Hello all!
Do you think this is a bounding box problem? He says it is reproducible with eps output.
Hmm. It may well be - but I'm not sure where the bounding box problem is actually occurring.
With an EPS file embedded in PPT, Arnaud, the problem you are seeing may be because EPS includes a PNG image which may well be truncated due to the same bug. EPS files, however, are rendered in a slightly different way, and will include the complete text shape if you select the 'Text' output option. Try opening the file in InkScape, if you don't have access to Illustrator, and you should see the full consensus line.
Unfortunately, I can't reproduce this on my own system. The EPS (text/lines) and PNG files exported from a wrapped view of the default alignment all look fine when imported into Adobe Illustrator (development branch of Jalview (Build Date: 15 June 2012), Java version: 1.6.0_33 x86_64 Mac OS X 10.6.8). You can try this version yourself from :
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/develop/webstart/jalview.jnlp
If you still have the same problems, Could you send me the output of the Jalview Java console (open this from the Desktop's Tools menu) ? It would also help if you could send an example PNG, EPS and jalview project that reproduces the problem.
Jim.
···
On 25/06/2012 09:33, Geoff Barton wrote:
OK - I'll move the discussion to the list, but for those other jalview-discuss folk listening, I'll say here that the EPS file Arnaud provided confirmed my growing suspicion that this is a font issue. The EPS file was definitely using a font that I don't have on my system (the logo wasn't rendered correctly at all), which explains why I couldn't reproduce the problem.
The quickest work around is probably to pick another font to render the alignment, and repeat until you don't see the issue. If you have the same problem with several fonts picked at random, then we'll have to dig deeper.
Jim.
(see http://issues.jalview.org/browse/JAL-1128 for next comments...).
···
On Mon Jun 25 16:47:40 2012, arnaud.muller@crp-sante.lu wrote:
Dear Jim,
Many thanks for spending for that.
I've updated Java with the latest available version; as you can see in
the console output,
and used the Development Branch Build.
Results remains the same as you can see there:
http://issues.jalview.org/browse/JAL-1128-> testCH.png
Dear all,
Many thanks for that fix. I’ve selected another font (SansSerif) and it’s much better now!
Either the PNG and the EPS (text) look fine.
You can find an updated PNG there:
http://issues.jalview.org/secure/thumbnail/10345/10345
Thanks again and have an excellent day!
Arnaud
On Mon Jun 25 16:47:40 2012, arnaud.muller@crp-sante.lu wrote:
> Dear Jim,
>
> Many thanks for spending for that.
> I've updated Java with the latest available version; as you can see in
> the console output,
> and used the Development Branch Build.
> Results remains the same as you can see there:
> http://issues.jalview.org/browse/JAL-1128-> testCH.png
OK - I'll move the discussion to the list, but for those other
jalview-discuss folk listening, I'll say here that the EPS file Arnaud
provided confirmed my growing suspicion that this is a font issue. The
EPS file was definitely using a font that I don't have on my system
(the logo wasn't rendered correctly at all), which explains why I
couldn't reproduce the problem.
The quickest work around is probably to pick another font to render the
alignment, and repeat until you don't see the issue. If you have the
same problem with several fonts picked at random, then we'll have to
dig deeper.
Jim.
(see http://issues.jalview.org/browse/JAL-1128 for next comments...).
Hi All,
Our web site using the applet version of the jalview. We have problem using the feature “Copy Consensus Sequence” We can see it by right clicking on the “Consensus” Label which bring up the context menu, and it’s the last option. After we choose that option, there is nothing get transfer to the clipboard, is there a way to get around it?
Thanks,
Wei
Our web site using the applet version of the jalview. We have problem using the feature “Copy Consensus Sequence” We can see it by right clicking on the “Consensus” Label which bring up the context menu, and it’s the last option. After we choose that option, there is nothing get transfer to the clipboard, is there a way to get around it?
Not really. Since JalviewLite is an unsigned applet, it doesn’t have access to the system clipboard (http://docs.oracle.com/javase/tutorial/deployment/applet/security.html), and the ‘Copy Consensus Sequence’ function just copies the sequence to an internal clipboard (type shift+ctrl+V and you will see a new alignment window appear with the consensus sequence).
I’m not sure if the consensus sequence will be copied to the system clipboard if you sign the jalview applet jar then it might ‘just work’, but that’s fairly unlikely.
Jim.
···
Hello Wei
On 27/06/2012 17:21, Wei Jen wrote:
Thanks Jim,
We did sign the jar file, and it doesn’t work for us.
We are trying to figure out a way, so user can get the consense sequence without moving to the full version (which kind of leave our site where we have some javascript code to interact with jalview).
Regards,
Wei
···
Hello Wei
On 27/06/2012 17:21, Wei Jen wrote:
You've two options - both involve patching the jalviewlite code.
1. Provide an additional method to get at the consensus sequence via javascript, and add a new button to your web page that gets the current jalview's consensus sequence and puts it into the system clipboard.
2. Change the copy consensus sequence action so that it also opens a text box showing the sequence. The user will then be able to copy and paste that sequence.
both are reasonably easy to accomplish. I'm not sure what you might prefer.
Jim.
···
On Thu Jun 28 17:37:49 2012, Wei Jen wrote:
Thanks Jim,
We did sign the jar file, and it doesn't work for us.
We are trying to figure out a way, so user can get the consense
sequence without moving to the full version (which kind of leave our
site where we have some javascript code to interact with jalview).
Thanks Jim, I like the option1, but I will discuss it with our team to see what’s the best option for us.
Once again, thanks for the quick responses.
Wei
···
From: Jim Procter [mailto:foreveremain@gmail.com]
To: jalview-discuss@jalview.org
Sent: Thu, 28 Jun 2012 12:50:56 -0400
Subject: Re: [Jalview-discuss] Question about Copy Consensus Sequence
On Thu Jun 28 17:37:49 2012, Wei Jen wrote:
Thanks Jim,
We did sign the jar file, and it doesn’t work for us.
We are trying to figure out a way, so user can get the consense
sequence without moving to the full version (which kind of leave our
site where we have some javascript code to interact with jalview).
You’ve two options - both involve patching the jalviewlite code.
-
Provide an additional method to get at the consensus sequence via
javascript, and add a new button to your web page that gets the current
jalview’s consensus sequence and puts it into the system clipboard.
-
Change the copy consensus sequence action so that it also opens a
text box showing the sequence. The user will then be able to copy and
paste that sequence.
both are reasonably easy to accomplish. I’m not sure what you might
prefer.
Jim.
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