Re: [Scaffoldhunter-devel] Solved [Feature Request #38 : Split Subsets by Scaffolds On a Specified Level]

[Shamshad A. <sha...@gm...>]

Hi,

Thanks for feedback. In the next patch you will find the fix of problems
you pointed out.

Thanks
Shamshad


On Thu, Apr 17, 2014 at 6:53 PM, Till Schäfer <til...@tu...
> wrote:

> Hi,
> i just updated the menu and added some categories as comments and also
> changed the ordering a little bit.
> -> your action should now go to "single subset filters" category.
>
> Viele Grüße
> Till
>
> Am Donnerstag, 17. April 2014, 15:01:53 schrieb Till Schäfer:
> > Hi,
> > it now seems to work for me.
> > It is good to see, that you used a worker thread for the splitting and
> animated the work, because it can take some tome to create many subsets.
> Furthermore i liked that you used the DbExceptionHandler.
> >
> > However, there are still some things to fix before we can integrate the
> patch:
> >
> > - The parent of the new subset should be the subset that is spitted.
> > - The split action should be accessible by right clicking on a subset
> (not only in the menu).
> > - The action should be located int the same section as union /
> intersection / difference / filter.
> > - ModelViewControler: The splitting should be implemented in the
> SubsetManager. The action should just call the method there (have a look at
> the other actions).
> > - Good Coding Style: use two lines of code if you want to define and
> initialize two variable: int ringLevel = subsetDialog.getRingLevel(), index
> = 1;
> > - Hint /  Good Coding Style: you can use the
> Scaffolds.SubtreePreorderIterable to iterate over all scaffolds in a
> subtree (e.v. in your method getMolecules)
> >
> >
> > Greetings
> > Till
> >
> > Am Mittwoch, 16. April 2014, 21:08:42 schrieb Shamshad Alam:
> > > Hi,
> > >
> > > Please, find the patch in attachment, apply and check it.
> > >
> > > Thanks
> > > Shamshad
> > >
> > >
> > >
> > > On Wed, Apr 16, 2014 at 3:21 PM, Till Schäfer <
> til...@tu...
> > > > wrote:
> > >
> > > > Hi,
> > > > lets go back to mailing list communication ;).
> > > >
> > > > Am Mittwoch, 16. April 2014, 14:57:34 schrieb Shamshad Alam:
> > > > > Hi,
> > > > >
> > > > > While working on this feature as you suggested I found that for a
> large
> > > > > dataset there are more than a hundred scaffolds at a given ring
> level and
> > > > > many of them contain a few (usually 1-10) molecules. So, after
> split up
> > > > > hundred of subsets which merely contain a few molecules are
> created. It
> > > > > makes Subset Manager Panel a little bit chaotic [Please refer to
> the
> > > > image
> > > > > attached to understand the situation well].
> > > > >
> > > > The features purpose is to be able to handle dataset of very large
> size
> > > > (i.e. about a million molecules). In this case one is not able to
> show all
> > > > molecules in a view, because of performance limitations. Therefore
> the
> > > > split is a way to handle the dataset step by step and it is a
> natural split
> > > > by the structure of the molecules (at least for a chemist ;-) ).
> > > >
> > > > As the number of molecules on level 1 ore 2 does not increase that
> much,
> > > > for larger datasets, this splitting makes sense for large datasets,
> but not
> > > > for small ones.
> > > >
> > > > To conclude: It is totally fine, that you create so many small
> datasets.
> > > >
> > > >
> > > > Regards,
> > > > Till
> > > >
> > > > > Should I go ahead to and create a patch for this implementation?
> > > >
> > > > >
> > > > > Or, we should include some further criteria such as subsets for
> only
> > > > those
> > > > > scaffolds which have more than n (a number specified by user)
> molecules
> > > > are
> > > > > created.
> > > > >
> > > > > Have you any other idea which makes this feature more usable?
> > > > >
> > > > > Thanks
> > > > > Shamshad
> > > > >
> > > > >
> > > > > On Tue, Apr 15, 2014 at 10:18 PM, Till Schäfer <
> > > > > til...@tu...> wrote:
> > > > >
> > > > > > Hi,
> > > > > >
> > > > > >
> > > > > > Am Dienstag, 15. April 2014, 21:30:29 schrieb Shamshad Alam:
> > > > > > > Hi,
> > > > > > >
> > > > > > > Thanks for feedback, and sorry for misunderstanding.
> > > > > > >
> > > > > > > You mean that n subsets will be created if there are n
> scaffolds at
> > > > ring
> > > > > > > level x. In this case, it will be tedious task to enter name
> of the
> > > > each
> > > > > > > subset to be created. So, what naming convention should I use?
> I
> > > > have an
> > > > > > > idea:
> > > > > > >
> > > > > > > --> User will enter the name of the subset which will act as a
> > > > prefix and
> > > > > > > we will add suffix 1 for first subset, 2 for second subset...,
> and n
> > > > for
> > > > > > > nth subset, to the name for each subset to be created (You may
> get
> > > > the
> > > > > > > better picture of idea in the image attached) .
> > > > > > Sounds good. The default name should be orientated towards the
> default
> > > > > > name schema of filters and random subset creation.
> > > > > >
> > > > > > Something like: "Split(Level 3) - n"
> > > > > >
> > > > > > where n refers to the counter.
> > > > > >
> > > > > > Regards,
> > > > > > Till
> > > > > >
> > > > > > >
> > > > > > > --> Please tell me if you have any better idea regarding this.
> > > > > > >
> > > > > > > Thanks
> > > > > > > Shamshad
> > > > > > >
> > > > > > >
> > > > > > > On Tue, Apr 15, 2014 at 5:36 PM, Till Schäfer <
> > > > > > til...@tu...
> > > > > > > > wrote:
> > > > > > >
> > > > > > > > Hi,
> > > > > > > > your patch just creates a single subset, where the top rings
> are
> > > > > > filtered
> > > > > > > > out. It does not SPLIT the subset.
> > > > > > > > See section "misunderstanding" in my previous mail.
> > > > > > > >
> > > > > > > > Greetings,
> > > > > > > > Till
> > > > > > > >
> > > > > > > > Am Montag, 14. April 2014, 09:10:46 schrieb Shamshad Alam:
> > > > > > > > > Hi,
> > > > > > > > >
> > > > > > > > > I have made the changes you suggested. You can find
> patches in
> > > > > > attached
> > > > > > > > > file with this mail.
> > > > > > > > >
> > > > > > > > > Thanks
> > > > > > > > > Shamshad
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Fri, Apr 11, 2014 at 9:58 PM, Till Schäfer <
> > > > > > > > til...@tu...
> > > > > > > > > > wrote:
> > > > > > > > >
> > > > > > > > > > Hi,
> > > > > > > > > > thx for the patch.
> > > > > > > > > > I just looked through the code and there was some
> > > > misunderstanding
> > > > > > > > > > regarding the task:
> > > > > > > > > > - You selected the molecules of all scaffolds on ring
> level x
> > > > and
> > > > > > > > created
> > > > > > > > > > a single subset from this.
> > > > > > > > > > - The feature request 38 asked for something diferent:
> > > > > > > > > >  -> for each of the scaffolds on level x, select the
> molecules
> > > > > > from the
> > > > > > > > > > scaffold and his subtree and create a new subset.
> > > > > > > > > >  -> that means we will have n subsets if there are n
> scaffolds
> > > > on
> > > > > > > > level x.
> > > > > > > > > >  -> that means we partition the subset (minus the
> molecules
> > > > from
> > > > > > lower
> > > > > > > > > > rings)
> > > > > > > > > >
> > > > > > > > > > The good message is, that your dialog seems to be
> reusable for
> > > > this
> > > > > > > > task.
> > > > > > > > > > We just need to change the description.
> > > > > > > > > > One small bug in the dialog: Only the visible rings are
> > > > > > selectable, not
> > > > > > > > > > the complete tree levels
> > > > > > > > > >
> > > > > > > > > > One further note: The action should be located in the
> subset
> > > > menu
> > > > > > and
> > > > > > > > > > therefore should be implemented at the same place, where
> also
> > > > the
> > > > > > patch
> > > > > > > > > > from najenson was imlemented (SubssetManager /
> SubsetActions).
> > > > > > > > > >
> > > > > > > > > > You can access the complete tree for a subset over
> > > > > > > > DbManager.getScaffolds.
> > > > > > > > > > Please wrap each of the DbManager calls in a
> DbExceptionHandler
> > > > > > (you
> > > > > > > > will
> > > > > > > > > > find some examples in the SubsetManger).
> > > > > > > > > >
> > > > > > > > > > Regards,
> > > > > > > > > > Till
> > > > > > > > > >
> > > > > > > > > > Am Mittwoch, 9. April 2014, 15:19:28 schrieb Shamshad
> Alam:
> > > > > > > > > > > Hi,
> > > > > > > > > > >
> > > > > > > > > > > Feature Request #38 has been implemented, and you can
> find
> > > > > > related
> > > > > > > > > > patches
> > > > > > > > > > > in attachment.
> > > > > > > > > > >
> > > > > > > > > > > When you will execute the application after applying
> > > > patches, a
> > > > > > tool
> > > > > > > > bar
> > > > > > > > > > > button (to make subset from ring) will appear at the
> right
> > > > side
> > > > > > of
> > > > > > > > export
> > > > > > > > > > > toolbar button. Follow that button to create a new
> subset at
> > > > > > > > specified
> > > > > > > > > > ring
> > > > > > > > > > > level.
> > > > > > > > > > >
> > > > > > > > > > > Thanks
> > > > > > > > > > > Shamshad
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > --
> > > > > > > > > > Dipl.-Inf. Till Schäfer
> > > > > > > > > > TU Dortmund University
> > > > > > > > > > Chair 11 - Algorithm Engineering
> > > > > > > > > > Otto-Hahn-Str. 14 / Room 237
> > > > > > > > > > 44227 Dortmund, Germany
> > > > > > > > > >
> > > > > > > > > > e-mail: til...@cs...
> > > > > > > > > > phone: +49(231)755-7706
> > > > > > > > > > fax: +49(231)755-7740
> > > > > > > > > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> > > > > > > > > > pgp:
> > > > > > > > > >
> > > > > > > >
> > > > > >
> > > >
> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > --
> > > > > > > > Dipl.-Inf. Till Schäfer
> > > > > > > > TU Dortmund University
> > > > > > > > Chair 11 - Algorithm Engineering
> > > > > > > > Otto-Hahn-Str. 14 / Room 237
> > > > > > > > 44227 Dortmund, Germany
> > > > > > > >
> > > > > > > > e-mail: til...@cs...
> > > > > > > > phone: +49(231)755-7706
> > > > > > > > fax: +49(231)755-7740
> > > > > > > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> > > > > > > > pgp:
> > > > > > > >
> > > > > >
> > > >
> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > > --
> > > > > > Dipl.-Inf. Till Schäfer
> > > > > > TU Dortmund University
> > > > > > Chair 11 - Algorithm Engineering
> > > > > > Otto-Hahn-Str. 14 / Room 237
> > > > > > 44227 Dortmund, Germany
> > > > > >
> > > > > > e-mail: til...@cs...
> > > > > > phone: +49(231)755-7706
> > > > > > fax: +49(231)755-7740
> > > > > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> > > > > > pgp:
> > > > > >
> > > >
> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > > --
> > > > Dipl.-Inf. Till Schäfer
> > > > TU Dortmund University
> > > > Chair 11 - Algorithm Engineering
> > > > Otto-Hahn-Str. 14 / Room 237
> > > > 44227 Dortmund, Germany
> > > >
> > > > e-mail: til...@cs...
> > > > phone: +49(231)755-7706
> > > > fax: +49(231)755-7740
> > > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> > > > pgp:
> > > >
> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79
> > > >
> > >
> > >
> > >
> > >
> >
> --
> Dipl.-Inf. Till Schäfer
> TU Dortmund University
> Chair 11 - Algorithm Engineering
> Otto-Hahn-Str. 14 / Room 237
> 44227 Dortmund, Germany
>
> e-mail: til...@cs...
> phone: +49(231)755-7706
> fax: +49(231)755-7740
> web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> pgp:
> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79
>



-- 
-Shamshad Alam

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