Target part order list file

Note: The content on this page is not complete, and (for the time being) is merely meant to supplement this deprecated j5 manual page.

With the implementation of support for EMPTY parts in j5 v3.4.0, in the Part Name column field, if "EMPTY" is listed, the part will be treated as an EMPTY part.

What are EMPTY parts?

In a single construct design (i.e. in non-combinatorial designs), target parts named "EMPTY" will effectively be ignored. In other words, a single construct design target part order list file with a row designating an "EMPTY" part is equivalent to the same file with that row removed. Or put yet another way, in the assembled construct, the part preceding the EMPTY part will be followed immediately by the part following the EMPTY part.

Note: "EMPTY" parts do not need to be defined in the parts list input file.

Note: for rows with "EMPTY" in the first Part Name column, all other columns are ignored (e.g. it is not important or necessary to indicate if the EMPTY part is to be placed in the forward or reverse direction).

Note: EMPTY parts are removed/ignored prior to verifying Eugene rules. This means that any Eugene rules referencing an "EMPTY" part will be ignored.

In a combinatorial design, if a target part bin exclusively contains EMPTY parts, that bin will effectively be ignored. This is analogous (bins to parts) to the above explained for EMPTY parts in a single construct design.

In a combinatorial design, if a particular target part bin contains (but not exclusively) one or more EMPTY parts, j5 will attempt to achieve full combinatorial assembly piece re-use (or at least maximize assembly piece re-use) by (where possible) forcing overhangs/overlaps to be contained exclusively upstream or downstream of this particular bin.

Here is an example CSV file that contains EMPTY parts. It is in the combinatorial mode format, but it should also make the single construct mode clear as well. It has examples of EMPTY target parts, and target bins that contain no EMPTY parts, mixtures of EMPTY and non-EMPTY (i.e. normal) parts, and exclusively EMPTY parts.

Note: In this example file, a target bin is named (>Bin column field) ">EMPTY", but this specific bin name is not treated differently than any other bin name.