Class Fusions

The class Fusions is a collection class for the Fusion class.

Overview

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

Fusions

New()

item(index: Integer): Fusion {read-only}

add(ByRef NewFusion: Fusion): void

addRange(ByRef NewFusions: Fusions): void

clone(): Object {Implements ICloneable.Clone}

contains(ByRef FusionToCheck: Fusion): Boolean

count(): Integer

getEnumerator(): IEnumerator {Implements IEnumerable.GetEnumerator}

toString(): String

toString(format: String): String

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 Fusions object.

Interfaces

ICloneable

is implemented with the clone function.

IEnumerable

is implemented with the getEnumerator function.

Enumerations

The class does not provide enumerations.

Properties

Default Public ReadOnly Property item(ByVal index As Integer) As Fusion

Returns the fusion object at the specified index.

Property Value

• the fusion object at the specified index.

Parameters

• index: the index of the fusion object to be retrieved. The index is zero-based.

Exceptions

• ArgumentOutOfRangeException: if index is less than 0 or if index is equal to or greater than count.

Remarks

• This property provides the ability to access a specific Fusion object in the Fusions object by using the following syntax: myFusions(index).

Methods

Public Sub add(ByRef NewFusion As Fusion)

Adds a reference to NewFusion to the internal collection.

Parameters

• NewFusion: a reference to the fusion object to be added.

Remarks

• If an equal fusion object is found in the collection, the previous object is cloned and its multiplicators are increased by the multiplicators of the NewFusion. Equality is determined with Fusion.equals(NewFusion, False).
• A reference is added to the collection, hence later changes to the original object may result in changes to the object in the collection. If such changes cannot be excluded and would cause problems, a clone should be added instead.

Public Sub addRange(ByRef NewFusions As Fusions)

Adds all the fusion objects contained in NewFusions to the internal collection using the add() function.

Parameters

• NewFusions: a reference to a fusions object whose fusion objects are to be added to the collection.

Remarks

• The function uses the add() function for each fusion object in NewFusions. For remarks on this process, see the add() function.

Public Function clone() As Object Implements ICloneable.Clone

Returns a deep copy of this fusions object. All its internal fusion objects are also copied.

Return Value

• a deep copy of this fusions object.

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. That is, all fusion objects in the internal collection will be cloned using Fusion.clone.

Public Function contains(ByRef FusionToCheck As Fusion) As Boolean

Checks if FusionToCheck can be found in the internal collection.

Return Value

• true, if FusionToCheck is in the internal collection.
• false, otherwise.

Parameters

• FusionToCheck: a reference to the Fusion object to locate in the Fusions object.

Remarks

• Equality is determined by Fusion.equals(NewFusion, False).

Public Function count() As Integer

Returns the number of fusion objects stored in this collection.

Return Value

• the number of fusion objects.

Remarks

• The index is zero-based, hence the maximum index is count - 1.

Public Function getEnumerator() As IEnumerator Implements IEnumerable.GetEnumerator

Returns an enumerator that can iterate through the collection of Fusion objects of this Fusions object.

Implements

• IEnumerable.GetEnumerator

Public Shadows Function toString() As String

Returns a textual representation of the Fusions object. The fusion objects are separated by commata.

Return Value

• a textual representation of the Fusions object.

Remarks

• The function actually passes through to toString("E") which calls Fusion.toString("E") for each fusion object.
• There is no general way for the description of fusions. See also the remarks at Fusion.toString(format).

Public Shadows Function toString(ByVal format As String) As String

Returns a textual representation of the Fusions object in the specified format. The fusion objects are separated by commata.

Return Value

• a textual representation of the Fusions object.

Parameters

• format: a short description of the format. For defined values, see Fusion.toString(format).

Remarks

• There is no general way for the description of fusions. See also the remarks at Fusion.toString(format).

Interaction with other classes

Classes using Fusions

A Fusions object is member of the Karyotype object and the Aberration object. In a Chromosome object, Fusions are calculated on request.

Classes used by Fusions

A Fusions object may contain 0, 1 or many Fusion objects.