scaffoldhunter-devel — Discussion list for Scaffold Hunter developers

Re: [Scaffoldhunter-devel] States of Bugs

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

Hi, 
one more hint regarding the new state in-progress. If you select this state you should always assign an owner. 

Regards,
Till

Am Mittwoch, 20. August 2014, 14:52:42 schrieb Till Schäfer:
> Hi, 
> i have changed the bug tracker to accept different states of a bug / feature request.
> 
> States until now: open, unread, open-accepted, pending, closed, wont-fix
> 
> This states did not really follow our workflow and we only used: open, close, wont-fix and very rarely pending.
> 
> Now i have changed the Tracker to the following states:
> Open States:
> - open: the default state for new bugs / feature requests
> - in-progress: somebody is currently working on the bug / feature. In this state nobody else should grab the bug without contacting its owner! We can save some mails like "on which features / bugs are you currently working" with this state. 
> - needs-info: the bug / feature is stalled, because further information are needed from the reporter to fix it. Is similar to the old state pending (but it describes better what our use case is)
> Closed States:
> - closed: the bug  / feature 
> - wont-fix: we decided to not fix the bug / not implement the feature
> - invalid: The bug report doe not follow some minimal conditions (e.g. The bug reported is no bug but a feature ;-), Spam, unclear description). May be used after a needs-info request is not responded for a longer time
> - duplicate: The bug was already reported. Please add a reference to the duplicate bug in this case.
> 
> Please follow the new states in feature or discuss them if they don't fit your needs. 
> 
> Regards, 
> Till
> 
> 
-- 
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

Re: [Scaffoldhunter-devel] States of Bugs

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

Hi, 
i added one more open state:
- needs-review: If you have fixed a bug / implemented a feature, but you want somebody else to review it before closing the bug, this is the right state. You should go for this if you have changed a larger part and want to be sure you have not introduced new bugs.  This is also a good way to tell the reporter of a bug, that he should test, if the bug is also resolved for him. In the later case you should also write a comment with the request to retest and specify the version / branch he should use. For a general review you might want to add a hint, what parts should be reviewed more precisely than others. 

Regards,
Till

Am Mittwoch, 20. August 2014, 14:52:42 schrieb Till Schäfer:
> Hi, 
> i have changed the bug tracker to accept different states of a bug / feature request.
> 
> States until now: open, unread, open-accepted, pending, closed, wont-fix
> 
> This states did not really follow our workflow and we only used: open, close, wont-fix and very rarely pending.
> 
> Now i have changed the Tracker to the following states:
> Open States:
> - open: the default state for new bugs / feature requests
> - in-progress: somebody is currently working on the bug / feature. In this state nobody else should grab the bug without contacting its owner! We can save some mails like "on which features / bugs are you currently working" with this state. 
> - needs-info: the bug / feature is stalled, because further information are needed from the reporter to fix it. Is similar to the old state pending (but it describes better what our use case is)
> Closed States:
> - closed: the bug  / feature 
> - wont-fix: we decided to not fix the bug / not implement the feature
> - invalid: The bug report doe not follow some minimal conditions (e.g. The bug reported is no bug but a feature ;-), Spam, unclear description). May be used after a needs-info request is not responded for a longer time
> - duplicate: The bug was already reported. Please add a reference to the duplicate bug in this case.
> 
> Please follow the new states in feature or discuss them if they don't fit your needs. 
> 
> Regards, 
> Till
> 
> 
-- 
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

[Scaffoldhunter-devel] States of Bugs

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

Hi, 
i have changed the bug tracker to accept different states of a bug / feature request.

States until now: open, unread, open-accepted, pending, closed, wont-fix

This states did not really follow our workflow and we only used: open, close, wont-fix and very rarely pending.

Now i have changed the Tracker to the following states:
Open States:
- open: the default state for new bugs / feature requests
- in-progress: somebody is currently working on the bug / feature. In this state nobody else should grab the bug without contacting its owner! We can save some mails like "on which features / bugs are you currently working" with this state. 
- needs-info: the bug / feature is stalled, because further information are needed from the reporter to fix it. Is similar to the old state pending (but it describes better what our use case is)
Closed States:
- closed: the bug  / feature 
- wont-fix: we decided to not fix the bug / not implement the feature
- invalid: The bug report doe not follow some minimal conditions (e.g. The bug reported is no bug but a feature ;-), Spam, unclear description). May be used after a needs-info request is not responded for a longer time
- duplicate: The bug was already reported. Please add a reference to the duplicate bug in this case.

Please follow the new states in feature or discuss them if they don't fit your needs. 

Regards, 
Till

-- 
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

Re: [Scaffoldhunter-devel] Inefficient Export Interface

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

Hi,

Ok, it's possible to replace only interfaces and I'll do that.

Thanks,
Shamshad


On Thu, Aug 7, 2014 at 4:00 PM, Till Schäfer <til...@tu...>
wrote:

> Hi,
> if you just replace the old interface and the new interface is compatible
> with the GUI access, you should not worry about the other steps. Someone
> else will fix the GUI later.
>
> Regards,
> Till
>
> Am Donnerstag, 7. August 2014, 15:54:50 schrieben Sie:
> > Hi,
> >
> > Ok, how can we avoid the duplicate code? Is it good idea to modify GUI
> > after all branches are merged at the end of GSoC?
> >
> > Thanks,
> > Shamshad
> >
> >
> > On Thu, Aug 7, 2014 at 3:23 PM, Till Schäfer <
> til...@tu...>
> > wrote:
> >
> > > Hi,
> > > thats fine, so we still need to adjust the GUI, but we do not have
> > > duplicate code.
> > >
> > > Regards,
> > > Till
> > >
> > > Am Donnerstag, 7. August 2014, 12:21:48 schrieb Shamshad Alam:
> > > > Hi Till,
> > > >
> > > > I saw the GUI of data export and observed that if we make change in
> model
> > > > interface it won't affect the GUI. we have to modify GUI in order to
> run
> > > > export task in background with progress dialog. All other codes are
> > > usable.
> > > >
> > > > Thanks,
> > > > Shamshad
> > > >
> > > >
> > > >
> > > > On Wed, Aug 6, 2014 at 7:17 PM, Till Schäfer <
> > > til...@tu...>
> > > > wrote:
> > > >
> > > > > To make it short: your interface sounds reasonable. Do you plan to
> > > replace
> > > > > to reorganize the GUI export as well to fit you interface? (i am
> always
> > > > > afraid of redundant code)
> > > > >
> > > > > Regards,
> > > > > Till
> > > > >
> > > > > Am Dienstag, 5. August 2014, 12:45:13 schrieb Shamshad Alam:
> > > > > > Hi everyone,
> > > > > >
> > > > > > While I was implementing command to export dataset / subset in
> the
> > > sdf /
> > > > > > csv file I saw
> > > > > > scaffold hunter has classes which implements data export,
> however,
> > > they
> > > > > are
> > > > > > less efficient because they do not support ProgressListener which
> > > results
> > > > > > in unresponsive GUI when we export large dataset. Moreover the
> export
> > > > > > interfaces are implemented in model package and they are using
> > > > > JOptionPane
> > > > > > which is a GUI. The ExportInterface should have method like
> > > getName() and
> > > > > > getDescription(), which make any exporter self explanatory. [see
> the
> > > > > > interface in the package edu.udo.scaffoldhunter.model.dataexport
> and
> > > its
> > > > > > implementation in sub packages].
> > > > > >
> > > > > > The proposed interface and its abstract implementation is
> attached
> > > with
> > > > > the
> > > > > > mail.
> > > > > >
> > > > > > If there is more efficient solution is possible in different way
> let
> > > me
> > > > > > know. I'll try to implement that if possible within the time
> frame.
> > > > > >
> > > > > > 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
> > > > >
> > > > >
> > > > >
> > >
> ------------------------------------------------------------------------------
> > > > > Infragistics Professional
> > > > > Build stunning WinForms apps today!
> > > > > Reboot your WinForms applications with our WinForms controls.
> > > > > Build a bridge from your legacy apps to the future.
> > > > >
> > > > >
> > >
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> > > > > _______________________________________________
> > > > > Scaffoldhunter-devel mailing list
> > > > > Sca...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
> > > > >
> > > >
> > > >
> > > >
> > > >
> > > --
> > > 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
> > >
> > >
> > >
> ------------------------------------------------------------------------------
> > > Infragistics Professional
> > > Build stunning WinForms apps today!
> > > Reboot your WinForms applications with our WinForms controls.
> > > Build a bridge from your legacy apps to the future.
> > >
> > >
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> > > _______________________________________________
> > > Scaffoldhunter-devel mailing list
> > > Sca...@li...
> > > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
> > >
> >
> >
> >
> >
> --
> 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
>
>
> ------------------------------------------------------------------------------
> Infragistics Professional
> Build stunning WinForms apps today!
> Reboot your WinForms applications with our WinForms controls.
> Build a bridge from your legacy apps to the future.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> _______________________________________________
> Scaffoldhunter-devel mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
>



-- 

Shamshad Alam
+91 9911631198 | India
G+: +ShamshadAlamNpti
FB: shamshad.saralindia
IN: http://lnkd.in/b_EzeeN

Re: [Scaffoldhunter-devel] Inefficient Export Interface

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

Hi, 
if you just replace the old interface and the new interface is compatible with the GUI access, you should not worry about the other steps. Someone else will fix the GUI later. 

Regards, 
Till

Am Donnerstag, 7. August 2014, 15:54:50 schrieben Sie:
> Hi,
> 
> Ok, how can we avoid the duplicate code? Is it good idea to modify GUI
> after all branches are merged at the end of GSoC?
> 
> Thanks,
> Shamshad
> 
> 
> On Thu, Aug 7, 2014 at 3:23 PM, Till Schäfer <til...@tu...>
> wrote:
> 
> > Hi,
> > thats fine, so we still need to adjust the GUI, but we do not have
> > duplicate code.
> >
> > Regards,
> > Till
> >
> > Am Donnerstag, 7. August 2014, 12:21:48 schrieb Shamshad Alam:
> > > Hi Till,
> > >
> > > I saw the GUI of data export and observed that if we make change in model
> > > interface it won't affect the GUI. we have to modify GUI in order to run
> > > export task in background with progress dialog. All other codes are
> > usable.
> > >
> > > Thanks,
> > > Shamshad
> > >
> > >
> > >
> > > On Wed, Aug 6, 2014 at 7:17 PM, Till Schäfer <
> > til...@tu...>
> > > wrote:
> > >
> > > > To make it short: your interface sounds reasonable. Do you plan to
> > replace
> > > > to reorganize the GUI export as well to fit you interface? (i am always
> > > > afraid of redundant code)
> > > >
> > > > Regards,
> > > > Till
> > > >
> > > > Am Dienstag, 5. August 2014, 12:45:13 schrieb Shamshad Alam:
> > > > > Hi everyone,
> > > > >
> > > > > While I was implementing command to export dataset / subset in the
> > sdf /
> > > > > csv file I saw
> > > > > scaffold hunter has classes which implements data export, however,
> > they
> > > > are
> > > > > less efficient because they do not support ProgressListener which
> > results
> > > > > in unresponsive GUI when we export large dataset. Moreover the export
> > > > > interfaces are implemented in model package and they are using
> > > > JOptionPane
> > > > > which is a GUI. The ExportInterface should have method like
> > getName() and
> > > > > getDescription(), which make any exporter self explanatory. [see the
> > > > > interface in the package edu.udo.scaffoldhunter.model.dataexport and
> > its
> > > > > implementation in sub packages].
> > > > >
> > > > > The proposed interface and its abstract implementation is attached
> > with
> > > > the
> > > > > mail.
> > > > >
> > > > > If there is more efficient solution is possible in different way let
> > me
> > > > > know. I'll try to implement that if possible within the time frame.
> > > > >
> > > > > 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
> > > >
> > > >
> > > >
> > ------------------------------------------------------------------------------
> > > > Infragistics Professional
> > > > Build stunning WinForms apps today!
> > > > Reboot your WinForms applications with our WinForms controls.
> > > > Build a bridge from your legacy apps to the future.
> > > >
> > > >
> > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> > > > _______________________________________________
> > > > Scaffoldhunter-devel mailing list
> > > > Sca...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
> > > >
> > >
> > >
> > >
> > >
> > --
> > 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
> >
> >
> > ------------------------------------------------------------------------------
> > Infragistics Professional
> > Build stunning WinForms apps today!
> > Reboot your WinForms applications with our WinForms controls.
> > Build a bridge from your legacy apps to the future.
> >
> > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Scaffoldhunter-devel mailing list
> > Sca...@li...
> > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
> >
> 
> 
> 
> 
-- 
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

Re: [Scaffoldhunter-devel] Inefficient Export Interface

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

Hi,

Ok, how can we avoid the duplicate code? Is it good idea to modify GUI
after all branches are merged at the end of GSoC?

Thanks,
Shamshad


On Thu, Aug 7, 2014 at 3:23 PM, Till Schäfer <til...@tu...>
wrote:

> Hi,
> thats fine, so we still need to adjust the GUI, but we do not have
> duplicate code.
>
> Regards,
> Till
>
> Am Donnerstag, 7. August 2014, 12:21:48 schrieb Shamshad Alam:
> > Hi Till,
> >
> > I saw the GUI of data export and observed that if we make change in model
> > interface it won't affect the GUI. we have to modify GUI in order to run
> > export task in background with progress dialog. All other codes are
> usable.
> >
> > Thanks,
> > Shamshad
> >
> >
> >
> > On Wed, Aug 6, 2014 at 7:17 PM, Till Schäfer <
> til...@tu...>
> > wrote:
> >
> > > To make it short: your interface sounds reasonable. Do you plan to
> replace
> > > to reorganize the GUI export as well to fit you interface? (i am always
> > > afraid of redundant code)
> > >
> > > Regards,
> > > Till
> > >
> > > Am Dienstag, 5. August 2014, 12:45:13 schrieb Shamshad Alam:
> > > > Hi everyone,
> > > >
> > > > While I was implementing command to export dataset / subset in the
> sdf /
> > > > csv file I saw
> > > > scaffold hunter has classes which implements data export, however,
> they
> > > are
> > > > less efficient because they do not support ProgressListener which
> results
> > > > in unresponsive GUI when we export large dataset. Moreover the export
> > > > interfaces are implemented in model package and they are using
> > > JOptionPane
> > > > which is a GUI. The ExportInterface should have method like
> getName() and
> > > > getDescription(), which make any exporter self explanatory. [see the
> > > > interface in the package edu.udo.scaffoldhunter.model.dataexport and
> its
> > > > implementation in sub packages].
> > > >
> > > > The proposed interface and its abstract implementation is attached
> with
> > > the
> > > > mail.
> > > >
> > > > If there is more efficient solution is possible in different way let
> me
> > > > know. I'll try to implement that if possible within the time frame.
> > > >
> > > > 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
> > >
> > >
> > >
> ------------------------------------------------------------------------------
> > > Infragistics Professional
> > > Build stunning WinForms apps today!
> > > Reboot your WinForms applications with our WinForms controls.
> > > Build a bridge from your legacy apps to the future.
> > >
> > >
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> > > _______________________________________________
> > > Scaffoldhunter-devel mailing list
> > > Sca...@li...
> > > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
> > >
> >
> >
> >
> >
> --
> 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
>
>
> ------------------------------------------------------------------------------
> Infragistics Professional
> Build stunning WinForms apps today!
> Reboot your WinForms applications with our WinForms controls.
> Build a bridge from your legacy apps to the future.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> _______________________________________________
> Scaffoldhunter-devel mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
>



-- 

Shamshad Alam
+91 9911631198 | India
G+: +ShamshadAlamNpti
FB: shamshad.saralindia
IN: http://lnkd.in/b_EzeeN

Re: [Scaffoldhunter-devel] Inefficient Export Interface

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

Hi, 
thats fine, so we still need to adjust the GUI, but we do not have duplicate code. 

Regards,
Till

Am Donnerstag, 7. August 2014, 12:21:48 schrieb Shamshad Alam:
> Hi Till,
> 
> I saw the GUI of data export and observed that if we make change in model
> interface it won't affect the GUI. we have to modify GUI in order to run
> export task in background with progress dialog. All other codes are usable.
> 
> Thanks,
> Shamshad
> 
> 
> 
> On Wed, Aug 6, 2014 at 7:17 PM, Till Schäfer <til...@tu...>
> wrote:
> 
> > To make it short: your interface sounds reasonable. Do you plan to replace
> > to reorganize the GUI export as well to fit you interface? (i am always
> > afraid of redundant code)
> >
> > Regards,
> > Till
> >
> > Am Dienstag, 5. August 2014, 12:45:13 schrieb Shamshad Alam:
> > > Hi everyone,
> > >
> > > While I was implementing command to export dataset / subset in the sdf /
> > > csv file I saw
> > > scaffold hunter has classes which implements data export, however, they
> > are
> > > less efficient because they do not support ProgressListener which results
> > > in unresponsive GUI when we export large dataset. Moreover the export
> > > interfaces are implemented in model package and they are using
> > JOptionPane
> > > which is a GUI. The ExportInterface should have method like getName() and
> > > getDescription(), which make any exporter self explanatory. [see the
> > > interface in the package edu.udo.scaffoldhunter.model.dataexport and its
> > > implementation in sub packages].
> > >
> > > The proposed interface and its abstract implementation is attached with
> > the
> > > mail.
> > >
> > > If there is more efficient solution is possible in different way let me
> > > know. I'll try to implement that if possible within the time frame.
> > >
> > > 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
> >
> >
> > ------------------------------------------------------------------------------
> > Infragistics Professional
> > Build stunning WinForms apps today!
> > Reboot your WinForms applications with our WinForms controls.
> > Build a bridge from your legacy apps to the future.
> >
> > http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Scaffoldhunter-devel mailing list
> > Sca...@li...
> > https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
> >
> 
> 
> 
> 
-- 
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

Re: [Scaffoldhunter-devel] Inefficient Export Interface

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

Hi Till,

I saw the GUI of data export and observed that if we make change in model
interface it won't affect the GUI. we have to modify GUI in order to run
export task in background with progress dialog. All other codes are usable.

Thanks,
Shamshad



On Wed, Aug 6, 2014 at 7:17 PM, Till Schäfer <til...@tu...>
wrote:

> To make it short: your interface sounds reasonable. Do you plan to replace
> to reorganize the GUI export as well to fit you interface? (i am always
> afraid of redundant code)
>
> Regards,
> Till
>
> Am Dienstag, 5. August 2014, 12:45:13 schrieb Shamshad Alam:
> > Hi everyone,
> >
> > While I was implementing command to export dataset / subset in the sdf /
> > csv file I saw
> > scaffold hunter has classes which implements data export, however, they
> are
> > less efficient because they do not support ProgressListener which results
> > in unresponsive GUI when we export large dataset. Moreover the export
> > interfaces are implemented in model package and they are using
> JOptionPane
> > which is a GUI. The ExportInterface should have method like getName() and
> > getDescription(), which make any exporter self explanatory. [see the
> > interface in the package edu.udo.scaffoldhunter.model.dataexport and its
> > implementation in sub packages].
> >
> > The proposed interface and its abstract implementation is attached with
> the
> > mail.
> >
> > If there is more efficient solution is possible in different way let me
> > know. I'll try to implement that if possible within the time frame.
> >
> > 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
>
>
> ------------------------------------------------------------------------------
> Infragistics Professional
> Build stunning WinForms apps today!
> Reboot your WinForms applications with our WinForms controls.
> Build a bridge from your legacy apps to the future.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
> _______________________________________________
> Scaffoldhunter-devel mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel
>



-- 

Shamshad Alam
+91 9911631198 | India
G+: +ShamshadAlamNpti
FB: shamshad.saralindia
IN: http://lnkd.in/b_EzeeN

Re: [Scaffoldhunter-devel] Inefficient Export Interface

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

To make it short: your interface sounds reasonable. Do you plan to replace to reorganize the GUI export as well to fit you interface? (i am always afraid of redundant code)

Regards,
Till

Am Dienstag, 5. August 2014, 12:45:13 schrieb Shamshad Alam:
> Hi everyone,
> 
> While I was implementing command to export dataset / subset in the sdf /
> csv file I saw
> scaffold hunter has classes which implements data export, however, they are
> less efficient because they do not support ProgressListener which results
> in unresponsive GUI when we export large dataset. Moreover the export
> interfaces are implemented in model package and they are using JOptionPane
> which is a GUI. The ExportInterface should have method like getName() and
> getDescription(), which make any exporter self explanatory. [see the
> interface in the package edu.udo.scaffoldhunter.model.dataexport and its
> implementation in sub packages].
> 
> The proposed interface and its abstract implementation is attached with the
> mail.
> 
> If there is more efficient solution is possible in different way let me
> know. I'll try to implement that if possible within the time frame.
> 
> 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

[Scaffoldhunter-devel] Inefficient Export Interface

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

public interface Exporter {

    /**
     * the name of the exporter
     * @return name of the exporter
     */
    public String getName();

    /**
     * 
     * @return description of the exporter
     */
    public String getDescription();

    /**
     * Export data to file
     * 
     * @param molecules
     *            the {@code Iterable<IAtomContainer>} to export
     * @param properties
     *            The key in the map represent the header and the corresponding
     *            value represent the key of the {@code IAtomContainer}
     * @param filename
     *            the name of the file where you want to export the data
     */
    public void writeData(Iterable<IAtomContainer> molecules, Map<String, ? extends Object> properties, String filename);

    /**
     * Get the extension of the file
     * 
     * @return extension of file
     */
    public String getFileExtension();

    /**
     * 
     * @param listener
     *            {@code ProgressListener} to add
     */
    public void addProgressListener(ProgressListener<ExportStatus> listener);

    /**
     * 
     * @param listener
     *            {@code ProgressListener} to remove
     */
    public void removeProgressListener(ProgressListener<ExportStatus> listener);
}

Re: [Scaffoldhunter-devel] How can I use substructure implementation?

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

Hi,

I have implemented this feature with option to select a matcher from
Simple, VF2, and Fast Matchers.

Matchers are not working if we create   pattern graph or host graph with
false value of configure parameter

Thanks,
Shamshad
On Jul 28, 2014 5:07 PM, <nl...@us...> wrote:

> Hi Shamshad,
>
> the following code performs substructure search (without filtering) using
> our
> implementation:
>
> IAtomContainer acQuery = null; // input
> Collection<IAtomContainer> database = null; // input
>
> MoleculeGraph mgQuery = new MoleculeGraph(acQuery);
> SearchPattern sp = new SearchPattern(mgQuery, false);
>
> for (IAtomContainer molData : database) {
>     MoleculeGraph mgData = new MoleculeGraph(molData);
>     Matcher m = new MatcherFast(sp, mgData);
>     if (m.match()) {
>         // process matching molecule
>     }
> }
>
> Note that it is assumed that the query structure and the database have been
> loaded into the CDK datastructure IAtomContainer.
>
>
> Regards,
>   Nils
>
>
> On Wednesday 23 July 2014 23:24:13 Shamshad Alam wrote:
> > Hi,
> >
> > I am implementing filter command which allows user to filter dataset,
> > subset, sdf and csv files. I've used SMARTSQueryTool (available in CDK)
> to
> > filter structure. Now I'm looking for the ways to use substructure search
> > implementation available in scaffold hunter. I am still not able to
> > identify the entry point to substructure search.
> >
> > So, Could anyone help me with some demo code (or steps) to use the
> > substructure search implementation.
> >
> > Thanks,
> > Shamshad
>

Re: [Scaffoldhunter-devel] How can I use substructure implementation?

[<nl...@us...>]

Hi Shamshad,

the following code performs substructure search (without filtering) using our 
implementation:

IAtomContainer acQuery = null; // input
Collection<IAtomContainer> database = null; // input 

MoleculeGraph mgQuery = new MoleculeGraph(acQuery);
SearchPattern sp = new SearchPattern(mgQuery, false);

for (IAtomContainer molData : database) {
    MoleculeGraph mgData = new MoleculeGraph(molData);
    Matcher m = new MatcherFast(sp, mgData);
    if (m.match()) {
        // process matching molecule
    }
}

Note that it is assumed that the query structure and the database have been 
loaded into the CDK datastructure IAtomContainer.


Regards,
  Nils


On Wednesday 23 July 2014 23:24:13 Shamshad Alam wrote:
> Hi,
> 
> I am implementing filter command which allows user to filter dataset,
> subset, sdf and csv files. I've used SMARTSQueryTool (available in CDK) to
> filter structure. Now I'm looking for the ways to use substructure search
> implementation available in scaffold hunter. I am still not able to
> identify the entry point to substructure search.
> 
> So, Could anyone help me with some demo code (or steps) to use the
> substructure search implementation.
> 
> Thanks,
> Shamshad

[Scaffoldhunter-devel] How can I use substructure implementation?

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

Hi,

I am implementing filter command which allows user to filter dataset,
subset, sdf and csv files. I've used SMARTSQueryTool (available in CDK) to
filter structure. Now I'm looking for the ways to use substructure search
implementation available in scaffold hunter. I am still not able to
identify the entry point to substructure search.

So, Could anyone help me with some demo code (or steps) to use the
substructure search implementation.

Thanks,
Shamshad

-- 
-Shamshad Alam

+91 9911631198
Google: +ShamshadNpti

Re: [Scaffoldhunter-devel] Issue while Implementing Data Import

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

Hi Tills,

Thanks! I will learn the code and try to divide them into two part (Model
and Controller). It is also good to know that we shouldn't inherit
controller classes.

Thanks,
Shamshad


On Thu, Jul 17, 2014 at 9:36 PM, Till Schäfer <til...@tu...
> wrote:

> Hi,
>
>
> Am Donnerstag, 17. Juli 2014, 21:08:19 schrieb Shamshad Alam:
> > Hi everyone,
> >
> > I'm working on Command Line Interface and currently facing a problem
> while
> > implementing functionality to import dataset. There's already a class
> > 'edu.udo.scaffoldhunter.model.dataimport.Importer' available in SH to
> > manage import process. Importer class has runImport() method as an entry
> > point. But the runImport() method incorporates GUI and so I can't use
> this
> > method in CLI. However, some methods, such as
> > saveDatasetAndPropertyDefinitions(), which are defined with private
> > modifier in Importer class are useful in CLI too.
> >
> > At this point, I can either extends the Importer class, override
> > runImport() method and change accessibility of private methods which are
> > defined in Importer class to protected so that I can use them in extended
> > class or I can simply make the copy of whole code in Importer class and
> > then I'll modify it to met the requirement of CLI.
> >
> > In former case, which is an efficient solution, I will not modify any
> > internal code except methods' access modifier and will add some getter
> and
> > setter for the private field if it's required. Please let me know any
> issue
> > associated with such modification in any part of the existing code.
>
> Yes, Importer is a controller class. So it is the layer between the actual
> model an the GUI representation. However, it is uncommon to place such a
> class in the model package. Normally nothing in the model should reference
> anything GUI related. In my opinion this class should be moved in the
> corresponding gui package. If there are larger parts of gui independent
> functionality implemented in the controller class, they should be moved to
> a (new?) model class, such that they can be reused by the controller and
> your cli implementation.
>
> Regarding the method saveDatasetAndPropertyDefinition: i only see the
> ExceptionHandler as GUI dependent code (but i have not looked deeply in the
> code, so please check yourself again). In this case you can keep the
> unlocking in the controller and move the rest of the functionality to some
> model class.
>
> A last advice: please do not derive from the controller class for your cli
> code. This will destroy the model-view-controller design.
>
> Regards,
> Till
>
> >
> > 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
>



-- 
-Shamshad Alam

+91 9911631198

LinkedIn : in.linkedin.com/pub/shamshad-alam/58/939/70
GitHub: @shamshad-npti
Facbook: @shamshad.saralindia

Re: [Scaffoldhunter-devel] Issue while Implementing Data Import

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

Hi, 


Am Donnerstag, 17. Juli 2014, 21:08:19 schrieb Shamshad Alam:
> Hi everyone,
> 
> I'm working on Command Line Interface and currently facing a problem while
> implementing functionality to import dataset. There's already a class
> 'edu.udo.scaffoldhunter.model.dataimport.Importer' available in SH to
> manage import process. Importer class has runImport() method as an entry
> point. But the runImport() method incorporates GUI and so I can't use this
> method in CLI. However, some methods, such as
> saveDatasetAndPropertyDefinitions(), which are defined with private
> modifier in Importer class are useful in CLI too.
> 
> At this point, I can either extends the Importer class, override
> runImport() method and change accessibility of private methods which are
> defined in Importer class to protected so that I can use them in extended
> class or I can simply make the copy of whole code in Importer class and
> then I'll modify it to met the requirement of CLI.
> 
> In former case, which is an efficient solution, I will not modify any
> internal code except methods' access modifier and will add some getter and
> setter for the private field if it's required. Please let me know any issue
> associated with such modification in any part of the existing code.

Yes, Importer is a controller class. So it is the layer between the actual model an the GUI representation. However, it is uncommon to place such a class in the model package. Normally nothing in the model should reference anything GUI related. In my opinion this class should be moved in the corresponding gui package. If there are larger parts of gui independent functionality implemented in the controller class, they should be moved to a (new?) model class, such that they can be reused by the controller and your cli implementation.

Regarding the method saveDatasetAndPropertyDefinition: i only see the ExceptionHandler as GUI dependent code (but i have not looked deeply in the code, so please check yourself again). In this case you can keep the unlocking in the controller and move the rest of the functionality to some model class. 

A last advice: please do not derive from the controller class for your cli code. This will destroy the model-view-controller design.

Regards, 
Till 

> 
> 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

[Scaffoldhunter-devel] Issue while Implementing Data Import

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

Hi everyone,

I'm working on Command Line Interface and currently facing a problem while
implementing functionality to import dataset. There's already a class
'edu.udo.scaffoldhunter.model.dataimport.Importer' available in SH to
manage import process. Importer class has runImport() method as an entry
point. But the runImport() method incorporates GUI and so I can't use this
method in CLI. However, some methods, such as
saveDatasetAndPropertyDefinitions(), which are defined with private
modifier in Importer class are useful in CLI too.

At this point, I can either extends the Importer class, override
runImport() method and change accessibility of private methods which are
defined in Importer class to protected so that I can use them in extended
class or I can simply make the copy of whole code in Importer class and
then I'll modify it to met the requirement of CLI.

In former case, which is an efficient solution, I will not modify any
internal code except methods' access modifier and will add some getter and
setter for the private field if it's required. Please let me know any issue
associated with such modification in any part of the existing code.

Thanks,
Shamshad

-- 
-Shamshad Alam

+91 9911631198

LinkedIn : in.linkedin.com/pub/shamshad-alam/58/939/70
GitHub: @shamshad-npti
Facbook: @shamshad.saralindia

Re: [Scaffoldhunter-devel] Seeking Feedback On Command Line Interface (CLI)

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

Hi Nills,

Well, I missed something in the illustration. Currently in following
information is being saved with scaffolds -
1. SCAFFOLD (boolean) - to indicate it is an scaffold
2. NO_OF_MOLECULES (int) - number of molecules in the scaffold.
3. RING_SIZE (int) - number of ring in the scaffold
4. PARENT_COUNT (int) - number of parents
5. PARENT_0, PARENT_1.... PARENT_N (string) - smiles string of the nth
parent

So, tree/network structure is preserved in file. Molecules are unaffected
i.e. they are saved without adding any additional property to identify
which scaffold they belong to.

>> technical question: Does your....

This is really an issue. If we keep all the molecules in memory it will
consume a lot of memory and if we open a file, write the molecule to it,
and close it then for each molecule again it's not an efficient way.

I'm currently storing scaffolds and molecules in a map (Map<String,
OutputScaffold[1]>) which of course stays in memory. In my opinion after
processing certain number of molecules (say 1000) we should write the
structure to the temp files and at the end of the process we should merge
all such temp files. However, not sure it would the efficient and yet it is
little vague to me. How can we handle it more efficiently? Have you any
other idea?

[1] - OutputScaffold has following fields -

    private static class OutputScaffold {
        private String smiles;
        private List<String> parents;
        private List<String> children;
        private List<IMolecule> molecules;
        private int ringSize;
   }

Thanks,
Shamshad


On Thu, Jul 3, 2014 at 1:22 PM, <nl...@us...> wrote:

> Hi Shamshad,
>
> thank you for the illustration. So currently the tree/network structure is
> not
> saved? I think this is a very important feature. One solution might be to
> assign a unique id to every scaffold. Then each molecule can have a
> property
> "SCAFFOLD_ID" that identifies the associated scaffold. A scaffold could
> have
> an additional property "PARENT_SCAFFOLD_IDS" that contains a single
> scaffold
> id in case of a tree and a list of parent scaffolds for networks.
>
> A technical question: Does your approach require to keep all molecules and
> scaffolds in memory? Avoiding this would be great and would allow to use
> the
> CLI with very large data sets.
>
>
> Regards,
>   Nils
>
> On Wednesday 02 July 2014 21:49:49 Shamshad Alam wrote:
> > Hi Nils,
> >
> > Nice suggestions!
> >
> > I'm currently saving scaffolds and associated molecules in a single sdf
> > file. The file structure can be better understood with the help of
> attached
> > illustration.
> >
> > Thanks,
> > Shamshad
> >
> > On Wed, Jul 2, 2014 at 1:58 PM, <nl...@us...> wrote:
> > > Hi Shamshad,
> > >
> > > I think it would be good not only to write out the scaffolds, but also
> the
> > > molecules with an additional property that identifies the associated
> > > scaffold.
> > > How do you plan to save the tree/network structure?
> > > An additional parameter --min-ring-size might also be useful.
> > >
> > >
> > > Regards,
> > >
> > >   Nils
> > >
> > > On Wednesday 25 June 2014 08:37:11 Shamshad Alam wrote:
> > > > Hi,
> > > >
> > > > I am working on Command Line Interface (CLI) which is a GSoC-2014
> > >
> > > project.
> > >
> > > > And I would like get some  feedback on the commands and parameters
> used
> > > > with commands in CLI.
> > > >
> > > > In the first phase, our aim is to implement the commands to generate
> > > > Scaffold tree from the molecules in the SDF file or in the database.
> We
> > >
> > > are
> > >
> > > > also offering user to specify the ring size of the scaffolds which
> are
> > > > to
> > > > be included in output. The generated scaffold is saved in the sdf
> file
> > >
> > > that
> > >
> > > > can be further used for analysis. An SDF file is required to generate
> > > > scaffold tree from the file and connection data is needed to make
> > > > connection with database to generate scaffold tree from database.
> > > >
> > > > In the later stages we have planned to implement filtering by
> structure
> > >
> > > and
> > >
> > > > substructure e. g. only certain subtrees based on the structure /
> > > > substructure search will saved in output.
> > > >
> > > > These are proposed commands and their parameters so far:
> > > >
> > > > (1) generate : This command is used to generate scaffold tree /
> network
> > >
> > > and
> > >
> > > > it needs a source of molecules like sdf file and a destination file
> to
> > >
> > > save
> > >
> > > > generated scaffolds. It is used in combination with following
> parameters
> > >
> > > -
> > >
> > > > (a) To generate scaffold tree / network loading molecules from file
> > > > -n | --network : Use this parameter to generate scaffold network,
> > > > absence
> > > > of this parameter means you want to generate scaffold tree
> > > > -i | --input-file <file_location> : Specify location of input file to
> > >
> > > read
> > >
> > > > molecules from.
> > > > -o | --output-file <file_location> : Specify file in which generated
> > > > scaffold would be saved
> > > > -m | --max-ring-size <number> : Specify the maximum ring size of
> > > > scaffold
> > > > that should be included in the output
> > > >
> > > > (b) To generate scaffold tree / network by loading molecules from
> > >
> > > Scaffold
> > >
> > > > Hunter database
> > > > -c | --connection-name <connection-name> : Name of the connection
> that
> > > > would be used for connection with the database to retrieve molecules.
> > > > -d |  --dataset <dataset_name> : Specify name of the dataset to
> retrieve
> > > > molecules from and generate scaffold tree
> > > > -o | --output-file <file_location> : Specify file in which generated
> > > > scaffold would be saved
> > > > -m | --max-ring-size <number> : Specify the maximum ring size of
> > > > scaffold
> > > > that should be included in the output
> > > > -n | --network : Use this parameter to generate scaffold network,
> > > > absence
> > > > of this parameter means you want to generate scaffold tree
> > > >
> > > > These are some examples of 'generate' command :
> > > >
> > > > (a) Read molecules from file
> > > >
> > > > sh generate -i <input-file>
> > > > Read molecules from input file and generate scaffold tree. Generated
> > > > tree
> > > > is saved in a file automatically.
> > > >
> > > > sh generate -i <input-file> -o scaffold.sdf
> > > > Read molecules from input file and generate scaffold tree. Generated
> > > > tree
> > > > is saved in scaffold.sdf.
> > > >
> > > > sh generate -i <input-file> -o scaffold-2.sdf -n
> > > > Read molecules from input file and generate scaffold 'network'.
> > > > Generated
> > > > network is saved in scaffold-2.sdf.
> > > >
> > > > sh generate -i <input-file> -o scaffold-3.sdf -m 5
> > > > Read molecules from input file and generate scaffold tree. Generated
> > > > tree
> > > > is saved in scaffold-3.sdf. All scaffolds with rings more than 5 are
> not
> > > > saved.
> > > >
> > > > (b) Read molecules from database
> > > >
> > > > sh generate -c <connection-name>
> > > > Read molecules from database which connection data is pointed by
> > > > <connection-name> and generate scaffold tree. Generated tree is
> saved in
> > > > file automatically.
> > > >
> > > > sh generate -c <connection-name> -o scaffold.sdf
> > > > Read molecules from database which connection data is pointed by
> > > > <connection-name> and generate scaffold tree. Generated tree is
> saved in
> > > > scaffold.sdf.
> > > >
> > > > Similarly, you can use -n to generate network and -m <number> to
> limit
> > >
> > > the
> > >
> > > > ring size as you've done in scaffold tree generation from file.
> > > >
> > > > (2) connection [list | save | delete] : This command is used to
> manage
> > > > connection data which is required for connection with database. It is
> > > > followed by list, save or delete action. These are parameters
> supported
> > >
> > > by
> > >
> > > > the command :
> > > >
> > > > -c | --connection-name <name> : name of the connection
> > > > -t | --database-type : Type of database (mySql, HSQLDB)
> > > > -u | --url : Url of the mySql database server or file location of
> HSQLDB
> > > > -n | --database-name : Name of the database
> > > > -un | --user-name : user name to login
> > > > -p | --password : password of the database (You can avoid this
> parameter
> > > > and specify it at runtime during connection is made to database)
> > > >
> > > > Here is some uses of connection command -
> > > >
> > > > sh connection list
> > > > display the names of available connections on screen
> > > >
> > > > sh connection list -c <name>
> > > > display the details of particular connection data pointed by name
> > >
> > > excluding
> > >
> > > > password
> > > >
> > > > sh connection delete -c <name>
> > > > delete the connection data pointed by the name
> > > >
> > > > connection save -c <name> -t <hsqldb | mysql> -u <url> -n
> > > > <database-name>
> > > > -un <user-name>
> > > > save a new connection data with specified name which can be used
> later
> > > > to
> > > > make connection with database
> > > >
> > > > Feedback -
> > > >
> > > > We are seeking your feedback on implemented commands and proposed
> > > > parameters to make the command line interface more useful. So, please
> > >
> > > give
> > >
> > > > your inputs to a few questions given here :
> > > > 1. What are the features of scaffold hunter you want to use in
> command
> > >
> > > line
> > >
> > > > interface?
> > > > 2. Do you find the parameters provided for scaffold tree / network
> > > > generation user friendly?
> > > > 3. Do you need some more parameters to control the generation
> strategy?
> > > > 4. Do you think some proposed parameters are redundant? If so, please
> > > > specify the name of those parameters.
> > > >
> > > > You may also put any other suggestions regarding command line
> interface
> > > >
> > > > Thanks,
> > > > Shamshad
>



-- 
-Shamshad Alam

+91 9911631198

LinkedIn : in.linkedin.com/pub/shamshad-alam/58/939/70
GitHub: @shamshad-npti
Facbook: @shamshad.saralindia

Re: [Scaffoldhunter-devel] Seeking Feedback On Command Line Interface (CLI)

[<nl...@us...>]

Hi Shamshad,

thank you for the illustration. So currently the tree/network structure is not 
saved? I think this is a very important feature. One solution might be to 
assign a unique id to every scaffold. Then each molecule can have a property 
"SCAFFOLD_ID" that identifies the associated scaffold. A scaffold could have 
an additional property "PARENT_SCAFFOLD_IDS" that contains a single scaffold 
id in case of a tree and a list of parent scaffolds for networks.

A technical question: Does your approach require to keep all molecules and 
scaffolds in memory? Avoiding this would be great and would allow to use the 
CLI with very large data sets.


Regards,
  Nils

On Wednesday 02 July 2014 21:49:49 Shamshad Alam wrote:
> Hi Nils,
> 
> Nice suggestions!
> 
> I'm currently saving scaffolds and associated molecules in a single sdf
> file. The file structure can be better understood with the help of attached
> illustration.
> 
> Thanks,
> Shamshad
> 
> On Wed, Jul 2, 2014 at 1:58 PM, <nl...@us...> wrote:
> > Hi Shamshad,
> > 
> > I think it would be good not only to write out the scaffolds, but also the
> > molecules with an additional property that identifies the associated
> > scaffold.
> > How do you plan to save the tree/network structure?
> > An additional parameter --min-ring-size might also be useful.
> > 
> > 
> > Regards,
> > 
> >   Nils
> > 
> > On Wednesday 25 June 2014 08:37:11 Shamshad Alam wrote:
> > > Hi,
> > > 
> > > I am working on Command Line Interface (CLI) which is a GSoC-2014
> > 
> > project.
> > 
> > > And I would like get some  feedback on the commands and parameters used
> > > with commands in CLI.
> > > 
> > > In the first phase, our aim is to implement the commands to generate
> > > Scaffold tree from the molecules in the SDF file or in the database. We
> > 
> > are
> > 
> > > also offering user to specify the ring size of the scaffolds which are
> > > to
> > > be included in output. The generated scaffold is saved in the sdf file
> > 
> > that
> > 
> > > can be further used for analysis. An SDF file is required to generate
> > > scaffold tree from the file and connection data is needed to make
> > > connection with database to generate scaffold tree from database.
> > > 
> > > In the later stages we have planned to implement filtering by structure
> > 
> > and
> > 
> > > substructure e. g. only certain subtrees based on the structure /
> > > substructure search will saved in output.
> > > 
> > > These are proposed commands and their parameters so far:
> > > 
> > > (1) generate : This command is used to generate scaffold tree / network
> > 
> > and
> > 
> > > it needs a source of molecules like sdf file and a destination file to
> > 
> > save
> > 
> > > generated scaffolds. It is used in combination with following parameters
> > 
> > -
> > 
> > > (a) To generate scaffold tree / network loading molecules from file
> > > -n | --network : Use this parameter to generate scaffold network,
> > > absence
> > > of this parameter means you want to generate scaffold tree
> > > -i | --input-file <file_location> : Specify location of input file to
> > 
> > read
> > 
> > > molecules from.
> > > -o | --output-file <file_location> : Specify file in which generated
> > > scaffold would be saved
> > > -m | --max-ring-size <number> : Specify the maximum ring size of
> > > scaffold
> > > that should be included in the output
> > > 
> > > (b) To generate scaffold tree / network by loading molecules from
> > 
> > Scaffold
> > 
> > > Hunter database
> > > -c | --connection-name <connection-name> : Name of the connection that
> > > would be used for connection with the database to retrieve molecules.
> > > -d |  --dataset <dataset_name> : Specify name of the dataset to retrieve
> > > molecules from and generate scaffold tree
> > > -o | --output-file <file_location> : Specify file in which generated
> > > scaffold would be saved
> > > -m | --max-ring-size <number> : Specify the maximum ring size of
> > > scaffold
> > > that should be included in the output
> > > -n | --network : Use this parameter to generate scaffold network,
> > > absence
> > > of this parameter means you want to generate scaffold tree
> > > 
> > > These are some examples of 'generate' command :
> > > 
> > > (a) Read molecules from file
> > > 
> > > sh generate -i <input-file>
> > > Read molecules from input file and generate scaffold tree. Generated
> > > tree
> > > is saved in a file automatically.
> > > 
> > > sh generate -i <input-file> -o scaffold.sdf
> > > Read molecules from input file and generate scaffold tree. Generated
> > > tree
> > > is saved in scaffold.sdf.
> > > 
> > > sh generate -i <input-file> -o scaffold-2.sdf -n
> > > Read molecules from input file and generate scaffold 'network'.
> > > Generated
> > > network is saved in scaffold-2.sdf.
> > > 
> > > sh generate -i <input-file> -o scaffold-3.sdf -m 5
> > > Read molecules from input file and generate scaffold tree. Generated
> > > tree
> > > is saved in scaffold-3.sdf. All scaffolds with rings more than 5 are not
> > > saved.
> > > 
> > > (b) Read molecules from database
> > > 
> > > sh generate -c <connection-name>
> > > Read molecules from database which connection data is pointed by
> > > <connection-name> and generate scaffold tree. Generated tree is saved in
> > > file automatically.
> > > 
> > > sh generate -c <connection-name> -o scaffold.sdf
> > > Read molecules from database which connection data is pointed by
> > > <connection-name> and generate scaffold tree. Generated tree is saved in
> > > scaffold.sdf.
> > > 
> > > Similarly, you can use -n to generate network and -m <number> to limit
> > 
> > the
> > 
> > > ring size as you've done in scaffold tree generation from file.
> > > 
> > > (2) connection [list | save | delete] : This command is used to manage
> > > connection data which is required for connection with database. It is
> > > followed by list, save or delete action. These are parameters supported
> > 
> > by
> > 
> > > the command :
> > > 
> > > -c | --connection-name <name> : name of the connection
> > > -t | --database-type : Type of database (mySql, HSQLDB)
> > > -u | --url : Url of the mySql database server or file location of HSQLDB
> > > -n | --database-name : Name of the database
> > > -un | --user-name : user name to login
> > > -p | --password : password of the database (You can avoid this parameter
> > > and specify it at runtime during connection is made to database)
> > > 
> > > Here is some uses of connection command -
> > > 
> > > sh connection list
> > > display the names of available connections on screen
> > > 
> > > sh connection list -c <name>
> > > display the details of particular connection data pointed by name
> > 
> > excluding
> > 
> > > password
> > > 
> > > sh connection delete -c <name>
> > > delete the connection data pointed by the name
> > > 
> > > connection save -c <name> -t <hsqldb | mysql> -u <url> -n
> > > <database-name>
> > > -un <user-name>
> > > save a new connection data with specified name which can be used later
> > > to
> > > make connection with database
> > > 
> > > Feedback -
> > > 
> > > We are seeking your feedback on implemented commands and proposed
> > > parameters to make the command line interface more useful. So, please
> > 
> > give
> > 
> > > your inputs to a few questions given here :
> > > 1. What are the features of scaffold hunter you want to use in command
> > 
> > line
> > 
> > > interface?
> > > 2. Do you find the parameters provided for scaffold tree / network
> > > generation user friendly?
> > > 3. Do you need some more parameters to control the generation strategy?
> > > 4. Do you think some proposed parameters are redundant? If so, please
> > > specify the name of those parameters.
> > > 
> > > You may also put any other suggestions regarding command line interface
> > > 
> > > Thanks,
> > > Shamshad

Re: [Scaffoldhunter-devel] Seeking Feedback On Command Line Interface (CLI)

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

Hi, 
with defined properties i mean: 
- sdf/cvs: all properties that occur in any of the molecules. Regarding csv, there is usually a header column that gives you the names. For sdf file format you will need  to iterate over the complete sdf and collect the individual properties for each molecule. They are identified by a string name. 
- internal dataset: there is a list of propertyDefinitions for each dataset. That are the properties, which are present for an imported dataset. 

-> for im/export it will be important to select the properties one want to import/export together with the molecule / scaffold structure. 

Regards, 
Till 

Am Mittwoch 02 Juli 2014, 07:14:28 schrieb Shamshad Alam:
> Hi Tills,
> 
> Thanks! Good to hear from you. All points are comprehensible except the
> term "defined properties" in second point. Does it refer to molecular
> properties?
> 
> >> show the *defined properties* and some statistics (e.g. size) about an
> sdf, csv file, without actually doing anything with the file
> 
> Thanks,
> Shamshad
> 
> 
> 
> On Tue, Jul 1, 2014 at 6:09 PM, Till Schäfer <til...@tu...>
> wrote:
> 
> > Hi,
> > here are some wishes, that came into my mind:
> > - import/merging sdf and csv into the scaffold hunter database over
> > command line
> > - show the defined properties and some statistics (e.g. size) about an
> > sdf, csv file, without actually doing anything with the file (this can be
> > useful for later import / merging.
> > - export an internal database over the command line
> > - show the defined properties and some statistics (e.g. size) about an
> > internal dataset / subset, without actually doing anything with the file
> > (this can be useful for later import / merging.
> > - add a subset switch for each operation that uses data from the scaffold
> > hunter database
> > - clustering -> as for scaffold network / tree generation, but with
> > clustering
> > - generate a subset based on a filter, split a subset by scaffold tree
> > structure, random subset generation
> >   -> this should be possible to in a way, such that we can store the
> > subset in the database, or store it directly in a file.
> >  -> it should be possible to read an sdf/csv, filter it and store it
> > directly to a file (without any sh database operation involved)
> > - apply a calc plugin to data
> >  -> pathways: read from file / database -> generate property  -> store to
> > file / database
> > - the tree generation code should have an option to specify the rules,
> > which are used to generate a scaffold tree
> > - delete an internal database / subset
> > - ... :-)
> >
> > Regards,
> > Till
> >
> > Am Mittwoch, 25. Juni 2014, 08:37:11 schrieb Shamshad Alam:
> > > Hi,
> > >
> > > I am working on Command Line Interface (CLI) which is a GSoC-2014
> > project.
> > > And I would like get some  feedback on the commands and parameters used
> > > with commands in CLI.
> > >
> > > In the first phase, our aim is to implement the commands to generate
> > > Scaffold tree from the molecules in the SDF file or in the database. We
> > are
> > > also offering user to specify the ring size of the scaffolds which are to
> > > be included in output. The generated scaffold is saved in the sdf file
> > that
> > > can be further used for analysis. An SDF file is required to generate
> > > scaffold tree from the file and connection data is needed to make
> > > connection with database to generate scaffold tree from database.
> > >
> > > In the later stages we have planned to implement filtering by structure
> > and
> > > substructure e. g. only certain subtrees based on the structure /
> > > substructure search will saved in output.
> > >
> > > These are proposed commands and their parameters so far:
> > >
> > > (1) generate : This command is used to generate scaffold tree / network
> > and
> > > it needs a source of molecules like sdf file and a destination file to
> > save
> > > generated scaffolds. It is used in combination with following parameters
> > -
> > > (a) To generate scaffold tree / network loading molecules from file
> > > -n | --network : Use this parameter to generate scaffold network, absence
> > > of this parameter means you want to generate scaffold tree
> > > -i | --input-file <file_location> : Specify location of input file to
> > read
> > > molecules from.
> > > -o | --output-file <file_location> : Specify file in which generated
> > > scaffold would be saved
> > > -m | --max-ring-size <number> : Specify the maximum ring size of scaffold
> > > that should be included in the output
> > >
> > > (b) To generate scaffold tree / network by loading molecules from
> > Scaffold
> > > Hunter database
> > > -c | --connection-name <connection-name> : Name of the connection that
> > > would be used for connection with the database to retrieve molecules.
> > > -d |  --dataset <dataset_name> : Specify name of the dataset to retrieve
> > > molecules from and generate scaffold tree
> > > -o | --output-file <file_location> : Specify file in which generated
> > > scaffold would be saved
> > > -m | --max-ring-size <number> : Specify the maximum ring size of scaffold
> > > that should be included in the output
> > > -n | --network : Use this parameter to generate scaffold network, absence
> > > of this parameter means you want to generate scaffold tree
> > >
> > > These are some examples of 'generate' command :
> > >
> > > (a) Read molecules from file
> > >
> > > sh generate -i <input-file>
> > > Read molecules from input file and generate scaffold tree. Generated tree
> > > is saved in a file automatically.
> > >
> > > sh generate -i <input-file> -o scaffold.sdf
> > > Read molecules from input file and generate scaffold tree. Generated tree
> > > is saved in scaffold.sdf.
> > >
> > > sh generate -i <input-file> -o scaffold-2.sdf -n
> > > Read molecules from input file and generate scaffold 'network'. Generated
> > > network is saved in scaffold-2.sdf.
> > >
> > > sh generate -i <input-file> -o scaffold-3.sdf -m 5
> > > Read molecules from input file and generate scaffold tree. Generated tree
> > > is saved in scaffold-3.sdf. All scaffolds with rings more than 5 are not
> > > saved.
> > >
> > > (b) Read molecules from database
> > >
> > > sh generate -c <connection-name>
> > > Read molecules from database which connection data is pointed by
> > > <connection-name> and generate scaffold tree. Generated tree is saved in
> > > file automatically.
> > >
> > > sh generate -c <connection-name> -o scaffold.sdf
> > > Read molecules from database which connection data is pointed by
> > > <connection-name> and generate scaffold tree. Generated tree is saved in
> > > scaffold.sdf.
> > >
> > > Similarly, you can use -n to generate network and -m <number> to limit
> > the
> > > ring size as you've done in scaffold tree generation from file.
> > >
> > > (2) connection [list | save | delete] : This command is used to manage
> > > connection data which is required for connection with database. It is
> > > followed by list, save or delete action. These are parameters supported
> > by
> > > the command :
> > >
> > > -c | --connection-name <name> : name of the connection
> > > -t | --database-type : Type of database (mySql, HSQLDB)
> > > -u | --url : Url of the mySql database server or file location of HSQLDB
> > > -n | --database-name : Name of the database
> > > -un | --user-name : user name to login
> > > -p | --password : password of the database (You can avoid this parameter
> > > and specify it at runtime during connection is made to database)
> > >
> > > Here is some uses of connection command -
> > >
> > > sh connection list
> > > display the names of available connections on screen
> > >
> > > sh connection list -c <name>
> > > display the details of particular connection data pointed by name
> > excluding
> > > password
> > >
> > > sh connection delete -c <name>
> > > delete the connection data pointed by the name
> > >
> > > connection save -c <name> -t <hsqldb | mysql> -u <url> -n <database-name>
> > > -un <user-name>
> > > save a new connection data with specified name which can be used later to
> > > make connection with database
> > >
> > > Feedback -
> > >
> > > We are seeking your feedback on implemented commands and proposed
> > > parameters to make the command line interface more useful. So, please
> > give
> > > your inputs to a few questions given here :
> > > 1. What are the features of scaffold hunter you want to use in command
> > line
> > > interface?
> > > 2. Do you find the parameters provided for scaffold tree / network
> > > generation user friendly?
> > > 3. Do you need some more parameters to control the generation strategy?
> > > 4. Do you think some proposed parameters are redundant? If so, please
> > > specify the name of those parameters.
> > >
> > > You may also put any other suggestions regarding command line interface
> > >
> > > 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

Re: [Scaffoldhunter-devel] Seeking Feedback On Command Line Interface (CLI)

[<nl...@us...>]

Hi Shamshad,

I think it would be good not only to write out the scaffolds, but also the 
molecules with an additional property that identifies the associated scaffold. 
How do you plan to save the tree/network structure? 
An additional parameter --min-ring-size might also be useful.


Regards,
  Nils

On Wednesday 25 June 2014 08:37:11 Shamshad Alam wrote:
> Hi,
> 
> I am working on Command Line Interface (CLI) which is a GSoC-2014 project.
> And I would like get some  feedback on the commands and parameters used
> with commands in CLI.
> 
> In the first phase, our aim is to implement the commands to generate
> Scaffold tree from the molecules in the SDF file or in the database. We are
> also offering user to specify the ring size of the scaffolds which are to
> be included in output. The generated scaffold is saved in the sdf file that
> can be further used for analysis. An SDF file is required to generate
> scaffold tree from the file and connection data is needed to make
> connection with database to generate scaffold tree from database.
> 
> In the later stages we have planned to implement filtering by structure and
> substructure e. g. only certain subtrees based on the structure /
> substructure search will saved in output.
> 
> These are proposed commands and their parameters so far:
> 
> (1) generate : This command is used to generate scaffold tree / network and
> it needs a source of molecules like sdf file and a destination file to save
> generated scaffolds. It is used in combination with following parameters -
> (a) To generate scaffold tree / network loading molecules from file
> -n | --network : Use this parameter to generate scaffold network, absence
> of this parameter means you want to generate scaffold tree
> -i | --input-file <file_location> : Specify location of input file to read
> molecules from.
> -o | --output-file <file_location> : Specify file in which generated
> scaffold would be saved
> -m | --max-ring-size <number> : Specify the maximum ring size of scaffold
> that should be included in the output
> 
> (b) To generate scaffold tree / network by loading molecules from Scaffold
> Hunter database
> -c | --connection-name <connection-name> : Name of the connection that
> would be used for connection with the database to retrieve molecules.
> -d |  --dataset <dataset_name> : Specify name of the dataset to retrieve
> molecules from and generate scaffold tree
> -o | --output-file <file_location> : Specify file in which generated
> scaffold would be saved
> -m | --max-ring-size <number> : Specify the maximum ring size of scaffold
> that should be included in the output
> -n | --network : Use this parameter to generate scaffold network, absence
> of this parameter means you want to generate scaffold tree
> 
> These are some examples of 'generate' command :
> 
> (a) Read molecules from file
> 
> sh generate -i <input-file>
> Read molecules from input file and generate scaffold tree. Generated tree
> is saved in a file automatically.
> 
> sh generate -i <input-file> -o scaffold.sdf
> Read molecules from input file and generate scaffold tree. Generated tree
> is saved in scaffold.sdf.
> 
> sh generate -i <input-file> -o scaffold-2.sdf -n
> Read molecules from input file and generate scaffold 'network'. Generated
> network is saved in scaffold-2.sdf.
> 
> sh generate -i <input-file> -o scaffold-3.sdf -m 5
> Read molecules from input file and generate scaffold tree. Generated tree
> is saved in scaffold-3.sdf. All scaffolds with rings more than 5 are not
> saved.
> 
> (b) Read molecules from database
> 
> sh generate -c <connection-name>
> Read molecules from database which connection data is pointed by
> <connection-name> and generate scaffold tree. Generated tree is saved in
> file automatically.
> 
> sh generate -c <connection-name> -o scaffold.sdf
> Read molecules from database which connection data is pointed by
> <connection-name> and generate scaffold tree. Generated tree is saved in
> scaffold.sdf.
> 
> Similarly, you can use -n to generate network and -m <number> to limit the
> ring size as you've done in scaffold tree generation from file.
> 
> (2) connection [list | save | delete] : This command is used to manage
> connection data which is required for connection with database. It is
> followed by list, save or delete action. These are parameters supported by
> the command :
> 
> -c | --connection-name <name> : name of the connection
> -t | --database-type : Type of database (mySql, HSQLDB)
> -u | --url : Url of the mySql database server or file location of HSQLDB
> -n | --database-name : Name of the database
> -un | --user-name : user name to login
> -p | --password : password of the database (You can avoid this parameter
> and specify it at runtime during connection is made to database)
> 
> Here is some uses of connection command -
> 
> sh connection list
> display the names of available connections on screen
> 
> sh connection list -c <name>
> display the details of particular connection data pointed by name excluding
> password
> 
> sh connection delete -c <name>
> delete the connection data pointed by the name
> 
> connection save -c <name> -t <hsqldb | mysql> -u <url> -n <database-name>
> -un <user-name>
> save a new connection data with specified name which can be used later to
> make connection with database
> 
> Feedback -
> 
> We are seeking your feedback on implemented commands and proposed
> parameters to make the command line interface more useful. So, please give
> your inputs to a few questions given here :
> 1. What are the features of scaffold hunter you want to use in command line
> interface?
> 2. Do you find the parameters provided for scaffold tree / network
> generation user friendly?
> 3. Do you need some more parameters to control the generation strategy?
> 4. Do you think some proposed parameters are redundant? If so, please
> specify the name of those parameters.
> 
> You may also put any other suggestions regarding command line interface
> 
> Thanks,
> Shamshad

Re: [Scaffoldhunter-devel] Seeking Feedback On Command Line Interface (CLI)

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

Hi Tills,

Thanks! Good to hear from you. All points are comprehensible except the
term "defined properties" in second point. Does it refer to molecular
properties?

>> show the *defined properties* and some statistics (e.g. size) about an
sdf, csv file, without actually doing anything with the file

Thanks,
Shamshad



On Tue, Jul 1, 2014 at 6:09 PM, Till Schäfer <til...@tu...>
wrote:

> Hi,
> here are some wishes, that came into my mind:
> - import/merging sdf and csv into the scaffold hunter database over
> command line
> - show the defined properties and some statistics (e.g. size) about an
> sdf, csv file, without actually doing anything with the file (this can be
> useful for later import / merging.
> - export an internal database over the command line
> - show the defined properties and some statistics (e.g. size) about an
> internal dataset / subset, without actually doing anything with the file
> (this can be useful for later import / merging.
> - add a subset switch for each operation that uses data from the scaffold
> hunter database
> - clustering -> as for scaffold network / tree generation, but with
> clustering
> - generate a subset based on a filter, split a subset by scaffold tree
> structure, random subset generation
>   -> this should be possible to in a way, such that we can store the
> subset in the database, or store it directly in a file.
>  -> it should be possible to read an sdf/csv, filter it and store it
> directly to a file (without any sh database operation involved)
> - apply a calc plugin to data
>  -> pathways: read from file / database -> generate property  -> store to
> file / database
> - the tree generation code should have an option to specify the rules,
> which are used to generate a scaffold tree
> - delete an internal database / subset
> - ... :-)
>
> Regards,
> Till
>
> Am Mittwoch, 25. Juni 2014, 08:37:11 schrieb Shamshad Alam:
> > Hi,
> >
> > I am working on Command Line Interface (CLI) which is a GSoC-2014
> project.
> > And I would like get some  feedback on the commands and parameters used
> > with commands in CLI.
> >
> > In the first phase, our aim is to implement the commands to generate
> > Scaffold tree from the molecules in the SDF file or in the database. We
> are
> > also offering user to specify the ring size of the scaffolds which are to
> > be included in output. The generated scaffold is saved in the sdf file
> that
> > can be further used for analysis. An SDF file is required to generate
> > scaffold tree from the file and connection data is needed to make
> > connection with database to generate scaffold tree from database.
> >
> > In the later stages we have planned to implement filtering by structure
> and
> > substructure e. g. only certain subtrees based on the structure /
> > substructure search will saved in output.
> >
> > These are proposed commands and their parameters so far:
> >
> > (1) generate : This command is used to generate scaffold tree / network
> and
> > it needs a source of molecules like sdf file and a destination file to
> save
> > generated scaffolds. It is used in combination with following parameters
> -
> > (a) To generate scaffold tree / network loading molecules from file
> > -n | --network : Use this parameter to generate scaffold network, absence
> > of this parameter means you want to generate scaffold tree
> > -i | --input-file <file_location> : Specify location of input file to
> read
> > molecules from.
> > -o | --output-file <file_location> : Specify file in which generated
> > scaffold would be saved
> > -m | --max-ring-size <number> : Specify the maximum ring size of scaffold
> > that should be included in the output
> >
> > (b) To generate scaffold tree / network by loading molecules from
> Scaffold
> > Hunter database
> > -c | --connection-name <connection-name> : Name of the connection that
> > would be used for connection with the database to retrieve molecules.
> > -d |  --dataset <dataset_name> : Specify name of the dataset to retrieve
> > molecules from and generate scaffold tree
> > -o | --output-file <file_location> : Specify file in which generated
> > scaffold would be saved
> > -m | --max-ring-size <number> : Specify the maximum ring size of scaffold
> > that should be included in the output
> > -n | --network : Use this parameter to generate scaffold network, absence
> > of this parameter means you want to generate scaffold tree
> >
> > These are some examples of 'generate' command :
> >
> > (a) Read molecules from file
> >
> > sh generate -i <input-file>
> > Read molecules from input file and generate scaffold tree. Generated tree
> > is saved in a file automatically.
> >
> > sh generate -i <input-file> -o scaffold.sdf
> > Read molecules from input file and generate scaffold tree. Generated tree
> > is saved in scaffold.sdf.
> >
> > sh generate -i <input-file> -o scaffold-2.sdf -n
> > Read molecules from input file and generate scaffold 'network'. Generated
> > network is saved in scaffold-2.sdf.
> >
> > sh generate -i <input-file> -o scaffold-3.sdf -m 5
> > Read molecules from input file and generate scaffold tree. Generated tree
> > is saved in scaffold-3.sdf. All scaffolds with rings more than 5 are not
> > saved.
> >
> > (b) Read molecules from database
> >
> > sh generate -c <connection-name>
> > Read molecules from database which connection data is pointed by
> > <connection-name> and generate scaffold tree. Generated tree is saved in
> > file automatically.
> >
> > sh generate -c <connection-name> -o scaffold.sdf
> > Read molecules from database which connection data is pointed by
> > <connection-name> and generate scaffold tree. Generated tree is saved in
> > scaffold.sdf.
> >
> > Similarly, you can use -n to generate network and -m <number> to limit
> the
> > ring size as you've done in scaffold tree generation from file.
> >
> > (2) connection [list | save | delete] : This command is used to manage
> > connection data which is required for connection with database. It is
> > followed by list, save or delete action. These are parameters supported
> by
> > the command :
> >
> > -c | --connection-name <name> : name of the connection
> > -t | --database-type : Type of database (mySql, HSQLDB)
> > -u | --url : Url of the mySql database server or file location of HSQLDB
> > -n | --database-name : Name of the database
> > -un | --user-name : user name to login
> > -p | --password : password of the database (You can avoid this parameter
> > and specify it at runtime during connection is made to database)
> >
> > Here is some uses of connection command -
> >
> > sh connection list
> > display the names of available connections on screen
> >
> > sh connection list -c <name>
> > display the details of particular connection data pointed by name
> excluding
> > password
> >
> > sh connection delete -c <name>
> > delete the connection data pointed by the name
> >
> > connection save -c <name> -t <hsqldb | mysql> -u <url> -n <database-name>
> > -un <user-name>
> > save a new connection data with specified name which can be used later to
> > make connection with database
> >
> > Feedback -
> >
> > We are seeking your feedback on implemented commands and proposed
> > parameters to make the command line interface more useful. So, please
> give
> > your inputs to a few questions given here :
> > 1. What are the features of scaffold hunter you want to use in command
> line
> > interface?
> > 2. Do you find the parameters provided for scaffold tree / network
> > generation user friendly?
> > 3. Do you need some more parameters to control the generation strategy?
> > 4. Do you think some proposed parameters are redundant? If so, please
> > specify the name of those parameters.
> >
> > You may also put any other suggestions regarding command line interface
> >
> > 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
>



-- 
-Shamshad Alam

+91 9911631198

LinkedIn : in.linkedin.com/pub/shamshad-alam/58/939/70
GitHub: @shamshad-npti
Facbook: @shamshad.saralindia

Re: [Scaffoldhunter-devel] Seeking Feedback On Command Line Interface (CLI)

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

Hi, 
here are some wishes, that came into my mind: 
- import/merging sdf and csv into the scaffold hunter database over command line
- show the defined properties and some statistics (e.g. size) about an sdf, csv file, without actually doing anything with the file (this can be useful for later import / merging. 
- export an internal database over the command line
- show the defined properties and some statistics (e.g. size) about an internal dataset / subset, without actually doing anything with the file (this can be useful for later import / merging. 
- add a subset switch for each operation that uses data from the scaffold hunter database
- clustering -> as for scaffold network / tree generation, but with clustering 
- generate a subset based on a filter, split a subset by scaffold tree structure, random subset generation
  -> this should be possible to in a way, such that we can store the subset in the database, or store it directly in a file.  
 -> it should be possible to read an sdf/csv, filter it and store it directly to a file (without any sh database operation involved)
- apply a calc plugin to data 
 -> pathways: read from file / database -> generate property  -> store to file / database 
- the tree generation code should have an option to specify the rules, which are used to generate a scaffold tree
- delete an internal database / subset
- ... :-)

Regards,
Till

Am Mittwoch, 25. Juni 2014, 08:37:11 schrieb Shamshad Alam:
> Hi,
> 
> I am working on Command Line Interface (CLI) which is a GSoC-2014 project.
> And I would like get some  feedback on the commands and parameters used
> with commands in CLI.
> 
> In the first phase, our aim is to implement the commands to generate
> Scaffold tree from the molecules in the SDF file or in the database. We are
> also offering user to specify the ring size of the scaffolds which are to
> be included in output. The generated scaffold is saved in the sdf file that
> can be further used for analysis. An SDF file is required to generate
> scaffold tree from the file and connection data is needed to make
> connection with database to generate scaffold tree from database.
> 
> In the later stages we have planned to implement filtering by structure and
> substructure e. g. only certain subtrees based on the structure /
> substructure search will saved in output.
> 
> These are proposed commands and their parameters so far:
> 
> (1) generate : This command is used to generate scaffold tree / network and
> it needs a source of molecules like sdf file and a destination file to save
> generated scaffolds. It is used in combination with following parameters -
> (a) To generate scaffold tree / network loading molecules from file
> -n | --network : Use this parameter to generate scaffold network, absence
> of this parameter means you want to generate scaffold tree
> -i | --input-file <file_location> : Specify location of input file to read
> molecules from.
> -o | --output-file <file_location> : Specify file in which generated
> scaffold would be saved
> -m | --max-ring-size <number> : Specify the maximum ring size of scaffold
> that should be included in the output
> 
> (b) To generate scaffold tree / network by loading molecules from Scaffold
> Hunter database
> -c | --connection-name <connection-name> : Name of the connection that
> would be used for connection with the database to retrieve molecules.
> -d |  --dataset <dataset_name> : Specify name of the dataset to retrieve
> molecules from and generate scaffold tree
> -o | --output-file <file_location> : Specify file in which generated
> scaffold would be saved
> -m | --max-ring-size <number> : Specify the maximum ring size of scaffold
> that should be included in the output
> -n | --network : Use this parameter to generate scaffold network, absence
> of this parameter means you want to generate scaffold tree
> 
> These are some examples of 'generate' command :
> 
> (a) Read molecules from file
> 
> sh generate -i <input-file>
> Read molecules from input file and generate scaffold tree. Generated tree
> is saved in a file automatically.
> 
> sh generate -i <input-file> -o scaffold.sdf
> Read molecules from input file and generate scaffold tree. Generated tree
> is saved in scaffold.sdf.
> 
> sh generate -i <input-file> -o scaffold-2.sdf -n
> Read molecules from input file and generate scaffold 'network'. Generated
> network is saved in scaffold-2.sdf.
> 
> sh generate -i <input-file> -o scaffold-3.sdf -m 5
> Read molecules from input file and generate scaffold tree. Generated tree
> is saved in scaffold-3.sdf. All scaffolds with rings more than 5 are not
> saved.
> 
> (b) Read molecules from database
> 
> sh generate -c <connection-name>
> Read molecules from database which connection data is pointed by
> <connection-name> and generate scaffold tree. Generated tree is saved in
> file automatically.
> 
> sh generate -c <connection-name> -o scaffold.sdf
> Read molecules from database which connection data is pointed by
> <connection-name> and generate scaffold tree. Generated tree is saved in
> scaffold.sdf.
> 
> Similarly, you can use -n to generate network and -m <number> to limit the
> ring size as you've done in scaffold tree generation from file.
> 
> (2) connection [list | save | delete] : This command is used to manage
> connection data which is required for connection with database. It is
> followed by list, save or delete action. These are parameters supported by
> the command :
> 
> -c | --connection-name <name> : name of the connection
> -t | --database-type : Type of database (mySql, HSQLDB)
> -u | --url : Url of the mySql database server or file location of HSQLDB
> -n | --database-name : Name of the database
> -un | --user-name : user name to login
> -p | --password : password of the database (You can avoid this parameter
> and specify it at runtime during connection is made to database)
> 
> Here is some uses of connection command -
> 
> sh connection list
> display the names of available connections on screen
> 
> sh connection list -c <name>
> display the details of particular connection data pointed by name excluding
> password
> 
> sh connection delete -c <name>
> delete the connection data pointed by the name
> 
> connection save -c <name> -t <hsqldb | mysql> -u <url> -n <database-name>
> -un <user-name>
> save a new connection data with specified name which can be used later to
> make connection with database
> 
> Feedback -
> 
> We are seeking your feedback on implemented commands and proposed
> parameters to make the command line interface more useful. So, please give
> your inputs to a few questions given here :
> 1. What are the features of scaffold hunter you want to use in command line
> interface?
> 2. Do you find the parameters provided for scaffold tree / network
> generation user friendly?
> 3. Do you need some more parameters to control the generation strategy?
> 4. Do you think some proposed parameters are redundant? If so, please
> specify the name of those parameters.
> 
> You may also put any other suggestions regarding command line interface
> 
> 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

[Scaffoldhunter-devel] Development for GSoC continues

[Karsten K. <kar...@ud...>]

Congratulations to our Google Summer of Code students, all of whom
succeeded to pass their midterm evaluation.

We would like to thank them for their contribution, and look
forward to further development work done over the next weeks.

We expect that the new features under development will add a lot of
value to Scaffold Hunter!

Best,
    Karsten

[Scaffoldhunter-devel] Seeking Feedback On Command Line Interface (CLI)

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

Hi,

I am working on Command Line Interface (CLI) which is a GSoC-2014 project.
And I would like get some  feedback on the commands and parameters used
with commands in CLI.

In the first phase, our aim is to implement the commands to generate
Scaffold tree from the molecules in the SDF file or in the database. We are
also offering user to specify the ring size of the scaffolds which are to
be included in output. The generated scaffold is saved in the sdf file that
can be further used for analysis. An SDF file is required to generate
scaffold tree from the file and connection data is needed to make
connection with database to generate scaffold tree from database.

In the later stages we have planned to implement filtering by structure and
substructure e. g. only certain subtrees based on the structure /
substructure search will saved in output.

These are proposed commands and their parameters so far:

(1) generate : This command is used to generate scaffold tree / network and
it needs a source of molecules like sdf file and a destination file to save
generated scaffolds. It is used in combination with following parameters -
(a) To generate scaffold tree / network loading molecules from file
-n | --network : Use this parameter to generate scaffold network, absence
of this parameter means you want to generate scaffold tree
-i | --input-file <file_location> : Specify location of input file to read
molecules from.
-o | --output-file <file_location> : Specify file in which generated
scaffold would be saved
-m | --max-ring-size <number> : Specify the maximum ring size of scaffold
that should be included in the output

(b) To generate scaffold tree / network by loading molecules from Scaffold
Hunter database
-c | --connection-name <connection-name> : Name of the connection that
would be used for connection with the database to retrieve molecules.
-d |  --dataset <dataset_name> : Specify name of the dataset to retrieve
molecules from and generate scaffold tree
-o | --output-file <file_location> : Specify file in which generated
scaffold would be saved
-m | --max-ring-size <number> : Specify the maximum ring size of scaffold
that should be included in the output
-n | --network : Use this parameter to generate scaffold network, absence
of this parameter means you want to generate scaffold tree

These are some examples of 'generate' command :

(a) Read molecules from file

sh generate -i <input-file>
Read molecules from input file and generate scaffold tree. Generated tree
is saved in a file automatically.

sh generate -i <input-file> -o scaffold.sdf
Read molecules from input file and generate scaffold tree. Generated tree
is saved in scaffold.sdf.

sh generate -i <input-file> -o scaffold-2.sdf -n
Read molecules from input file and generate scaffold 'network'. Generated
network is saved in scaffold-2.sdf.

sh generate -i <input-file> -o scaffold-3.sdf -m 5
Read molecules from input file and generate scaffold tree. Generated tree
is saved in scaffold-3.sdf. All scaffolds with rings more than 5 are not
saved.

(b) Read molecules from database

sh generate -c <connection-name>
Read molecules from database which connection data is pointed by
<connection-name> and generate scaffold tree. Generated tree is saved in
file automatically.

sh generate -c <connection-name> -o scaffold.sdf
Read molecules from database which connection data is pointed by
<connection-name> and generate scaffold tree. Generated tree is saved in
scaffold.sdf.

Similarly, you can use -n to generate network and -m <number> to limit the
ring size as you've done in scaffold tree generation from file.

(2) connection [list | save | delete] : This command is used to manage
connection data which is required for connection with database. It is
followed by list, save or delete action. These are parameters supported by
the command :

-c | --connection-name <name> : name of the connection
-t | --database-type : Type of database (mySql, HSQLDB)
-u | --url : Url of the mySql database server or file location of HSQLDB
-n | --database-name : Name of the database
-un | --user-name : user name to login
-p | --password : password of the database (You can avoid this parameter
and specify it at runtime during connection is made to database)

Here is some uses of connection command -

sh connection list
display the names of available connections on screen

sh connection list -c <name>
display the details of particular connection data pointed by name excluding
password

sh connection delete -c <name>
delete the connection data pointed by the name

connection save -c <name> -t <hsqldb | mysql> -u <url> -n <database-name>
-un <user-name>
save a new connection data with specified name which can be used later to
make connection with database

Feedback -

We are seeking your feedback on implemented commands and proposed
parameters to make the command line interface more useful. So, please give
your inputs to a few questions given here :
1. What are the features of scaffold hunter you want to use in command line
interface?
2. Do you find the parameters provided for scaffold tree / network
generation user friendly?
3. Do you need some more parameters to control the generation strategy?
4. Do you think some proposed parameters are redundant? If so, please
specify the name of those parameters.

You may also put any other suggestions regarding command line interface

Thanks,
Shamshad

-- 
-Shamshad Alam

+91 9911631198 | India

Re: [Scaffoldhunter-devel] Saving session fails

[Anjenson <hot...@gm...>]

Hi Till,

Thanks for your advice it helped. :)
Well, the actual reason was that I tried to store Scaffold in ViewState. 
Still it is not used in program so I can simply remove it and now 
everything works fine.

All the best,
     Andrew

On 06/13/2014 02:57 PM, Till Schäfer wrote:
> Hi,
> this sql error normally occurs if you save a too long string in a field, that has a size limitation.
>
> The error occurs for the following command in the GUI Controller:
> db.saveOrUpdate(dbSession);
>
> Could it be, that some part of your ViewState or ViewConfig references some other part of your code? For example if you have registered a change listener on your ViewState, all registered listeners and all objects that are referenced by this objects (and so on) are also saved!
>
> So as a general rule: ViewState and ViewConfig should never reference anything outside their own class.
>
> Greetings
> Till
>
> Am Mittwoch, 11. Juni 2014, 21:18:48 schrieb Anjenson:
>> Hi everyone,
>>
>> While working on MoleculeCloud view and I faced a problem with saving
>> session when finishing program.
>> It is not related to the size of packets as not much is stored in State
>> class on the moment of closing.
>> I have no idea about how saving process works and how to debug it.
>> I hope that there is someone on the list who can describe the process of
>> saving so that at least I could understand it.
>>
>> I attach error logs to this mail. I will be happy to receive any advice
>> or help.
>>
>> Regards,
>>       Andrew Zhilka