Also could you try if the following script correctly selects all highlights:

tell document 1 of application "Skim"
    set theSel to {}
    tell current page
        repeat with theNote in notes
            if type of theNote is highlight note then
                set theSel to join theSel to selection of theNote
            end if
        end repeat
    end tell
    set selection to theSel
end tell

Christiaan

On 8/16/07, Christiaan Hofman <[EMAIL PROTECTED]> wrote:
>
> Can you send the PDF, as I haven't seen a PDF that has this problem.
>
> Christiaan
>
> On 16 Aug 2007, at 8:17 PM, Maxwell, Adam R wrote:
>
> >
> >
> >
> > On 08/16/07 11:07, "Christiaan Hofman" <[EMAIL PROTECTED]> wrote:
> >
> >> I don't see your problem. What is the problem with PDFSelection? It
> >> works for me, even when the highlighted text consists of completely
> >> random parts.
> >
> > See attached.  If I select the top highlight, then shift-click on
> > the two
> > lower discrete highlights to merge them, the top two highlights
> > vanish.  Not
> > necessarily a problem in PDFSelection per se; my guess is that it's
> > the
> > initWithSelection:markupType: method's determination of quad points
> > based on
> > selection.  Only a guess, since I don't have time to look at it in
> > detail.
> > Shift-clicking seems to work fine with discontiguous highlights on
> > the same
> > line of the same column.
> >
> > --
> > Adam
> >
> > <Picture
> > 1.png>----------------------------------------------------------------
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