Re: [Scaffoldhunter-devel] export clustering results

[Till S. <til...@tu...>]

Hi, 
SH currently does not support an export of the clustering results yet. The clustering results are stored as serialized session data in an XML format and stored in a single database field (session_data.session_data). The results are therefore not so easy to extract from the database directly, but it should be possible to reconstruct them with an XML Parser. Alternatively, if you are just interested in the flat clustering (and not the hierarchy) you can create  and export a subset for each cluster by clicking the horizontal dendrogram bar of each clusters LCA (lowest common ancestor) to select the complete cluster/subtree at once (its might be a bit cumbersome for many clusters). If you are familiar with Java, you can also simply modify SH and create a custom export by grabbing the root node of the dendrogram, which is stored as an attribute of the dendrogram view.  The node class is called HierarchicalClusterNode. It simply has a left and right child  or contains a reference to the associated molecule, in the case of leaf nodes.

If you are interested in a functionality to automatically create subsets based on the partitioning implied by the cluster selection bar (the red bar which is draggable) or to export the complete hierarchy, please open a feature request at [1]. If you can elaborate your goal a bit deeper, we can also think about other workarounds.

Regards,
Till

[1] https://sourceforge.net/p/scaffoldhunter/feature-requests/?source=navbar

Am Donnerstag, 14. Juli 2016, 12:27:14 schrieb Gonzalo Colmenarejo:
> Hi,
> 
> how can I export the clustering results appearing in the SH? Or at least is
> it there in the database? If yes what would be the tables involved?
> 
> Thanks
> 
> Gonzalo
-- 
Dipl.-Inf. Till Schäfer
TU Dortmund University
Chair 11 - Algorithm Engineering
Otto-Hahn-Str. 14 / Room 237
44227 Dortmund, Germany

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