cmbi / vase

Visualization of Alignments Structures and Entropy

VASE

Visualization of Alignments Structures and Entropy

Configuration:

The configuration file is at src/main/resources/config.properties

If you want the users to be able to submit custom structures, then you must set 'hsspcache' to a valid writable directory.

If you only want VASE to display the content of a series of VASE-format xml files, then you can set 'xmlonly' to true and set the 'cache' path to the directory where the files are located.

Build & Install

VASE requires maven 2 to compile. (http://maven.apache.org/) You can build the war file by running "mvn package" from the root directory. Then deploy it.

vase's Issues

alignment page responsiveness

The larger an alignment (rows * columns) the slower the page responds to column selections by the user. (plot/table/alignment/jmol) The javascript takes more time to find all the elements that match the selection.

licensing

There's no licence yet to release VASE under. When a licence is chosen, the headers of the source files must be adapted.

adapt alignment page to window size

The alignment page has two scrollable divs: alignment and table, plus several plots that can have variable sizes. We need to make the page adapt to the browser's window size somehow, because now they just have a fixed width.

The user must always get a page where all items fit in one window without the need for scolling to see other items in the page. Individual panels, like tablesshould be scrollable instead.

using the correct 3-letter code for non-canonical amino acids

Whenever the alignment page needs to display a pdb file with non-canonical amino acids (example: 1hw4). Those amino acids are identified with the three letter code 'XAA'. Jmol can't handle this, it needs the three letter code as is in the PDB file.

null pointer config

If certain fields are not set in the config files, it can cause null pointer exceptions. We must adapt VASE to handle missing settings. For example, if the hssp cache directory is not set, then the job submission page should not be displayed.

entries listing on homepage

At the moment, the homepage is just blank. We could use it for listing all the files in cache.

Form too large

It appears that jetty (and maybe other server applications) has a data size limit on the post requests. This can cause trouble when a large pdb structure is submitted to the restful service.

We need to find a way to remove this limit. HSSPSoap doesn't seem to have it.

readme file

VASE still needs a readme file. It must explain how VASE must be configured(setting directory paths etc. )

Incorrect xssp-rest url

The URL for xssp-rest is incorrect:

private static String hsspRestURL = "http://127.0.0.1:5000/api";//"http://www.cmbi.ru.nl/xssp/api";

1f88/A residues out of sync

When selecting certain residues near the C-terminus in 1f88/A, the table highlights a different residue from the model/alignment.

PDB ID form does not accept capitalized letters

No results are found when a capitalized PDB ID is used for the 'Enter a Structure ID' field. I think '1CRN' should also be allowed (not only '1crn', in particular since the alignment title also shows capitalized identifiers).