[Bioclipse-devel] the new splash screen is great!

[<daniel.kroeni@gm...>]

bXVzdCBiZSBzYWlkISA9KQpkYW5pZWwK

Re: [Bioclipse-devel] Multiple Jmols?

[Ola Spjuth <ola.spjuth@fa...>]

Hi,

If you want you can write a plugin for this. Just add a new perspective,
call it MultipleJmolPerspective or whatever, and set up as many
JmolViews as you like. Should not be too complicated. Add actions "Show
in Jmol 1", "Show in Jmol 2" etc, for molecules/scripts. It might
require a new JmolView (the current allows only for a single instance)
but that should be more or less copy/paste.

Cheers,

   .../Ola


On Wed, 2006-03-29 at 17:13 +0200, Egon Willighagen wrote:
> On Wednesday 29 March 2006 17:10, Mark Southern wrote:
> > Iterate through them and animate them, yes, but how would you see all
> > the different views all at the same time? There is only one Jmol view
> > that displays one molecule at a time.
> 
> What I meant is, you could show more than one time point in one view, on top 
> of each other...
> 
> What's the reason for comparing two time points?
> 
> Egon
> 

RE: [Bioclipse-devel] Multiple Jmols?

[Mark Southern <southern@sc...>]

I'm not aware how to do that.

The specific experiment I am talking about is the incorporation of
deuterium into a protein.

Consider only one peptide: 30-45. After 30 seconds there might be a low
incorporation of deuterium and I might color the peptide sequence blue.
After 5 hours it might have a higher incorporation of deuterium and I
might color it red.

e.g.

select 30-45;
color blue;

select 30-45;
color red;


I cannot display both of these at the same time, it will either show
blue or red. I would need to have two molecules open, one showing each.
Rather than step through these (up to ~10 time points) the scientists
prefer to be able to see all at the same time.

M.



-----Original Message-----
From: bioclipse-devel-admin@...
[mailto:bioclipse-devel-admin@...] On Behalf Of Egon
Willighagen
Sent: Wednesday, March 29, 2006 10:14 AM
To: bioclipse-devel@...
Subject: Re: [Bioclipse-devel] Multiple Jmols?

On Wednesday 29 March 2006 17:10, Mark Southern wrote:
> Iterate through them and animate them, yes, but how would you see all
> the different views all at the same time? There is only one Jmol view
> that displays one molecule at a time.

What I meant is, you could show more than one time point in one view, on
top=20
of each other...

What's the reason for comparing two time points?

Egon

--=20
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6


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Re: [Bioclipse-devel] Multiple Jmols?

[Egon Willighagen <egonw@us...>]

On Wednesday 29 March 2006 17:10, Mark Southern wrote:
> Iterate through them and animate them, yes, but how would you see all
> the different views all at the same time? There is only one Jmol view
> that displays one molecule at a time.

What I meant is, you could show more than one time point in one view, on top 
of each other...

What's the reason for comparing two time points?

Egon

-- 
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6

RE: [Bioclipse-devel] Multiple Jmols?

[Mark Southern <southern@sc...>]

Iterate through them and animate them, yes, but how would you see all
the different views all at the same time? There is only one Jmol view
that displays one molecule at a time.

Am I missing something?

M.

-----Original Message-----
From: bioclipse-devel-admin@...
[mailto:bioclipse-devel-admin@...] On Behalf Of Egon
Willighagen
Sent: Wednesday, March 29, 2006 10:04 AM
To: bioclipse-devel@...
Subject: Re: [Bioclipse-devel] Multiple Jmols?

On Wednesday 29 March 2006 16:34, Mark Southern wrote:
> What the users would like to do is have a Jmol open for each time
point
> so that they can see all the views of the protein on screen at the
same
> time. This is of course possible but currently a pain to open 10
> different Jmols, align them on screen, load the structures and render
> the scripts.

Why not load them into one Jmol view?

Then you can iteratate through them, animate them, and show them all at
the=20
same time...

Egon

--=20
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6


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Re: [Bioclipse-devel] Multiple Jmols?

[Egon Willighagen <egonw@us...>]

On Wednesday 29 March 2006 16:34, Mark Southern wrote:
> What the users would like to do is have a Jmol open for each time point
> so that they can see all the views of the protein on screen at the same
> time. This is of course possible but currently a pain to open 10
> different Jmols, align them on screen, load the structures and render
> the scripts.

Why not load them into one Jmol view?

Then you can iteratate through them, animate them, and show them all at the 
same time...

Egon

-- 
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6

[Bioclipse-devel] Multiple Jmols?

[Mark Southern <southern@sc...>]

Hi all,

=20

This came up as part of a discussion here yesterday:=20

=20

We generate RasMol script files that differentially color peptides along
a protein structure in Jmol. There is one script file for each of a
number of time points (~10). The user steps between the scripts to see
the differences between them.

=20

I want to move toward using bioclipse for this task but currently we are
using Jmol on it's own.=20

=20

What the users would like to do is have a Jmol open for each time point
so that they can see all the views of the protein on screen at the same
time. This is of course possible but currently a pain to open 10
different Jmols, align them on screen, load the structures and render
the scripts.

=20

In terms of design, does it make sense to have the Jmol plugin (or any
graphical plugin) have the ability to have multiple views open at the
same time, of would it be better to have a separate plugin for this that
wraps them?

=20

=20

Best wishes,

=20

Mark.

=20

=20

=20

Re: [Bioclipse-devel] BiojavaResource

[Valentin Ruano <valentin.ruano@gm...>]

Once upon a time I bumped into a file whose type I wanted to know and after
some search I found this program whose name I dont remember now based on
neural networks.
He had already pretrained nets for major types but you could create your
own. It was fast and returned a reability index sorting candidate types by
probability. No extensions needed.

Nonetheless I dont remember the name of the program, neither its license
although it was for free so freeware shareware or even FOSS. I will try to
find it but cant promisse; a simple google search does not show it and I
remember it took me a while to find it amongst comercial software of the
same sort back then.

Perhaps is too sofisticated but it is also a cool idea and a general
solution to the problem.


On 3/28/06, Emig, Robin <Robin.Emig@...> wrote:
>
>
>        I like your idea of check one parser, then the next, etc. That
> may just solve all the problems. However, In my opinion, if we want to
> make something that works for as many people as possible, then we cannot
> rely on extensions alone. Maybe I'm using a sledge hammer for a nail,
> but this is one area I find most people get VERY frustrated with.
>        File extensions work as long as the user knows what's going on.
> VectorNTI has a bad habit of exporting sequences in a file .gb which is
> actually a fasta file. In addition some websites allow the download of
> fasta files, but by default add a .txt extension, resulting in
> .fasta.txt . This causes a problem when users try to open a file they
> see as .fasta because windows default hides the .txt extension.
>        One thing to keep in mind is that sometimes the same file can be
> opened up in different ways...
>
> Example...
> PDB file as a sequence file
> .fasta is this a group of sequences, or an alignment
> .msf - normally an alignment, but what if I want just a group of
> sequences?
> .seq -maybe I want to edit the file as a text file (ie replace X's with
> N's, etc, inspect to find out why parsing doesn't work, etc)
> 2c,
> -Robin
>
>
> -----Original Message-----
> From: bioclipse-devel-admin@...
> [mailto:bioclipse-devel-admin@...] On Behalf Of Ola
> Spjuth
> Sent: Tuesday, March 28, 2006 9:25 AM
> To: Mark Southern
> Cc: Bioclipse-devel ML
> Subject: RE: [Bioclipse-devel] BiojavaResource
>
> Hi,
>
> I have been thinking a lot about this and decided:
>
> For Bioclipse vers 1.0:
>        Use file extensions and levels to decide original type
>        On parse, decide final type that could be other than original
> type
>
> For future versions we could:
>        Implement a scanner to read e.g. first 10 rows and decide FAST
> the
> actual file format/BioResourceType
>
> I don't really see how your proposal differs from my implementation,
> given that the parser can handle multiple types. If the parser cannot
> parse a file, it returns null and the next parser (with a lower level)
> can give it a try.
>
> > Only some types of file perhaps? A .pdb file is pretty much always a
> pdb
> > file but a .seq file can be swissprot, fasta or several others.
>
> This is exactly the way it works now. I think we already have the
> functionality implemented in Bioclipse. Let me know if I have
> misunderstood things.
>
> Cheers,
>
>   .../Ola
>
>
> On Tue, 2006-03-28 at 11:59 -0500, Mark Southern wrote:
> >
> > -----Original Message-----
> > From: Mark Southern
> > Sent: Tuesday, March 28, 2006 11:59 AM
> > To: 'Emig, Robin'
> > Subject: RE: [Bioclipse-devel] BiojavaResource
> >
> > I like this idea too. Meta data about the user's files would need to
> be
> > stored though, else the next time they start bioclipse they'd be asked
> > the same questions.
> >
> > Only some types of file perhaps? A .pdb file is pretty much always a
> pdb
> > file but a .seq file can be swissprot, fasta or several others.
> >
> >
> > Mark.
> >
> > -----Original Message-----
> > From: bioclipse-devel-admin@...
> > [mailto:bioclipse-devel-admin@...] On Behalf Of
> Emig,
> > Robin
> > Sent: Monday, March 27, 2006 6:46 PM
> > To: egonw@...; bioclipse-devel@...
> > Subject: RE: [Bioclipse-devel] BiojavaResource
> >
> > I'm a big fan of the way MOE and Mesquite load files
> >
> > Allow user to open ANY file
> > Then go to another dialog to actually parse it
> >
> > Text version of parse dialog....
> > We can use the biojava stuff to guess the file, and then read in....
> > ------------------------------------------------------------
> > - File Data:          | Open file as...   | Example format
> > -                     | Sequence: Fasta   | >sequencename annotations
> > - >sequence blah blah | Sequence: MSF     | sequence
> > - ATGAMGIALMD         | Alignment: MSF    | sequence
> > - KLKLKLKPRLKTLK      | Sequence: Genbank |
> > -                     | Recommend: Sequence:Fasta |
> > ------------------------------------------------------------
> >
> > -Robin
> >
> > -----Original Message-----
> > From: bioclipse-devel-admin@...
> > [mailto:bioclipse-devel-admin@...] On Behalf Of Egon
> > Willighagen
> > Sent: Sunday, March 26, 2006 9:33 PM
> > To: bioclipse-devel@...
> > Subject: Re: [Bioclipse-devel] BiojavaResource
> >
> > On Sunday 26 March 2006 21:36, Mark Southern wrote:
> > > I propose that we use org.biojava.bio.seq.io.SeqIOTools to guess the
> > > type of sequence file and autoload it. Something like:
> >
> > CDK uses such an algorithm for chem files too.
> >
> > > The guessFileType() method IS deprecated in biojava but in many
> years
> > of
> > > using it, it has not failed me.
> >
> > You could set up a number of test cases.
> >
> > > In a gui application such as bioclipse
> > > it makes sense to try to best deal with what ever the user throws at
> > > you!
> >
> > Egon
> >
> > --
> > egonw@...
> > Blog: http://chem-bla-ics.blogspot.com/
> > GPG: 1024D/D6336BA6
> >
> >
> > -------------------------------------------------------
> > This SF.Net email is sponsored by xPML, a groundbreaking scripting
> > language
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> > webcast
> > and join the prime developer group breaking into this new coding
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=3D121642
> > _______________________________________________
> > Bioclipse-devel mailing list
> > Bioclipse-devel@...
> > https://lists.sourceforge.net/lists/listinfo/bioclipse-devel
> >
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2
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>
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>

RE: [Bioclipse-devel] BiojavaResource

[Emig, Robin <Robin.Emig@pi...>]

	I like your idea of check one parser, then the next, etc. That
may just solve all the problems. However, In my opinion, if we want to
make something that works for as many people as possible, then we cannot
rely on extensions alone. Maybe I'm using a sledge hammer for a nail,
but this is one area I find most people get VERY frustrated with.
	File extensions work as long as the user knows what's going on.
VectorNTI has a bad habit of exporting sequences in a file .gb which is
actually a fasta file. In addition some websites allow the download of
fasta files, but by default add a .txt extension, resulting in
.fasta.txt . This causes a problem when users try to open a file they
see as .fasta because windows default hides the .txt extension.=20
	One thing to keep in mind is that sometimes the same file can be
opened up in different ways...

Example...
PDB file as a sequence file
.fasta is this a group of sequences, or an alignment
.msf - normally an alignment, but what if I want just a group of
sequences?
.seq -maybe I want to edit the file as a text file (ie replace X's with
N's, etc, inspect to find out why parsing doesn't work, etc)
2c,
-Robin


-----Original Message-----
From: bioclipse-devel-admin@...
[mailto:bioclipse-devel-admin@...] On Behalf Of Ola
Spjuth
Sent: Tuesday, March 28, 2006 9:25 AM
To: Mark Southern
Cc: Bioclipse-devel ML
Subject: RE: [Bioclipse-devel] BiojavaResource

Hi,

I have been thinking a lot about this and decided:

For Bioclipse vers 1.0:
	Use file extensions and levels to decide original type
	On parse, decide final type that could be other than original
type

For future versions we could:
	Implement a scanner to read e.g. first 10 rows and decide FAST
the
actual file format/BioResourceType

I don't really see how your proposal differs from my implementation,
given that the parser can handle multiple types. If the parser cannot
parse a file, it returns null and the next parser (with a lower level)
can give it a try.

> Only some types of file perhaps? A .pdb file is pretty much always a
pdb
> file but a .seq file can be swissprot, fasta or several others.

This is exactly the way it works now. I think we already have the
functionality implemented in Bioclipse. Let me know if I have
misunderstood things.

Cheers,

   .../Ola


On Tue, 2006-03-28 at 11:59 -0500, Mark Southern wrote:
>=20
> -----Original Message-----
> From: Mark Southern=20
> Sent: Tuesday, March 28, 2006 11:59 AM
> To: 'Emig, Robin'
> Subject: RE: [Bioclipse-devel] BiojavaResource
>=20
> I like this idea too. Meta data about the user's files would need to
be
> stored though, else the next time they start bioclipse they'd be asked
> the same questions.
>=20
> Only some types of file perhaps? A .pdb file is pretty much always a
pdb
> file but a .seq file can be swissprot, fasta or several others.
>=20
>=20
> Mark.
>=20
> -----Original Message-----
> From: bioclipse-devel-admin@...
> [mailto:bioclipse-devel-admin@...] On Behalf Of
Emig,
> Robin
> Sent: Monday, March 27, 2006 6:46 PM
> To: egonw@...; bioclipse-devel@...
> Subject: RE: [Bioclipse-devel] BiojavaResource
>=20
> I'm a big fan of the way MOE and Mesquite load files
>=20
> Allow user to open ANY file
> Then go to another dialog to actually parse it
>=20
> Text version of parse dialog....
> We can use the biojava stuff to guess the file, and then read in....
> ------------------------------------------------------------
> - File Data:          | Open file as...   | Example format
> -                     | Sequence: Fasta   | >sequencename annotations
> - >sequence blah blah | Sequence: MSF     | sequence
> - ATGAMGIALMD         | Alignment: MSF    | sequence
> - KLKLKLKPRLKTLK      | Sequence: Genbank |
> -                     | Recommend: Sequence:Fasta |
> ------------------------------------------------------------
>=20
> -Robin
>=20
> -----Original Message-----
> From: bioclipse-devel-admin@...
> [mailto:bioclipse-devel-admin@...] On Behalf Of Egon
> Willighagen
> Sent: Sunday, March 26, 2006 9:33 PM
> To: bioclipse-devel@...
> Subject: Re: [Bioclipse-devel] BiojavaResource
>=20
> On Sunday 26 March 2006 21:36, Mark Southern wrote:
> > I propose that we use org.biojava.bio.seq.io.SeqIOTools to guess the
> > type of sequence file and autoload it. Something like:
>=20
> CDK uses such an algorithm for chem files too.
>=20
> > The guessFileType() method IS deprecated in biojava but in many
years
> of
> > using it, it has not failed me.=20
>=20
> You could set up a number of test cases.
>=20
> > In a gui application such as bioclipse=20
> > it makes sense to try to best deal with what ever the user throws at
> > you!
>=20
> Egon
>=20
> --=20
> egonw@...
> Blog: http://chem-bla-ics.blogspot.com/
> GPG: 1024D/D6336BA6
>=20
>=20
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking scripting
> language
> that extends applications into web and mobile media. Attend the live
> webcast
> and join the prime developer group breaking into this new coding
> territory!
>
http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D110944&bid=3D241720&dat=3D1=
21642
> _______________________________________________
> Bioclipse-devel mailing list
> Bioclipse-devel@...
> https://lists.sourceforge.net/lists/listinfo/bioclipse-devel
>=20
> This communication is for use by the intended recipient and contains
> information that may be Privileged, confidential or copyrighted under
> applicable law. If you are not the intended recipient, you are hereby
> formally notified that any use, copying or distribution of this
e-mail,
> in whole or in part, is strictly prohibited. Please notify the sender
by
> return e-mail and delete this e-mail from your system. Unless
explicitly
> and conspicuously designated as "E-Contract Intended", this e-mail
does
> not constitute a contract offer, a contract amendment, or an
acceptance
> of a contract offer. This e-mail does not constitute a consent to the
> use of sender's contact information for direct marketing purposes or
for
> transfers of data to third parties.
>=20
> Francais Deutsch Italiano  Espanol  Portugues  Japanese  Chinese
Korean
>=20
>            http://www.DuPont.com/corp/email_disclaimer.html
>=20
>=20
> -------------------------------------------------------
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> language
> that extends applications into web and mobile media. Attend the live
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/bioclipse-devel
>=20
>=20
> -------------------------------------------------------
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> that extends applications into web and mobile media. Attend the live
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RE: [Bioclipse-devel] Sequence Spread Sheet

[Emig, Robin <Robin.Emig@pi...>]

Here is some additional info..
-Robin

-----Original Message-----
From: Carl Manaster [mailto:carl.manaster@...]=20
Sent: Saturday, March 25, 2006 4:39 PM
To: Emig, Robin
Cc: Ola Spjuth
Subject: Re: [Bioclipse-devel] Sequence Spread Sheet

Hi, Robin,

There's a lot I don't understand here.  My background is programming,
and I've learned the limited amount I needed to about sequencing, so
where what you're asking for doesn't match what I've worked on in the
past, I'll need more fleshed-out examples.

My desire to put chromatograms into the cells comes from my work on
InSNP <http://www.mucosa.de/insnp/>; and SGCaller
<http://www.mucosa.de/sgcaller/help/automatic_calling.html>;, where the
program focusses the user's attention on a tiny bit of the
chromatogram, generally grouping multiple chromatograms together.=20
Particularly in InSNP, this was a very nice approach: navigate in the
pixel-wide sequence represenations to show zoomed-in
chromatogram-level detail.  I'd love for the spreadsheet to be able to
do the job of InSNP, but I am afraid that may be too ambitious (it's
more important to me that it be general-purpose than that it be good
at any one particular purpose).

More comments inline.

>         Very interesting thanks. One feature that exists in our
> alignment tool, as well as in PFAAT(partially due to my request) Is
the
> ability to hide columns, in fact our program automatically hides all
> columns which do not contain variation. However, once you do that, you
> tend to loose sense of distance. The trade off is you can see all the
> differences much more easier than the "pale" method you have come up
> with. Both I think are useful.

I'd like to see a screenshot of this.  I would think that losing the
distance-sense would be a big drawback, but maybe I just don't have
enough experience with the kinds of problems you're working on.


>         I think a good idea would be to brainstorm what are the kind
of
> things we would like to see in an alignment. Whether or not we care
> about all of them is another matter, but could help with initial model
> design. For instance, I hadn't thought of display chromatograms (which
> are basically continuous). Here is an initial list I can come up with:
>
> 1) DNA, RNA, Amino acid alignment

Sure.  Probably a variety of alignment algorithms (pluggable).  In
InSNP, the alignment is very simple because we are aligning to a
reference that is assumed to be good, so variations are basically
measured from that.  In more conventional MSA situations, all the
sequences are "equal" in value, so deciding whether to treat a
particular mutation as an insertion or a deletion is less simple.=20
There are lots of good programs out there and I would try to take
advantage of them.  I gather Biojava (of which I'm hoping to make
extensive use) doesn't do MSA, but I haven't looked into it very much.


> 2) More than one of the above ie
>
>  M   *
> ATG TAG
>  M   M
> ATG ATG

Graphically this could be a bit of a challenge for the "stripes" view
because each amino acid is, like each base, only one pixel wide.  If
we puffed out the AAs to fill, they would look longer than they really
are; also coloring gets increasingly complex if we're trying to do
color by reference and have meaningful colors across sequence types.=20
But I'm sure there are things we could do.


> 3) Chromatograms (note these generally are considered continuous)
>
>   A  T  G
> _/-\_/\_/^^\

Here I'd like to be able to specify the range of bases to display,
also which bases (ACGT) to display, and ideally to overlap multiple
chromatograms as mentioned above.


> 4) Contact Maps
>
> MARTGIPLKRTS
>   |_____|

I don't know what this means.

---
This is a contact map between amino acids in the three dimensional
structure of the protein. Ie R contacts with K, they get more
complicated, but I couldn't find a better example


> 5) Conservation Profile
>         a) graph
>         b) sequence logos

Again, I'm not clear on this.
http://weblogo.berkeley.edu/


> 6) Annotations (ie instead of sequence, display R group pKa *value*)
>     a) sequence level (like a name or assay value), column level (like
a
> watch this column), position in sequence level (this position in this
> sequence has a mutation, * it)

--- initial alignment
MTAGLP
MTPSLA
MAASLV

  *  *              Column level alignment (important positions)
MTAGLP
MTPSLA
MAASLV

Take a look at PFAAT, it actually does a really good job on the above,
BUT they made it protein only.....

But if you had annotated the amino acids, you could display (made up
numbers) instead...


0 13.6 0 0 8.6 2.6
0 13.6 2.6 2.3 0
0 0.0  0.0 2.3 3.3


Sorry; I'm lost again.


> 7) Graphics (ie beta sheet/alpha helix)

Here, I'd like to take advantage of the rest of Bioclipse; maybe the
Jmol component can do this?  I intend for the sequence spreadsheet to
be very tightly focussed on sequence, and that it can reach out to
other components that are good at other things.  But maybe you have
something else in mind?  I don't mean to say this is how it has to be,
just this is how I've been thinking about it.


---
Think of this more as an annotation, that this region is in an
alphahelix. In general I was thinking of display graphics for
annotations. Ie what if this position was hydrogen bonding with the
ligand, and we display and O:H picture , maybe it is phosphoralated,
etc, etc.


> 8) Boxes for groups of columns, or sequences
>         Similar to what you have shown in your document with different
> colors, but with actual boxes and labels around them

Can you mock up an example?  Pictures always work best for me.

----
See attached, (note totally made up)



> 9) "Overview" single pixel color diagram (ie minimap)
>         a) could also be a view of the sequence annotation

Is this like the "sequence chart" in InSNP?

-- this is that mini-map version on the left in your program


> 10) Walking property value (ie unit of a bar chart)

I can see how this could be useful.  It could extend into other
domains as well; an in-cell bar chart could be handy in lots of
places.  The immediate problem I have is that it represents a
multivalued entity - a series of numbers rather than an individual
number, and spreadsheets typically hold only single-valued entities
(so things like how to enter or display as text need a lot of careful
thought).  Of course, sequences are themselves multivalued, but their
natural representation as strings makes this less of an issue.  Until
I start wanting chromatograms and then it's a whole new kettle of
fish...  Anyway, I know what you mean here and I agree it would be
nice.

> 11) Sequence Alignment offsets (ie for comparative genomics, or blast
> search type alignments) (spice, Vnti blast, have examples of this)

Again, a graphical example would help me.  There is a simple FIND
function in the current program that gives the offset of a
subsequence, but I sense you want something more sophisticated here.


Actually, the more I think of it, this doesn't make sense here, it would
for more of a simple two sequence alignment, but not really anything
else.

Thanks for your continued interest.

Peace,
--Carl

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RE: [Bioclipse-devel] BiojavaResource

[Ola Spjuth <ola.spjuth@fa...>]

Hi,

I have been thinking a lot about this and decided:

For Bioclipse vers 1.0:
	Use file extensions and levels to decide original type
	On parse, decide final type that could be other than original type

For future versions we could:
	Implement a scanner to read e.g. first 10 rows and decide FAST the
actual file format/BioResourceType

I don't really see how your proposal differs from my implementation,
given that the parser can handle multiple types. If the parser cannot
parse a file, it returns null and the next parser (with a lower level)
can give it a try.

> Only some types of file perhaps? A .pdb file is pretty much always a pdb
> file but a .seq file can be swissprot, fasta or several others.

This is exactly the way it works now. I think we already have the functionality implemented in Bioclipse. Let me know if I have misunderstood things.

Cheers,

   .../Ola


On Tue, 2006-03-28 at 11:59 -0500, Mark Southern wrote:
> 
> -----Original Message-----
> From: Mark Southern 
> Sent: Tuesday, March 28, 2006 11:59 AM
> To: 'Emig, Robin'
> Subject: RE: [Bioclipse-devel] BiojavaResource
> 
> I like this idea too. Meta data about the user's files would need to be
> stored though, else the next time they start bioclipse they'd be asked
> the same questions.
> 
> Only some types of file perhaps? A .pdb file is pretty much always a pdb
> file but a .seq file can be swissprot, fasta or several others.
> 
> 
> Mark.
> 
> -----Original Message-----
> From: bioclipse-devel-admin@...
> [mailto:bioclipse-devel-admin@...] On Behalf Of Emig,
> Robin
> Sent: Monday, March 27, 2006 6:46 PM
> To: egonw@...; bioclipse-devel@...
> Subject: RE: [Bioclipse-devel] BiojavaResource
> 
> I'm a big fan of the way MOE and Mesquite load files
> 
> Allow user to open ANY file
> Then go to another dialog to actually parse it
> 
> Text version of parse dialog....
> We can use the biojava stuff to guess the file, and then read in....
> ------------------------------------------------------------
> - File Data:          | Open file as...   | Example format
> -                     | Sequence: Fasta   | >sequencename annotations
> - >sequence blah blah | Sequence: MSF     | sequence
> - ATGAMGIALMD         | Alignment: MSF    | sequence
> - KLKLKLKPRLKTLK      | Sequence: Genbank |
> -                     | Recommend: Sequence:Fasta |
> ------------------------------------------------------------
> 
> -Robin
> 
> -----Original Message-----
> From: bioclipse-devel-admin@...
> [mailto:bioclipse-devel-admin@...] On Behalf Of Egon
> Willighagen
> Sent: Sunday, March 26, 2006 9:33 PM
> To: bioclipse-devel@...
> Subject: Re: [Bioclipse-devel] BiojavaResource
> 
> On Sunday 26 March 2006 21:36, Mark Southern wrote:
> > I propose that we use org.biojava.bio.seq.io.SeqIOTools to guess the
> > type of sequence file and autoload it. Something like:
> 
> CDK uses such an algorithm for chem files too.
> 
> > The guessFileType() method IS deprecated in biojava but in many years
> of
> > using it, it has not failed me. 
> 
> You could set up a number of test cases.
> 
> > In a gui application such as bioclipse 
> > it makes sense to try to best deal with what ever the user throws at
> > you!
> 
> Egon
> 
> -- 
> egonw@...
> Blog: http://chem-bla-ics.blogspot.com/
> GPG: 1024D/D6336BA6
> 
> 
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RE: [Bioclipse-devel] BiojavaResource

[Emig, Robin <Robin.Emig@pi...>]

Yes, I think this is how the JBoss IDE (maybe eclipse in general)
handles opening up xml files as text, xml, or specific config files, I
like it. Plus, we could always just default to the recommended so the
user only has to click ok.
-Robin

-----Original Message-----
From: Mark Southern [mailto:southern@...]=20
Sent: Tuesday, March 28, 2006 8:59 AM
To: Emig, Robin
Subject: RE: [Bioclipse-devel] BiojavaResource

I like this idea too. Meta data about the user's files would need to be
stored though, else the next time they start bioclipse they'd be asked
the same questions.

Only some types of file perhaps? A .pdb file is pretty much always a pdb
file but a .seq file can be swissprot, fasta or several others.


Mark.

-----Original Message-----
From: bioclipse-devel-admin@...
[mailto:bioclipse-devel-admin@...] On Behalf Of Emig,
Robin
Sent: Monday, March 27, 2006 6:46 PM
To: egonw@...; bioclipse-devel@...
Subject: RE: [Bioclipse-devel] BiojavaResource

I'm a big fan of the way MOE and Mesquite load files

Allow user to open ANY file
Then go to another dialog to actually parse it

Text version of parse dialog....
We can use the biojava stuff to guess the file, and then read in....
------------------------------------------------------------
- File Data:          | Open file as...   | Example format
-                     | Sequence: Fasta   | >sequencename annotations
- >sequence blah blah | Sequence: MSF     | sequence
- ATGAMGIALMD         | Alignment: MSF    | sequence
- KLKLKLKPRLKTLK      | Sequence: Genbank |
-                     | Recommend: Sequence:Fasta |
------------------------------------------------------------

-Robin

-----Original Message-----
From: bioclipse-devel-admin@...
[mailto:bioclipse-devel-admin@...] On Behalf Of Egon
Willighagen
Sent: Sunday, March 26, 2006 9:33 PM
To: bioclipse-devel@...
Subject: Re: [Bioclipse-devel] BiojavaResource

On Sunday 26 March 2006 21:36, Mark Southern wrote:
> I propose that we use org.biojava.bio.seq.io.SeqIOTools to guess the
> type of sequence file and autoload it. Something like:

CDK uses such an algorithm for chem files too.

> The guessFileType() method IS deprecated in biojava but in many years
of
> using it, it has not failed me.=20

You could set up a number of test cases.

> In a gui application such as bioclipse=20
> it makes sense to try to best deal with what ever the user throws at
> you!

Egon

--=20
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6


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RE: [Bioclipse-devel] BiojavaResource

[Mark Southern <southern@sc...>]

-----Original Message-----
From: Mark Southern=20
Sent: Tuesday, March 28, 2006 11:59 AM
To: 'Emig, Robin'
Subject: RE: [Bioclipse-devel] BiojavaResource

I like this idea too. Meta data about the user's files would need to be
stored though, else the next time they start bioclipse they'd be asked
the same questions.

Only some types of file perhaps? A .pdb file is pretty much always a pdb
file but a .seq file can be swissprot, fasta or several others.


Mark.

-----Original Message-----
From: bioclipse-devel-admin@...
[mailto:bioclipse-devel-admin@...] On Behalf Of Emig,
Robin
Sent: Monday, March 27, 2006 6:46 PM
To: egonw@...; bioclipse-devel@...
Subject: RE: [Bioclipse-devel] BiojavaResource

I'm a big fan of the way MOE and Mesquite load files

Allow user to open ANY file
Then go to another dialog to actually parse it

Text version of parse dialog....
We can use the biojava stuff to guess the file, and then read in....
------------------------------------------------------------
- File Data:          | Open file as...   | Example format
-                     | Sequence: Fasta   | >sequencename annotations
- >sequence blah blah | Sequence: MSF     | sequence
- ATGAMGIALMD         | Alignment: MSF    | sequence
- KLKLKLKPRLKTLK      | Sequence: Genbank |
-                     | Recommend: Sequence:Fasta |
------------------------------------------------------------

-Robin

-----Original Message-----
From: bioclipse-devel-admin@...
[mailto:bioclipse-devel-admin@...] On Behalf Of Egon
Willighagen
Sent: Sunday, March 26, 2006 9:33 PM
To: bioclipse-devel@...
Subject: Re: [Bioclipse-devel] BiojavaResource

On Sunday 26 March 2006 21:36, Mark Southern wrote:
> I propose that we use org.biojava.bio.seq.io.SeqIOTools to guess the
> type of sequence file and autoload it. Something like:

CDK uses such an algorithm for chem files too.

> The guessFileType() method IS deprecated in biojava but in many years
of
> using it, it has not failed me.=20

You could set up a number of test cases.

> In a gui application such as bioclipse=20
> it makes sense to try to best deal with what ever the user throws at
> you!

Egon

--=20
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6


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RE: [Bioclipse-devel] BiojavaResource

[Emig, Robin <Robin.Emig@pi...>]

I'm a big fan of the way MOE and Mesquite load files

Allow user to open ANY file
Then go to another dialog to actually parse it

Text version of parse dialog....
We can use the biojava stuff to guess the file, and then read in....
------------------------------------------------------------
- File Data:          | Open file as...   | Example format
-                     | Sequence: Fasta   | >sequencename annotations
- >sequence blah blah | Sequence: MSF     | sequence
- ATGAMGIALMD         | Alignment: MSF    | sequence
- KLKLKLKPRLKTLK      | Sequence: Genbank |
-                     | Recommend: Sequence:Fasta |
------------------------------------------------------------

-Robin

-----Original Message-----
From: bioclipse-devel-admin@...
[mailto:bioclipse-devel-admin@...] On Behalf Of Egon
Willighagen
Sent: Sunday, March 26, 2006 9:33 PM
To: bioclipse-devel@...
Subject: Re: [Bioclipse-devel] BiojavaResource

On Sunday 26 March 2006 21:36, Mark Southern wrote:
> I propose that we use org.biojava.bio.seq.io.SeqIOTools to guess the
> type of sequence file and autoload it. Something like:

CDK uses such an algorithm for chem files too.

> The guessFileType() method IS deprecated in biojava but in many years
of
> using it, it has not failed me.=20

You could set up a number of test cases.

> In a gui application such as bioclipse=20
> it makes sense to try to best deal with what ever the user throws at
> you!

Egon

--=20
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6


-------------------------------------------------------
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and join the prime developer group breaking into this new coding
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Re: [Bioclipse-devel] BiojavaResource

[Egon Willighagen <egonw@us...>]

On Sunday 26 March 2006 21:36, Mark Southern wrote:
> I propose that we use org.biojava.bio.seq.io.SeqIOTools to guess the
> type of sequence file and autoload it. Something like:

CDK uses such an algorithm for chem files too.

> The guessFileType() method IS deprecated in biojava but in many years of
> using it, it has not failed me. 

You could set up a number of test cases.

> In a gui application such as bioclipse 
> it makes sense to try to best deal with what ever the user throws at
> you!

Egon

-- 
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6

Re: [Bioclipse-devel] bc_biojava plugin / svn authorization error.

[Egon Willighagen <egonw@us...>]

Hi Mark,

(very nice screenshot!)

On Sunday 26 March 2006 21:19, Mark Southern wrote:
> I updated SequenceView.java in the bc_bioclipse project but I was unable
> to update the jars/biojava.jar file to the latest live version of
> biojava (svn authorization problem).

Is it not supposed to go into bc_biojava?

> Authorization failed
>
> svn: Commit failed (details follow):
>
> svn: MKACTIVITY of
> '/svnroot/bioclipse/!svn/act/e07f0d20-3261-9146-8fac-3a24d8d0d6f8':
> authorization failed (https://svn.sourceforge.net)

I checked, and you do have write access.

> Do I not have permissions for this folder? I need to update to the
> latest biojava because the SequenceView depends on files that are only
> in the biojava CVS.

Join #IRC today... then we'll try to figure it out.

Egon

-- 
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6

[Bioclipse-devel] BiojavaResource

[Mark Southern <southern@sc...>]

When parsing, the BiojavaResource only attempts to read a fasta protein
sequence file.

=20

We probably want to work with many different sequence formats and we
aren't always going to know what format we are going to receive. We also
probably want to be able to handle DNA sequences also.

=20

=20

I propose that we use org.biojava.bio.seq.io.SeqIOTools to guess the
type of sequence file and autoload it. Something like:

=20

File file =3D new File(bioFirst.getPath());

try{

    SequenceIterator iter =3D ( SequenceIterator )
SeqIOTools.fileToBiojava(

            SeqIOTools.guessFileType(file), new BufferedReader(new
FileReader(file))

    );

      while(iter.hasNext())

{    =20

    sequenceDB.addSequence(iter.nextSequence());

}

}

catch(Exception ex){

    logger.error("There was an error opening sequence: " + file);

}

=20

=20

=20

The guessFileType() method IS deprecated in biojava but in many years of
using it, it has not failed me. In a gui application such as bioclipse
it makes sense to try to best deal with what ever the user throws at
you!

=20

=20

~Mark.

=20

=20

[Bioclipse-devel] bc_biojava plugin / svn authorization error.

[Mark Southern <southern@sc...>]

I updated SequenceView.java in the bc_bioclipse project but I was unable
to update the jars/biojava.jar file to the latest live version of
biojava (svn authorization problem).

=20

=20

Authorization failed

svn: Commit failed (details follow):

svn: MKACTIVITY of
'/svnroot/bioclipse/!svn/act/e07f0d20-3261-9146-8fac-3a24d8d0d6f8':
authorization failed (https://svn.sourceforge.net)

=20

=20

=20

Do I not have permissions for this folder? I need to update to the
latest biojava because the SequenceView depends on files that are only
in the biojava CVS.

=20

=20

=20

Thank you!

Re: [Bioclipse-devel] wiki is being spamed

[Ola Spjuth <ola.spjuth@fa...>]

Hi all,

I have now set up so that editing pages on the wiki requires
registration. Seemed like the only reasonable way to get rid of spammers
using bots.

So from now on, please register in order to edit the wiki. Done in a
breeze.

Cheers,

   .../Ola


On Sat, 2006-03-25 at 13:29, Egon Willighagen wrote:
> Ola, 
> 
> the wiki is being spamed, but I cannot put IP addresses in the black list at:
> 
> http://wiki.bioclipse.net/index.php?title=Special:Ipblocklist
> 
> Egon
-- 
Ola Spjuth
Dept of pharmaceutical biosciences
Uppsala University, Sweden

[Bioclipse-devel] wiki is being spamed

[Egon Willighagen <egonw@us...>]

Ola, 

the wiki is being spamed, but I cannot put IP addresses in the black list at:

http://wiki.bioclipse.net/index.php?title=Special:Ipblocklist

Egon

-- 
egonw@...
Blog: http://chem-bla-ics.blogspot.com/
GPG: 1024D/D6336BA6

Re: [Bioclipse-devel] Problems downloading Bioclipse

[Ola Spjuth <ola.spjuth@fa...>]

I agree.
Let us add 128M to the bioclipse.product VM-settings.

I have been unable to do much work this week due to my eye surgery but
hopefully I will be up to speed next week again.

Cheers,

   .../Ola


On Fri, 2006-03-24 at 17:46, Stefan Kuhn wrote:
> Ola,
> well, the solution isn't to hard, as you could see. I am just wondering why 
> nobody else has memory problems. We should perhaps make sure that the 
> distributions we make in the future start up with more than 64m, which is not 
> a lot. At least 128 should be no problem on today's computers.
> Stefan
> 
> Am Friday 24 March 2006 16:57 schrieb Miguel Rojas Cherto:
> > Ei all,
> >
> > I had done a new import from Bioclipse. And now I found the following
> > problem: The bioclipse platform can't be instanced. I've got this
> > error:
> >
> >
> > !ENTRY org.eclipse.osgi 2006-03-24 16:07:35.99
> > !MESSAGE Application error
> > !STACK 1
> > java.lang.OutOfMemoryError: Java heap space
> >
> >
> >
> > Had anybody the same problem or know the solution?
> >
> > cheers,
> >  Miquel
-- 
Ola Spjuth
Dept of pharmaceutical biosciences
Uppsala University, Sweden

Re: [Bioclipse-devel] Problems downloading Bioclipse

[Ola Spjuth <ola.spjuth@fa...>]

Never experienced it,
Try VM-args: -Xmx128M or a large enough setting.

Cheers,

   .../Ola


On Fri, 2006-03-24 at 16:57, Miguel Rojas Cherto wrote:
> Ei all,
> 
> I had done a new import from Bioclipse. And now I found the following
> problem: The bioclipse platform can't be instanced. I've got this
> error: 
> 
> 
> !ENTRY org.eclipse.osgi 2006-03-24 16:07:35.99
> !MESSAGE Application error
> !STACK 1
> java.lang.OutOfMemoryError: Java heap space
> 
> 
> 
> Had anybody the same problem or know the solution?
> 
> cheers,
> Miquel
-- 
Ola Spjuth
Dept of pharmaceutical biosciences
Uppsala University, Sweden

Re: [Bioclipse-devel] Problems downloading Bioclipse

[Stefan Kuhn <stefan.kuhn@un...>]

Ola,
well, the solution isn't to hard, as you could see. I am just wondering w=
hy=20
nobody else has memory problems. We should perhaps make sure that the=20
distributions we make in the future start up with more than 64m, which is=
 not=20
a lot. At least 128 should be no problem on today's computers.
Stefan

Am Friday 24 March 2006 16:57 schrieb Miguel Rojas Cherto:
> Ei all,
>
> I had done a new import from Bioclipse. And now I found the following
> problem: The bioclipse platform can't be instanced. I've got this
> error:
>
>
> !ENTRY org.eclipse.osgi 2006-03-24 16:07:35.99
> !MESSAGE Application error
> !STACK 1
> java.lang.OutOfMemoryError: Java heap space
>
>
>
> Had anybody the same problem or know the solution?
>
> cheers,
>  Miquel

--=20
Stefan Kuhn M. A.
Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de)
Z=C3=BClpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7428   Fax: +49 (0) 221-470-7786
My public PGP key is available at http://pgp.mit.edu

[Bioclipse-devel] Problems downloading Bioclipse

[Miguel Rojas Cherto <miguel.rojas@un...>]

Ei all,

I had done a new import from Bioclipse. And now I found the following
problem: The bioclipse platform can't be instanced. I've got this
error: 


!ENTRY org.eclipse.osgi 2006-03-24 16:07:35.99
!MESSAGE Application error
!STACK 1
java.lang.OutOfMemoryError: Java heap space



Had anybody the same problem or know the solution?

cheers,
 Miquel

[Fwd: Re: [Bioclipse-devel] Bioclipse listed on eclipse.org]

[Ola Spjuth <ola.spjuth@fa...>]

-----Forwarded Message-----
From: Ola Spjuth <ola.spjuth@...>
To: Daniel Kröni <daniel.kroeni@...>
Subject: Re: [Bioclipse-devel] Bioclipse listed on eclipse.org
Date: Fri, 24 Mar 2006 14:44:51 +0100

Hi Daniel,

On Fri, 2006-03-24 at 11:48, Daniel Kröni wrote:
> thanks!
> 
> about the mail i wrote 10mins before.. forget it! =)
> your preference pages are correctly registered and so is your initializer.
> do you really have instantiate and call the PreferenceInitializer by your own?

I actually don't know! Because of testing it was convenient for me to
programatically call it.

> 
> and you have an activator class too (BioclipsePlugin). why don't you
> use, activate this bundle?

I got the impression that a bundle activator was not needed and maybe
even outdated for RCP applications, but I am by no means sure about it.
What would be the benefit of including it?

Cheers,

   .../Ola
-- 
Ola Spjuth
Dept of pharmaceutical biosciences
Uppsala University, Sweden