From standley at protein.osaka-u.ac.jp  Thu Apr  3 03:58:46 2008
From: standley at protein.osaka-u.ac.jp (Daron Standley)
Date: Thu Apr  3 03:58:54 2008
Subject: [Jalview-discuss] jalview.ButtonAlignApplet
Message-ID: <9C01561A-538A-4651-B42A-CD059EDFE24D@protein.osaka-u.ac.jp>

Hi-

I am just getting started using the latest jalview, and I am confused  
on a few points:

1. I can't seem to find "jalview.ButtonAlignApplet" in the  
jalviewApplet.jar file, although this
code seems to be used in many of the examples I find on the web.

2. I can find and use "jalview/bin/JalviewLite.class". However, I  
wonder if this will allow me to display
alignments in the form:

<PARAM name="numseqs" value=3>
<PARAM name="seq1" value="ALSDKFHLKRHELKHASLDKHLKHR">
<PARAM name="seq2" value="ALSDKFHLKRHE-----LDKHLKHR">
<PARAM name="seq3" value="ALSDKFHLKRHELKHALKFL-HLKHR">

I can not get this to work using the jalviewLite class.  I get  an  
error where the button should be
saying Jalview can't open "NO FILE".

3. Assuming I eventually figure out how to do #2 (above) I am  
wondering if I can then display a single sequence
along with some properties (conservation, secondary structure,  
functional residues, etc.)  I am hoping this
will be a nice way to present such properties at the Protein Data  
Bank Japan (currently we only show a the
FASTA sequence in a text window).

Thanks in advance, and sorry if my question is not clear. I am not  
very familiar with java.

Best regards,

Daron
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From jimp at compbio.dundee.ac.uk  Thu Apr  3 09:28:21 2008
From: jimp at compbio.dundee.ac.uk (Jim Procter)
Date: Thu Apr  3 09:28:34 2008
Subject: [Jalview-discuss] jalview.ButtonAlignApplet
In-Reply-To: <9C01561A-538A-4651-B42A-CD059EDFE24D@protein.osaka-u.ac.jp>
References: <9C01561A-538A-4651-B42A-CD059EDFE24D@protein.osaka-u.ac.jp>
Message-ID: <47F49525.5080408@compbio.dundee.ac.uk>

Hello Daron.

Daron Standley wrote:
> 1. I can't seem to find "jalview.ButtonAlignApplet" in 
> the jalviewApplet.jar file, although this 
> code seems to be used in many of the examples I find on the web. 
>
You can be almost 100% certain that all these examples are using the old 
version of Jalview, which had a package structure like 
jalview.<classname> for many of the classes. Jalview 2 has a class 
structure like jalview.<mainpackage>.<class> for nearly all of its 
source code.
> 2. I can find and use "jalview/bin/JalviewLite.class".
That is most definitely the one to use. You'll find examples of the 
applet being launched here:
http://www.jalview.org/examples/applet.html
http://www.jalview.org/examples/appletParameters.html

> However, I wonder if this will allow me to display
> alignments in the form: 
>
> <PARAM name="numseqs" value=3>
> <PARAM name="seq1" value="ALSDKFHLKRHELKHASLDKHLKHR">
> <PARAM name="seq2" value="ALSDKFHLKRHE-----LDKHLKHR">
> <PARAM name="seq3" value="ALSDKFHLKRHELKHALKFL-HLKHR">
These parameters are wrong. The format for passing an alignment as 
applet parameters is given on the appletParameters link above. Firstly - 
you don't need numseqs at all, and secondly, jalview searches for 
parameters called 'sequence<i>' - where <i> is 1,2,3,.... The value of 
each sequence<i> parameter is the i'th line of the alignment file. For 
example:
<param name="sequence1" value="s1  a-cde">
<param name="sequence2" value="s2  apcde">
<param name="sequence3" value="s3  a--de">

Each line specifies a sequence name and alignment row in PFAM format.
> I can not get this to work using the jalviewLite class.  I get  an 
> error where the button should be
> saying Jalview can't open "NO FILE".
this is the generic error that the applet gives when the formats or 
parameters are incorrect. Always check on the browser's Java console for 
more information about what has caused  the error.

> 3. Assuming I eventually figure out how to do #2 (above) I am 
> wondering if I can then display a single sequence
> along with some properties (conservation, secondary structure, 
> functional residues, etc.)  I am hoping this
> will be a nice way to present such properties at the Protein Data Bank 
> Japan (currently we only show a the 
> FASTA sequence in a text window).
all possible. Have a look at the current development version of the 
applet's parameters and (rudimentary) API. Secondary structure 
annotation is passed into Jalview via it's own alignment annotations 
file format, and sequence features (ie DAS style sequence annotation) 
can be read from GFF or via a Jalview Features file. You don't need to 
create these files statically - the location of a servlet that generates 
the appropriate annotation file is all that's necessary.

> Thanks in advance, and sorry if my question is not clear. I am not 
> very familiar with java.
no problem. Now if only it were possible to eliminate all incorrect 
documentation ;)

hope it helps..
Jim

-- 
-------------------------------------------------------------------
J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk 
The University of Dundee is a Scottish Registered Charity, No. SC015096.

From standley at protein.osaka-u.ac.jp  Thu Apr  3 09:52:20 2008
From: standley at protein.osaka-u.ac.jp (Daron Standley)
Date: Thu Apr  3 09:52:29 2008
Subject: [Jalview-discuss] jalview.ButtonAlignApplet
In-Reply-To: <47F49525.5080408@compbio.dundee.ac.uk>
References: <9C01561A-538A-4651-B42A-CD059EDFE24D@protein.osaka-u.ac.jp>
	<47F49525.5080408@compbio.dundee.ac.uk>
Message-ID: <03756E92-EF22-46F8-830A-3DF816B9942A@protein.osaka-u.ac.jp>

Hi Jim,

Thanks so much.  Your advice cleared up all my problems, and I now  
understand why things weren't working.

One minor point: I could access the link:

http://www.jalview.org/examples/appletParameters.html

but not:

  http://www.jalview.org/examples/applet.html

Don't know if thats significant or not.

Thanks again. As soon as I can get a prototype working I can hand  
this off to the java experts, and they will make it beautiful.
Hopefully we will have jalview running here shortly.

-Daron


On Apr 3, 2008, at 5:28 PM, Jim Procter wrote:

> Hello Daron.
>
> Daron Standley wrote:
>> 1. I can't seem to find "jalview.ButtonAlignApplet" in the  
>> jalviewApplet.jar file, although this code seems to be used in  
>> many of the examples I find on the web.
> You can be almost 100% certain that all these examples are using  
> the old version of Jalview, which had a package structure like  
> jalview.<classname> for many of the classes. Jalview 2 has a class  
> structure like jalview.<mainpackage>.<class> for nearly all of its  
> source code.
>> 2. I can find and use "jalview/bin/JalviewLite.class".
> That is most definitely the one to use. You'll find examples of the  
> applet being launched here:
> http://www.jalview.org/examples/applet.html
> http://www.jalview.org/examples/appletParameters.html
>
>> However, I wonder if this will allow me to display
>> alignments in the form:
>> <PARAM name="numseqs" value=3>
>> <PARAM name="seq1" value="ALSDKFHLKRHELKHASLDKHLKHR">
>> <PARAM name="seq2" value="ALSDKFHLKRHE-----LDKHLKHR">
>> <PARAM name="seq3" value="ALSDKFHLKRHELKHALKFL-HLKHR">
> These parameters are wrong. The format for passing an alignment as  
> applet parameters is given on the appletParameters link above.  
> Firstly - you don't need numseqs at all, and secondly, jalview  
> searches for parameters called 'sequence<i>' - where <i> is  
> 1,2,3,.... The value of each sequence<i> parameter is the i'th line  
> of the alignment file. For example:
> <param name="sequence1" value="s1  a-cde">
> <param name="sequence2" value="s2  apcde">
> <param name="sequence3" value="s3  a--de">
>
> Each line specifies a sequence name and alignment row in PFAM format.
>> I can not get this to work using the jalviewLite class.  I get  an  
>> error where the button should be
>> saying Jalview can't open "NO FILE".
> this is the generic error that the applet gives when the formats or  
> parameters are incorrect. Always check on the browser's Java  
> console for more information about what has caused  the error.
>
>> 3. Assuming I eventually figure out how to do #2 (above) I am  
>> wondering if I can then display a single sequence
>> along with some properties (conservation, secondary structure,  
>> functional residues, etc.)  I am hoping this
>> will be a nice way to present such properties at the Protein Data  
>> Bank Japan (currently we only show a the FASTA sequence in a text  
>> window).
> all possible. Have a look at the current development version of the  
> applet's parameters and (rudimentary) API. Secondary structure  
> annotation is passed into Jalview via it's own alignment  
> annotations file format, and sequence features (ie DAS style  
> sequence annotation) can be read from GFF or via a Jalview Features  
> file. You don't need to create these files statically - the  
> location of a servlet that generates the appropriate annotation  
> file is all that's necessary.
>
>> Thanks in advance, and sorry if my question is not clear. I am not  
>> very familiar with java.
> no problem. Now if only it were possible to eliminate all incorrect  
> documentation ;)
>
> hope it helps..
> Jim
>
> -- 
> -------------------------------------------------------------------
> J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk  
> The University of Dundee is a Scottish Registered Charity, No.  
> SC015096.
>
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-discuss@jalview.org
> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss

From jimp at compbio.dundee.ac.uk  Thu Apr 17 09:33:35 2008
From: jimp at compbio.dundee.ac.uk (James Procter)
Date: Thu Apr 17 09:34:01 2008
Subject: [Jalview-discuss] Re: JalView and Phylip output
In-Reply-To: <480706A9.3000104@unil.ch>
References: <480706A9.3000104@unil.ch>
Message-ID: <48070B5F.1030608@compbio.dundee.ac.uk>

Hi Sebastian.

Thanks for the email. I've forwarded this to the jalview-discuss list
because I suspect this is of general interest.

Sebastien Moretti wrote:
> Do you plan to add a phylip format output to Jalview ?
it wasn't planned originally. Our preferred route for phylogeny
calculations was to pass the alignment to TOPALi (www.topali.org) or use
phylogeny web services (which don't exist as yet).

> I know that there is a 'problem' with the fact that strict phylip format
> must have sequence names cut to the 10th characters. 
yep - its only a problem if you care about the names - there would have
to be some user investigation concerning that. jalview doesn't need
unique names (in principal), but the tree-matching display requires
unambiguous correspondence. If phylip analyses were implemented via a
web service then all of that kind of housekeeping could  be hidden away
from the user.

> But, now, more and more software, like PhyML or PAML, use names longer
> than 10: 30 for PAML, no limit (?) for PhyML.
true. They still require unique names, however.

> What do you think to add a strict phylip format output and a non-strict
> one ?
It would be of use - but a switch would be needed between the strict and
non-strict when generating a PHYLIP formatted aligment. Otherwise, from
the looks of the format,
(http://evolution.genetics.washington.edu/phylip/doc/sequence.html) it
would be a very easy implementation since it is practically the same as
PFAM (except for the interleaved/not interleaved aspect).

> Do you know when the release with AMSA format support will be available ?
The jalview paper is still being written, and we originally planned to
delay the release of 2.4 until after it was submitted. However, I
suspect the 'official' release may happen before that now.

thanks for the mail!
Jim

-- 
-------------------------------------------------------------------
J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
From besnoitia at gmail.com  Fri Apr 25 19:09:37 2008
From: besnoitia at gmail.com (James Wasmuth)
Date: Fri Apr 25 19:09:48 2008
Subject: [Jalview-discuss] Loading annotations
Message-ID: <6af8a6450804251109y525633pf6f72bfd4fa04e02@mail.gmail.com>

Hi All,

I wish to use an annotation file to decorate my alignment. I created a dummy
file (below) and used File->Load Features/Annotations. The file is called
features.txt.

I am greated with an error box saying that jalview,
"Couldn't load file /tmp/features.txt
Formats currently supported are
Fasta, MSF, Clustal, BLC, PIR, MSP and Pfam"

Can someone enlighten me as to how I can load in my file? The alignment is
displayed when I try this.

many thanks
-james

>less features.txt
tash red

tash_domain    Tp_2992.1    -1    263    281    tash
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From jcohn at lanl.gov  Fri Apr 25 20:33:40 2008
From: jcohn at lanl.gov (Judith Cohn)
Date: Fri Apr 25 20:33:59 2008
Subject: [Jalview-discuss] Loading annotations
In-Reply-To: <6af8a6450804251109y525633pf6f72bfd4fa04e02@mail.gmail.com>
References: <6af8a6450804251109y525633pf6f72bfd4fa04e02@mail.gmail.com>
Message-ID: <0A1C257A-BFFA-48F5-A17F-BC5E8DB6BDB9@lanl.gov>

Hi,

I am using Jalview 2.3  (though the about option says 6.1).  I do the  
same thing.  I load a .aln file (from clustalw) then from the  
alignment window in Jalview I choose Load Features/Annotations and it  
works.  An example of the beginning of a features file (which I  
create automatically in a Java program):

dpa1	111111
d1gv1a1_O	d1gv1a1	-1	6	6	dpa1

The main difference I see in my file versus yours (at least as  
included in the email) is that I used tabs and your snippet appears  
to have spaces between columns.
Note:  I use the numeric designation of a color so that I can get  
gradations of the same color.

Judith


On Apr 25, 2008, at 12:09 PM, James Wasmuth wrote:
> Hi All,
>
> I wish to use an annotation file to decorate my alignment. I  
> created a dummy file (below) and used File->Load Features/ 
> Annotations. The file is called features.txt.
>
> I am greated with an error box saying that jalview,
> "Couldn't load file /tmp/features.txt
> Formats currently supported are
> Fasta, MSF, Clustal, BLC, PIR, MSP and Pfam"
>
> Can someone enlighten me as to how I can load in my file? The  
> alignment is displayed when I try this.
>
> many thanks
> -james
>
> >less features.txt
> tash red
>
> tash_domain    Tp_2992.1    -1    263    281    tash
>
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-discuss@jalview.org
> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss



--------------------

Judith Cohn, Ph.D.
Information Science (CCS-3)
Mail Stop B256
Los Alamos National Lab
Los Alamos, NM 87545
phone:  505-665-0999
email:  jcohn@lanl.gov




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From besnoitia at gmail.com  Fri Apr 25 20:50:10 2008
From: besnoitia at gmail.com (James Wasmuth)
Date: Fri Apr 25 20:50:17 2008
Subject: [Jalview-discuss] Loading annotations
In-Reply-To: <4B0DB441-CFED-4B9C-9162-F733BB28DEBA@lanl.gov>
References: <6af8a6450804251109y525633pf6f72bfd4fa04e02@mail.gmail.com>
	<4B0DB441-CFED-4B9C-9162-F733BB28DEBA@lanl.gov>
Message-ID: <6af8a6450804251250ia20b856x617158d96a33ce31@mail.gmail.com>

Thanks Judith.

there was a space in the first line instead of a space <embarrassed smile>.
Fixed that and it works!

-james


On Fri, Apr 25, 2008 at 3:32 PM, Judith Cohn <jcohn@lanl.gov> wrote:

> Hi,
> I am using Jalview 2.3  (though the about option says 6.1).  I do the same
> thing.  I load a .aln file (from clustalw) then from the alignment window in
> Jalview I choose Load Features/Annotations and it works.  An example of the
> beginning of a features file (which I create automatically in a Java
> program):
>
> dpa1 111111
> d1gv1a1_O d1gv1a1 -1 6 6 dpa1
>
> The main difference I see in my file versus yours (at least as included in
> the email) is that I used tabs and your snippet appears to have spaces
> between columns.
> Note:  I use the numeric designation of a color so that I can get
> gradations of the same color.
>
> Judith
>
>
> On Apr 25, 2008, at 12:09 PM, James Wasmuth wrote:
>
> Hi All,
>
> I wish to use an annotation file to decorate my alignment. I created a
> dummy file (below) and used File->Load Features/Annotations. The file is
> called features.txt.
>
> I am greated with an error box saying that jalview,
> "Couldn't load file /tmp/features.txt
> Formats currently supported are
> Fasta, MSF, Clustal, BLC, PIR, MSP and Pfam"
>
> Can someone enlighten me as to how I can load in my file? The alignment is
> displayed when I try this.
>
> many thanks
> -james
>
> >less features.txt
> tash red
>
> tash_domain    Tp_2992.1    -1    263    281    tash
>
> _______________________________________________
> Jalview-discuss mailing list
> Jalview-discuss@jalview.org
> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
>
>
>
>
> --------------------
>
> Judith Cohn, Ph.D.
> Information Science (CCS-3)
> Mail Stop B256
> Los Alamos National Lab
> Los Alamos, NM 87545
> phone:  505-665-0999
> email:  jcohn@lanl.gov
>
>
>
>
>
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