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java.lang.Objectorg.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
org.biojavax.bio.seq.io.EMBLxmlFormat
public class EMBLxmlFormat
Format reader for EMBLxml files. This version of EMBLxml 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.ac.uk/embl/Documentation/DTD/EMBL_dtd.txt
Nested Class Summary | |
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static class |
EMBLxmlFormat.Terms
Implements some EMBLxml-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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EMBLxmlFormat()
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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 EMBLxml format if the second XML line contains the phrase "http://www.ebi.ac.uk/schema/EMBL_schema.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 EMBLxml format if the second XML line contains the phrase "http://www.ebi.ac.uk/schema/EMBL_schema.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 DNA 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 DNA 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. |
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. Namespace is ignored as EMBLxml has no concept of it. |
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 EMBLXML_FORMAT
protected static final String ENTRY_GROUP_TAG
protected static final String ENTRY_TAG
protected static final String ENTRY_ACCESSION_ATTR
protected static final String ENTRY_NAME_ATTR
protected static final String ENTRY_DIVISION_ATTR
protected static final String ENTRY_CREATED_ATTR
protected static final String ENTRY_RELCREATED_ATTR
protected static final String ENTRY_UPDATED_ATTR
protected static final String ENTRY_RELUPDATED_ATTR
protected static final String ENTRY_VER_ATTR
protected static final String SEC_ACC_TAG
protected static final String DESC_TAG
protected static final String KEYWORD_TAG
protected static final String REFERENCE_TAG
protected static final String CITATION_TAG
protected static final String CITATION_ID_ATTR
protected static final String CITATION_TYPE_ATTR
protected static final String CITATION_DATE_ATTR
protected static final String CITATION_NAME_ATTR
protected static final String CITATION_VOL_ATTR
protected static final String CITATION_ISSUE_ATTR
protected static final String CITATION_FIRST_ATTR
protected static final String CITATION_LAST_ATTR
protected static final String CITATION_PUB_ATTR
protected static final String CITATION_PATENT_ATTR
protected static final String CITATION_INSTITUTE_ATTR
protected static final String CITATION_YEAR_ATTR
protected static final String DBREFERENCE_TAG
protected static final String DBREF_DB_ATTR
protected static final String DBREF_PRIMARY_ATTR
protected static final String DBREF_SEC_ATTR
protected static final String CONSORTIUM_TAG
protected static final String TITLE_TAG
protected static final String EDITOR_TAG
protected static final String AUTHOR_TAG
protected static final String PATENT_TAG
protected static final String LOCATOR_TAG
protected static final String REFERENCE_POSITION_TAG
protected static final String REF_POS_BEGIN_ATTR
protected static final String REF_POS_END_ATTR
protected static final String COMMENT_TAG
protected static final String FEATURE_TAG
protected static final String FEATURE_NAME_ATTR
protected static final String ORGANISM_TAG
protected static final String NAMESET_TAG
protected static final String SCINAME_TAG
protected static final String COMNAME_TAG
protected static final String TAXID_TAG
protected static final String LINEAGE_TAG
protected static final String TAXON_TAG
protected static final String QUALIFIER_TAG
protected static final String QUALIFIER_NAME_ATTR
protected static final String LOCATION_TAG
protected static final String LOCATION_TYPE_ATTR
protected static final String LOCATION_COMPL_ATTR
protected static final String LOCATION_ELEMENT_TAG
protected static final String LOC_ELEMENT_TYPE_ATTR
protected static final String LOC_ELEMENT_ACC_ATTR
protected static final String LOC_ELEMENT_VER_ATTR
protected static final String LOC_ELEMENT_COMPL_ATTR
protected static final String BASEPOSITION_TAG
protected static final String BASEPOSITION_TYPE_ATTR
protected static final String BASEPOSITION_EXTENT_ATTR
protected static final String SEQUENCE_TAG
protected static final String SEQUENCE_TYPE_ATTR
protected static final String SEQUENCE_LENGTH_ATTR
protected static final String SEQUENCE_TOPOLOGY_ATTR
protected static final String SEQUENCE_VER_ATTR
protected static final Pattern xmlSchema
Constructor Detail |
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public EMBLxmlFormat()
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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