Interface Functions Detail
void assignValueByKey(it, key, value);
Add or update a key-value pair of the current annotation.
Parameters
it
|
The AnnotationTreeIterator to |
key
|
The key whose value should be changed. Type: ContainerConcept. |
value
|
The value that should be assigned. Type: ContainerConcept. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
void clearValues(it);
Clear all key-value pairs of a given annotation.
Parameters
it
|
The AnnotationTreeIterator to clear all key-value pairs of the current annotation. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
TIter createLeftChild(it);
Create a new leftmost child of the current node and returns an iterator to it.
Parameters
it
|
The AnnotationTreeIterator to create a left child for. |
Returns
TIter |
Iterator to the new child. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
TIter createRightChild(it);
Creates a new rightmost child of the current node and returns an iterator to it.
Parameters
it
|
The AnnotationTreeIterator that was just created. |
Returns
TIter |
Iterator to the new child. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
TIter createSibling(it);
Creates a new right sibling of the current node and return an iterator to it.
Parameters
it
|
The AnnotationTreeIterator to create the sibling for. |
Returns
TIter |
Iterator to the new sibling. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
TAnnotation getAnnotation(it);
Returns the current annotation.
Parameters
it
|
The AnnotationTreeIterator to query for its annotation. |
Returns
TAnnotation |
A reference to the AnnotationStoreElement the iterator points to. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TName getName(it);
Returns the identifier of the current annotation.
Parameters
it
|
An AnnotationTreeIterator to query. |
Returns
TName |
The name of the current annotation. This is a reference to the corresponding position in annotationNameStore. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
TName getParentName(it);
Returns the identifier of the parent node in the annotationt ree of the current annotation.
Parameters
it
|
The AnnotationTreeIterator to get the name for. |
Returns
TName |
The name of the parent of the current annotation. This is a reference to the corresponding value in
annotationNameStore. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TSeq getType(it);
Returns the type name of the current annotation.
Parameters
it
|
The AnnotationTreeIterator to query for its type. |
Returns
The |
name of the current annotation, e.g. "exon" or "mRNA". This is a reference to an entry in annotationTypeStore. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
CharString getUniqueName(it);
Returns a unique name of the current annotation.
Parameters
it
|
The AnnotationTreeIterator to query. |
Returns
CharString |
A unique name of the current annotation. |
Some annotation file formats do not require that every annotation has a non-empty name. This function returns the
name if non-emtpy and otherwise generates one using the type an id.
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
bool getValueByKey(it, key);
bool getValueByKey(value, it, key);
Retrieve a key's value in the current annotation.
Parameters
it
|
The AnnotationTreeIterator for which to retrieve the key. |
key
|
The key to get the value for. |
value
|
The resulting value. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
bool goDown(it);
Move the iterator down to the leftmost child in the annotation tree.
Parameters
it
|
The AnnotationTreeIterator to move. |
Returns
bool |
true if the iterator could be moved and false otherwise. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
void goNextUp(it);
Go to the next node in preorder DFS skipping the current node's subtree.
Parameters
it
|
The AnnotationTreeIterator to |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
void goNextUp(it);
Go to the next node in preorder DFS skipping the subtrees of the current node and all of its siblings.
Parameters
it
|
The AnnotationTreeIterator to |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
bool goRight(it);
Move the iterator right to the next sibling in the annotation tree.
Parameters
it
|
The AnnotationTreeIterator to move. |
Returns
bool |
true if the iterator could be moved and false otherwise. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
void goRoot(it);
Move the iterator down to the tree root.
Parameters
it
|
The AnnotationTreeIterator to move. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
void goTo(it, annoId);
Moves the iterator to an arbitrary node giving its annotationId.
Parameters
it
|
The AnnotationTreeIterator to move. |
annoId
|
The id of the annotation to move to. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
bool goUp(it);
Move the iterator down to the parent in the annotation tree.
Parameters
it
|
The AnnotationTreeIterator to move. |
Returns
bool |
true if the iterator could be moved and false otherwise. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
bool isLastChild(it);
Returns a boolean value that indicates whether the current node is the last child.
Parameters
it
|
The AnnotationTreeIterator to query. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
bool isLeaf(it);
Return a boolean indicating whether the annotation is a leaf.
Parameters
it
|
The AnnotationTreeIterator to query. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
bool isRoot(it);
Return a boolean indicating whether the annotation is the root.
Parameters
it
|
The AnnotationTreeIterator to query. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
TIter nodeDown(it);
Returns a new iterator to the first child node of the current annotation in the annotation tree.
Parameters
it
|
The AnnotationTreeIterator to query. |
Returns
TIter |
Iterator to the first child node of it. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
TIter nodeRight(it);
Returns a new iterator to the right sibling of the current annotation in the annotation tree.
Parameters
it
|
The AnnotationTreeIterator to query. |
Returns
TIter |
Iterator to the right sibling of it. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
TIter nodeUp(it);
Returns a new iterator to the parent node of the current annotation in the annotation tree.
Parameters
it
|
The AnnotationTreeIterator to query. |
Returns
TIter |
Iterator to the parent node. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
void setName(it, name);
Sets the identifier of the current annotation.
Parameters
it
|
Iterator to the annotation to set the name for. |
name
|
The new identifier of the annotation pointed to by it. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also
void setType(it, typeName);
Sets the type name of the current annotation.
Parameters
it
|
The iterator to the annotation to set the type name for. |
typeName
|
The name of the type (e.g. "exon" or "mRNA"). Type: ContainerConcept. |
Data Races
If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.
See Also