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

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Hi Shamshad,

thanks for your work on this feature request. Your patch (with some further 
modifications) has now been committed to the SVN repository.

Regards,
  Nils

On Friday 18 April 2014 17:42:38 Shamshad Alam wrote:
> Hi,
> 
> Please, find revised version in attachment.
> 
> Thanks
> Shamshad
> 
> On Thu, Apr 17, 2014 at 9:18 PM, Shamshad Alam 
<sha...@gm...>wrote:
> > 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=0xD84D
> >> ED79>> 
> >> > > > > > > > --
> >> > > > > > > > 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=0xD84D
> >> ED79>> 
> >> > > > > > --
> >> > > > > > 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=0xD84D
> >> ED79>> 
> >> > > > --
> >> > > > 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=0xD84D
> >> ED79
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> --
> >> 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=0xD84D
> >> ED79> 
> > --
> > -Shamshad Alam
> > 
> > +91 9911631198
> > 
> > LinkedIn : in.linkedin.com/pub/shamshad-alam/58/939/70
> > GitHub: @shamshad-npti
> > Facbook: @shamshad.saralindia

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

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