org.biojava3.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

Methods

Modifier and Type	Method and Description
String	getAttribute(String key) Get the attribute value for this key.
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,Object>	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,Object> userData()

Get HashMap of user data.

Returns:

The user HashMap.