public class FastaFormat extends RichSequenceFormat.HeaderlessFormat
RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat
Modifier and Type | Field and Description |
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protected static java.util.regex.Pattern |
aminoAcids |
protected static java.util.regex.Pattern |
dp |
static java.lang.String |
FASTA_FORMAT
The name of this format
|
protected static java.util.regex.Pattern |
hp |
protected static java.util.regex.Pattern |
readableFiles |
Constructor and Description |
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FastaFormat() |
Modifier and Type | Method and Description |
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boolean |
canRead(java.io.BufferedInputStream stream)
Check to see if a given stream is in our format.
|
boolean |
canRead(java.io.File file)
Check to see if a given file is in our format.
|
java.lang.String |
getDefaultFormat()
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation. |
FastaHeader |
getHeader() |
SymbolTokenization |
guessSymbolTokenization(java.io.BufferedInputStream stream)
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.
|
SymbolTokenization |
guessSymbolTokenization(java.io.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.
|
void |
processHeader(java.lang.String line,
RichSeqIOListener rsiol,
Namespace ns)
Parse the Header information from the Fasta Description line
|
boolean |
readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rsiol,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse
sequence symbols.
|
boolean |
readSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
SeqIOListener listener)
Read a sequence and pass data on to a SeqIOListener.
|
void |
setHeader(FastaHeader header) |
void |
writeSequence(Sequence seq,
Namespace ns)
Writes a sequence out to the outputstream given by beginWriting() using the default format of the
implementing class.
|
void |
writeSequence(Sequence seq,
java.io.PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
writeSequence(Sequence seq,
java.lang.String format,
java.io.PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
beginWriting, finishWriting
getElideComments, getElideFeatures, getElideReferences, getElideSymbols, getLineWidth, getPrintStream, setElideComments, setElideFeatures, setElideReferences, setElideSymbols, setLineWidth, setPrintStream
public static final java.lang.String FASTA_FORMAT
protected static final java.util.regex.Pattern hp
protected static final java.util.regex.Pattern dp
protected static final java.util.regex.Pattern readableFiles
protected static final java.util.regex.Pattern aminoAcids
public boolean canRead(java.io.File file) throws java.io.IOException
canRead
in interface RichSequenceFormat
canRead
in class RichSequenceFormat.BasicFormat
file
- the File
to check.java.io.IOException
- in case the file is inaccessible.public SymbolTokenization guessSymbolTokenization(java.io.File file) throws java.io.IOException
guessSymbolTokenization
in interface RichSequenceFormat
guessSymbolTokenization
in class RichSequenceFormat.BasicFormat
file
- the File
object to guess the format of.SymbolTokenization
to read the file with.java.io.IOException
- if the file is unrecognisable or inaccessible.public boolean canRead(java.io.BufferedInputStream stream) throws java.io.IOException
stream
- the BufferedInputStream
to check.java.io.IOException
- in case the stream is inaccessible.public SymbolTokenization guessSymbolTokenization(java.io.BufferedInputStream stream) throws java.io.IOException
stream
- the BufferedInputStream
object to guess the format of.SymbolTokenization
to read the stream with.java.io.IOException
- if the stream is unrecognisable or inaccessible.public boolean readSequence(java.io.BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) throws IllegalSymbolException, java.io.IOException, ParseException
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
public boolean readRichSequence(java.io.BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rsiol, Namespace ns) throws IllegalSymbolException, java.io.IOException, ParseException
reader
- the input sourcesymParser
- the tokenizer which understands the sequence being readrsiol
- the listener to send sequence events tons
- the namespace to read sequences into.IllegalSymbolException
- if the tokenizer couldn't understand one of the
sequence symbols in the file.java.io.IOException
- if there was a read error.ParseException
public void processHeader(java.lang.String line, RichSeqIOListener rsiol, Namespace ns) throws java.io.IOException, ParseException
line
- rsiol
- ns
- java.io.IOException
ParseException
public void writeSequence(Sequence seq, java.io.PrintStream os) throws java.io.IOException
writeSequence
writes a sequence to the specified
PrintStream, using the default format.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.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 void writeSequence(Sequence seq, Namespace ns) throws java.io.IOException
seq
- the sequence to writens
- the namespace to write it withjava.io.IOException
- in case it couldn't write somethingpublic java.lang.String getDefaultFormat()
getDefaultFormat
returns the String identifier for
the default sub-format written by a SequenceFormat
implementation.String
.public FastaHeader getHeader()
public void setHeader(FastaHeader header)