anndata.ann package

Subpackages

• anndata.ann.annlabel package
  • Submodules
  • anndata.ann.annlabel.label module
  • anndata.ann.annlabel.tag module
  • anndata.ann.annlabel.tagcompare module
  • anndata.ann.annlabel.tagtypes module
  • Module contents
• anndata.ann.annlocation package
  • Submodules
  • anndata.ann.annlocation.disjoint module
  • anndata.ann.annlocation.duration module
  • anndata.ann.annlocation.durationcompare module
  • anndata.ann.annlocation.interval module
  • anndata.ann.annlocation.intervalcompare module
  • anndata.ann.annlocation.localization module
  • anndata.ann.annlocation.localizationcompare module
  • anndata.ann.annlocation.location module
  • anndata.ann.annlocation.point module
  • Module contents

Submodules

anndata.ann.annotation module

filename

sppas.src.anndata.ann.annotation.py

author

Brigitte Bigi

contact

develop@sppas.org

summary

Representation of an annotation.

class anndata.ann.annotation.sppasAnnotation(location, labels=[])

Bases: sppas.src.anndata.metadata.sppasMetaData

Represents an annotation.

A sppasAnnotation() is a container for:

• a sppasLocation()

• a list of sppasLabel()

Example

>>> location = sppasLocation(sppasPoint(1.5, radius=0.01))
>>> labels = sppasLabel(sppasTag("foo"))
>>> ann = sppasAnnotation(location, labels)

__init__(location, labels=[])

Create a new sppasAnnotation instance.

Parameters

• location – (sppasLocation) the location(s) where the annotation happens

• labels – (sppasLabel, list) the label(s) to stamp this annotation, or a list of them.

add_tag(tag, score=None, label_idx=0)

Append an alternative tag in a label.

Parameters

• tag – (sppasTag)

• score – (float)

• label_idx – (int)

Raises

AnnDataTypeError, IndexError

append_label(label)

Append a label into the list of labels.

Parameters

label – (sppasLabel)

contains_localization(localization)

Return True if the given localization is in the location.

contains_tag(tag, function='exact', reverse=False, label_idx=0)

Return True if the given tag is in the label.

Parameters

• tag – (sppasTag)

• function – Search function

• reverse – Reverse the function.

• label_idx – (int)

copy()

Return a full copy of the annotation.

The location, the labels and the metadata are all copied. The ‘id’ of the returned annotation is then the same.

Returns

sppasAnnotation()

get_all_points()

Return the list of a copy of all points of this annotation.

get_best_tag(label_idx=0)

Return the tag with the highest score of a label or an empty str.

Parameters

label_idx – (int)

get_highest_localization()

Return a copy of the sppasPoint with the highest loc.

get_label_type()

Return the current type of tags, or an empty string.

get_labels()

Return the list of sppasLabel() of this annotation.

get_labels_best_tag()

Return a list with the best tag of each label.

get_location()

Return the sppasLocation() of this annotation.

get_lowest_localization()

Return a copy of the sppasPoint with the lowest localization.

get_parent()

Return the parent tier or None.

get_score()

Return the score of this annotation or None if no score is set.

is_labelled()

Return True if at least a sppasTag exists and is not None.

label_is_bool()

Return True if the type of the labels is ‘bool’.

label_is_filled()

Return True if at least one BEST tag is filled.

label_is_float()

Return True if the type of the labels is ‘float’.

label_is_int()

Return True if the type of the labels is ‘int’.

label_is_string()

Return True if the type of the labels is ‘str’.

location_is_disjoint()

Return True if the location is made of sppasDisjoint locs.

location_is_interval()

Return True if the location is made of sppasInterval locs.

location_is_point()

Return True if the location is made of sppasPoint locs.

remove_tag(tag, label_idx=0)

Remove an alternative tag of the label.

Parameters

• tag – (sppasTag) the tag to be removed of the list.

• label_idx – (int)

serialize_labels(separator='\n', empty='', alt=True)

DEPRECATED. Return labels serialized into a string.

TODO: REMOVE THIS METHOD. Use aioutils.serialize_labels() instead.

Parameters

• separator – (str) String to separate labels.

• empty – (str) The text to return if a tag is empty or not set.

• alt – (bool) Include alternative tags

Returns

(str)

set_best_localization(localization)

Set the best localization of the location.

Parameters

localization – (sppasBaseLocalization)

set_labels(labels=[])

Fix/reset the list of labels of this annotation.

Parameters

labels – (sppasLabel, list) the label(s) to stamp this annotation, or a list of them.

Raises

AnnDataTypeError, TypeError, CtrlVocabContainsError, HierarchyContainsError, HierarchyTypeError

set_parent(parent=None)

Set a parent tier.

Parameters

parent – (sppasTier) The parent tier of this annotation.

Raises

CtrlVocabContainsError, HierarchyContainsError, HierarchyTypeError

set_score(score=None)

Set or reset the score to this annotation.

Parameters

score – (float)

validate()

Validate the annotation.

Check if the labels and location match the requirements.

Raises

TypeError, CtrlVocabContainsError, HierarchyContainsError, HierarchyTypeError

validate_label(label)

Validate the label.

Check if the label matches the requirements of this annotation.

Raises

CtrlVocabContainsError, TypeError

validate_location()

Validate the location of the annotation.

Raises

anndata.ann.annset module

filename

sppas.src.anndata.ann.annset.py

author

Brigitte Bigi

contact

develop@sppas.org

summary

Manager for a set of annotations.

class anndata.ann.annset.sppasAnnSet

Bases: sppas.src.structs.basefset.sppasBaseSet

Manager for a set of annotations.

Mainly used with the data that are the result of the tier filter system. A sppasAnnSet() manages a dictionary with:

• key: an annotation

• value: a list of strings

__init__()

Create a sppasAnnSet instance.

copy()

Make a deep copy of self.

Overridden to return a sppasAnnSet() instead of a sppasBaseSet().

to_tier(name='AnnSet', annot_value=False)

Create a tier from the data set.

Parameters

• name – (str) Name of the tier to be returned

• annot_value – (bool) format of the resulting annotation label. By default, the label of the annotation is used. Instead, its value in the data set is used.

Returns

(sppasTier)

Module contents