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Class Complex Karyotype Aberration Score

Class ChromosomeData

The class ChromosomeData provides information on the chromosome set used for the analysis and some functions for general use with chromosomes.

Overview

Constructors
Interfaces
Enumerations
Properties
Methods
Interaction with other classes
Internal Views

ChromosomeData

---

MapViewer

checkBandExistence(Band: Band): Boolean

getBandSet(Resolution: eResolutionLevel, ByRef BandSet: Band(), ByRef BandNames: String())

getBandsForFragment(Fragment: Fragment, Resolution: eResolutionLevel): Bands

getColorForChromosome(Chromosome: String): System.Drawing.Color

getDefaultDrawSequence(): String

getInstallDir(): String

getMapViewLink(Band: Band): String

getMapViewURL(Band: Band): String

getMaximumChromosomeHeight(): Integer

getMaximumChromosomeNumber(): Integer

getMaximumResolutionForBand(Chromosome: String, BandNumber: String): eResolutionLevel

resetChromosomeUserColor(): Void

setChromosomeUserColor(Chromosome: String, ByRef UserColor: System.Drawing.Color)

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

The class does not have any constructor. All its function are class methods, not instance methods, thus no instance of this class is needed.

Interfaces

This class does not implement an interface.

Enumerations

The class provides enumerations for the description of the resolution of the chromosome and for properties needed for drawing a chromosome.

Enum eResolutionLevel

This enumeration describes the level of resolution of chromosome banding.

Value	Meaning
ResolutionNone	The resolution could not be determined or has not yet been determined.
ResolutionChromosome	Only the chromosome number is given.
ResolutionArm	Chromosome and arm are known.
Resolution1Digit	Chromosome, arm and 1 digit are known.
Resolution2Digit	Chromosome, arm and 2 digits are known.
Resolution400Bands	The band can be detected at a resolution of 400 band per haploid set.
Resolution500Bands	The band can be detected at a resolution of 500 band per haploid set.
Resolution550Bands	The band can be detected at a resolution of 550 band per haploid set.
Resolution800Bands	The band can be detected at a resolution of 800 band per haploid set.

Enum ePaintWidth

This enumeration describes the width a chromosome band is drawn with.
Note: There is no value for a centromer or a band close to a centromer because centromers can be detected with a logic of its own.

Value	Meaning
PaintWidthNormal	a "normal" band drawn at full width
PaintWidthSatellite	a satellite band drawn with diminished width

Enum ePaintStyle

This enumeration describes the style a chromosome band is drawn with.

Value	Meaning
PaintStyleNone	The style is unknown.
PaintStyleTransparent	Only the circumference of the band is drawn, its area is transparent. This corresponds to a Giemsa negative band.
PaintStyleLight	The circumference of the band is drawn and its area is filled with a pattern of lines on a diagonal from upper left to lower right. This corresponds to a heterochromatic regions which stains a little.
PaintStyleDark	The circumference of the band is drawn and its area is filled with a pattern of thick lines close to each other on a diagonal from upper right to lower left. This corresponds to a heterochromatic regions which stains strongly.
PaintStyleFull	The band is filled fully. This corresponds to a Giemsa positive band.
PaintStyleWeak	The band is filled fully, but the color is reduced to a light grey (or similar). This corresponds to a band which is only slightly Giemsa positive.
PaintStyleMiddle	The band is filled fully, but the color is reduced to a medium grey (or similar). This corresponds to a band which is Giemsa positive at a reduced level.
PaintStyleStrong	The band is filled fully, but the color is reduced to a dark grey (or similar). This corresponds to a band which is strongly Giemsa positive, but not yet fully dark.

Properties

The class provides one property:

Public Shared Property MapViewer() As String

Gets or sets the external resource with which chromosomal bands are linked.

Property Value

an external resource chromosomal bands are linked with.

Parameter

None.

Remarks

Possible values are "NCBI" for the map viewer at the National Center for Biotechnology Information and "Ensemble" for the map viewer of the Ensembl group (a joint project between EMBL - EBI and the Sanger Institute).

Internal Processing

If links change, or another map viewer is to be integrated, the getMapViewURL function must be adjusted.

Methods

All methods of the class are class methods, i.e. they are marked "shared".

Public Shared Function checkBandExistence(ByRef Band As Band) As Boolean

Checks if a band number with which Band is described was defined in the chromosome set given in the resources file.

Return Value

true: the band exists.
false: the band does not exist.

Parameters

Band: a reference to a Band object describing the band number to be checked for proper existence.

Remarks

This function does not raise an exception if the Band was not found. If an exception in such cases is desired, use the Band.checkExistence() function instead.

Examples

With the standard set of human chromosomes, checkBandExistence returns true for 9q34.12, and false for 9q34.21, resp.

Public Shared Sub getBandSet(ByVal Resolution As eResolutionLevel, ByRef BandSet As Band(), ByRef BandNames As String())

Provides an array of Band objects and an array of String with the band names of all bands visible at the given banding resolution.

Return Value

there is no direct return value, but two arrays are passed by reference and changed within the function.

Parameters

Resolution: the desired banding resolution. Its values are defined in the eResolutionLevel enumeration.
BandSet: a reference to an array of Band objects. This array will be filled with the band objects of the desired resolution in due order.
BandNames: a reference to an array of string. This array will be filled with the names of the bands of the desired resolution in due order.

Remarks

The arrays are calculated for each resolution only once and stored in class variables.
Be careful when changing the properties of a band in a BandSet returned from this function: this will also change the original Band object. Using the Band.clone() function could circumvent problems arising therefrom.

Public Shared Function getBandsForFragment(ByRef Fragment As Fragment, ByVal Resolution As eResolutionLevel) As Bands

Returns a Bands object containing all the bands residing on the Fragment at the given banding resolution.

Return Value

the bands contained in the fragment.

Parameters

Fragment: a reference to a Fragment object whose bands are to be determined.
Resolution: the desired banding resolution. Its values are defined in the eResolutionLevel enumeration.

Exceptions

Exception: the bands must exist.

Internals

The function gets a BandSet with all chromosomal bands at the desired resolution level and searches for band names starting with or equalling the names of the start and end band of the fragment. Bands from the BandSet are then copied into the returned Bands object.
For start and end bands, clones are established and there broken level set to the broken levels of the bands in Fragment.

Public Shared Function getColorForChromosome(ByVal Chromosome As String) As System.Drawing.Color

Returns the color to be used for drawing the chromosome. It may have been modified by the user with the setChromosomeUserColor function; for getting the default color, the user settings may be invalidated using the resetChromosomeUserColor function.

Return Value

the color to be used for drawing the chromosome.

Parameters

Chromosome: The number of the chromosome.

Remarks

If no chromosome number is given, returns "gray".
Default colors are defined in the resources file.

Examples

For chromosome # 13, getColorForChromosome originally returns "DarkOrange".

Internals

Internally, two hashtables storing the chromosome colors exist. The default table is loaded from the resources file and remains unchanged. The "user" table is originally copied from the default table and may be changed or re-copied from the default. The function always looks into the "user" table.

Public Shared Function getDefaultDrawSequence() As String

Returns the sequence in which chromosomes are to be drawn when a set of all chromosomes is to be displayed.

Return Value

a string showing the sequence in which chromosomes are to be drawn.

Remarks

Chromosome numbers are delimited by commata (",").
Line breaks are shown with the symbol "BR".
The default is defined in the resources file.

Examples

Within the standard CyDAS package, the chromosomes are defined to be drawn in three lines as follows: "1,2,3,4,5,6,7,X,BR,8,9,10,11,12,13,14,15,BR,16,17,18,19,20,21,22,Y". This sequence shows the same number of chromosomes in every line and an order of descending lenght, thus providing a good use of space.

Public Shared Function getInstallDir() As String

Shows where the ISCNAnalyser.dll was installed.

Return Value

The directory where the ISCNAnalyser.dll was installed.

Internals

The installation directory is internally required for finding the resources file.
The ISCNAnalyser dll can be registered; then its location can be queried from the registry.
When debugging the program, the dll is registered during the build action in the bin/ directory of the project folder. Here, setting the gbUseDefaultLocation variable to true and hard coding the location in LoadResources helps circumvent some problems.
Also when using the dll on a web server (.aspx), the gbUseDefaultLocation variable should be set to true and the location in LoadResources hard coded.

Public Shared Function getMapViewLink(ByRef Band As Band) As String

Returns HTML code showing the band number in exact notation linked with map viewer information for that band.

Parameters

Band: a reference to a Band object describing the band whose information is to be obtained from the map viewer.

Remarks

The method does not at all check the band for existence. If a band does not exist, the map viewer will show an error when the link is followed.
The band is expected to be a band on a human chromosome. The link URL is hard coded.
Also hard coded is the target (new browser window) and a javascript function "getLink(document,this)" which can be used for other programming purposes.
For getting the URL only, use the getMapViewURL function instead.
The type of map viewer is set in the MapViewer property.

Examples

With band "2q21", getMapViewLink returns for the NCBI map viewer "<a href="http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?TAXID=9606&CHR=2&MAPS=ideogr%5B2pter%3A2qter%5D%2CugHs%2Cmit%5B1.00%3A243415958.00%5D%2Cgenes%5B1.00%3A243415958.00%5D&BEG=2q21&END= 2q21&thmb=on" target="_blank" onclick="getLink(document,this)">2q21</a>"

Public Shared Function getMapViewURL(ByRef Band As Band) As String

Retuns a URL pointing to a map viewer information for that band.

Parameters

Band: a reference to a Band object describing the band whose information is to be obtained from the map viewer.

Remarks

The method does not at all check the band for existence. If a band does not exist, the map viewer will show an error when the link is followed.
The band is expected to be a band on a human chromosome. The link URL is hard coded.
If HTML code linking the number of the band with the URL is required, use the getMapViewLink function instead.
The type of map viewer is set in the MapViewer property.

Examples

With band "2q21", getMapViewLink returns for the NCBI map viewer "http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?TAXID=9606&CHR=2&MAPS=ideogr%5B2pter%3A2qter%5D%2CugHs%2Cmit%5B1.00%3A243415958.00%5D%2Cgenes%5B1.00%3A243415958.00%5D&BEG=2q21&END= 2q21&thmb=on"

Public Shared Function getMaximumChromosomeHeight() As Integer

Returns the maximum height of a chromosome ideogram in pixels.

Return Value

the maximum height of a chromosome ideogram.

Remarks

The maximum chromosome height is defined in the resources file. It is used for pre-sizing the bitmaps of chromosome ideograms.

Examples

Within the standard CyDAS package, getMaximumChromosomeHeight returns 1650.

Public Shared Function getMaximumChromosomeNumber() As Integer

Returns the maximum number a chromosome can have.

Return Value

the maximum number of a chromosome.

Remarks

The maximum number of a chromosome is defined in the resources file. With distinct species, distinct maximum numbers are likely to be needed.
It is not the number of chromosomes in a normal karyotype of that species.
Besides chromosomes with numbers starting from 1, "X" and "Y" are valid for denoting chromosomes.

Examples

Within the standard CyDAS package, the resource file defines human chromosomes, and thus getMaximumChromosomeNumber returns 22.

Public Shared Function getMaximumResolutionForBand(ByVal Chromosome As String, ByVal BandNumber As String) As eResolutionLevel

Returns the maximum value of the ResolutionLevel which the band described by its chromosome and band number fulfills.

Parameters

Chromosome: the number of the chromosome.
BandNumber: the number of the band (including arm, but without the chromosome number)

Remarks

Values for the resolution level are defined in the enumeration eResolutionLevel.

Examples

With chromosome 13 and band number q14, getMaximumResolutionForBand returns "Resolution400Bands".

Public Shared Sub resetChromosomeUserColor()

Resets the colors used for drawing chromosome ideograms to the default colors.

Remarks

The colors can be set using the setChromosomeUserColor function and can be retrieved with the getColorForChromosome function. More information about colors can be found among the remarks at getColorForChromosome.

Public Shared Sub setChromosomeUserColor(ByVal Chromosome As String, ByRef UserColor As System.Drawing.Color)

Changes the color to be used for drawing an ideogram of the respective chromosome.

Parameters

Chromosome: the number of the chromosome whose number is to be changed.
UserColor: the color to be used for the ideogram of that chromosome.

Remarks

The colors can be reset to the deafult values using the resetChromosomeUserColor function and can be retrieved with the getColorForChromosome function. More information about colors can be found among the remarks at getColorForChromosome.

Interaction with other classes

Classes using ChromosomeData

The ChromosomeData class is used by Band objects to query their existence and paint data, by Fragment objects to determine contained bands, and by the CyDASGraphics class.

Classes used by ChromosomeData

The ChromosomeData class itself makes use of some other classes of the CyDAS project, but always transiently only.

Internal Views

All functions start with a call to the init() function which determines if the resources were already loaded from the resources file, and if necessary loads them. The data will then be held in class variables in order to speed up the functions.