gmod-cmap — Discussion of the CMAP comparative map viewer

Re: [gmod-cmap] Problem CMAP with feature_name displaying in CMAP

[Ken Youens-C. <kc...@cs...>]

On Jan 20, 2009, at 11:14 AM, Chantal Hamelin wrote:

> Hi,
>
> We have created a map in CMAP where there are features such as  
> markers and QTLs. QTLs were first named with a number but we changed  
> our mind and decided to rename them by concatening the trait name  
> and the number. For instance the QTL n°1195 for the trait Days to  
> flowering became Days_to_flowering_1195. We changed directly the  
> feature_name in the cmap_feature table in CMAP but the result is the  
> following (see below), only one map (no 10) over 12 displays the  
> QTLs with their new names, the others maps still displays the QTLs  
> with their old feature_name (a number). We saw also that if we  
> change the total magnification on map 10 (for instance we choose 2)  
> the QTLs are displayed with their old name (a number). Afterwards if  
> we use the previous magnification the old QTL names (numbers) are  
> still displayed, we cannot display again the QTLs with their new  
> names.
> A detail is that the map 10 is the one which has the fewer number of  
> markers and QTLs.
> It seems that the feature_name displayed varies with the  
> magnification of the map but we don't understand why at the original  
> magnification one map only (no 10) if displayed as we want.
>
>
> Can you help us ?

Chantal,

Have you reset the cache?  If not, use "cmap_admin.pl" on the server  
where CMap is running and choose "[10] Purge the cache to view new  
data."  I believe that should help.

> Another problem is the length varchar(32) of the feature_name in  
> table cmap_feature, can we increase this length ?


Yes, just use the "ALTER TABLE" command in MySQL.  It shouldn't hurt  
anything, but remember to do this again in the future should you move  
to a new db.

ky

[gmod-cmap] Problem CMAP with feature_name displaying in CMAP

[Chantal H. <cha...@ci...>]

Hi,

We have created a map in CMAP where there are features such as markers 
and QTLs. QTLs were first named with a number but we changed our mind 
and decided to rename them by concatening the trait name and the number. 
For instance the QTL n°1195 for the trait Days to flowering became 
Days_to_flowering_1195. We changed directly the feature_name in the 
cmap_feature table in CMAP but the result is the following (see below), 
only one map (no 10) over 12 displays the QTLs with their new names, the 
others maps still displays the QTLs with their old feature_name (a 
number). We saw also that if we change the total magnification on map 10 
(for instance we choose 2) the QTLs are displayed with their old name (a 
number). Afterwards if we use the previous magnification the old QTL 
names (numbers) are still displayed, we cannot display again the QTLs 
with their new names.
A detail is that the map 10 is the one which has the fewer number of 
markers and QTLs.
It seems that the feature_name displayed varies with the magnification 
of the map but we don't understand why at the original magnification one 
map only (no 10) if displayed as we want.
Another problem is the length varchar(32) of the feature_name in table 
cmap_feature, can we increase this length ?

Can you help us ?

Best regards.



?cmap

-- 
Chantal HAMELIN
CIRAD - Département Systèmes Biologiques
UMR Développement et Amélioration des Plantes - Equipe Intégration des données                      

TA A96/03
Avenue Agropolis
34398 Montpellier Cedex 5
FRANCE


Tél : (33) 4 67 61 59 75
Fax : (33) 4 67 61 56 05	
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