Recent changes to feature-requests

#13 extension of IO data formats

2018-07-06T06:11:09.353000Z

Agreed :)

Export of statistical results

2011-08-09T13:40:08Z

the command "File->Export Data" should be able to export information of various statistical tests, e.g. exporting the resulting value of the wilcoxon-test. at the moment this information is just accessable via the tooltip of each node

extension of IO data formats

2010-10-26T09:57:16Z

- BioPax (input, output) to be able to access network databases
- improve SBML input, support for output

Obtaining Kegg Pathways

2010-10-26T07:28:27Z

The power of the Kegg Pathway downloader of VANTED could be increased by adding
an additional functionality: a simple method which gets a species and a set of Kegg pathway IDs
in the form (path:)?KOxxxxx returning the set of graphs.
E.g. VANTED NETS could diretly integrate KEGG pathways in this way.

program arguments should support URLs

2010-10-13T08:19:55Z

The code for loading defined graph files upon start of the program (VANTED/KGML-ED) currently just supports loading local files. This needs to be enhanced to support download and loading of files, residing on any web-servery, as specified by an URL.

Offending code:

if (args!=null) {
for (String f : args) {
File ft = new File(f);
if (ft.exists() && ft.canRead())
MainFrame.getInstance().loadGraph(ft);
}
}

Another loadGraph command also supports URLs, this needs to be called if the argument is an URL.

using "Maven" for lib handling

2010-10-06T13:12:27Z

should get rid of the problems with different lib-versions and allows to reduce the set of libs by removing unneeded ones

algorithms in the menus

2010-10-06T13:09:56Z

check all menu entries:
- consistently (plant/series/line/condition) and intuitively named
- sorted into the correct (named) menugroup
- some algorithms may be grouped (such as the cluster id commands)
- the description (when you enter parameters) should also be checked

improving attribute handling via gui

2010-10-06T13:06:55Z

new attributeditors for setting the gradient, arrow head and edge docking are useful, as the values of these attributes have different meanings (eg arrow head will be scaled according to the thickness of the tail, if the value is between 0 and 1, edge docking is just a string)

most or a selected set of attributes should be deleteable via gui, eg. clusterid, label, mappingdata...

improving flux data visualisation in vanted

2010-10-05T06:09:27Z

it would be nice to improve the flux data visualisation in vanted.

1) import: flux data should be importable by a template, where you specifiy just the flux (eg a reaction a -> b+c should be entered in a way like "a^b+c" and vanted itself creates a small reaction node to implement the hypergraph functionality. at the moment the user has to do it manually by specifying "a->r1", "r1->b" and "r1->c" (technical hint: perhaps a novel data importer would be nice)
2) coupling of data and edge thickness: the flux data should be mapped onto an edge and the shape itself shall react on this data. at the moment the user has to set the thickness of the a) tail and the thickness of the b) arrow manually. these attributes should just scale a) the relation between data and edge thickness (eventually even non-linear (if you have many small, but one big flux)) and b) the relation between tail and arrow-thickness
3) fixing all the redrawing bugs (change of thickness needs redraw)

make image export more user-friendly

2010-09-28T13:46:13Z

(png and probably also jpg is already quite nice)

pdf: the dialog is the same as for svg

all: clipping is not performed properly
- minxy is not clipped (so there may be space in your image in the top-left corner)
- maxxy is clipped to close to the node right- and bottom-most shapes (perhaps more space?)
- surrounding cluster colors are clipepd away