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java.lang.Objectorg.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat
org.biojavax.bio.seq.io.FastaFormat
public class FastaFormat
Format object representing FASTA files. These files are almost pure sequence data.
Nested Class Summary |
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Nested classes/interfaces inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat |
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RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat |
Field Summary | |
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protected static Pattern |
aminoAcids
|
protected static Pattern |
dp
|
static String |
FASTA_FORMAT
The name of this format |
protected static Pattern |
hp
|
protected static Pattern |
readableFiles
|
Constructor Summary | |
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FastaFormat()
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Method Summary | |
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boolean |
canRead(BufferedInputStream stream)
Check to see if a given stream is in our format. |
boolean |
canRead(File file)
Check to see if a given file is in our format. |
String |
getDefaultFormat()
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation. |
FastaHeader |
getHeader()
|
SymbolTokenization |
guessSymbolTokenization(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(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(String line,
RichSeqIOListener rsiol,
Namespace ns)
Parse the Header information from the Fasta Description line |
boolean |
readRichSequence(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(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,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream, using the default format. |
void |
writeSequence(Sequence seq,
String format,
PrintStream os)
writeSequence writes a sequence to the specified
PrintStream , using the specified format. |
Methods inherited from class org.biojavax.bio.seq.io.RichSequenceFormat.HeaderlessFormat |
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beginWriting, finishWriting |
Methods inherited from class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat |
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getElideComments, getElideFeatures, getElideReferences, getElideSymbols, getLineWidth, getPrintStream, setElideComments, setElideFeatures, setElideReferences, setElideSymbols, setLineWidth, setPrintStream |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String FASTA_FORMAT
protected static final Pattern hp
protected static final Pattern dp
protected static final Pattern readableFiles
protected static final Pattern aminoAcids
Constructor Detail |
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public FastaFormat()
Method Detail |
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public boolean canRead(File file) throws IOException
canRead
in interface RichSequenceFormat
canRead
in class RichSequenceFormat.BasicFormat
file
- the File
to check.
IOException
- in case the file is inaccessible.public SymbolTokenization guessSymbolTokenization(File file) throws 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.
IOException
- if the file is unrecognisable or inaccessible.public boolean canRead(BufferedInputStream stream) throws IOException
stream
- the BufferedInputStream
to check.
IOException
- in case the stream is inaccessible.public SymbolTokenization guessSymbolTokenization(BufferedInputStream stream) throws IOException
stream
- the BufferedInputStream
object to guess the format of.
SymbolTokenization
to read the stream with.
IOException
- if the stream is unrecognisable or inaccessible.public boolean readSequence(BufferedReader reader, SymbolTokenization symParser, SeqIOListener listener) throws IllegalSymbolException, 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.
IOException
- if an error occurs while reading from the
stream.
ParseException
public boolean readRichSequence(BufferedReader reader, SymbolTokenization symParser, RichSeqIOListener rsiol, Namespace ns) throws IllegalSymbolException, 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.
IOException
- if there was a read error.
ParseException
public void processHeader(String line, RichSeqIOListener rsiol, Namespace ns) throws IOException, ParseException
line
- rsiol
- ns
-
IOException
ParseException
public void writeSequence(Sequence seq, PrintStream os) throws 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.
IOException
public void writeSequence(Sequence seq, String format, PrintStream os) throws 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.
IOException
- if an error occurs.public void writeSequence(Sequence seq, Namespace ns) throws IOException
seq
- the sequence to writens
- the namespace to write it with
IOException
- in case it couldn't write somethingpublic 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)
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