OpenSWATH - GUI Models

The main models used by the GUI are the PeptideTree and the DataModel models

MSData Data model Module

Contains classes that provide access to the raw data

MSData

TreeModels Module

Contains classes that provide access to the peptide / protein data

TreeNode

TreeModel

PeptideTreeNode

PeptideTree

SWATH MS Run Module

SingleChromatogramFile

class openswathgui.models.SingleChromatogramFile.SingleChromatogramFile(run, filename, load_in_memory=False, precursor_mapping=None, sequences_mapping=None, protein_mapping={})

Data Model for a single file from one run.

One run may contain multiple mzML files

Attributes:
runid: Current run id
Private Attributes:
  • _run: A pymzml.run.Reader object
  • _filename: Original filename
  • _basename: Original filename basename
  • _precursor_mapping: Dictionary { FullPrecursorName : [transition_id, transition_id] }
  • _sequences_mapping: Dictionary { StrippedSequence : [FullPrecursorName, FullPrecursorName]}
getTransitionCount()

Get total number of transitions

get_all_peptide_sequences()

Get all (stripped) sequences

get_all_precursor_ids()

Get all precursor ids (full sequence + charge)

get_data_for_precursor(precursor)

Retrieve raw data for a specific precursor - data will be as list of pairs (timearray, intensityarray)

get_data_for_transition(transition_id)

Retrieve raw data for a specific transition

get_id()
get_precursors_for_sequence(sequence)

Get all precursors mapping to one stripped sequence

get_sequence_for_protein(protein)
get_transitions_for_precursor(precursor)

Return the transition names for a specific precursor

get_transitions_with_mass_for_precursor(precursor)

Return the transition names prepended with the mass for a specific precursor

SwathRun

SwathRunCollection

ChromatogramTransition Module

ChromatogramTransition

class openswathgui.models.ChromatogramTransition.ChromatogramTransition(name, charge, subelements, peptideSequence=None, fullName=None, datatype='Precursor')

Bases: object

Internal tree structure object representing one row in the in the left side tree.

This is the bridge between the view and the data model

Pointers to objects of ChromatogramTransition are passed to callback functions when the selection of the left side tree changes. The object needs to have store information about all the column present in the rows (PeptideSequence, Charge, Name) which are requested by the PeptideTree model.

Also it needs to know how to access the raw data as well as meta-data for a certain transition. This is done through getData, getLabel etc.

getCharge()

Get charge of precursor

int:
Charge
getData(run)

Get raw data for a certain object

If we have a single precursors or a peptide with only one precursor, we show the same data as for the precursor itself. For a peptide with multiple precursors, we show all precursors as individual curves. For a single transition, we simply plot that transition.

run : SwathRun
SwathRun object which will be used to retrieve data
list of pairs (timearray, intensityarray):
Returns the raw data of the chromatograms for a given run. The dataformat is a list of transitions and each transition is a pair of (timearray,intensityarray)
getIntensity(run)

Get the intensity for a specific run and current precursor

run : SwathRun
SwathRun object which will be used to retrieve data
float:
The intensity for a specific run and current precursor
getLabel(run)

Get the labels for a curve (corresponding to the raw data from getData call) for a certain object.

If we have a single precursors or a peptide with only one precursor, we show the same data as for the precursor itself. For a peptide with multiple precusors, we show all precursors as individual curves. For a single transition, we simply plot that transition.

run : SwathRun
SwathRun object which will be used to retrieve data
list of str:
The labels to display for each line in the graph
getName()

Get name of precursor

str:
Name of precursor
getPeptideSequence()
getProbScore(run)

Get the probabilistic score for a specific run and current precursor

run : SwathRun
SwathRun object which will be used to retrieve data
float:
The probabilistic score for a specific run and current precursor
getRange(run)

Get the data range (leftWidth/rightWidh) for a specific run

run : SwathRun
SwathRun object which will be used to retrieve data
list of float:
A pair of floats representing the data range (leftWidth/rightWidh) for a specific run
getSubelements()
getType()