History

The History tab in the sidebar lists every change made to the open document since it was opened, newest first, and takes the document back to any of them. It is the same history the Undo and Redo buttons walk through one step at a time, laid out so a whole editing session can be read at once.

Made from

A document that came out of a simulated reaction, such as a fragment, a PCR product, a ligation or an assembly (see What a product was made from), has a Made from section at the top of the tab. Collapsed, it says how the document was made (_Ligation of 2 parts, circular_). Expanded, it shows the tree. The document is at the top, and under each molecule are the ones it was made from, then the ones those were made from, and so on. Each molecule shows:

• its name, and how it was made: _Digest with BamHI and EcoRI · 397–3,082_, _PCR with Forward and Reverse · proofreading_, with the primers under it;
• its length, topology and the short form of its checksum;
• Open, when this browser still holds that exact molecule: in an open tab, which it brings to the front, or among the documents kept in this browser, which it opens. A molecule is matched by its checksum, not its name, so a file edited since it was used does not count, and a renamed one still does. Otherwise it says not in this browser.

Under the tree, Protocol… builds a page for the bench from it: see Protocol for a product.

At the top, this document means the document is still the molecule that was made; edited since means its bases have changed since. The list below says how.

The section only appears for a document made in PlasmidPop, read from a file that carries the PlasmidPop-made-from: block, or opened from a SnapGene .dna file that carries SnapGene's own history. SnapGene's tree reads the same way, with two differences: it keeps no checksums, so every molecule in it says not in this browser, and what it did that PlasmidPop does not — flip, newFileFromSelection, changeMethylation — is shown under SnapGene's own word for it. Everything can also be used with the keyboard: Tab reaches the section and each Open, and Enter or Space expands and collapses it.

Reading the list

Each row is one recorded change:

• the step number, counting from the state the document started in;
• what was done, in the same words the Undo tooltip uses: _Insert 3 bases_, _Paste 120 bases_, _Edit feature_, _Set origin_, _Make circular_;
• the time the change was made;
• what it did to the document: +12 bp, −3 bp, +1 feature, circular or linear. A change that moves none of those, such as a rename, has nothing to show here.

The current state is highlighted. Changes that have been undone are greyed and sit above it; they stay until a new change replaces them.

The last row is where the history starts: Opened document for a file, or New document for one started from scratch, with the size and feature count it had then. Only the most recent 200 changes are kept, so in a long session the oldest row reads Oldest kept state instead.

A named state is kept even then. When its step goes past the 200, it moves to Named states from before the oldest kept below the list, with its name, what the step was and when. Undo cannot reach it any more, but clicking it brings it back as a change of its own (_Back to “name”_, which Undo takes back as usual), and its ⋯ menu can rename it, mark changes since it, or Forget it.

Runs of typing are one step

Typing base after base is one thing you did, so it is recorded as one change: a row that reads _Insert 12 bases_, and one Ctrl+Z that takes all twelve back. Holding Backspace or Delete merges the same way.

A run ends, and the next keystroke starts a fresh row, when you

• pause for two seconds or more,
• move the caret or click elsewhere,
• reach 60 bases in one run,
• undo, redo or jump to another state,
• download the document, so the version you have a file of stays a row you can return to, or
• choose Mark from here in the Edits menu.

Switching between typing, Backspace and Delete also starts a new row, and a paste is always a row of its own however short it is.

Jumping to a state

Click any row to put the document in that state. Rows below the current one are undone to, rows above are redone to; Latest at the top of the panel redoes everything that was undone. Nothing is thrown away by jumping, so you can go back and forth freely. Making a new change from a state in the middle does drop the changes above it, exactly as Undo followed by typing does.

The selection is cleared on a jump, because positions from the old state may not exist in the new one.

Naming a state

A state you will want to come back to — _before the Gibson_, _clean backbone_, _sent for sequencing_ — can be given a name, so it is found by what it is rather than by its step number.

1. Click ⋯ at the right of the row and choose Name….
2. Type the name and press Enter. Escape leaves the row as it was.

The name then heads the row, in the accent colour, with what the step did under it. Rename… in the same menu changes it; Clear name, or emptying the field and pressing Enter, takes it off. The row at the bottom — Opened document or New document — already has a name and cannot be given another; every step above it can.

Once anything is named, Named only at the top of the panel lists just the named rows; click it again for the whole list.

Naming is not an edit. It does not add a row, Undo does not take it off, and the document is not changed or marked as changed by it: a name is a note about the history, and an Undo step for it would leave Undo one step short of the state you just named. The name is kept with the history across reloads (see After a reload).

A named row also ends a run of typing: if you name the row you are typing in and carry on typing, the new bases go into a row of their own, so the state you named stays as you named it.

What a step changed

⋯ ▸ What changed shows what that one step did: the document just before it against the document just after it, in the same review a working copy's download and Compare with… show — the summary, the map with the change marked, each changed stretch of bases, and what became of the features. It is only a look: nothing is undone, and Close or Escape puts it away. The starting row has no step before it, so it has nothing to show.

Marking changes since a state

⋯ ▸ Mark changes since this makes that state what the edit marks measure from, as Mark in the views does after Compare with…: the sequence view and the map mark everything that differs from it, the Edits menu reads _Compared with_ and the state's name (or _step 4_, or _the opened document_), and Next change / Previous change (Alt+N, Alt+Shift+N) go through those changes. Choose another baseline in the Edits menu to go back. Like a comparison, it is for this session: after a reload the marks measure Since opened again.

The version you have a file of

The row whose state matches the last download — or, in a document opened from a file and not yet edited, the file it was read from — is tagged on disk. It is the same information as the dot next to the document name in the toolbar, but it says which state your file holds, so you can see how far the document has moved since. Downloading moves the tag to the current row. A working copy you have not downloaded yet has no such row: its history starts at the contents of the file it came from.

Elsewhere

• The ▾ next to Undo and Redo in the toolbar opens a short version of the same list as a menu.
• Ctrl+Z and Ctrl+Shift+Z step one change at a time. See Editing the sequence and Keyboard shortcuts.

After a reload

The history is kept in this browser's storage beside the document, so a reload, a crash, or closing the tab and opening the document again from Recent files — or opening a file identical to it — brings the list back as you left it: the same rows, times and current state, with the undone rows still greyed above it and reachable with Redo or a click. What does change:

• A run of typing that was going on when the page went is finished; the next keystroke starts a new row.
• Since opened in the Edits menu still measures from the state the history starts at, the Opened document row — or, for a working copy, from the file it came from — not from the moment of the reload.
• The on disk tag and the dot beside the document name stay on the row you last downloaded, so undoing to that row clears the dot as before. A working copy you have never downloaded has the dot after a reload too.
• Mark from here and Compared with come back as Since opened, as they always have.

The stored history is limited to the 200 most recent changes, like the list, and to about 4 MB per document. A long session on a very large document can go over that: the oldest rows are then left out of the stored copy, and after the next reload the list starts at Oldest kept state. Named states are kept longest. One whose row is left out comes back under Named states from before the oldest kept, stored whole, and it counts towards the 4 MB; to make room for named states, Since opened and the on disk tag give way first. Only when not even the current document would fit beside them are named states left out, the oldest first. On a plasmid none of this comes near the limit; on a document of a megabase or more, each named state that has left the list costs about as much as the document. A document of more than about four million bases keeps no stored history, and reopens with an empty list.

The history lives only in this browser. It is not written to the files you download or into share links (the Made from tree is: it belongs to the molecule, not to the editing session), and Remove on the start screen deletes it with the document; closing a tab does not.