Constraint Element Description

When describing a constraint element, the element_name consists of two parts separated by two hyphens:

part1–part2

Each part represents one of the algorithms the constraint is imposed on.

If the algorithm is presented as a single element in a schema (like ORF or Pattern), the algorithm’s part has the format:

algorithm_element_name.unit

If the algorithm is presented as two subelements in a schema (like Repeats or Primer), the algorithm’s part has the format:

algorithm_element_name.left

or:

algorithm_element_name.right

depending on the subelement the constraint is imposed on.

You should also specify the constraint type parameter (currently, the only available type is distance):

type: distance;

And specify one of the distance types, for example:

distance-type: end-to-start;

Example 1: The constraint is imposed on myORF and myPattern algorithm elements:

myORF.unit–myPattern.unit {

type: distance; distance-type: start-to-start;

Other parameters

}

Example 2: The constraint is imposed on the myORF algorithm element and the left myRepeats algorithm subelement:

myORF.unit–myRepeats.left {

type: distance; distance-type: start-to-end;

}

The available constraint elements are described in the Constraint Elements chapter.