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Class Marker

Overview

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

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()

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)

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)

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

ICloneable

Enumerations

Properties

CountMin As Integer

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

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

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

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

Return Value

• A copy of the Marker object.

Implements

• ICloneable.Clone

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

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

• ArgumentException: is thrown when obj cannot be cast into Marker type.

Implements

• IComparable.CompareTo

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

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

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