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 relatedSequenceAnnotation
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 fromSequenceAnnotationGenerator.getGeneratedAnnotationGroup()
. Note: SequenceAnnotationGroups are not used for associated individual annotations with other individual annotations. Individual annotations can be associated that way usingSequenceAnnotation.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, includingSequenceAnnotation.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, includingSequenceAnnotation.TYPE_PRIMER_BIND
andSequenceAnnotation.TYPE_PRIMER_BIND_REVERSE
.static SequenceAnnotationGroup
STRUCTURE
A group of 3d structure annotations, includingSequenceAnnotation.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
All Methods Static Methods Instance Methods Concrete Methods 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 typestatic java.util.List<SequenceAnnotationGroup>
getAnnotationGroups()
Get all available annotation groupsjava.util.List<java.lang.String>
getAnnotationTypes()
Get all of the annotations types contained within this groupjava.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()
-
-
-
Field Detail
-
STRUCTURE
public static final SequenceAnnotationGroup STRUCTURE
A group of 3d structure annotations, includingSequenceAnnotation.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, includingSequenceAnnotation.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, includingSequenceAnnotation.TYPE_PRIMER_BIND
andSequenceAnnotation.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 groupannotationTypes
- the annotation types this group contains. Usually, one ofSequenceAnnotation
.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 classjava.lang.Object
-
equals
public boolean equals(java.lang.Object o)
- Overrides:
equals
in classjava.lang.Object
-
hashCode
public int hashCode()
- Overrides:
hashCode
in classjava.lang.Object
-
-