revise menu structure and names of base conceptual objects

[epruesse]

The current menu structure and the names of the "things" that form the base conceptual objects in ARB are a bit counter intuitive.

Important: Update help files for each change to menu structure

See also #56

[epruesse]

My thoughts so far:

Species

The term is reflected in the database, which would be a good reason to keep it. It's not quite correct, though. We really talk about "individuals" or "sequence entries" as identified by accession (+start) here.

Sequence

Might be better to call this menu "alignment".

SAI

Filter would be an intuitive term. SAIs store per-column data, so "Columns" might work too.

Probes

Should go to Tools, I think.

Properties

Should become a sub menu in a new "Edit" menu.

[westram]

My thoughts so far:

Species

The term is reflected in the database, which would be a good reason to keep it. It's not quite correct, though. We really talk about "individuals" or "sequence entries" as identified by accession (+start) here.

As described ​here

Sequence

Might be better to call this menu "alignment".

ok for me.

SAI

Filter would be an intuitive term. SAIs store per-column data, so "Columns" might work too.

The term "Filter" is already used for filters - filters may be created using SAI. Every filter could be represented by an SAI, but not the other way round. "Columns" doesn't fit well. We could use "Column information" or "Column associated information" (short "CAI") or just stick with "SAI"

Probes

Should go to Tools, I think.

I don't agree. Probe stuff is one of ARBs key features, should stay on top.

Properties

Should become a sub menu in a new "Edit" menu.

I dont like the idea of an "Edit" menu. You could really put nearly every ARB_NT-menu-item into there, because they all somehow edit some data.

The menus we currently have in ARB_NT are object-based: Species, Sequence, SAI, Probes, Trees. Even "File" (which could become "Database").

"Tools" and "Properties" do not fit into that scheme. Several entries could be moved away from there, e.g.

• Name server admin → Species
• admin → File ("Database")
• Tree options / Tree colors & fonts → Tree
• WWW → Species

but some rest will remain and wont fit into any of the other menus. So i guess we'll always have some "Tools", "Esoteric" or "Other crap" menu left.

[epruesse]

Replying to westram:

As described ​here

Nice. Might help if that was more exposed somehow.

SAI

Filter would be an intuitive term. SAIs store per-column data, so "Columns" might work too.

The term "Filter" is already used for filters - filters may be created using SAI. Every filter could be represented by an SAI, but not the other way round. "Columns" doesn't fit well. We could use "Column information" or "Column associated information" (short "CAI") or just stick with "SAI"

That's a coders POV.

I've yet to hear a say "SAI". They all call those things filters (even the "ecoli filter" and the "helix filter"). The thinking is that e.g. "PVP Filter" is applied with "123456" sensitivity. So an SAI is a parametrizable filter. That a filter in the code is something built from parameters and an SAI isn't really relevant to the .

Probes

Should go to Tools, I think.

I don't agree. Probe stuff is one of ARBs key features, should stay on top.

Ok.

Properties

Should become a sub menu in a new "Edit" menu.

I dont like the idea of an "Edit" menu. You could really put nearly every ARB_NT-menu-item into there, because they all somehow edit some data.

Well, undo/redo we have, but we lack copy/paste and I'm not even sure what that would do. Select/Find? is also often found in Edit, so that's overlap with Species.

I just checked a few programs. FF, TB and Gimp have the "Preferences…" in Edit. Inkscape and Scribus keep them in File. LibreOffice? has them under Tools . Emacs … has them in ~/.emacs.

How about "File→ARB Preferences" then?

The menus we currently have in ARB_NT are object-based: Species, Sequence, SAI, Probes, Trees. Even "File" (which could become "Database").

I'd stick to file. It's what you expext as leftmost menu containing new/open/save/save-as, import/export, (print), quit.

"Tools" and "Properties" do not fit into that scheme. Several entries could be moved away from there, e.g.

• Name server admin → Species

So next to "sync IDs". Sounds right.

• admin → File ("Database")

That one contains only "re-repair ". Is that even necessary? What does it do?

• Tree options / Tree colors & fonts → Tree

Only if we elect to store those in the ARB file in the future. OpenOffice? used to not separate settings that were "per " clearly from what's "per file" — and that was a major pain.

• WWW → Species

but some rest will remain and wont fit into any of the other menus. So i guess we'll always have some "Tools", "Esoteric" or "Other crap" menu left.

Well. We could have File→Launch→{remote arb, second arb, xterm}. That'd leave the specieals. GDE is redundant anyway and the WL one — is it even needed anymore? Hide if $USER!=ludwig?

[westram]

Ticket retargeted after milestone deleted