org.biojava.bio.seq.io

Interface SeqFileFormer

All Superinterfaces:

SeqIOListener

All Known Implementing Classes:

EmblFileFormer, GenbankFileFormer, ProteinRefSeqFileFormer, SwissprotFileFormer

Deprecated.

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

public interface SeqFileFormer
extends SeqIOListener

Objects implementing the SeqFileFormer interface are responsible for the detailed formatting of sequence data prior to writing to a PrintStream. Some file formats, such as Fasta, are very simple and don't require a SeqFileFormer.

Since:

1.2

Author:

Keith James

Method Summary

Methods

Modifier and Type	Method and Description
String	formatLocation(Feature theFeature) Deprecated. Formats the location of a feature.
StringBuffer	formatLocation(StringBuffer sb, Location loc, StrandedFeature.Strand strand) Deprecated. formatLocation creates a String representation of a Location.
PrintStream	getPrintStream() Deprecated. getPrintStream returns the PrintStream to which an instance will write the formatted data.
void	setPrintStream(PrintStream stream) Deprecated. setPrintStream informs an instance which PrintStream to use.

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

addFeatureProperty, addSequenceProperty, addSymbols, endFeature, endSequence, setName, setURI, startFeature, startSequence

Method Detail

getPrintStream

PrintStream getPrintStream()

Deprecated.

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.

Returns:

the PrintStream which will be written to.

setPrintStream

void setPrintStream(PrintStream stream)

Deprecated.

setPrintStream informs an instance which PrintStream to use.

Parameters:

stream - a PrintStream to write to.

formatLocation

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

Deprecated.

formatLocation creates a String representation of a Location. The strand may not be relevant for all formats (e.g. it is relevant for Genbank and EMBL, but not for SwissProt). In such cases the implementation may accept a strand of 'unknown', '0' or '.'. A StringBuffer is used to allow avoidance of expensive String manipulations on (potentially very large numbers of) locations.

Parameters:

sb - a StringBuffer to append the location to.

loc - a Location to format.

strand - a StrandedFeature.Strand indicating any relevant strandedness.

Returns:

a StringBuffer with the location appended.

formatLocation

String formatLocation(Feature theFeature)

Deprecated.

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