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Delivered-To: andrew@compbio.dundee.ac.uk
Subject: Re: Minor bug in JalviewLite.java ?
From: Franck Valentin <franckv@ebi.ac.uk>
To: Andrew Waterhouse <andrew@compbio.dundee.ac.uk>
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Date: Wed, 26 Oct 2005 09:50:24 +0100
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X-Spam-Score: -3.0Hi Andrew,
thanks for this swift response !
Don't worry about a new version, I've changed the line in the code and
will use the modified version at the moment.
We'll use jalview 2 to display results from muscle, a new alignment tool
that will be available on the EBI web pages. So at the moment it meets
the features we want (thanks for adding trees !).Franck
On Wed, 2005-10-26 at 09:06, Andrew Waterhouse wrote:
> Morning Franck,
>
> How soon do you need the new applet jar file? Its extremely straight
> forward to build one right now, but if you wanted extra features it
> might be a while till we release the next version of Jalview.
>
> Andrew
>
> At 14:11 25/10/2005, you wrote:
> >Hi Andrew,
> >
> >On Tue, 2005-10-25 at 10:54, Andrew Waterhouse wrote:
> > > Hi Franck,
> > >
> > > We can add the function to use either applet.getCodeBase() or not, to
> > > get the best of both worlds.
> >
> >Great idea !
> > >
> > > if(!file.startsWith("http://") && !file.startsWith("file://"))
> > > file = applet.getCodeBase() + file;
> > >
> >
> >You can also use a more generic test to tests URLS (I've taken this
> >example from one of my ongoing projects but haven't tested it yet...) :
> > // If no protocol is defined
> > // (See http://www.ietf.org/rfc/rfc2396.txt chap 3)
> > if (! st.matches("\\A\\w*(\\w|\\d|\\+|-|\\.):.+$")) {
> > file = applet.getCodeBase() + file;
> > }
> >
> > > Of course the file will still need to sit on the same server that the
> > > jar file is served from.
> > >
> > > On another point, there were a number of HTML output options in
> > > Jalview 1+ (used by PFAM) which are not currently implemented in
> > > Jalview 2+. Are these functions useful to you, and are there any new
> > > features you would like added to Jalview applet/application?
> >
> >Thanks ! I don't know yet if we'll use theses functionalities and I'll
> >asked my team leader if he thinks about something.
> >
> >Cheers
> >
> >Franck
> > >
> > > Andrew
> > >
> > > At 09:55 25/10/2005, Franck Valentin wrote:
> > > >Hi,
> > > >
> > > >I will use the applet version of jalview for one of our services
> > > >available at Services | EMBL-EBI.
> > > >I have a little problem because the file for the sequences I use
> > > >(applet's parameter 'file') is not in a subdirectory of
> > > >jalviewApplet.jar as required by the applet.
> > > >This is defined in jalview.bin.JalviewLite, function init() :
> > > >file = applet.getCodeBase() + file;
> > > >
> > > >Do you think you can remove this line as it is not necessary and limits
> > > >the places where the input sequences can be ?
> > > >
> > > >Have a good day !
> > > >Cheers
> > > >
> > > >Franck