Package com.biomatters.geneious.publicapi.documents.sequence

Class SequenceAnnotationGroup

java.lang.Object

com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotationGroup

public final class SequenceAnnotationGroup
extends java.lang.Object

An immutable class representing a collection of related SequenceAnnotation types.

Annotations in the same group are positioned in the same row as each other if possible in the sequence viewer. SequenceAnnotationGroups may also be returned from SequenceAnnotationGenerator.getGeneratedAnnotationGroup().

Note: SequenceAnnotationGroups are not used for associated individual annotations with other individual annotations. Individual annotations can be associated that way using SequenceAnnotation.KEY_ANNOTATION_GROUP.

Field Summary

Fields

Modifier and Type	Field	Description
static SequenceAnnotationGroup	EDITING_HISTORY	A group of annotations created when a sequence is manually editing, including SequenceAnnotation.TYPE_EDITING_HISTORY_REPLACEMENT, SequenceAnnotation.TYPE_EDITING_HISTORY_INSERTION, SequenceAnnotation.TYPE_EDITING_HISTORY_DELETION.
static SequenceAnnotationGroup	PRIMER	A group of annotations created when designing primers, including SequenceAnnotation.TYPE_PRIMER_BIND and SequenceAnnotation.TYPE_PRIMER_BIND_REVERSE.
static SequenceAnnotationGroup	STRUCTURE	A group of 3d structure annotations, including SequenceAnnotation.TYPE_HELIX, SequenceAnnotation.TYPE_STRAND, SequenceAnnotation.TYPE_COIL, SequenceAnnotation.TYPE_TURN.

Constructor Summary

Constructors

Constructor	Description
SequenceAnnotationGroup(java.lang.String groupName, java.lang.String... annotationTypes)	construct a new SequenceAnnotationGroup with the specified name and types

Method Summary

Modifier and Type	Method	Description
boolean	equals(java.lang.Object o)
static SequenceAnnotationGroup	getAnnotationGroup(java.lang.String annotationType)	Get the annotation group that contains this annotation type
static java.util.List<SequenceAnnotationGroup>	getAnnotationGroups()	Get all available annotation groups
java.util.List<java.lang.String>	getAnnotationTypes()	Get all of the annotations types contained within this group
java.lang.String	getGroupName()	Get a name suitable for displaying to an end user describing the annotation types within this group.
int	hashCode()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

STRUCTURE

public static final SequenceAnnotationGroup STRUCTURE

A group of 3d structure annotations, including SequenceAnnotation.TYPE_HELIX, SequenceAnnotation.TYPE_STRAND, SequenceAnnotation.TYPE_COIL, SequenceAnnotation.TYPE_TURN.

EDITING_HISTORY

public static final SequenceAnnotationGroup EDITING_HISTORY

A group of annotations created when a sequence is manually editing, including SequenceAnnotation.TYPE_EDITING_HISTORY_REPLACEMENT, SequenceAnnotation.TYPE_EDITING_HISTORY_INSERTION, SequenceAnnotation.TYPE_EDITING_HISTORY_DELETION.

PRIMER

public static final SequenceAnnotationGroup PRIMER

A group of annotations created when designing primers, including SequenceAnnotation.TYPE_PRIMER_BIND and SequenceAnnotation.TYPE_PRIMER_BIND_REVERSE.

Constructor Detail

SequenceAnnotationGroup

public SequenceAnnotationGroup(java.lang.String groupName,
                               java.lang.String... annotationTypes)

construct a new SequenceAnnotationGroup with the specified name and types

Parameters:

groupName - a human readable name for this group

annotationTypes - the annotation types this group contains. Usually, one of SequenceAnnotation.TYPE_*. If no types are specified, the group is assumed to contain a single type matching the group name

Method Detail

getAnnotationGroups

public static java.util.List<SequenceAnnotationGroup> getAnnotationGroups()

Get all available annotation groups

Returns:

all available annotation groups

getAnnotationGroup

public static SequenceAnnotationGroup getAnnotationGroup(java.lang.String annotationType)

Get the annotation group that contains this annotation type

Parameters:

annotationType - the annotation type to get the group for (case insensitive)

Returns:

the annotation group that contains this annotation type or null if this annotation type is not a member of any group.

getAnnotationTypes

public java.util.List<java.lang.String> getAnnotationTypes()

Get all of the annotations types contained within this group

Returns:

all of the annotations types contained within this group

getGroupName

public java.lang.String getGroupName()

Get a name suitable for displaying to an end user describing the annotation types within this group.

Returns:

a name suitable for displaying to an end user describing the annotation types within this group.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object