Recent changes to nbrowse-feature-requests-bugs

metadata switch after session loading won't work

Monty Schulman — Wed, 21 Jul 2010 22:06:32 -0000

After loading session file - if user wishes to select different species or database - meta data will not load properly.

problem showing initial go term slection

Monty Schulman — Thu, 01 Apr 2010 14:48:16 -0000

There is a problem showing inital go term selection. The problem is caused by to go terms loading too late after the initial database query. Queries need to be combined into one thread.

pop up needed to indicate no gene interaction

Monty Schulman — Thu, 01 Apr 2010 14:43:59 -0000

A popup is needed to indicate there is no gene interaction.

synonym db loader should add ids as common

Mark Gibson — Fri, 26 Mar 2010 14:47:35 -0000

\so the db is such that if a node/gene has an id/node_primary_name but no common name then
one must put the id in the node synonyms data load file for the server/nbrowse-db/dataloader_node_syn.pl perl script.
If one neglects to do this - as tair has done as its easy to forget - it screws up nbrowse - in that the
nodes actually wont come in with out the common synonym. tair has understandably asked to make this process easier/ more robust.
One easy fix would be to add functionality to the end of dataloader_node_syn script that after all syns are loaded it does a check to see if
there are any nodes that lack a common synonym - and if so then add the id as a common syn. this would be easy to add - and make that part
of the loading easier on folks putting together loading files - one less thing to remember thats sort of tedious to remember

make gui of node attribute query

Mark Gibson — Thu, 25 Mar 2010 20:35:45 -0000

currently can query node attributes with post fix
make user friendly gui

acyclic edges for same node drawn on each other

Monty Schulman — Wed, 24 Mar 2010 18:37:02 -0000

Acyclic edges for same node are drawn on one another. AT5G35750 in TAIR is good example of this. They need to be separated out.

nb1 nb2 diff

Mark Gibson — Tue, 23 Mar 2010 21:59:33 -0000

modifying user docs from nb1 to nb2 points up differences - some interesting some less so:

- Display this # of hops from node - this we want folks have asked for this!

- Hide nodes with more than this many edges - i would think you would want the opposite - whats the use case here?

- rotate on a scroll bar (with zoom) - in nb2 rotate is an obscure mouse option

- anchor all nodes as handy button - todo

- adjust layout - im guessing this is the same as our layout button?

- save list of nodes (not edges)

- find and display all miRNAs predicted - is this the same as miRNA filter in nb2 - does it get special status in nb1 - or is it different?

its useful to go through nb1 user docs

node sizes not always uniform

Monty Schulman — Fri, 12 Mar 2010 20:09:29 -0000

When using the edge filter, and generating new nodes in an existing graph, the new nodes will be the default size. If user changes the node size, the node sizes will not be uniform.

need to have formula setting for spring layout

Monty Schulman — Mon, 01 Mar 2010 14:47:50 -0000

Need to provide formula setting for spring layout. Need to provide formula dialog so that user can use it for doing Spring Layout.
It should be: value1 * edge_value ^ value2 + value3. It will be applied to C1 in formula for edge attraction.

need to able to to shrink nodes to dots

Monty Schulman — Mon, 01 Mar 2010 14:41:46 -0000

Need to be able to shrink to dots when viewing graphs with many edges and using zoom to look at specific ones.