Minor bug in JalviewLite.java ?

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Delivered-To: andrew@midge.compbio.dundee.ac.uk
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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Hi 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 http://www.ebi.ac.uk/services/.
> > > >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