IdTransferer

Class Definition

class spectra_cluster.analyser.id_transferer.IdTransferer(add_to_identified=False, add_to_unidentified=True, include_all_identified=False)

The IdTransferer analyser transfers identifications to spectra part of a cluster.

The analysis is run by calling ‘process_cluster’ repeatedly. The transferred identifications are stored in the ‘identification_references’ member variable.

Variables:identification_references – A list of IdentificationReferences

__init__(add_to_identified=False, add_to_unidentified=True, include_all_identified=False)

Creates a default IdTransferer object.

Parameters:

• add_to_identified – If set identifications are added to identified spectra.
• add_to_unidentified – If set identifications are added to unidentified spectra.
• include_all_identified – If set identified spectra that are not part of reliable clusters are returned as well. Additionally, if add_to_identified is set to false and include_all_identified is set to true, the original identifications are returned unchanged.

static extract_main_cluster_psms(cluster)

Extracts the most common identification(s) from a cluster and returns it as a PSM object.

Parameters:cluster – Cluster to extract the most common PSM from. Returns:Most common PSMs as a list

process_cluster(cluster)

Transfers ids to spectra based on the cluster’s properties

Parameters:cluster – The cluster to process

IdentificationReference

class spectra_cluster.analyser.id_transferer.IdentificationReference(filename, spec_id, psms, changed_through_clustering, spectrum)

Contains the main identification data.

Variables:

• filename – The original peak list filename
• spec_id – The spectrum’s id within the source file
• psms – A list of PSM objects
• changed_through_clustering – Logical indicating whether the identification details were changed through the clustering.
• spectrum – The complete spectrum object

__init__(filename, spec_id, psms, changed_through_clustering, spectrum)

Creates a new instance of the identification reference.

Parameters:

• filename – Original peak list filename.
• spec_id – The spectrum’s id within this file.
• psms – A list of PSM objects
• changed_through_clustering – Logical indicating whether the identification details were changed through the