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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.UniProtFormat
public class UniProtFormat
Format reader for UniProt files. This version of UniProt format will generate and write RichSequence objects. Loosely Based on code from the old, deprecated, org.biojava.bio.seq.io.EMBLLikeFormat object.
Nested Class Summary | |
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static class |
UniProtFormat.Terms
Implements some UniProt-specific terms. |
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 java.lang.String |
ACCESSION_TAG
|
protected static java.lang.String |
AUTHORS_TAG
|
protected static java.lang.String |
COMMENT_TAG
|
protected static java.lang.String |
CONSORTIUM_TAG
|
protected static java.lang.String |
DATABASE_XREF_TAG
|
protected static java.lang.String |
DATE_TAG
|
protected static java.lang.String |
DEFINITION_TAG
|
protected static java.util.regex.Pattern |
dp
|
protected static java.lang.String |
END_SEQUENCE_TAG
|
protected static java.lang.String |
FEATURE_TAG
|
protected static java.util.regex.Pattern |
fp
|
protected static java.lang.String |
GENE_TAG
|
protected static java.util.regex.Pattern |
headerLine
|
protected static java.lang.String |
KEYWORDS_TAG
|
protected static java.lang.String |
LOCATION_TAG
|
protected static java.lang.String |
LOCUS_TAG
|
protected static java.util.regex.Pattern |
lp
|
protected static java.lang.String |
ORGANELLE_TAG
|
protected static java.lang.String |
ORGANISM_TAG
|
protected static java.lang.String |
RC_LINE_TAG
|
protected static java.lang.String |
REFERENCE_TAG
|
protected static java.lang.String |
REFERENCE_XREF_TAG
|
protected static java.lang.String |
RP_LINE_TAG
|
protected static java.util.regex.Pattern |
rppat
|
protected static java.lang.String |
SOURCE_TAG
|
protected static java.lang.String |
START_SEQUENCE_TAG
|
protected static java.lang.String |
TAXON_TAG
|
protected static java.lang.String |
TITLE_TAG
|
static java.lang.String |
UNIPROT_FORMAT
The name of this format |
Constructor Summary | |
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UniProtFormat()
|
Method Summary | |
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boolean |
canRead(java.io.BufferedInputStream stream)
Check to see if a given stream is in our format. A stream is in UniProt format if the first line matches the UniProt format for the ID line. |
boolean |
canRead(java.io.File file)
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. A file is in UniProt format if the first line matches the UniProt format for the ID line. |
java.lang.String |
getDefaultFormat()
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation. |
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. Always returns a protein tokenizer. |
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. 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. Always returns a protein tokenizer. |
boolean |
readRichSequence(java.io.BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
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 |
writeSequence(Sequence seq,
Namespace ns)
Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. Namespace is ignored as UniProt has no concept of it. |
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. |
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 java.lang.String UNIPROT_FORMAT
protected static final java.lang.String LOCUS_TAG
protected static final java.lang.String ACCESSION_TAG
protected static final java.lang.String DEFINITION_TAG
protected static final java.lang.String DATE_TAG
protected static final java.lang.String SOURCE_TAG
protected static final java.lang.String ORGANELLE_TAG
protected static final java.lang.String ORGANISM_TAG
protected static final java.lang.String TAXON_TAG
protected static final java.lang.String GENE_TAG
protected static final java.lang.String DATABASE_XREF_TAG
protected static final java.lang.String REFERENCE_TAG
protected static final java.lang.String RP_LINE_TAG
protected static final java.lang.String REFERENCE_XREF_TAG
protected static final java.lang.String AUTHORS_TAG
protected static final java.lang.String CONSORTIUM_TAG
protected static final java.lang.String TITLE_TAG
protected static final java.lang.String LOCATION_TAG
protected static final java.lang.String RC_LINE_TAG
protected static final java.lang.String KEYWORDS_TAG
protected static final java.lang.String COMMENT_TAG
protected static final java.lang.String FEATURE_TAG
protected static final java.lang.String START_SEQUENCE_TAG
protected static final java.lang.String END_SEQUENCE_TAG
protected static final java.util.regex.Pattern lp
protected static final java.util.regex.Pattern rppat
protected static final java.util.regex.Pattern dp
protected static final java.util.regex.Pattern fp
protected static final java.util.regex.Pattern headerLine
Constructor Detail |
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public UniProtFormat()
Method Detail |
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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 rlistener, Namespace ns) throws IllegalSymbolException, java.io.IOException, ParseException
reader
- the input sourcesymParser
- the tokenizer which understands the sequence being readrlistener
- 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 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 with
java.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
.
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