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Class Markers

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()

Interfaces

ICloneable

IEnumerable

Enumerations

Properties

Public ReadOnly Property CountMax() As Integer

Property Value

• a value indicating the sum of maximum copy numbers of the marker chromosomes in this collection.

Remarks

• CountMax and CountMin are increased whenever a Marker object is added to the collection.

Public ReadOnly Property CountMin() As Integer

Property Value

• a value indicating the sum of minimum copy numbers of the marker chromosomes in this collection.

Remarks

• CountMax and CountMin are increased whenever a Marker object is added to the collection.

Default Public ReadOnly Property item(ByVal Index As Integer) As Marker

Property Value

• the marker chromosome at the specified position of the collection.

Parameters

• 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 Marker object in the Markers object by using the following syntax: myMarkers(index).
• The property is read-only.

Methods

Public Sub add(ByRef AdditionalMarker As Marker)

Return Value

• None.

Parameters

• AdditionalMarker: a reference to the Marker to be added to the collection.

Exceptions

• ArgumentNullException: the AdditionalMarker to be added must not be a null reference.

Remarks

• The values for minimum copies and maximum copies of markers in the collection is increased.
• A reference to the AdditionalMarker is added to the collection, not a clone of it.

Public Function clone() As Object Implements ICloneable.Clone

Return Value

• A deep copy of the Markers object.

Parameters

• None.

Implements

• ICloneable.Clone

Remarks

• A deep copy copies not only the elements of the internal collection, but it does also copy the objects that the references refer to; i.e. the Marker objects contained are also cloned using Marker.clone().

Public Function count() As Integer

Public Function GetEnumerator() As IEnumerator Implements IEnumerable.GetEnumerator

Implements

• IEnumerable.GetEnumerator

Remarks

• The underlying collection is sorted first.

Public Function indexOf(ByRef MarkerToFind As Marker) As Integer

Return Value

• the index of the specified marker object in the collection.
• -1, if the specified marker is not contained in the collection.

Parameters

• MarkerToFind: a reference to the marker object to be located in the internal colelction.

Remarks

• Though this function is similar to the indexOf() function of collection classes, it does not implement it since the parameter is passed by reference for performance reasons.

Public Sub removeAt(ByVal Index As Integer)

Return Value

• None.

Parameters

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

Exceptions

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

Remarks

• The elements that follow the removed element move up to occupy the vacated spot. The indexes of the elements that are moved are also updated.
• Internally, the function calls ArrayList.removeAt().

Public Overloads Overrides Function toString() As String

Return Value

• a textual description of the Marker chromosomes.

Remarks

• delegates to toString("L").

Public Overloads Overrides Function toString(format As String) As String

Return Value

• a textual description of the Marker chromosomes.

Parameters

• format: "S" means short format. Here, no distinction between individually distinguishable marker chromosomes is made and a representation showing the added values of copy numbers is given.

"L" means long format (default). Here, markers are sorted according to their numbers and are written in a comma separated list. Marker.toString() is called for each Marker object.

Remarks

• If an unknown format is specified, the long format will be taken by default.

Interaction with other classes

Classes using Markers

Classes used by Markers