Hi Betina,
It's kind of hard for me to determine for sure what's going one without
access to the data. But there's quite a bit that goes on for generating
the ID to be used in the URL. You might want to create your own
instance of DisplayPrefsI (which can be extended from
DefaultDisplayPrefs) to handle your URL generation. Of particular
interest should be DefaultDisplayPrefs.generateURL() and
DefaultDisplayPrefs.getIdForURL(). If you at least set breakpoints
at those locations you can see how the IDs are being generated
for each different feature.
If you end up writing your own DisplayPrefsI instance, you can
load by adding the following to your style file:
DisplayPreferences "apollo.config.MyDisplayPrefs"
Hope this helps.
Cheers,
Ed
On Mon, 6 Jul 2009, Betina Porcel wrote:
Hi Ed, Jonathan, and all the Apollo's out there!
I understand what you mean both mean, but unfortunately, that's not the case
:-( !
When I'm saying "gene modle" I'm talking about a feature on the results
pannel (the black one).
I'm using the Apollo default stuff (as for the name adapter). But when
trying to link to my GGB using "Get info for this feature via web", sometimes
is working and sometimes not (even though the data in the chadodb is the same
for both cases).
The only difference so far is that is working pretty well for spliced gene
models but not for single-exon ones! (perhaps that's the reason? The way in
which I can select the model?).
I mean, if the gene model is a multi-exon one:
-> I click on one intron or double click in the model
-> the whole model is highlighted in red
-> use the "Get info for this feature via web" and I'm arriving where I
wanted: Apollo is using the feature'sID to get the correct region on the GGB,
like in the example below:
DEBUG: SDP: firstFeature = [SeqFeature Gaze:84722-84862 (id
GSCHCE00002483001): type = Gaze:Chcr_wss_Gaze, biotype = null, range =
84722-84862, parent = GSCHCT00002483001]
........
isRightMouseButton = true, isMiddleMouseButton = false, isLeftMouseButton =
false, apollo.util.IOUtil.isMac = false, evt.isAltDown() = false;
evt.isControlDown() = false
DEBUG: loading web page
https://www.genoscope.cns.fr/secure-nda/XXXXXXXX/cgi-bin/gbrowse/XXXXXXXX/?name=GSCHCT00002483001
the information on the chadodb for this gene model being
select * from feature where name='GSCHCT00002483001';
feature_id | dbxref_id | organism_id | name | uniquename
| residues | seqlen | md5checksum | type_id | is_analysis | is_obsolete |
timeaccessioned | timelastmodified
------------+-----------+-------------+-------------------+-------------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+----------------------------
6080134 | | 14 | GSCHCT00002483001 | GSCHCT00002483001
| | | | 319 | t | f |
2009-06-26 11:35:14.957132 | 2009-06-26 11:35:14.957132
BUT when using a single-exon model (so, double clicking on the model, the
whole model highlighted in red and use the "Get info for this feature via
web" from the pop-up menu) is not working at all
DEBUG: SDP: firstFeature = [SeqFeature Gaze:76296-77840 (id
GSCHCE00002478001): type = Gaze:Chcr_wss_Gaze, biotype = null, range =
76296-77840, parent = GSCHCT00002478001]
.........
DEBUG: MouseButtonEvent: got right mouse event.
DEBUG: Mon Jul 06 17:18:34 CEST 2009 MouseButtonEvent: checking for middle
mouse event.
JVM = 1.6.0_07
isRightMouseButton = true, isMiddleMouseButton = false, isLeftMouseButton =
false, apollo.util.IOUtil.isMac = false, evt.isAltDown() = false;
evt.isControlDown() = false
DEBUG: loading web page
https://www.genoscope.cns.fr/secure-nda/Chondrus/cgi-bin/gbrowse/chondrus/?name=Gaze:76296-77840
select * from feature where name='GSCHCT00002478001';
feature_id | dbxref_id | organism_id | name | uniquename
| residues | seqlen | md5checksum | type_id | is_analysis | is_obsolete |
timeaccessioned | timelastmodified
------------+-----------+-------------+-------------------+-------------------+----------+--------+-------------+---------+-------------+-------------+----------------------------+----------------------------
6073878 | | 14 | GSCHCT00002478001 | GSCHCT00002478001
| | | | 319 | t | f |
2009-06-26 11:35:14.957132 | 2009-06-26 11:35:14.957132
I guess the problem is just the way to select the model (since it's a
single-exon one, it's difficult to be sure that I've chosen it as a model and
not as the exon itself!), is there another way to select a model, when it's
only one exon?!?
Thanks in advanced,
Betina
Ed Lee a écrit :
Hi Betina,
Just to make sure we're on the same page, when you say "gene model" you
mean a feature in the annotation panel, correct? The URL link uses
the feature's ID, so as Jonathan mentioned, you'll want to have your
name adapter define how the IDs should be set.
Cheers,
Ed
On Tue, 30 Jun 2009, Jonathan Crabtree wrote:
Hi Betina,
If you haven't overridden the Apollo default (e.g. by defining your own
name
adapter and/or display preferences class) then I think it's quite possible
that the analysis name plus the genomic coordinates _is_ the id/display
name
of the feature in question. I think this is what Apollo uses in the chado
JDBC adapter when it doesn't have anything better to use (and no
database-specific alternative has been provided via one of the files I
just
mentioned--I forget which one, probably the display preferences file.) If
you select "Show labels" for the tier in question you should be able to
see
if this is the case.
Jonathan
On Tue, Jun 30, 2009 at 11:32 AM, Betina Porcel <[email protected]>
wrote:
Hi everybody!
Here the problem: I'm using (still!) Apollo1.10.0 connected to a
Chado DB, and I'm having problems when trying to get additional
information for a feature via the web. My Apollo is linked to
the GBrowse, as shown in the xxx.tiers file
[Type]
tiername : Gene Integration
typename : Gaze
resulttype : Gaze:XXXX_wss_Gaze
color : 0,0,255
usescore : true
glyph : DrawableResultFeatureSet
column : SCORE
column : GENOMIC_RANGE
column : query_frame
sortbycolumn : GENOMIC_RANGE
weburl :
https://www.genoscope.cns.fr/secure-nda/XXXXX/cgi-bin/gbrowse/XXXX/?name=
1) launch apollo on my Linux (Java version: 1.6.0_04) -> OK
2) search for my gene model -> OK
But when selecting the gene model feature, it doesn't always
get the right link using the "Get info for this feature via web"
when working, it points out on
thehttps://www.genoscope.cns.fr/secure-nda/XXXXX/cgi-bin/gbrowse/XXXX/?name=GS
CHCT00011788001
but sometimes just get
https://www.genoscope.cns.fr/secure-nda/XXXXX/cgi-bin/gbrowse/XXXX/?name=Ga
ze:164606-163765
so, the name (in the analysis table from Chado) and the
start-end of the genomic region (instead of the gene model ID).
Any ideas why this can happen?
Thanks a lot!!
Betina
--------------------------------------------------
Betina Porcel
Analyse de séquences de génomes eucaryotes
(Coordination Plateforme d'Annotation Experte)
Genoscope - Institut de Génomique - CEA
2, rue Gaston Crémieux CP5706
91057 Evry CEDEX France
Tel: +33 (0)1 60 87 25 20
Fax: +33 (0)1 60 87 25 14
E-mail: [email protected]
--------------------------------------------------
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