org.biojava.nbio.genome.parsers.gff

Interface FeatureI

All Known Implementing Classes:

Feature

public interface FeatureI

A feature on a sequence (for example, an exon or a gene), defined by a location and a set of attributes encoded as key/value pairs.

Author:

Hanno Hinsch

Method Summary

Modifier and Type	Method and Description
String	getAttribute(String key) Get the attribute value for this key.
HashMap<String,String>	getAttributes()
String	group() Get the group id of the feature.
boolean	hasAttribute(String key) Check if the feature has a value defined for the specified key.
boolean	hasAttribute(String key, String value) Check if the feature attributes include the specified key/value pair.
Location	location() Get the location of the feature.
String	seqname() Get the sequence name.
String	toString() A string representation of the feature.
String	type() Get the feature type, for example, "exon", "CDS", etc.
HashMap<String,String>	userData() Get HashMap of user data.

Method Detail

location

Location location()

Get the location of the feature.

Returns:

The location.

group

String group()

Get the group id of the feature. The group id is defined in the GFF1 format; features that share a common group id are presumed to be part of some logical group. For example, a gene might be represented by several exon features that all share the same group id.

The exact meaning of a feature's group id, or even its existence, is not guaranteed by this interface. An understanding of a particular file's data format is necessary to properly interpret the group id.

Returns:

The group id. This may be an empty string.

type

String type()

Get the feature type, for example, "exon", "CDS", etc.

Returns:

The type.

seqname

String seqname()

Get the sequence name.

Returns:

Sequence name.

getAttribute

String getAttribute(String key)

Get the attribute value for this key.

Parameters:

key - The key.

Returns:

The corresponding value. Null if the key has no value defined .

hasAttribute

boolean hasAttribute(String key)

Check if the feature has a value defined for the specified key.

Parameters:

key - The key.

Returns:

True if a value is defined for this key.

hasAttribute

boolean hasAttribute(String key,
                     String value)

Check if the feature attributes include the specified key/value pair.

Parameters:

key - The key.

value - The value.

Returns:

True if the feature's value for this key matches the specified value.

toString

String toString()

A string representation of the feature.

Overrides:

toString in class Object

Returns:

The string.

userData

HashMap<String,String> userData()

Get HashMap of user data.

Returns:

The user HashMap.

getAttributes

HashMap<String,String> getAttributes()