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Analysis is performed by a series of steps and is aborted when an error was encountered. In case of such an error, a description of the error will be placed into ErrorDescription property (variable: mstrError) of the object.
This parser is not a strict parser. It will accept some deviations from the standard ISCN.
Since the singular items in the formula are separated by a comma, the first step of analysis is splitting the ISCN formula into an array of its elements. Leading and trailing spaces are removed from each element.
Elements are then analysed in a defined series: first, some information is taken from the last elements, then chromosome count and sex chromosomes from the first elements, remaining elements are aberrations and analysed by the Aberration class. Afterwards, the karyotype object sums up the information from its aberration objects.
The last element possible is "[cp]" denoting that the karyotype is composite; the number of metaphases may be included (results are stored in the variables mbooCompositeKaryotype and mnCloneSize, resp.).
An "inc" statement (meaning incomplete information; also "[inc]" is accepted) may come before the [cp] statement (the result is stored in the variable mbooIncompleteKaryotype).
Analysis is performed by comparing the last non-empty element of the array with an appropriate pattern (a Perl regular expression). In case of a match, the matched region is removed from the element.
It is stored in moDMin. The number of dmin is added to the "unclassified" section of the CKAS variable moCKAS.
The marker object performs analysis of this marker chromosome (see also: Analysis of Marker Chromosomes). It is then added to the collection of marker chromosome mcMarkers.
If the last element did no more match the "mar" pattern, the total number of marker chromosomes is added to the "unclassified" section of the CKAS variable moCKAS.
An element is thought to describe such a ring chromosome, if it contains an "r" which may follow a combination of the characters "+-~x?" and numbers and spaces or which may be followed by a combination of the characters "c-~x?" and numbers and spaces. The element must not contain other characters.
A Ring object is instantiated with the element. It performs analysis of this ring shaped marker chromosome (see also: Analysis of Ring Shaped Marker Chromosomes). It is then added to the collection of ring shaped marker chromosomes mcRings.
If the last element did no more match the above pattern, the total number of ring shaped marker chromosomes is added to the "unclassified" section of the CKAS variable moCKAS.
The minimum and maximum numbers of chromosomes are stored in mnChromosomeCount and mnChromosomeCountMax, the ploidy level in mnPloidyLevel. If no ploidy level was given in the chromosome count field, ploidy is calculated by dividing the arithmetic medium of chromosome count by 23.
The sex chromosome field may consist of the characters "XYc?" only. If the element contains any other character, it is treated as an aberration (see below).
An element may contain two aberrations linked with "or". If the sequence "or" is found, the element is split into its two aberrations which are both marked questionable (i.e. with a leading question mark).
For an aberration, only digits, "normal" characters, and "+-x~();" are acceptable.
Each aberration is then passed into the constructor of the Aberration class. The aberration object then analyses this aberration (see Analysis of Aberrations). In case of derivative chromosomes (aberrations starting with "der" or "ider"), the fragment composition similiar to the ISCN detailed notation must be calculated (see Calculation of Derivative Chromosomes).
If the aberration was found valid, its aberration type is queried. If it is an "idem" aberration, it is stored in moIdemAberration, else it is added to the collection of aberrations mcAberrations.
In contrast to the ISCN manual, any arbitrary order of aberrations in the aberration section of the formula is accepted.
The collection of aberrations is searched for non-expanded aberrations ("isExpanded" property). Such aberrations receive their break points from other aberrations of the karyotype by the help of string comparison. An expanded aberration replaces then the original aberration.
Since with CKAS, descriptions of derivative chromosomes have to reveal their constituting aberrations, but duplicates of the aberrations must be recognised, the aberrations are added to the collection with the CombineMultiplicators parameter set to true.
The break points collection (type Bands) gets its content from mcAberrations. At this point, all break points can be checked for their existence on (human) chromosomes: non-existent break points - likely to be due to typos - are a common problem.
Fusions (also called "junctions" in the website of NCBI) and structural aberrations are also calculated from mcAberrations.
While quantitative aberrations can be easily summed up for non-der-aberrations, der-aberrations need balancing. E.g. with "46,XY,der(4)t(4;9)(p14;p21),der(9)t(4;9)(p14;p21)t(9;22)(q34;q11),der(22)t(9;22)(q34;q11)", all three translocations are balanced, but for each single derivative chromosome gains and losses were found.
If no error was encountered, the ISCN formula is rebuild from the elements and the karyotype is marked valid.