Many documents in Geneious Prime are the output of an operation run on a set of input documents. The input documents of the operation are known as the parents of the output, and the output documents the descendants (or children) of the input. Those parent documents may themselves be the descendants of other documents, each with their own parents, and so on. In many situations it is useful to preserve this hierarchy, so that future alterations, for example the re-calling of a base, or the addition of a new annotation, can be transferred downstream to the molecules aﬀected by this change in a parent.
An active link between a child and its parents means that when you modify any of the parent documents, you will be given the choice of propagating these changes to the child. When this modiﬁcation aﬀects a part of the parent involved in creating the child, the change will be immediately visible in the child. Modiﬁcations include things like editing the residues of a sequence, adding new annotations, or changing the meta-data associated with the document.
Propagating a change to a parent document causes Geneious to rerun every operation that links that parent actively to one or more child documents, with the altered parent document (and any other parents) as input. Geneious stores the options that the operation was originally run with so that it can reproduce the original operation’s conditions exactly, and afterwards matches up the newly regenerated child documents with any former children, and replace their contents where possible.
Occasionally, one or more of the parent documents has been altered to a point where an operation can no longer be rerun, or a necessary parent document is inaccessible. In this case, Geneious will inform you of the failure, and attempt to be as speciﬁc as possible about the cause of the failure (Figure 6.1 )
Inactive links do not propagate changes from parent to child. Inactive links are created in two diﬀerent ways; ﬁrstly, when you choose not to propagate changes, that active link becomes temporarily inactive. Secondly, if an operation does not support creation of active links, or was told not to create them, all links between its parents and children will be permanently inactive. All operations in Geneious Prime at least create inactive links.
The following operations in Geneious Prime can produce actively linked documents:
Note: Extract and Translate will not create active links by default. To do so, you must select the Actively link source and extracted documents checkbox in the relevant dialog (see Figure 6.2 ), otherwise they will be created with permanently inactive links.