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java.lang.Objectorg.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
org.biojavax.bio.seq.io.UniProtXMLFormat
public class UniProtXMLFormat
Format reader for UniProtXML files. This version of UniProtXML format will generate and write RichSequence objects. Loosely Based on code from the old, deprecated, org.biojava.bio.seq.io.GenbankXmlFormat object. Understands http://www.ebi.uniprot.org/support/docs/uniprot.xsd
Nested Class Summary | |
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static class |
UniProtXMLFormat.Terms
Implements some UniProtXML-specific terms. |
Nested classes/interfaces inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat |
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RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat |
Constructor Summary | |
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UniProtXMLFormat()
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Method Summary | |
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void |
beginWriting()
Informs the writer that we want to start writing. |
boolean |
canRead(BufferedInputStream stream)
Check to see if a given stream is in our format. A stream is in UniProtXML format if the second XML line contains the phrase "http://www.uniprot.org/support/docs/uniprot.xsd". |
boolean |
canRead(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 UniProtXML format if the second XML line contains the phrase "http://www.uniprot.org/support/docs/uniprot.xsd". |
void |
finishWriting()
Informs the writer that are done writing. |
String |
getDefaultFormat()
getDefaultFormat returns the String identifier for
the default sub-format written by a SequenceFormat
implementation. |
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. Always returns a protein tokenizer. |
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. 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(BufferedReader reader,
SymbolTokenization symParser,
RichSeqIOListener rlistener,
Namespace ns)
Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. If namespace is null, then the namespace of the sequence in the fasta is used. |
boolean |
readSequence(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. If namespace is null, then the sequence's own namespace is used. |
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.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 UNIPROTXML_FORMAT
protected static final String ENTRY_GROUP_TAG
protected static final String ENTRY_TAG
protected static final String ENTRY_VERSION_ATTR
protected static final String ENTRY_NAMESPACE_ATTR
protected static final String ENTRY_CREATED_ATTR
protected static final String ENTRY_UPDATED_ATTR
protected static final String COPYRIGHT_TAG
protected static final String ACCESSION_TAG
protected static final String NAME_TAG
protected static final String TEXT_TAG
protected static final String REF_ATTR
protected static final String TYPE_ATTR
protected static final String KEY_ATTR
protected static final String ID_ATTR
protected static final String EVIDENCE_ATTR
protected static final String VALUE_ATTR
protected static final String STATUS_ATTR
protected static final String NAME_ATTR
protected static final String PROTEIN_TAG
protected static final String PROTEIN_TYPE_ATTR
protected static final String DOMAIN_TAG
protected static final String COMPONENT_TAG
protected static final String GENE_TAG
protected static final String ORGANISM_TAG
protected static final String DBXREF_TAG
protected static final String PROPERTY_TAG
protected static final String LINEAGE_TAG
protected static final String TAXON_TAG
protected static final String GENELOCATION_TAG
protected static final String GENELOCATION_NAME_TAG
protected static final String REFERENCE_TAG
protected static final String CITATION_TAG
protected static final String TITLE_TAG
protected static final String EDITOR_LIST_TAG
protected static final String AUTHOR_LIST_TAG
protected static final String PERSON_TAG
protected static final String CONSORTIUM_TAG
protected static final String LOCATOR_TAG
protected static final String RP_LINE_TAG
protected static final String RC_LINE_TAG
protected static final String RC_SPECIES_TAG
protected static final String RC_TISSUE_TAG
protected static final String RC_TRANSP_TAG
protected static final String RC_STRAIN_TAG
protected static final String RC_PLASMID_TAG
protected static final String COMMENT_TAG
protected static final String COMMENT_MASS_ATTR
protected static final String COMMENT_ERROR_ATTR
protected static final String COMMENT_METHOD_ATTR
protected static final String COMMENT_LOCTYPE_ATTR
protected static final String COMMENT_ABSORPTION_TAG
protected static final String COMMENT_ABS_MAX_TAG
protected static final String COMMENT_KINETICS_TAG
protected static final String COMMENT_KIN_KM_TAG
protected static final String COMMENT_KIN_VMAX_TAG
protected static final String COMMENT_PH_TAG
protected static final String COMMENT_REDOX_TAG
protected static final String COMMENT_TEMPERATURE_TAG
protected static final String COMMENT_LINK_TAG
protected static final String COMMENT_LINK_URI_ATTR
protected static final String COMMENT_EVENT_TAG
protected static final String COMMENT_ISOFORM_TAG
protected static final String COMMENT_INTERACTANT_TAG
protected static final String COMMENT_INTERACT_INTACT_ATTR
protected static final String COMMENT_INTERACT_LABEL_TAG
protected static final String COMMENT_ORGANISMS_TAG
protected static final String COMMENT_EXPERIMENTS_TAG
protected static final String NOTE_TAG
protected static final String KEYWORD_TAG
protected static final String PROTEIN_EXISTS_TAG
protected static final String ID_TAG
protected static final String FEATURE_TAG
protected static final String FEATURE_DESC_ATTR
protected static final String FEATURE_ORIGINAL_TAG
protected static final String FEATURE_VARIATION_TAG
protected static final String EVIDENCE_TAG
protected static final String EVIDENCE_CATEGORY_ATTR
protected static final String EVIDENCE_ATTRIBUTE_ATTR
protected static final String EVIDENCE_DATE_ATTR
protected static final String LOCATION_TAG
protected static final String LOCATION_SEQ_ATTR
protected static final String LOCATION_BEGIN_TAG
protected static final String LOCATION_END_TAG
protected static final String LOCATION_POSITION_ATTR
protected static final String LOCATION_POSITION_TAG
protected static final String SEQUENCE_TAG
protected static final String SEQUENCE_VERSION_ATTR
protected static final String SEQUENCE_LENGTH_ATTR
protected static final String SEQUENCE_MASS_ATTR
protected static final String SEQUENCE_CHECKSUM_ATTR
protected static final String SEQUENCE_MODIFIED_ATTR
protected static final Pattern rppat
protected static final Pattern xmlSchema
Constructor Detail |
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public UniProtXMLFormat()
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 rlistener, Namespace ns) throws IllegalSymbolException, 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.
IOException
- if there was a read error.
ParseException
public void beginWriting() throws IOException
IOException
- if writing fails.public void finishWriting() throws IOException
IOException
- if writing fails.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
.
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