org.biojava.bio.seq.io

Class EmblFileFormer

java.lang.Object

org.biojava.bio.seq.io.EmblFileFormer

All Implemented Interfaces:

SeqFileFormer, SeqIOListener

Deprecated.

Use org.biojavax.bio.seq.io framework instead

public class EmblFileFormer
extends Object
implements SeqFileFormer

EmblFileFormer performs the detailed formatting of EMBL entries for writing to a PrintStream. Currently the formatting of the header is not correct. This really needs to be addressed in the parser which is merging fields which should remain separate.

The event generator used to feed events to this class should enforce ordering of those events. This class will stream data directly to the PrintStream

.

This implementation requires that all the symbols be added in one block as is does not buffer the tokenized symbols between calls.

Since:

1.2

Author:

Keith James, Len Trigg (Taxon output), Lorna Morris

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	EmblFileFormer() Deprecated. Creates a new EmblFileFormer using System.out stream.
protected	EmblFileFormer(PrintStream stream) Deprecated. Creates a new EmblFileFormer using the specified stream.

Method Summary

Methods

Modifier and Type	Method and Description
void	addFeatureProperty(Object key, Object value) Deprecated. Notify the listener of a feature property.
void	addSequenceProperty(Object key, Object value) Deprecated. Notify the listener of a sequence-wide property.
void	addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) Deprecated. Notify the listener of symbol data.
void	endFeature() Deprecated. Mark the end of data associated with one specific feature.
void	endSequence() Deprecated. Notify the listener that processing of the sequence is complete.
String	formatLocation(Feature theFeature) Formats the location of a feature.
String	formatLocation(Location loc, StrandedFeature.Strand strand) formatLocation creates an EMBL/Genbank style representation of a Location.
StringBuffer	formatLocation(StringBuffer sb, Location loc, StrandedFeature.Strand strand) formatLocation creates an EMBL/Genbank style representation of a Location.
PrintStream	getPrintStream() Deprecated. getPrintStream returns the PrintStream to which an instance will write the formatted data.
void	setName(String id) Deprecated. Notify the listener that the current sequence is generally known by a particular name.
void	setPrintStream(PrintStream stream) Deprecated. setPrintStream informs an instance which PrintStream to use.
void	setURI(String uri) Deprecated. Notify the listener of a URI identifying the current sequence.
void	startFeature(Feature.Template templ) Deprecated. Notify the listener that a new feature object is starting.
void	startSequence() Deprecated. Start the processing of a sequence.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.biojava.bio.seq.io.SeqFileFormer

formatLocation, formatLocation

Constructor Detail

EmblFileFormer

protected EmblFileFormer()

Deprecated.

Creates a new EmblFileFormer using System.out stream.

EmblFileFormer

protected EmblFileFormer(PrintStream stream)

Deprecated.

Creates a new EmblFileFormer using the specified stream.

Parameters:

stream - a PrintStream.

Method Detail

getPrintStream

public PrintStream getPrintStream()

Deprecated.

Description copied from interface: SeqFileFormer

getPrintStream returns the PrintStream to which an instance will write the formatted data. If this has not been set, an implementation should default to System.out.

Specified by:

getPrintStream in interface SeqFileFormer

Returns:

the PrintStream which will be written to.

setPrintStream

public void setPrintStream(PrintStream stream)

Deprecated.

Description copied from interface: SeqFileFormer

setPrintStream informs an instance which PrintStream to use.

Specified by:

setPrintStream in interface SeqFileFormer

Parameters:

stream - a PrintStream to write to.

setName

public void setName(String id)
             throws ParseException

Deprecated.

Description copied from interface: SeqIOListener

Notify the listener that the current sequence is generally known by a particular name.

Specified by:

setName in interface SeqIOListener

Parameters:

id - the String that should be returned by getName for the sequence being parsed

Throws:

ParseException

startSequence

public void startSequence()
                   throws ParseException

Deprecated.

Description copied from interface: SeqIOListener

Start the processing of a sequence. This method exists primarily to enforce the life-cycles of SeqIOListener objects.

Specified by:

startSequence in interface SeqIOListener

Throws:

ParseException

endSequence

public void endSequence()
                 throws ParseException

Deprecated.

Description copied from interface: SeqIOListener

Notify the listener that processing of the sequence is complete.

Specified by:

endSequence in interface SeqIOListener

Throws:

ParseException

setURI

public void setURI(String uri)
            throws ParseException

Deprecated.

Description copied from interface: SeqIOListener

Notify the listener of a URI identifying the current sequence.

Specified by:

setURI in interface SeqIOListener

Throws:

ParseException

addSymbols

public void addSymbols(Alphabet alpha,
              Symbol[] syms,
              int start,
              int length)
                throws IllegalAlphabetException

Deprecated.

Description copied from interface: SeqIOListener

Notify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception

Specified by:

addSymbols in interface SeqIOListener

Parameters:

alpha - The alphabet of the symbol data

syms - An array containing symbols

start - The start offset of valid data within the array

length - The number of valid symbols in the array

Throws:

IllegalAlphabetException - if we can't cope with this alphabet.

addSequenceProperty

public void addSequenceProperty(Object key,
                       Object value)
                         throws ParseException

Deprecated.

Description copied from interface: SeqIOListener

Notify the listener of a sequence-wide property. This might be stored as an entry in the sequence's annotation bundle.

Specified by:

addSequenceProperty in interface SeqIOListener

Throws:

ParseException

startFeature

public void startFeature(Feature.Template templ)
                  throws ParseException

Deprecated.

Description copied from interface: SeqIOListener

Notify the listener that a new feature object is starting. Every call to startFeature should have a corresponding call to endFeature. If the listener is concerned with a hierarchy of features, it should maintain a stack of `open' features.

Specified by:

startFeature in interface SeqIOListener

Throws:

ParseException

endFeature

public void endFeature()
                throws ParseException

Deprecated.

Description copied from interface: SeqIOListener

Mark the end of data associated with one specific feature.

Specified by:

endFeature in interface SeqIOListener

Throws:

ParseException

addFeatureProperty

public void addFeatureProperty(Object key,
                      Object value)

Deprecated.

Description copied from interface: SeqIOListener

Notify the listener of a feature property.

Specified by:

addFeatureProperty in interface SeqIOListener

formatLocation

public String formatLocation(Feature theFeature)

Formats the location of a feature. This version is required when formatting remote locations, since the location field of a remote feature is the projection of that feature on the sequence. When a distinction is made between 'order' and 'join' this method will likely be extended for that also.

Parameters:

theFeature - The feature with the location to format

Returns:

String The formatted location

formatLocation

public String formatLocation(Location loc,
                    StrandedFeature.Strand strand)

formatLocation creates an EMBL/Genbank style representation of a Location. This is a convenience method only. The version which has a StringBuffer parameter (and returns the StringBuffer) is preferred. If a compound location is formatted using this method, it is returned as a join-type location rather than an order-type.

Parameters:

loc - a Location to format.

strand - a StrandedFeature.Strand indicating the Location's strand.

Returns:

a StringBuffer.

formatLocation

public StringBuffer formatLocation(StringBuffer sb,
                          Location loc,
                          StrandedFeature.Strand strand)

formatLocation creates an EMBL/Genbank style representation of a Location. Supported location forms:

   123
  <123 or >123
  (123.567)
  (123.567)..789
   123..(567.789)
  (123.345)..(567.789)
   123..456
  <123..567 or 123..>567 or <123..>567
   123^567
   AL123465:(123..567)
 

If a compound location is formatted using this method, it is returned as a join-type location rather than an order-type. To preserve the join/order distinction; and to format locations like AL123465:(123..567), use the formatLocation(Feature) method.

Parameters:

sb - a StringBuffer

loc - a Location to format.

strand - a StrandedFeature.Strand indicating the Location's strand.

Returns:

a StringBuffer.