Class Marker

The class Marker describes a marker chromosome.

Overview

Marker
New()
New(Description: String)
New(MinCount: Integer, MaxCount: Integer, Optional MarkerNumber: Integer = 0)
CountMax: Integer
CountMin: Integer
MarkerNumber: Integer
Metaphases: Integer
clone(): Object {Implements ICloneable.Clone}
compareTo(obj: Object): Integer {Implements IComparable.CompareTo}
toString(): String

Programming Language

  • Microsoft Visual Basic .Net.

Availability

Constructors

Public Sub New()

Instantiates a new Marker object.

Parameters

  • None.

Remarks

  • Though the class allows for the instantiation of a marker object with this constructor and setting its properties later, this constructor is not meant for general use, but for COM compatibility only.

Public Sub New(ByVal Description As String)

Instantiates a new Marker object.

Parameters

  • Description: a textual description of the marker chromosome.

Exceptions

  • ArgumentException: If the textual description of the marker chromosome does not meet the pattern (regular expression) used to recognize the constituents of it, an ArgumentException containing a description of the problem is thrown.

Remarks

  • The regular expression used for the analysis of the marker element will also accept several types of notation which are not allowed in the ISCN, e.g. "2xmar" instead of "+2mar" or "+marx1-3" instead of "+1~3mar".

Examples

  • myMarker = new Marker("+mar") initializes a Marker object representing one marker chromosome.
  • myMarker = new Marker("+mar1x2") initializes a Marker object representing marker chromosome 1 which is duplicated.

Public Sub New(ByVal MinCount As Integer, ByVal MaxCount As Integer, Optional ByVal MarkerNumber As Integer = 0)

Instantiates a new Marker object.

Parameters

  • MinCount: the minimum copy number for the marker.
  • MaxCount: the maximum copy number for the marker.
  • MarkerNumber: the number for a clonally distinguishable marker chromsosome.

Remarks

  • Here, a marker object is instantiated with setting its properties instead of using a textual description.

Examples

  • myMarker = new Marker(1,1) initializes a Marker object representing one marker chromosome ("+mar").
  • myMarker = new Marker(2,2,1) initialies a Marker object representing marker chromosome 1 which is duplicated ("+mar1x2").

Interfaces

IComparable

is implemented with the compareTo function.

ICloneable

is implemented with the clone function.

Enumerations

The class does not provide enumeration.

Properties

CountMin As Integer

Gets or sets a value indicating the minimum copy number of this marker chromosome.

Property Value

  • a value indicating the minimum copy number of this marker chromosome.

Remarks

  • if no range was specified, CountMax and CountMin will return the same values.
  • if no copy number was specified, CountMax and CountMin will by default return 1.
  • when changing the CountMin property, no actions are taken to enforce that CountMin is not greater than CountMax.

CountMax As Integer

Gets or sets a value indicating the maximum copy number of this marker chromosome.

Property Value

  • a value indicating the maximum copy number of this marker chromosome.

Remarks

  • if no range was specified, CountMax and CountMin will return the same values.
  • if no copy number was specified, CountMax and CountMin will by default return 1.
  • when changing the CountMax property, no actions are taken to enforce that CountMax is not less than CountMin.

MarkerNumber As Integer

Gets or sets a value indicating the number of this (clonally distinguishable) marker chromosome.

Property Value

  • the number of the marker chromosome.
  • 0, if it is not a clonally distinguishable marker.

Remarks

  • Only clonally distinguishable markers are numbered with a digit following the "mar" symbol. If markers are not clonally distinguishable, the number is internally represented by a 0 which will not be added to the "mar" symbol.

Public Property Metaphases() As Integer

Gets or sets the number of metaphases / cells the marker chromosome was found in.

Property Value

  • the number of metaphases the marker chromosome was found in.

Remarks

  • The number of metaphases an abnormality was found in is an optional value according to the ISCN manual (chapter 11.1.6).
  • It follows after the aberration proper in square brackets, e.g. "+mar[7]".

Methods

Public Function clone() As Object Implements ICloneable.Clone

Returns a copy of the Marker object.

Return Value

  • A copy of the Marker object.

Implements

Remarks

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

Public Function compareTo(ByVal obj As Object) As Integer Implements IComparable.CompareTo

Compares this instance to a specified Marker object and returns an indication of their relative values. Only the numbering of the marker chromosome is compared.

Return Value

  • <0: This instance has a lower number.
  • 0: The Marker objects have the same number.
  • >0: This instance has a higher number.

Parameters

  • obj: the Marker to be compared with this Marker.

Exceptions

Implements

Remarks

  • Markers are compared with their number only, their copy number does not matter. If no number is given, the marker number is set to zero.
  • This compareTo method allows for ordering marker chromosomes as defined in ISCN 1995.

Public Shadows Function toString() As String

Returns a textual description of the Marker chromosome strictly fulfilling the specification of ISCN 1995.

Return Value

  • a textual description of the Marker chromosome.

Remarks

  • Even when the input description did not fulfill the ISCN specification, the value returned by this method will do.

Interaction with other classes

Classes using Marker

Marker objects are collected in the Markers object.

Transient use of Marker objects occurs in the Karyotype object while the karyotype is analysed.