Aside from other problems in the Cloning menu, Digest into Fragments refuses to work.

The dialog offers the restriction sites found and clearly documented, and when enzymes are moved to Add list, the report is always a failure, with the name of the restriction site NOT found although it is clearly present and UGENE offered it as an available site (with 1 cut) anyway.

I have attached 3 figures.  Fig 1 shows user interface before calling the Cloning->Digest in Fragments function.  Fig 2 shows the Digest into Fragments dialog clearly showing the enzymes available and selected.  Fig 3 shows the report of failure

I am using version 1.10.2.

It may be related to where the "enzyme" group is.  The enzymes list usually is shown under Auto-annotations object, an object which I don't want the enzymes group listed under.  It seems counter-intuitive to me in a user interface to have sequence objects in one document (gb file) having annotation objects in another document file, so I make a significant effort to make sure that any annotations relevant or belonging to a sequence object has a single annotations object located in that same document.  Even if I use the "Save a copy..." I make the annotations object part of the document so that the sequence object is independent of annotations found in another document (physically distinct file).

I guess the basis or reasons for having an annotations object part of a different document distinct from--

and thus possibly unavailable to

--the sequence object in the active document have not been explained to me.

The same is true for Auto-annotations.  If an annotation is worthy enough to become part of a feature of the sequence object, why have it in a temporary object like Auto-annotations?  It is counter-intuitive for me.

So I typically move (by mouse click-dragging) the individual enzymes to the annotations object that is part of the permanent document record.  If later, I don't want either the enzyme group or an individual enzyme within the group as part of the annotations record, it's easy enough to delete the group or the item in the group.

So my enzymes group within the annotation object that is part of the document that contains the sequence object will contain items that may the accumulated selections (enzymes) of different compressed bairoch files.  For instance, I have two bairoch files, each one containing the enzymes cutting unique sites in two popular commercial vectors (pUC19, pKLAC2), usually in the region of the vector serving as a multiple cloning site.  So my generated construct molecules will thus contain restriction sites that might be a mix of the sites in these vectors and thus a mix of selected enzymes in their bairoch files.

When I call the Cloning->Digest into Fragments command, the command interface appears to be reading the group 'enzyme' which is not under the Auto-annotations object, but rather the annotation object that is in the active document.  The enzyme group contains items that have been moved by mouse drag from Auto-annotations object, and and the auto-annotation interface might possibly have been disabled by unselecting all enzymes (with the alert/warning) given.  (NOTE:  another bug is the listing enzymes under Auto-annotations which are the same enzymes in an enzyme group under the annotation object of the permanent document:  although the cuts are same positions in the sequence, the Digest into Fragments interface lists them as two cuts.)

If the command interface requires that the enzymes group be under the Auto-annotations object and not elsewhere in an enzymes group in another annotation, then the list of available enzymes should not appear in the command dialog, although it does.

If I were to guess where the bug is, the command is looking for the Auto-annotations object containing the enzyme group with the named item in order to find the sequence position for cutting, and not finding it.  At the first error, it exits and generates the error report.

I will attempt to see if the portable package has this same bug.

I did not thoroughly detail the state of the application when I was making my pointer clicks and drags unfortunately.  I am usually always able  to find the workaround for the application anyway to work with all Cloning submenu's three commands, which is probably for me the best feature of UGENE.  (I guess those attending high throughput genomic DNA sequencers who might be using it to track overlaps and look for contigs might have a different opinion.)

After the bug fixes you cited/logged are done, we can see how much the interface has improved.  Other improvements (to the interface) will likely go into the feature wish list rather than the bug list.

I appreciate the guide's explanation of the application's coding strategy:  document (file object), objects belonging to a document (sequence, annotation, etc), and within the annotation object user-configurable groups possibly containing subgroups, all of which contain standard or customizable items in the annotation object.  A centralized database will be an interesting adaptation.