Resources
Resources data are stored in an XML file, "Chromosomes.xml". It contains
a description of a full haploid set of chromosome of the species of interest
at relevant banding resultions.
The file included with the ISCNAnalyser describes human chromosomes.
For the analysis of other species, this file may be replaced with the respective
chromosome defintions of the species of interest in the same data format.
Note that the description of chromosomal bands must be compatible with
the description of human chromosomes (e.g. gorilla, chimpanzee). Note that
the description of the all acrocentric chromosomes of mice is not compatible
and cannot be analysed with this software.
It is a hierarchical description of the following units:
Programming Language
-
Microsoft Visual Basic .Net.
Availability
General data
General data provide information on the Genus whose chromosomes are describes
here, a default drawing order, the maximum height of a chromosome in pixels,
the maximum number of a chromosome and the number of chromosomes in an
haploid set.
| Name |
Meaning |
Type |
Amount |
| Genus |
name of the genus whose chrosomes are
described here. |
String |
1 |
| DrawSequence |
a comma separated list of chromosome numbers
showing the sequence in which chromosomes are to be drawn by default. |
String |
1 |
| MAX_CHROMOSOME_HEIGHT |
the height of the largest chromosome in
pixels when drawn at scale 1. A bigger than the actual value may be given,
but that would reduce performance. |
Integer |
1 |
| MAX_CHROMOSOME_NUMBER |
with the exception of the sex chromosomes,
chromosomes are numbered with numbers. This field contains the maximum
number given to a chromosome. |
Integer |
1 |
| CHROMOSOMES_PER_HAPLOID_SET |
the amount of chromosomes in an haploid
set. |
Integer |
1 |
| Chromosome |
description of a chromosome (see below) |
|
0, 1, or many |
Chromosome
A chromosome is identified by its number. A default color for drawing in
color is provided. A chromosome has 1 or 2 arms.
| Name |
Meaning |
Type |
Amount |
| Number |
number of the chrosome described here. |
Integer, X, Y |
1 |
| DefaultColor |
default color when drawing the chromosome
(must be a valid color name from the System.Drawing.KnownColor
collection). |
String |
1 |
| Arm |
description of a chromosome arm (see below) |
|
1 or 2 |
Arm
A chromosomal arm belongs to a chromosome and is identified by its full
name. The band number of its terminus is denoted at maximum resolution.
| Name |
Meaning |
Type |
Amount |
| Parentt |
number of the chrosome this arm belongs
to. |
Integer, X, Y |
1 |
| FullName |
the full name of the arm (e.g. "1p"). |
String |
1 |
| Name |
name of the arm only (e.g. "p") |
"p" or "q" |
1 |
| Terminus |
band number of the terminus at maximum
resolution (e.g. "3633" for p arm of #1) |
String |
1 |
| Landmark |
description of a landmark on the chromosomal
arm (see below) |
|
1 or many |
Landmark
A landmark describes a larger region on a chromosomal arm.
| Name |
Meaning |
Type |
Amount |
| Parentt |
the FullName of the arm the landmark belongs
to. |
String |
1 |
| FullName |
the full name of the landmark (e.g. "1p3"). |
String |
1 |
| Number |
the number only of the landmark (e.g.
"3" for landmark "1p3") |
String (Length 1) |
1 |
| Band |
description of a band belonging to this
landmark (see below). |
|
1 or many |
Band
A band describes a chromosomal band. Apart from its name and its place
in the hierarchical structure, information is provided about the banding
resolution satisfied with this band number and data for drawing.
| Name |
Meaning |
Type |
Amount |
| Parentt |
the FullName of the landmark the band
belongs to. |
String |
1 |
| FullName |
the full name of the band (e.g. "1p36"). |
String |
1 |
| Number |
the number only of the band (e.g. "36"
for landmark "1p36"). |
String (Length 2) |
1 |
| SatisfiesResolution |
the banding resolution satisfied with
this band number ("0" if less than 400 bphs). |
Integer |
1 |
| Height |
the height of the band in pixels. |
Integer |
1 |
| Paint |
the style for drawing the band. |
PaintStyle |
1 |
| SubBand |
description of a sub-band belonging to
this band (see below). |
|
0 or many |
PaintStyle
PaintStyle is an enumeration of styles for drawing a chromosomal band.
| Name |
Meaning |
| full |
all the area of the band is filled with
color. |
| dark |
the area of the band is filled with a
hatched pattern of thick lines from upper right to lower left. |
| light |
the area of the band is filled with a
hatched pattern of thin lines from upper left to lower right. |
| transparent |
the area of the band remains transparent,
only the conturs are drawn. |
| none |
the paint style for the band is not defined. |
Subband
At higher resolution, bands may resolve into subbands. The properties are
almost the same as with band.
| Name |
Meaning |
Type |
Amount |
| Parentt |
the FullName of the band or subband the
subband belongs to. |
String |
1 |
| FullName |
the full name of the band (e.g. "1p363"). |
String |
1 |
| Number |
the number only of the subband (e.g. "363"
for landmark "1p363"). |
String (Length 3 or more) |
1 |
| SatisfiesResolution |
the banding resolution satisfied with
this subband number ("0" if less than 400 bphs). |
Integer |
1 |
| Height |
the height of the subband in pixels. |
Integer |
1 |
| Paint |
the style for drawing the subband. |
PaintStyle |
1 |
| SubBand |
description of a sub-band belonging to
this subband. |
|
0 or many |
