retrive the current line width.Gets the print stream currently being written to.On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.guessSymbolTokenization
(File file) On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it.boolean
readRichSequence
(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener listener, Namespace ns) Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols.void
setElideComments
(boolean elideComments) Use this method to toggle reading of comments data.void
setElideFeatures
(boolean elideFeatures) Use this method to toggle reading of feature data.void
setElideReferences
(boolean elideReferences) Use this method to toggle reading of bibliographic reference data.void
setElideSymbols
(boolean elideSymbols) Use this method to toggle reading of sequence data.void
setLineWidth
(int width) Set the line width.void
Sets the stream to write to.void
writeSequence
(Sequence seq, Namespace ns) Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class.Methods inherited from interface org.biojava.bio.seq.io.SequenceFormat
getDefaultFormat, readSequence, writeSequence, writeSequence
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Method Details
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canRead
Check to see if a given file is in our format. Some formats may be able to determine this by filename, whilst others may have to open the file and read it to see what format it is in.- Parameters:
file
- theFile
to check.- Returns:
- true if the file is readable by this format, false if not.
- Throws:
IOException
- in case the file is inaccessible.
-
guessSymbolTokenization
On the assumption that the file is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the file. For formats that accept multiple tokenizations, its up to you how you do it.- Parameters:
file
- theFile
object to guess the format of.- Returns:
- a
SymbolTokenization
to read the file with. - Throws:
IOException
- if the file is unrecognisable or inaccessible.
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canRead
Check to see if a given stream is in our format.- Parameters:
stream
- theBufferedInputStream
to check.- Returns:
- true if the stream is readable by this format, false if not.
- Throws:
IOException
- in case the stream is inaccessible.
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guessSymbolTokenization
On the assumption that the stream is readable by this format (not checked), attempt to guess which symbol tokenization we should use to read it. For formats that only accept one tokenization, just return it without checking the stream. For formats that accept multiple tokenizations, its up to you how you do it.- Parameters:
stream
- theBufferedInputStream
object to guess the format of.- Returns:
- a
SymbolTokenization
to read the stream with. - Throws:
IOException
- if the stream is unrecognisable or inaccessible.
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setPrintStream
Sets the stream to write to.- Parameters:
os
- the PrintStream to write to.- Throws:
IOException
- if writing fails.
-
getPrintStream
Gets the print stream currently being written to.- Returns:
- the current print stream.
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beginWriting
Informs the writer that we want to start writing. This will do any initialisation required, such as writing the opening tags of an XML file that groups sequences together.- Throws:
IOException
- if writing fails.
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finishWriting
Informs the writer that are done writing. This will do any finalisation required, such as writing the closing tags of an XML file that groups sequences together.- Throws:
IOException
- if writing fails.
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readRichSequence
boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener listener, Namespace ns) throws BioException, IllegalSymbolException, IOException Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. Events are passed to the listener, and the namespace used for sequences read is the one given. If the namespace is null, then the default namespace for the parser is used, which may depend on individual implementations of this interface.- Parameters:
reader
- the input sourcesymParser
- the tokenizer which understands the sequence being readlistener
- the listener to send sequence events tons
- the namespace to read sequences into.- Returns:
- true if there is more to read after this, false otherwise.
- Throws:
BioException
- in case of parsing errors.IllegalSymbolException
- if the tokenizer couldn't understand one of the sequence symbols in the file.IOException
- if there was a read error.
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writeSequence
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is given, sequences will be written with that namespace, otherwise they will be written with the default namespace of the implementing class (which is usually the namespace of the sequence itself). If you pass this method a sequence which is not a RichSequence, it will attempt to convert it using RichSequence.Tools.enrich(). Obviously this is not going to guarantee a perfect conversion, so it's better if you just use RichSequences to start with!- Parameters:
seq
- the sequence to writens
- the namespace to write it with- Throws:
IOException
- in case it couldn't write something
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getLineWidth
int getLineWidth()Retrive the current line width. Defaults to 80.- Returns:
- the line width
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setLineWidth
Set the line width. When writing, the lines of sequence will never be longer than the line width. Defaults to 80.- Parameters:
width
- the new line width
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setElideSymbols
Use this method to toggle reading of sequence data.- Parameters:
elideSymbols
- set to true if you don't want the sequence data.
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getElideSymbols
boolean getElideSymbols()Is the format going to emit events when sequence data is read?- Returns:
- true if it is not otherwise false (false is default) .
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setElideFeatures
Use this method to toggle reading of feature data.- Parameters:
elideFeatures
- set to true if you don't want the feature data.
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getElideFeatures
boolean getElideFeatures()Is the format going to emit events when feature data is read?- Returns:
- true if it is not otherwise false (false is default).
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setElideReferences
Use this method to toggle reading of bibliographic reference data.- Parameters:
elideReferences
- set to true if you don't want the bibliographic reference data.
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getElideReferences
boolean getElideReferences()Is the format going to emit events when bibliographic reference data is read?- Returns:
- true if it is not otherwise false (false is default) .
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setElideComments
Use this method to toggle reading of comments data. Will also ignore remarks lines in bibliographic references.- Parameters:
elideComments
- set to true if you don't want the comments data.
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getElideComments
boolean getElideComments()Is the format going to emit events when comments data or remarks from bibliographic references are read?- Returns:
- true if it is not otherwise false (false is default).
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