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Class CKAS

The class CKAS describes a "Complex Karyotype Aberration Score". It consists of the number of ploidy changes, numerical changes (gains and losses of (derivative) chromosomes), balanced and unbalanced, resp., structural abberations and unclassified aberrations (e.g. markers).

The CKAS was introduced together with the ISCN in:
Jutta Bradtke, Harald Balz, Christa Fonatsch, Barbara Heinze, Anna Jauch, Brigitte Mohr, Claudia Schoch, Harald Rieder:
"Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation",
BMC Bioinformatics 2003, 4:4 (28 January 2003)

CKAS

New()

New(Ploidy: Integer, Numerical: Integer, Balanced: Integer, Unbalanced: Integer, Unclassified: Integer)

Ploidy: Integer

Numerical: Integer

Balanced: Integer

UnBalanced: Integer

Unclassified: Integer

add(ByRef SecondCKAS: CKAS): Void

addBalanced(AddValue: Integer): Void

addNumerical(AddValue: Integer): Void

addPloidy(AddValue: Integer): Void

addUnbalanced(AddValue: Integer): Void

addUnclassified(AddValue: Integer): Void

combine(ByRef SecondCKAS: CKAS): Void

clone(): Object {Implements ICloneable.clone}

getOverallCKAS: Integer

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 CKAS object. All its values are 0.

Public Sub New(ByVal Ploidy As Integer, ByVal Numerical As Integer, ByVal Balanced As Integer, ByVal Unbalanced As Integer, ByVal Unclassified As Integer)

Instantiates a new CKAS object.

Parameter

Ploidy: the ploidy value of the CKAS.
Numerical: the numerical value of the CKAS.
Balanced: the balanced value of the CKAS.
Unbalanced: the unbalanced value of the CKAS.
Unclassified: the unclassified value of the CKAS.

Remarks

There is no parameter for the overall value of the CKAS; it will be calculated when queried with getOverallCKAS.

Interfaces

ICloneable

is implemented with the clone function.

Enumerations

The class does not provide enumerations.

Properties

Properties are available for the constituents of the CKAS. Furthermore, there are addPropertyName(AddValue: Integer) functions which allow for an increase of the respective value by AddValue (see below under "Methods").

Ploidy: Integer

Gets or sets the value indicating the ploidy change in a karyotype. Ploidy is seen as the deviation from a "normal" diploid karyotype.

Numerical: Integer

Gets or sets the value indicating the amount of gains and losses of chromosomes in a karyotype. Only gains and losses of whole chromosomes (normal or derivative) is counted with this property.

Balanced: Integer

Gets or sets the value indicating the amount of balanced structural aberrations in a karyotype.

UnBalanced: Integer

Gets or sets the value indicating the amount of unbalanced structural aberrations in a karyotype.

Unclassified: Integer

Gets or sets the value indicating the amount of unclasified aberrations in a karyotype. "Unclassified" aberrations are those aberrations which could not be classified further, e.g. marker chromosomes, double minutes.

Methods

Public Sub add(ByRef SecondCKAS As CKAS)

Adds the property values of SecondCKAS to the property values of this instance.

Parameters

SecondCKAS: the CKAS object whose values are to be added to the values of this instance.

Public Sub addBalanced(ByVal AddValue As Integer)

Adds the amount given by AddValue to the Balanced constituent of the CKAS.

Parameters

AddValue: the value by which the Balanced constituent of the CKAS is to be increased.

Remarks

For decreasing, use a negative value of the AddValue parameter.

Public Sub addNumerical(ByVal AddValue As Integer)

Adds the amount given by AddValue to the Numerical constituent of the CKAS.

Parameters

AddValue: the value by which the Numerical constituent of the CKAS is to be increased.

Remarks

For decreasing, use a negative value of the AddValue parameter.

Public Sub addPloidy(ByVal AddValue As Integer)

Adds the amount given by AddValue to the Ploidy constituent of the CKAS.

Parameters

AddValue: the value by which the Ploidy constituent of the CKAS is to be increased.

Remarks

For decreasing, use a negative value of the AddValue parameter.

Public Sub addUnbalanced(ByVal AddValue As Integer)

Adds the amount given by AddValue to the Unbalanced constituent of the CKAS.

Parameters

AddValue: the value by which the Unbalanced constituent of the CKAS is to be increased.

Remarks

For decreasing, use a negative value of the AddValue parameter.

Public Sub addUnclassified(ByVal AddValue As Integer)

Adds the amount given by AddValue to the Unclassified constituent of the CKAS.

Parameters

AddValue: the value by which the Unclassified constituent of the CKAS is to be increased.

Remarks

For decreasing, use a negative value of the AddValue parameter.

Public Sub combine(ByRef SecondCKAS As CKAS)

Combines this instance with the SecondCKAS object by taking the maximum values for each property.

Parameters

SecondCKAS: the CKAS object which is to be combined with this instance.

Public Function clone() As Object Implements ICloneable.Clone

Returns a copy of the CKAS object.

Return Value

A copy of the CKAS object.

Implements

ICloneable.Clone

Remarks

The CKAS object does not contain data of reference type, cloning is done by copying all its class wide variables.

getOverallCKAS: Integer

Gets a value indicating the sum of all aberrations in a karyotype. The value is calculated on the fly when queried. It is the sum of all the constituents of the CKAS.

Interaction with other classes

Classes using CKAS

The CKAS class is part of the Karyotype and the Aberration objects.