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Class QualitativeAberration

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()

Public Sub New(ByRef QualitativeString As String, Optional ByVal MayContainUncertainties As Boolean = True, Optional ByVal Resolution As Band.eResolutionLevel = Band.eResolutionLevel.ResolutionNone)

Parameters

• QualitativeString: a textual description of the qualitative aberration using SCCN
• MayContainUncertainties: indicates whether uncertainties may be present in the description, true by default
• Resolution: level of banding resolution met by this description

Exceptions

• ArgumentException: If the textual description of the qualitative aberration does not meet the patterns (regular expressions) used to recognize its constituents, an ArgumentException containing a description of the problem is thrown.

Remarks

• The input string corresponds to the string returned by the "toString()" method

Examples

• myQualAberr = New QualitativeAberration("t(9)(q34)") initializes a QuantitativeAberration object describing a translocation at band 9q34.

Interfaces

IComparable

ICloneable

Enumerations

Enum eAberrationType

Value	Text	Meaning
eWholeChromosomeChange	whc	a whole chromosome has been gained or lost
eAddition	add	addition
eDeletion	del	any type of deletion
eDeletionTerminal	delt	deletion of a terminal fragment
eDeletionNonTerminal	deln	non-terminal deletion = deletion of an interstitial fragment
eDerivation	der	formation of a derivative chromosome
eDicentric	dic	formation of a dicentric chromosome
eDuplication	dup	duplication of a fragment
eFision	fis	fision of a chromosome at the centromer
eHomogeneouslyStainingRegion	hsr	insertion of a homogeneously staining region
eIdem	idem	"idem" notation
eIsomerization	i	formation of an iso-chromosome
eIsoDerivation	ider	formation of an iso-derivative chromosome
eIsoDicentric	idic	formation of an iso-dicentric chromosome
eInsertion	ins	any type of insertion
eInsertionIntraChromosomal	insa	insertion between two chromosomes (donor<>acceptor)
eInsertionInterChromosomal	insr	insertion in one chromosome (donor=acceptor)
eInversion	inv	inversion
eQuadruplication	qdp	quadruplication
eRing	r	formation of a ring chromosome
eTranslocation	t	any type of translocation
eTranslocation2Chromosomes	tbc	translocation involving two chromosomes with two break points
eTranslocation2Chromosomes4Breaks	tbcqb	translocation involving two chromosomes with four break points
eTranslocation3Chromosomes	ttc	translocation involving three chromosomes with three break points
eTranslocation3Chromosomes6Breaks	ttchb	translocation involving three chromosomes with six break points
eTranslocation4Chromosomes	tqc	translocation involving four chromosomes
eTranslocation5Chromosomes	tpc	translocation involving five chromosomes
eTranslocation6Chromosomes	thc	translocation involving six chromosomes
eTranslocation7Chromosomes	tsc	translocation involving seven chromosomes
eTranslocation8Chromosomes	tnc	translocation involving eight chromosomes
eTranslocation9Chromosomes	toc	translocation involving nine chromosomes
eTranslocation10Chromosomes	tdc	translocation involving ten chromosomes
eTelomericAssociation	tas	telomeric association
eTricentric	trc	formation of a tricentric chromosome
eTriplication	trp	triplication
eUnknownAberration	ukn	any type of non identified aberration

Properties

Public Property AberrationType As eAberrationType

Property Value

• a value indicating the type of this qualitative aberration.

Remarks

• The aberration type is generally set at the initialization of a QualitativeAberration object. There is no need to change it later.
• The values are described in the eAberrationType enumeration.

Public Property Band() As Band

Property Value

• the band involved in this QualitativeAberration.

Remarks

• The band is generally set at the initialization of a QualitativeAberration object; there is no need to change it later.
• When the band property is changed, the Resolution property is reset.

Public Property Quantity As Integer

Property Value

• a value indicating how often this abberation has occured.

Remarks

• During the analysis of a single karyotype, an aberration is counted once only and quantity is not increased if the aberration is found again because it is assumed that it happened only once and then derivative chromosomes containing more aberrations were formed based on the original aberration.
• If more karyotypes are analysed, aberrations occured independently from each other, hence a quantity must be used. This is performed inside the classes of the library only, actually write access to this property outside the library is not necessary though granted.

Public Property Questionable() As Boolean

Property Value

• a value indicating whether the QualitativeAberration is deemed questionable.

Remarks

• This value is generally set at the initialization of a QualitativeAberration object. There is no need to change it later.

Public Property Resolution() As ChromosomeData.eResolutionLevel

Property Value

• the banding resolution met by this QualitativeAberration.

Remarks

• If the resolution level is eResolutionLevelNone, the value is calculated by calling Band.getMaximumResolution().
• When setting the value, no actions are taken to ensure that the Band really meets the new resolution.

Methods

Public Function clone() As Object Implements ICloneable.Clone

Return Value

• A deep copy of the QualitativeAberration object.

Implements

• ICloneable.Clone

Remarks

• The function calls Band.clone(), hence the clone contains a clone of the constituent Band object.

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

Return Value

• <-100: This QualitativeAberration resides on a chromosome with lower number.
• -100: Both QualitativeAberrations are on the same chromosome, but this one is closer to the p-terminus.
• -1>=x>=99: The QualitativeAberrations share the chromosomal break point, but have different types.
• 0: The QualitativeAberrations are equal.
• 1<=x<=99: The QualitativeAberrations share the chromosomal break point, but have different types.
• +100: Both QualitativeAberrations are on the same chromosome, but this one is closer to the q-terminus.
• >+100: This QualitativeAberration resides on a chromosome with higher number.

Parameters

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

Exceptions

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

Implements

• IComparable.CompareTo

Remarks

• QualitativeAberrations are ordered according to the place of their occurence on the chromosome. Hence, comparison is in the first step delegated to the band class. If two different aberrations took place at the same position, they are ordered according to the eAberrationType enumeration.
• Additional information from the return value indicates that two objects reside on different chromosomes (values greater than 100), on different locations of the same chromosome (100), or on the same point of a chromosome (values less than 100).

Public Overloads Function equals(ByRef SecondQualitativeAberration As QualitativeAberration) As Boolean

Return Value

• true, if both aberration occured at the same place and are of the same type.
• false, otherwise.

Parameters

• SecondQualitativeAberration: the qualitative aberration to compare with the current QualitativeAberration.

Remarks

• Two QualitativeAberration objects are deemed equal, if they conatin the same band, the same type of qualitative aberration, the same quantity, and the same questionability.

Public Function expandToResolution(ByRef Resolution As Band.eResolutionLevel) As QualitativeAberration

Return Value

• a QualitativeAberration corresponding to this aberration at the given resolution.

Parameters

• Resolution: the banding resolution to be met by the aberration

Remarks

• Uses the Band.expandToResolution function.

Public Function getGainsLossesStructs(ByVal Resolution As Band.eResolutionLevel) As GainsLossesStructs

Return Value

• a GainsLossesStructs object listing the bands at the given resolution level with the number of gains, losses and structural (qualitative) aberrations having occured there.

Parameters

• Resolution: the banding resolution to be met by the list.

Remarks

• This return type is also used by the QuantitativeAberration object. For compatibilty, it contains both gains and losses as well as structural aberrations.

Public Function hasUncertainty() As Boolean

Return Value

• a value indicating if the QualitativeAberrartion has some uncertainty.

Parameters

• None.

Remarks

• The QualitativeAberrartion has some uncertainty when its Band has some uncertainty (call to Band.hasUncertainty()) or when it is marked Questionable.

Public Shadows Function toString() As String

Return Value

• a textual description of the quantitative aberration using SCCN.

Remarks

• delegates to 'toString("S")'.

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

Return Value

• a textual description of the quantitative aberration using SCCN.

Parameters

• format: "S" causes the ISCN to be used for the aberration type, "E" the expanded notation.

Remarks

• If an unknown format is specified, the standard format will be used.
• For the "extended" version, see also Enum eAberrationType).

Public Shared Function translateAberrationTypeToString(ByVal Type As eAberrationType, Optional ByVal format As String = "S") As String

Return Value

• a string describing the type of aberration given by the enumeration value.

Parameters

• Type: the type of aberration given by the enumeration value.
• format: "S" (=standard) will return a value according to ISCN, whereas "E" (=expanded) will return a value which allows for more differentiation (see also Enum eAberrationType).

Remarks

• If the format is not specified or an unknown format is specified, the value returned will be in the standard ISCN format.

Public Shared Function translateStringToAberrationType(ByVal AberrationString As String) As eAberrationType

Return Value

• an enumeration value corresponding to the string describing the type of aberration.

Parameters

• AberrationString: a textual description of the aberration type, either in ISCN or expanded format.

Interaction with other classes

Classes using QualitativeAberration

It is transiently used by the Aberration class during the analysis of a single aberration. A more indeirect use is by the Karyotype class via the QualitativeAberrations class.

Classes used by QualitativeAberration

The GainLossStruct and GainsLossesStructs classes are used in a function returning the latter type.