INSDseqFormat (biojava-legacy 1.9.1 API)

java.lang.Object
- org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat
- - org.biojavax.bio.seq.io.INSDseqFormat

All Implemented Interfaces:

SequenceFormat, RichSequenceFormat
```
public class INSDseqFormat
extends RichSequenceFormat.BasicFormat
```
Format reader for INSDseq files. This version of INSDseq 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.insdc.org/files/documents/INSD_V1.4.dtd Does NOT understand the "sites" keyword in INSDReference_position. Interprets this instead as an empty location. This is because there is no obvious way of representing the "sites" keyword in BioSQL. Note also that the INSDInterval tags and associate stuff are not read, as this is duplicate information to the INSDFeature_location tag which is already fully parsed. However, they are written on output, although there is no guarantee that the INSDInterval tags will exactly match the INSDFeature_location tag as it is not possible to exactly reflect its contents using these.

Since:

1.5

Author:

Alan Li (code based on his work), Richard Holland, George Waldon

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class INSDseqFormat.Terms
Implements some INSDseq-specific terms.
- Nested classes/interfaces inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat
  RichSequenceFormat.BasicFormat, RichSequenceFormat.HeaderlessFormat

Nested Classes
Modifier and Type	Class and Description
`static class`	`INSDseqFormat.Terms` Implements some INSDseq-specific terms.

Field Summary

Fields
Modifier and Type	Field and Description
`protected static String`	`ACC_VERSION_TAG`
`protected static String`	`ACCESSION_TAG`
`protected static String`	`AUTHOR_TAG`
`protected static String`	`AUTHORS_GROUP_TAG`
`protected static String`	`COMMENT_TAG`
`protected static String`	`CONSORTIUM_TAG`
`protected static String`	`CONTIG_TAG`
`protected static String`	`CREATE_DATE_TAG`
`protected static String`	`CREATE_REL_TAG`
`protected static String`	`DATABASE_XREF_TAG`
`protected static Pattern`	`dbxp`
`protected static String`	`DEFINITION_TAG`
`protected static String`	`DIVISION_TAG`
`protected static String`	`FEATURE_ACCESSION_TAG`
`protected static String`	`FEATURE_FROM_TAG`
`protected static String`	`FEATURE_INTERBP_TAG`
`protected static String`	`FEATURE_INTERVAL_TAG`
`protected static String`	`FEATURE_INTERVALS_GROUP_TAG`
`protected static String`	`FEATURE_ISCOMP_TAG`
`protected static String`	`FEATURE_KEY_TAG`
`protected static String`	`FEATURE_LOC_TAG`
`protected static String`	`FEATURE_OPERATOR_TAG`
`protected static String`	`FEATURE_PARTIAL3_TAG`
`protected static String`	`FEATURE_PARTIAL5_TAG`
`protected static String`	`FEATURE_POINT_TAG`
`protected static String`	`FEATURE_TAG`
`protected static String`	`FEATURE_TO_TAG`
`protected static String`	`FEATUREQUAL_NAME_TAG`
`protected static String`	`FEATUREQUAL_TAG`
`protected static String`	`FEATUREQUAL_VALUE_TAG`
`protected static String`	`FEATUREQUALS_GROUP_TAG`
`protected static String`	`FEATURES_GROUP_TAG`
`static String`	`INSDSEQ_FORMAT` The name of this format
`protected static String`	`INSDSEQ_TAG`
`protected static String`	`INSDSEQS_GROUP_TAG`
`protected static String`	`JOURNAL_TAG`
`protected static String`	`KEYWORD_TAG`
`protected static String`	`KEYWORDS_GROUP_TAG`
`protected static String`	`LENGTH_TAG`
`protected static String`	`LOCUS_TAG`
`protected static String`	`MOLTYPE_TAG`
`protected static String`	`ORGANISM_TAG`
`protected static String`	`OTHER_SEQID_TAG`
`protected static String`	`OTHER_SEQIDS_GROUP_TAG`
`protected static String`	`PUBMED_TAG`
`protected static String`	`REFERENCE_LOCATION_TAG`
`protected static String`	`REFERENCE_POSITION_TAG`
`protected static String`	`REFERENCE_TAG`
`protected static String`	`REFERENCES_GROUP_TAG`
`protected static String`	`REMARK_TAG`
`protected static String`	`SECONDARY_ACCESSION_TAG`
`protected static String`	`SECONDARY_ACCESSIONS_GROUP_TAG`
`protected static String`	`SEQUENCE_TAG`
`protected static String`	`SOURCE_TAG`
`protected static String`	`STRANDED_TAG`
`protected static String`	`TAXONOMY_TAG`
`protected static String`	`TITLE_TAG`
`protected static String`	`TOPOLOGY_TAG`
`protected static String`	`UPDATE_DATE_TAG`
`protected static String`	`UPDATE_REL_TAG`
`protected static Pattern`	`xmlSchema`
`protected static String`	`XREF_DBNAME_TAG`
`protected static String`	`XREF_ID_TAG`
`protected static String`	`XREF_TAG`

Constructor Summary

Constructors
Constructor and Description

INSDseqFormat()

Constructors
Constructor and Description
`INSDseqFormat()`

Method Summary

Methods
Modifier and Type	Method and Description
`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.
`boolean`	`canRead(File file)` Check to see if a given file is in our format.
`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.
`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.
`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.
`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
getElideComments, getElideFeatures, getElideReferences, getElideSymbols, getLineWidth, getPrintStream, setElideComments, setElideFeatures, setElideReferences, setElideSymbols, setLineWidth, setPrintStream

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - INSDSEQ_FORMAT
```
public static final String INSDSEQ_FORMAT
```
    The name of this format
    
    See Also:
    Constant Field Values
  - INSDSEQS_GROUP_TAG
```
protected static final String INSDSEQS_GROUP_TAG
```
    See Also:
    Constant Field Values
  - INSDSEQ_TAG
```
protected static final String INSDSEQ_TAG
```
    See Also:
    Constant Field Values
  - LOCUS_TAG
```
protected static final String LOCUS_TAG
```
    See Also:
    Constant Field Values
  - LENGTH_TAG
```
protected static final String LENGTH_TAG
```
    See Also:
    Constant Field Values
  - TOPOLOGY_TAG
```
protected static final String TOPOLOGY_TAG
```
    See Also:
    Constant Field Values
  - STRANDED_TAG
```
protected static final String STRANDED_TAG
```
    See Also:
    Constant Field Values
  - MOLTYPE_TAG
```
protected static final String MOLTYPE_TAG
```
    See Also:
    Constant Field Values
  - DIVISION_TAG
```
protected static final String DIVISION_TAG
```
    See Also:
    Constant Field Values
  - UPDATE_DATE_TAG
```
protected static final String UPDATE_DATE_TAG
```
    See Also:
    Constant Field Values
  - CREATE_DATE_TAG
```
protected static final String CREATE_DATE_TAG
```
    See Also:
    Constant Field Values
  - UPDATE_REL_TAG
```
protected static final String UPDATE_REL_TAG
```
    See Also:
    Constant Field Values
  - CREATE_REL_TAG
```
protected static final String CREATE_REL_TAG
```
    See Also:
    Constant Field Values
  - DEFINITION_TAG
```
protected static final String DEFINITION_TAG
```
    See Also:
    Constant Field Values
  - DATABASE_XREF_TAG
```
protected static final String DATABASE_XREF_TAG
```
    See Also:
    Constant Field Values
  - XREF_TAG
```
protected static final String XREF_TAG
```
    See Also:
    Constant Field Values
  - ACCESSION_TAG
```
protected static final String ACCESSION_TAG
```
    See Also:
    Constant Field Values
  - ACC_VERSION_TAG
```
protected static final String ACC_VERSION_TAG
```
    See Also:
    Constant Field Values
  - SECONDARY_ACCESSIONS_GROUP_TAG
```
protected static final String SECONDARY_ACCESSIONS_GROUP_TAG
```
    See Also:
    Constant Field Values
  - SECONDARY_ACCESSION_TAG
```
protected static final String SECONDARY_ACCESSION_TAG
```
    See Also:
    Constant Field Values
  - OTHER_SEQIDS_GROUP_TAG
```
protected static final String OTHER_SEQIDS_GROUP_TAG
```
    See Also:
    Constant Field Values
  - OTHER_SEQID_TAG
```
protected static final String OTHER_SEQID_TAG
```
    See Also:
    Constant Field Values
  - KEYWORDS_GROUP_TAG
```
protected static final String KEYWORDS_GROUP_TAG
```
    See Also:
    Constant Field Values
  - KEYWORD_TAG
```
protected static final String KEYWORD_TAG
```
    See Also:
    Constant Field Values
  - SOURCE_TAG
```
protected static final String SOURCE_TAG
```
    See Also:
    Constant Field Values
  - ORGANISM_TAG
```
protected static final String ORGANISM_TAG
```
    See Also:
    Constant Field Values
  - TAXONOMY_TAG
```
protected static final String TAXONOMY_TAG
```
    See Also:
    Constant Field Values
  - REFERENCES_GROUP_TAG
```
protected static final String REFERENCES_GROUP_TAG
```
    See Also:
    Constant Field Values
  - REFERENCE_TAG
```
protected static final String REFERENCE_TAG
```
    See Also:
    Constant Field Values
  - REFERENCE_LOCATION_TAG
```
protected static final String REFERENCE_LOCATION_TAG
```
    See Also:
    Constant Field Values
  - REFERENCE_POSITION_TAG
```
protected static final String REFERENCE_POSITION_TAG
```
    See Also:
    Constant Field Values
  - TITLE_TAG
```
protected static final String TITLE_TAG
```
    See Also:
    Constant Field Values
  - JOURNAL_TAG
```
protected static final String JOURNAL_TAG
```
    See Also:
    Constant Field Values
  - PUBMED_TAG
```
protected static final String PUBMED_TAG
```
    See Also:
    Constant Field Values
  - XREF_DBNAME_TAG
```
protected static final String XREF_DBNAME_TAG
```
    See Also:
    Constant Field Values
  - XREF_ID_TAG
```
protected static final String XREF_ID_TAG
```
    See Also:
    Constant Field Values
  - REMARK_TAG
```
protected static final String REMARK_TAG
```
    See Also:
    Constant Field Values
  - AUTHORS_GROUP_TAG
```
protected static final String AUTHORS_GROUP_TAG
```
    See Also:
    Constant Field Values
  - AUTHOR_TAG
```
protected static final String AUTHOR_TAG
```
    See Also:
    Constant Field Values
  - CONSORTIUM_TAG
```
protected static final String CONSORTIUM_TAG
```
    See Also:
    Constant Field Values
  - COMMENT_TAG
```
protected static final String COMMENT_TAG
```
    See Also:
    Constant Field Values
  - FEATURES_GROUP_TAG
```
protected static final String FEATURES_GROUP_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_TAG
```
protected static final String FEATURE_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_KEY_TAG
```
protected static final String FEATURE_KEY_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_LOC_TAG
```
protected static final String FEATURE_LOC_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_INTERVALS_GROUP_TAG
```
protected static final String FEATURE_INTERVALS_GROUP_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_INTERVAL_TAG
```
protected static final String FEATURE_INTERVAL_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_FROM_TAG
```
protected static final String FEATURE_FROM_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_TO_TAG
```
protected static final String FEATURE_TO_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_POINT_TAG
```
protected static final String FEATURE_POINT_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_ISCOMP_TAG
```
protected static final String FEATURE_ISCOMP_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_INTERBP_TAG
```
protected static final String FEATURE_INTERBP_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_ACCESSION_TAG
```
protected static final String FEATURE_ACCESSION_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_OPERATOR_TAG
```
protected static final String FEATURE_OPERATOR_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_PARTIAL5_TAG
```
protected static final String FEATURE_PARTIAL5_TAG
```
    See Also:
    Constant Field Values
  - FEATURE_PARTIAL3_TAG
```
protected static final String FEATURE_PARTIAL3_TAG
```
    See Also:
    Constant Field Values
  - FEATUREQUALS_GROUP_TAG
```
protected static final String FEATUREQUALS_GROUP_TAG
```
    See Also:
    Constant Field Values
  - FEATUREQUAL_TAG
```
protected static final String FEATUREQUAL_TAG
```
    See Also:
    Constant Field Values
  - FEATUREQUAL_NAME_TAG
```
protected static final String FEATUREQUAL_NAME_TAG
```
    See Also:
    Constant Field Values
  - FEATUREQUAL_VALUE_TAG
```
protected static final String FEATUREQUAL_VALUE_TAG
```
    See Also:
    Constant Field Values
  - SEQUENCE_TAG
```
protected static final String SEQUENCE_TAG
```
    See Also:
    Constant Field Values
  - CONTIG_TAG
```
protected static final String CONTIG_TAG
```
    See Also:
    Constant Field Values
  - dbxp
```
protected static final Pattern dbxp
```
  - xmlSchema
```
protected static final Pattern xmlSchema
```
- Constructor Detail
  - INSDseqFormat
```
public INSDseqFormat()
```
- Method Detail
  - canRead
```
public boolean canRead(File file)
                throws IOException
```
    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 INSDseq format if the second XML line contains the phrase "http://www.ebi.ac.uk/dtd/INSD_INSDSeq.dtd".
    
    Specified by:
    
    canRead in interface RichSequenceFormat
    
    Overrides:
    
    canRead in class RichSequenceFormat.BasicFormat
    
    Parameters:
    file - the File to check.
    
    Returns:
    true if the file is readable by this format, false if not.
    
    Throws:
    
    IOException - in case the file is inaccessible.
  - guessSymbolTokenization
```
public SymbolTokenization guessSymbolTokenization(File file)
                                           throws IOException
```
    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.
    
    Specified by:
    
    guessSymbolTokenization in interface RichSequenceFormat
    
    Overrides:
    
    guessSymbolTokenization in class RichSequenceFormat.BasicFormat
    
    Parameters:
    file - the File object to guess the format of.
    
    Returns:
    a SymbolTokenization to read the file with.
    
    Throws:
    
    IOException - if the file is unrecognisable or inaccessible.
  - canRead
```
public boolean canRead(BufferedInputStream stream)
                throws IOException
```
    Check to see if a given stream is in our format. A stream is in INSDseq format if the second XML line contains the phrase "http://www.ebi.ac.uk/dtd/INSD_INSDSeq.dtd".
    
    Parameters:
    stream - the BufferedInputStream to check.
    
    Returns:
    true if the stream is readable by this format, false if not.
    
    Throws:
    
    IOException - in case the stream is inaccessible.
  - guessSymbolTokenization
```
public SymbolTokenization guessSymbolTokenization(BufferedInputStream stream)
                                           throws IOException
```
    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. For formats that only accept one tokenization, just return it without checking the stream. For formats that accept multiple tokenizations, its up to you how you do it. Always returns a DNA tokenizer.
    
    Parameters:
    stream - the BufferedInputStream object to guess the format of.
    
    Returns:
    a SymbolTokenization to read the stream with.
    
    Throws:
    
    IOException - if the stream is unrecognisable or inaccessible.
  - readSequence
```
public boolean readSequence(BufferedReader reader,
                   SymbolTokenization symParser,
                   SeqIOListener listener)
                     throws IllegalSymbolException,
                            IOException,
                            ParseException
```
    Read a sequence and pass data on to a SeqIOListener.
    
    Parameters:
    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.
    
    Returns:
    a boolean indicating whether or not the stream contains any more sequences.
    
    Throws:
    
    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
  - readRichSequence
```
public boolean readRichSequence(BufferedReader reader,
                       SymbolTokenization symParser,
                       RichSeqIOListener rlistener,
                       Namespace ns)
                         throws IllegalSymbolException,
                                IOException,
                                ParseException
```
    Reads a sequence from the given buffered reader using the given tokenizer to parse sequence symbols. Events are passed to the listener, and the namespace used for sequences read is the one given. If the namespace is null, then the default namespace for the parser is used, which may depend on individual implementations of this interface.
    
    Parameters:
    reader - the input source
    symParser - the tokenizer which understands the sequence being read
    rlistener - the listener to send sequence events to
    ns - the namespace to read sequences into.
    
    Returns:
    true if there is more to read after this, false otherwise.
    
    Throws:
    
    IllegalSymbolException - if the tokenizer couldn't understand one of the sequence symbols in the file.
    
    IOException - if there was a read error.
    
    ParseException
  - beginWriting
```
public void beginWriting()
                  throws IOException
```
    Informs the writer that we want to start writing. This will do any initialisation required, such as writing the opening tags of an XML file that groups sequences together.
    
    Throws:
    
    IOException - if writing fails.
  - finishWriting
```
public void finishWriting()
                   throws IOException
```
    Informs the writer that are done writing. This will do any finalisation required, such as writing the closing tags of an XML file that groups sequences together.
    
    Throws:
    
    IOException - if writing fails.
  - writeSequence
```
public void writeSequence(Sequence seq,
                 PrintStream os)
                   throws IOException
```
    writeSequence writes a sequence to the specified PrintStream, using the default format.
    
    Parameters:
    seq - the sequence to write out.
    os - the printstream to write to.
    
    Throws:
    
    IOException
  - writeSequence
```
public void writeSequence(Sequence seq,
                 String format,
                 PrintStream os)
                   throws IOException
```
    writeSequence writes a sequence to the specified PrintStream, using the specified format.
    
    Parameters:
    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.
    
    Throws:
    
    IOException - if an error occurs.
  - writeSequence
```
public void writeSequence(Sequence seq,
                 Namespace ns)
                   throws IOException
```
    Writes a sequence out to the outputstream given by beginWriting() using the default format of the implementing class. If namespace is given, sequences will be written with that namespace, otherwise they will be written with the default namespace of the implementing class (which is usually the namespace of the sequence itself). If you pass this method a sequence which is not a RichSequence, it will attempt to convert it using RichSequence.Tools.enrich(). Obviously this is not going to guarantee a perfect conversion, so it's better if you just use RichSequences to start with! Namespace is ignored as INSDseq has no concept of it.
    
    Parameters:
    seq - the sequence to write
    ns - the namespace to write it with
    
    Throws:
    
    IOException - in case it couldn't write something
  - getDefaultFormat
```
public String getDefaultFormat()
```
    getDefaultFormat returns the String identifier for the default sub-format written by a SequenceFormat implementation.
    
    Returns:
    a String.

Class INSDseqFormat

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojavax.bio.seq.io.RichSequenceFormat

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.biojavax.bio.seq.io.RichSequenceFormat.BasicFormat

Methods inherited from class java.lang.Object

Field Detail

INSDSEQ_FORMAT

INSDSEQS_GROUP_TAG

INSDSEQ_TAG

LOCUS_TAG

LENGTH_TAG

TOPOLOGY_TAG

STRANDED_TAG

MOLTYPE_TAG

DIVISION_TAG

UPDATE_DATE_TAG

CREATE_DATE_TAG

UPDATE_REL_TAG

CREATE_REL_TAG

DEFINITION_TAG

DATABASE_XREF_TAG

XREF_TAG

ACCESSION_TAG

ACC_VERSION_TAG

SECONDARY_ACCESSIONS_GROUP_TAG

SECONDARY_ACCESSION_TAG

OTHER_SEQIDS_GROUP_TAG

OTHER_SEQID_TAG

KEYWORDS_GROUP_TAG

KEYWORD_TAG

SOURCE_TAG

ORGANISM_TAG

TAXONOMY_TAG

REFERENCES_GROUP_TAG

REFERENCE_TAG

REFERENCE_LOCATION_TAG

REFERENCE_POSITION_TAG

TITLE_TAG

JOURNAL_TAG

PUBMED_TAG

XREF_DBNAME_TAG

XREF_ID_TAG

REMARK_TAG

AUTHORS_GROUP_TAG

AUTHOR_TAG

CONSORTIUM_TAG

COMMENT_TAG

FEATURES_GROUP_TAG

FEATURE_TAG

FEATURE_KEY_TAG

FEATURE_LOC_TAG

FEATURE_INTERVALS_GROUP_TAG

FEATURE_INTERVAL_TAG

FEATURE_FROM_TAG

FEATURE_TO_TAG

FEATURE_POINT_TAG

FEATURE_ISCOMP_TAG

FEATURE_INTERBP_TAG

FEATURE_ACCESSION_TAG

FEATURE_OPERATOR_TAG

FEATURE_PARTIAL5_TAG

FEATURE_PARTIAL3_TAG

FEATUREQUALS_GROUP_TAG

FEATUREQUAL_TAG

FEATUREQUAL_NAME_TAG

FEATUREQUAL_VALUE_TAG

SEQUENCE_TAG

CONTIG_TAG

dbxp

xmlSchema

Constructor Detail

INSDseqFormat

Method Detail

canRead

guessSymbolTokenization

canRead

guessSymbolTokenization