Hi Lochana,
I think you sure will need Multi-threading to keep the UI responsive and
also some form of cache, meaning if you display 10 compounds in the
"viewport" of the table, keep a lot more in memory, maybe 100 both up or
down and when the user scrolls, adjust the cache accordingly but the
scrolling will be fluid and fast.
Use this with the RandomAccessSDFReader. I don't know it's performance
and I guess the indexing phase can take pretty long. Hence that should
be run in the background. Maybe you can extend it to use above mentioned
cache because it sill uses file access and that is always very, very
slow compared to memory.
Or create your own reader that can quickly jump to the desired record
but does not need any indexing. eg. if you display record 100 to 110,
and have as example records 50 to 150 in cache and user scrolls up 1
page read records 40-49 from the file into the cache. Hint: record 40
(assuming index 0-based) starts at the 40th occurrence of $$$$. So
maybe just indexing all $$$$ positions could suffice (no idea how fast
that is in a large file). With this I would probably cache more like in
the 1000 record range and not adjust cache for every single page change.
Anyway I don't think this can be made fast without some significant effort.
Best Regards,
Joos
Am 18.09.2013 19:46, schrieb lochana menikarachchi:
> Hi Everyone,
>
> I need to quickly load 5-10 molecules to a jTable from a large SD
> file(say 1 million structures). The table needs to be updated by
> loading only 5-10 structures as the user scrolls down the table. I
> tried various SDF readers in CDK. Iterating reader,
> RandomAccessSDFReader but, they are extremely slow compared to what
> MarvinView (written in java) has. MarvinView can load 5-10 structures
> from extremely large files in few seconds. I wonder how marvin does
> this?? Any suggestions to replicate this functionality with CDK??
>
> Thanks.
>
> Lochana
>
>
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