| Reached by | Tools → Analyze |
What it does
Opens a PDF — a paper, a protocol, a supplementary document — as a real tab in the project, page by page.
When you'd use this
The paper your construct came from, the protocol you are following, the supplementary file whose tables you are working against. These normally live in another window or another folder, and the cost is small but constant: you lose the thread every time you go and find it.
Keeping the document in the project means the paper sits beside the plasmid, the reads and the tables it produced. The bundled example is exactly that — a published Golden Gate assembly study open next to the supplementary tables it published, which are the same tables the fidelity calculations in this app are built on.
What this computes
It is a reader, and what it reports is what the document itself carries.
- The page count and the page you are on, with the pages rendered one at a time
- The text layer, when there is one — selectable and searchable. A scanned PDF with no text layer has nothing to select, and that is a property of the file rather than a failure here
- The format from the file's own
%PDF-header rather than its name, so a mislabelled file still opens and a file that only claims to be a PDF is refused with that reason instead of drawing a blank page. A document over 128 MB is refused with its size stated
There is no output file: this is a reader. Nothing is extracted, re-typeset or written back, and a figure you want in a report is a screenshot you take, not a conversion this performs.
Where it lives
Tools → Analyze → Open PDF, or the command palette. A .pdf also opens directly from the Files
rail and the file manager, and previews in place there. A file picked from another project is copied
into the open one so the tab survives a reload.
Inputs and outputs
Takes any .pdf, recognised by the file's own %PDF- header rather than its name — so a
mislabelled file still opens, and a file that only claims to be a PDF is refused with that reason
instead of drawing a blank page. Documents over 128 MB are refused with the size stated.
There is no output file: this is a reader.
How to read the result
One page is drawn at a time, with the page number as a control. Zoom re-renders the page at the new size rather than stretching a bitmap, which is the difference that matters when you zoomed in to read a gel lane or an axis label. Rotate handles a landscape figure or a sideways scan. The document's own title, author and PDF version are shown when it declares them.
Getting somewhere in a long document is three different questions and there is a control for each. If you know the page number, the Page control takes it. If you would recognise the page on sight — a figure, a table, the reference list — the page strip down the left draws every page small and clicking one jumps there. If the document carries its own bookmarks, a Section control lists them and names the one you are currently in; most journal PDFs carry none, and then the control is simply not there rather than being offered empty.
Text is selectable: an invisible, positioned copy of the page's text sits over the drawing, so a gene name or an accession can be copied straight out of the paper. The text is also searched with the rest of the project — a hit names the page it is on. Full detail: the PDF canvas.
The bundled reference manual is the long-document case: 223 pages with 142 bookmarks, which is what the strip and the Section control are there for.
Related
Sits beside the table viewer and the NumPy array viewer: the documents and data a project accumulates around the sequences it is really about.