Class CGHCollection

The class CGHCollection stores a set of cases which were analysed by CGH. Its basic item is a case.

Overview

• Constructors
• Interfaces
• Enumerations
• Properties
• Methods
• Interaction with other classes

CGHCollection

New()

item( index: Integer): CGHs {readonly; default}

addCase(ByRef NewCase: CGHs): Void

getEnumerator(): IEnumerator {Implements IEnumerable.GetEnumerator}

createMiningDataFromGainsLossesStructs(Resolution: ChromosomeData.eResolutionLevel): MiningInputData {Implements IMinable.createMiningDataFromGainsLossesStructs}

createMiningDataFromSCCNAberrations(Resolution: ChromosomeData.eResolutionLevel): MiningInputData {Implements IMinable.createMiningDataFromSCCNAberrations}

createMiningDataFromStandardAberrationElements(): MiningInputData {Implements IMinable.createMiningDataFromStandardAberrationElements}

Programming Language

• Microsoft Visual Basic .Net.

Availability

• Copyrighted but free software under the GNU Public License.
• Binaries and source code can be obtained from the Download section.

Constructors

Public Sub New()

Instantiates a new CGHCollection object.

The internal collection is empty. Cases are then added by the addCase function.

Interfaces

This class implements the following interfaces:

IEnumberable

is used for the enumeration of collections. It is implemented with the getEnumerator function.

IMinable

is a locally defined interface used for the generation of mining input from collections. It is implemented with the createMiningDataFromGainsLossesStructs, createMiningDataFromSCCNAberrations, and createMiningDataFromStandardAberrationElements functions.

Enumerations

The class does not provide enumerations.

Properties

item(ByVal index As Integer) As CGHs

Gets the case (a CGHs object) at the specified index.

Property Value

• the case at the specified index.

Parameter

• index: The zero-based index of the element to get.

Exceptions

• ArgumentOutOfRangeException: index is less than zero or index is equal to or greater than count.

Remarks

• This property provides the ability to access a specific case (CGHs object) in this collection by using the following syntax: myCGHCollection(index).
• The property is read only. For adding a case, use the addCase function. No functionality is provided for removing an aberration.

Methods

Public Sub addCase(ByRef NewCase As CGHs)

Adds a new case to the internal collection.

Parameters

• NewCase: a reference to a CGHs object describing the case to be added.

Remarks

• A reference to he case is added. Hence, changing the properties of the original case after its addition to the collection will also cause changes of the case in the collection.
• No functionality for removing a case is provided.

Public Function getEnumerator() As IEnumerator Implements IEnumerable.GetEnumerator

Returns an enumerator that can iterate through the collection of cases (CGHs objects) of this collection.

Implements

• IEnumerable.GetEnumerator

Remarks

• The underlying collection is not sorted.

Public Function createMiningDataFromGainsLossesStructs(Optional ByVal Resolution As ChromosomeData.eResolutionLevel = ChromosomeData.eResolutionLevel.ResolutionArm) As MiningInputData Implements IMinable.createMiningDataFromGainsLossesStructs

Creates a MiningInputData object from the cytoband list of aberrations (GainsLossesStructs) calculated from the data of this collection.

Return Value

• a MiningInputData object based on the cytoband list.

Parameters

• Resolution: the resolution required for the calculation of the cytoband list.

Implements

• ISCNAnalyser.IMinable.createMiningDataFromGainsLossesStructs

Remarks

• If no resolution is given, the resolution will be set to chromosomal arm.
• The function calculates the cytoband list for each case at the required resolution and adds it to the mining data.
• At the level of the chromosomal bands, the function inquires if an aberration did occur there; its quantity does not matter.

Public Function createMiningDataFromSCCNAberrations(Optional ByVal Resolution As ChromosomeData.eResolutionLevel = ChromosomeData.eResolutionLevel.ResolutionNone) As MiningInputData Implements IMinable.createMiningDataFromSCCNAberrations

Creates a MiningInputData object from the SCCN aberrations (QuantitativeAberrations and QualitativeAberrations) calculated from the data of this collection.

Return Value

• a MiningInputData object based on the SCCN aberrations.

Parameters

• Resolution: the resolution required for the calculation of the SCCN aberrations.

Implements

• ISCNAnalyser.IMinable.createMiningDataFromSCCNAberrations

Remarks

• If no resolution is given, the resolution will be set to none.
• The function calculates the SCCN aberations for each case at the required resolution and adds them to the mining data.
• CGH data do not give raise to QualitativeAberrations.
• Only the occurence of an SCCN aberration, but not its quantity, is relevant in this function.

Public Function createMiningDataFromStandardAberrationElements() As MiningInputData Implements IMinable.createMiningDataFromStandardAberrationElements

Creates a MiningInputData object from the standard aberration elements (CGH aberrations) calculated from the data of this collection.

Return Value

• a MiningInputData object based on the standard CGH aberrations.

Implements

• ISCNAnalyser.IMinable.createMiningDataFromStandardAberrationElements

Remarks

• Only the occurence of an aberration, but not its quantity, is relevant in this function.

Interaction with other classes

Classes using CGHCollection

The CGHCollection class is a top level class in the ISCNAnalyser dll. It is not linked from other classes.

Classes used by CGHCollection

The CGHCollection class contains a set of CGHs objects representing the cases.

For mining purposes, GainsLossesStructs and QuantitativeAberrations objects are calculated. The connection with the CyDASMining dll, especially the MiningInputData, is important. For interchangability of CGH cases and ISCN cases for mining purposes, the interface IMinable was created in the ISCNAnalyser dll.