MutableFeature

All children of this parent

Positive, always greater than or equal to start. For discontinuous features, equivalent to maximum ending position among all ranges.

The ID attribute of this feature, or null if no such attribute

The length of the feature, equivalent to end - start + 1

Discontinuous annotations are represented in featureTree as a single Feature object with a multiplicity equal to the number of discontinuous segments of the annotation. ranges represents all the start-end ranges of this discontinuous feature while phases represents all the phases.

Alias for parent[0]

Alias for phases[0]

All phases for this feature. Continuous features will only have one, while discontinuous features will have several. Size is equal to ranges.size. A feature of type "CDS" (or synonym) may not have any Phase.UNSPECIFIED in its phases property.

Alias for ranges[0]

All start-end IntRanges that define this feature. Continuous features will only have one, while discontinuous features will have several. Size is equal to phases.size. All ranges are positive.

Positive, always less than or equal to end. For discontinuous features, equivalent to the minimum starting position among all ranges.

Associates value with tag in the attributes of this feature.

Associates all elements of values with tag in the attributes of this feature.

Adds a discontinuous region of this feature, with range and phase.

All attributes as tag-values pairs.

Return all ancestors of this feature in a depth-first order. Multiple parentage will result in duplicate values.

The String representation of this Feature as it appears as a row in a GFF file.

All attribute values for tag.

All children of this parent of type type (including its synonyms), or all children if type is null.

Clears all associations with tag in the attributes of this feature.

Deletes this MutableFeature from its MutableGenome. Subsequent calls to read or write to this or any descendants that become orphaned as a result of this deletion will throw DeletedAccessException.

All descendants of this parent of type type (including its synonyms) in depth-first order, or all descendants if type is null. Iterating over the descendants while modifying the topology of the tree will produce a ConcurrentModificationException (non-topological modifications are permissible). Multiple parentage will result in duplicate values

Inserts a feature with the specified properties as the child of this feature. If this MutableParent is not a MutableGenome, the inserted type must have a part-of relationship with this feature's type. This means that either the part-of relationship was explicitly defined by the user or exists in the Sequence Ontology.

Alias for insert for features without discontinuous regions. Behaves analogously.

Iterates over children

Associates tag with value in the attributes of this feature. Removes all other associations with tag that may have existed prior.

Associates tag with the elements of values in the attributes of this feature. Removes all other associations with tag that may have existed prior.

Sets the discontinuous regions of this feature to be those specified in discontinuities.

Sets the discontinuous region of the feature at index to be of range and phase.

Sets the id to new.

Make this feature continuous with a phase phase.

Makes this feature continuous with a range range.

Sorts the children by comparator.

Prepends this feature to MutableParent.descendants.