scaffoldhunter-devel — Discussion list for Scaffold Hunter developers

Re: [Scaffoldhunter-devel] Saving session fails

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

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
-- 
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
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[Scaffoldhunter-devel] Saving session fails

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

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

[Scaffoldhunter-devel] Tutorial about Database Access in SH

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

Hi, 
the Tutorial [1] covers database access and error handling (e.g. database connection loss). 

@GSOC Students: Whenever you come in touch with DbManager. Please read this! It is essential to do correct error handling!

Greetings, 
Till

[1] http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=database_access:devel&#using_the_dbexceptionhandler

-- 
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
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[Scaffoldhunter-devel] Guide for Lazy Loadingof Properties in the Wiki

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

Hi, 
i just created a small guide [1] about how the lazy loading of properties is done in Scaffold Hunter. 

Greetings,
Till

[1] http://scaffoldhunter.sourceforge.net/wiki/doku.php?id=lazy_loading_prop: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
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[Scaffoldhunter-devel] ProperyType and Property loading (lazy) / was: [Scaffoldhunter] Heatmap and Dendrograms

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

Hi, 
this mail contains some general information about how to handle properties, so i am also forwarding this mail to the devel mailing list. 

TO ALL GSOC PARTICIPANTS: please update your branches to apply the trunk changes listed below.

Am Dienstag, 27. Mai 2014, 10:52:53 schrieb Werner Sturm:
> Hi,
> 
> I have just checked in new code which fills the property list in the 
> left sidebar with all numerical PropertyDefintions. I am not completely 
> sure which properties we should use for the HeatMap. I selected all 
> PropertyDefinitions which are not of the types String-Property and 
> Scaffold-Property via getDataset().getPropertyDefinitions(). Are there 
> some more?
Dataset.getPropertyDefinitions() is the right way to get all defined properties for the current session / dataset. 

As you mentioned, a PropertyDefinition distinguishes between scaffold and molecule properties and you should only use the molecule properties for your view. 
Furthermore, there is a PropertyType. You should only use PropertyType.NumProperty for the Heatmap as you are interested in numerical properties only. All other PropertyTypes are meant for something different (e.g. BitString for Clustering and this BitString representation should be never presented to the user as it is not human readable). 

PropertyDefinition.isStringProperty() should be only used if you are interested in the format of a property on the Database level (i.e. its numerical or string representation). So it is important to distinguish between PropertyType which is the semantic (e.g. numerical value) and isStringProperty which gives you the representation (e.g. String, which may still represent some numerical value or some base encoded bit pattern!)
Currently there is no PropertyType other than NumProperty  that is stored as a numerical representation and therefore your implementation currently works as expected. However, you should use the semantic check (PropertyDefintion.getPropertyType() == PropertyType.NumProperty), because we might add another PropertyType, which users a numerical representation. 

I will change the JavaDoc to make this more clear and changed the name of the method. Therefore please update your branch to get the modifications from trunk. 

> 
> Before that, I tried to go through the result of the clustering 
> (HierarchicalClusterNode<Molecule>) to collect all numerical distinct 
> PropertyDefinitions of every molecule contained in the 
> HierarchicalClusterNode. This resulted in an empty set of 
> PropertyDefintions and actually I don't understand why. I called 
> molecule.getNumProperties() to get all NumProperties and 
> property.getType() to get its PropertyDefinition. Why does it not work?

Beside the fact that scanning the complete tree is not efficient and therefore should be avoided, i guess this has to do with lazy loading of properties.

In order to minimize RAM usage, Scaffold Hunter is using a lazy loading mechanism of properties. That means that you cannot access a property by simply calling Structure.getNumProperties(), Structure.getNumPropertyValue(), Structure.getStringProperties() or Structure.getStringPropertyValue(), because it might not be loaded. 

In order to load a property from the database you must call DbManager.lockAndLoad() for that property before accessing it. Please take care to unload them with DbManager.unlockAndUnload() after you do no need the properties anymore. 
Structures and therefore also Properties are shared between the Views. That means the lazy loading mechanism takes care, that a property is loaded only once. A property might be loaded even if you did not lock it yourself, but you should lock it anyway because the other locker might unlock it while you use the property!. 

Best Practice: unlock a Property as soon as possible, but try to avoid unnecessary lock unlock lock unlock ... circles. 
Attention: If you forget to unlock a property, you are causing a memory leak that even remain after your view is closed!

In your case i think that all properties where unloaded after the clustering. Therefore you get an empty list.


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
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[Scaffoldhunter-devel] Package Structure and Modularization / Re: [Scaffoldhunter] Heatmaps and Dendrograms

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

Hi, 
this mail contains some useful informations for all other developers that want to understand the package structure. 

Am Donnerstag, 15. Mai 2014, 00:26:38 schrieb Werner Sturm:
> - Maybe I will reuse the class ColorLegend located in 
> "edu.udo.scaffoldhunter.view.treemap.sidebar" as well. Should it be 
> placed in a more general package to avoid dependency on another view? I 
> do not know which package might be appropriate.
> 
> - To conform to the current package structure I should create the package
> "edu.udo.scaffoldhunter.view.heatmap" but it is not recommended that the 
> HeatMap package depends on several other views on the same package level.
Yes, all HeatMap specific code should go to that specific package. Everything else, that is reused by different views, should go to some common package and not depend on any of the views directly. That means it should not have any parameters, attributes, etc. of any class that is defined in the view package. If you need some concrete methods defined in the view package, define an interface for it in the common package and implement that interface by the specific view. 
One common package is the view.util package. However, as the name util suggests this is mainly for some small helpers such as the above mentioned color legend.  If you want to share larger parts (more that a single class) such as the complete dendrogram implementation, please create a new package view.components and a subpackage for the component (e.g. as dendrogram).

> 
> - I will also have to refactor/generalize some classes of DendrogramView 
> because they directly depend on DendrogramView (see 
> ClusteringController). 
Sounds reasonable. The ClusteringController is still not ideal in the above mentioned manner. This is a perfect example where we should create an interface, that provides the methods that always need to be present for the controller. For example the interface should contain a clusteringFinished(); method that can be called by the controller. This is similar to an listener / observer design pattern, but you have only a single observer which is passed to the controller in the constructor.
> Abstracting a view + state with clustering 
> functionality (ClusterController, StartClusteringPanel, etc.) might be a 
> solution.
i would not introduce some abstract "clustering view" class. Simply use the interface approach described above. Inheritance from a common superclass is always somewhat inflexible and i guess you cannot share much of functionality by doing so. Try to create small modules instead if you like to reuse functionality in different views.

> 
> - I might have to move classes located in the package 
> "edu.udo.scaffoldhunter.view.dendrogram" because I have to reuse several 
> classes (e.g., StartClusteringPanel, DendrogramEdge, DendrogramViewNode, 
> etc.). In this case DendrogramViewNode has to be renamed as well. 
> Creating a separate Dendrogram module would be nice but I think it takes 
> time which I need for other tasks till mid-term.
> Or maybe heatmap is a sub-package of dendrogram? (don't really like this 
> idea so far)
The ideal case is described above, but it could understand if you do not want to refactor the complete dendrogram view. This can take a reasonable amount of time. I would like to propose a golden middle way. Do not touch the dendrogram view where it  leads to heavy refactoring, but create / design your view in a manner, that you use reusable components, such as the dendrogram. This allows us to reuse your component later in the dendrogram view and the adaption of your components in the dendrogram view can be done by somebody else. This is still much less work for us than if we have to extract the component from two views which have them integrated without any component concept. 

> 
> I have not finished investigating these packages yet but these points 
> represent my current considerations and maybe you have a suggestion how 
> code should be organized to conform to current code structure.
> 
Looks good. The thought are going in the right direction. 

[1] https://en.wikipedia.org/wiki/Composition_over_inheritance


Greetings 
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
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Re: [Scaffoldhunter-devel] Command Line Interface

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

Hi Till,

it is community bonding, Till, all comments welcome :-)

Best,
    Karsten

Am 30.04.2014 19:07, schrieb Till Schäfer:
> Hi, 
> although i am not your mentor: i highly encourage to use http://jcommander.org/ for the CLI parsing / interpretation. 
> 
> Greetings,
> Till
> 
> Am Mittwoch, 30. April 2014, 13:27:20 schrieb Shamshad Alam:
>> Hi,
>>
>> Please, suggest me what tools, libraries, documentations, and literature I
>> should learn which will help me during the project.
>>
>> Sometime ago while I was browsing mailing list of scaffold hunter I found a
>> few information such as packages edu.udo.scaffoldhunter.model.clustering,
>> and edu.udo.scaffoldhunter.model.treegen are important for this project.
>> And Scaffold Hunter is already using JCommander for argument parsing[1].
>>
>> But, from that it is not to much clear what would be exactly scope of the
>> project etc. So, please help me to get started with this project.
>>
>> Thanks
>> Shamshad
>>
>> [1] https://sourceforge.net/p/scaffoldhunter/mailman/message/32049522/
>>
>>


-- 
Karsten Klein
Information Visualization Group
The University of Sydney

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Re: [Scaffoldhunter-devel] Command Line Interface

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

Hi, 
although i am not your mentor: i highly encourage to use http://jcommander.org/ for the CLI parsing / interpretation. 

Greetings,
Till

Am Mittwoch, 30. April 2014, 13:27:20 schrieb Shamshad Alam:
> Hi,
> 
> Please, suggest me what tools, libraries, documentations, and literature I
> should learn which will help me during the project.
> 
> Sometime ago while I was browsing mailing list of scaffold hunter I found a
> few information such as packages edu.udo.scaffoldhunter.model.clustering,
> and edu.udo.scaffoldhunter.model.treegen are important for this project.
> And Scaffold Hunter is already using JCommander for argument parsing[1].
> 
> But, from that it is not to much clear what would be exactly scope of the
> project etc. So, please help me to get started with this project.
> 
> Thanks
> Shamshad
> 
> [1] https://sourceforge.net/p/scaffoldhunter/mailman/message/32049522/
> 
> 
-- 
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
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[Scaffoldhunter-devel] Command Line Interface

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

Hi,

Please, suggest me what tools, libraries, documentations, and literature I
should learn which will help me during the project.

Sometime ago while I was browsing mailing list of scaffold hunter I found a
few information such as packages edu.udo.scaffoldhunter.model.clustering,
and edu.udo.scaffoldhunter.model.treegen are important for this project.
And Scaffold Hunter is already using JCommander for argument parsing[1].

But, from that it is not to much clear what would be exactly scope of the
project etc. So, please help me to get started with this project.

Thanks
Shamshad

[1] https://sourceforge.net/p/scaffoldhunter/mailman/message/32049522/

-- 
-Shamshad Alam

+91 9911631198

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

Re: [Scaffoldhunter-devel] Zoom Browsing

[Karsten K. <ka...@us...>]

Hi Andrew,

indeed the emphasis here is on "optional". It is good to quickly
flick through the selected elements without changing the view, where
it is of advantage to see where in the tree your current element is.
On the other hand, one would want to look at the element and
neighborhood more closely sometimes by having the zooming linked
to the browsing.

Best,
    Karsten

Am 29.04.2014 19:04, schrieb nl...@us...:
> Hi Andrew,
> 
> is this related to the feature request #16 [1]? It would be great to have this 
> feature as an option since the user not always wants to change the view when 
> browsing the selection.
> 
> 
> Regards,
>   Nils
> 
> [1] https://sourceforge.net/p/scaffoldhunter/feature-requests/16/
> 
> On Monday 28 April 2014 23:09:48 Anjenson wrote:
>> Hi,
>>
>> I have been thinking a lot about how to implement this feature in a good
>> way, but I suddenly came out with a peculiar solution that is to use
>> /focusMolecule/ method from /View/ classes. The simplicity makes me
>> confused and I would be really grateful if anyone could review it.
>>
>> Regards,
>> Andrew "Anjenson" Zhilka
>>
>> P.S.
>> My changes are attached.
> 
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Re: [Scaffoldhunter-devel] Zoom Browsing

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

Hi Nils,

On 04/29/2014 12:04 PM, nl...@us... wrote:
> Hi Andrew,
>
> is this related to the feature request #16 [1]?
Yes, that is the one in question.
>   It would be great to have this
> feature as an option since the user not always wants to change the view when
> browsing the selection.
OK, but is the way it is implemented (I mean excluding optionality) normal?

Regards,
Andrew "Anjenson" Zhilka

Re: [Scaffoldhunter-devel] Zoom Browsing

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

Hi Andrew,

is this related to the feature request #16 [1]? It would be great to have this 
feature as an option since the user not always wants to change the view when 
browsing the selection.


Regards,
  Nils

[1] https://sourceforge.net/p/scaffoldhunter/feature-requests/16/

On Monday 28 April 2014 23:09:48 Anjenson wrote:
> Hi,
> 
> I have been thinking a lot about how to implement this feature in a good
> way, but I suddenly came out with a peculiar solution that is to use
> /focusMolecule/ method from /View/ classes. The simplicity makes me
> confused and I would be really grateful if anyone could review it.
> 
> Regards,
> Andrew "Anjenson" Zhilka
> 
> P.S.
> My changes are attached.

[Scaffoldhunter-devel] Zoom Browsing

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

Hi,

I have been thinking a lot about how to implement this feature in a good 
way, but I suddenly came out with a peculiar solution that is to use 
/focusMolecule/ method from /View/ classes. The simplicity makes me 
confused and I would be really grateful if anyone could review it.

Regards,
Andrew "Anjenson" Zhilka

P.S.
My changes were attached in earlier mail.

[Scaffoldhunter-devel] Zoom Browsing

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

Hi,

I have been thinking a lot about how to implement this feature in a good 
way, but I suddenly came out with a peculiar solution that is to use 
/focusMolecule/ method from /View/ classes. The simplicity makes me 
confused and I would be really grateful if anyone could review it.

Regards,
Andrew "Anjenson" Zhilka

P.S.
My changes are attached.

[Scaffoldhunter-devel] GSOC - Welcome

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

Dear Accepted GSOC Participants, 
welcome on board! We look forward to work with you and are curious to see some new Scaffold Hunter features emerging. 

What will come next:
- In the next days the mentors will contact you and will arrange an online meeting with you (the mentors will write how this meeting will take place). In this meeting you will be introduced in the concrete goals of your project. 
- We will release Scaffold Hunter 2.3.1 in the next days. Some of you already contributed to this release. THX.  After the release each of you will get a SVN branch, where you can keep your code. Please do not use an external repository, because this will make your changes harder to reintegrate if your project is successful. Furthermore, we have already set up our repository to send emails on code changes and this makes it easier (for us mentors) to keep track of your work. To get write access to the repository, your will have to create a sourceforge account (if you do not already have one). Please send your account name to your mentors. 

General things to say (Your mentors will tell you something similar in the first meeting, but it is better to say this twice than missing a point)
- During the project keep in regular touch with your mentors. If you are stuck or the time schedule gets delayed talk to your mentors. If there is a reason, that you cannot work for some days on the project, talk to your mentors (in advance). Be responsive to mails.
- Respect the deadlines. 
- Submit your work often and in small pieces (without compilation errors). This will give use the chance to see problems / review your code early and this can save you a lot of work! We will not review all of your work a day before the evaluation! It will also help you to organize your work.
- We highly recommend to use eclipse and the eclipse project file! Many things are already configured in a way, that will help you to do your work in a way we expect your work to be. It is the only environment, where we can help you if you run in troubles with compiling / running your code / having  library dependency problems / etc. 
- Read the Java Code Conventions and format your code accordingly. The eclipse projects formatter is already configured correctly. Try to keep a common style and way to do the things, especially if you are extending existing code. Inspect how it is done in other parts of the SH. (There are some bad examples in the code. This is a general advice, but there might be good reasons to do things differently.)
- DOCUMENTATION! Always write meaningful JavaDocs for each of your public methods and classes. We will not accept undocumented Code!
- We expect your work to be free of warnings (and of course errors) at the time of the deadlines. The eclipse project is already configured in a way, that missing javadocs, etc will give you a warning.
- Use the logger and never use system.out.printline for console messages. 
- Keep your repository clean and well structured. Delete / do not submit temporary files if they are not needed for testing by the mentors. 


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

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

Hi Shamshad,

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


Regards,
  Nils

On Friday 18 April 2014 17:42:38 Shamshad Alam wrote:
> Hi,
> 
> Please, find revised version in attachment.
> 
> Thanks
> Shamshad
> 
> On Thu, Apr 17, 2014 at 9:18 PM, Shamshad Alam 
<sha...@gm...>wrote:
> > Hi,
> > 
> > Thanks for feedback. In the next patch you will find the fix of problems
> > you pointed out.
> > 
> > Thanks
> > Shamshad
> > 
> > 
> > On Thu, Apr 17, 2014 at 6:53 PM, Till Schäfer <
> > 
> > til...@tu...> wrote:
> >> Hi,
> >> i just updated the menu and added some categories as comments and also
> >> changed the ordering a little bit.
> >> -> your action should now go to "single subset filters" category.
> >> 
> >> Viele Grüße
> >> Till
> >> 
> >> Am Donnerstag, 17. April 2014, 15:01:53 schrieb Till Schäfer:
> >> > Hi,
> >> > it now seems to work for me.
> >> > It is good to see, that you used a worker thread for the splitting and
> >> 
> >> animated the work, because it can take some tome to create many subsets.
> >> Furthermore i liked that you used the DbExceptionHandler.
> >> 
> >> > However, there are still some things to fix before we can integrate the
> >> 
> >> patch:
> >> > - The parent of the new subset should be the subset that is spitted.
> >> > - The split action should be accessible by right clicking on a subset
> >> 
> >> (not only in the menu).
> >> 
> >> > - The action should be located int the same section as union /
> >> 
> >> intersection / difference / filter.
> >> 
> >> > - ModelViewControler: The splitting should be implemented in the
> >> 
> >> SubsetManager. The action should just call the method there (have a look
> >> at
> >> the other actions).
> >> 
> >> > - Good Coding Style: use two lines of code if you want to define and
> >> 
> >> initialize two variable: int ringLevel = subsetDialog.getRingLevel(),
> >> index
> >> = 1;
> >> 
> >> > - Hint /  Good Coding Style: you can use the
> >> 
> >> Scaffolds.SubtreePreorderIterable to iterate over all scaffolds in a
> >> subtree (e.v. in your method getMolecules)
> >> 
> >> > Greetings
> >> > Till
> >> > 
> >> > Am Mittwoch, 16. April 2014, 21:08:42 schrieb Shamshad Alam:
> >> > > Hi,
> >> > > 
> >> > > Please, find the patch in attachment, apply and check it.
> >> > > 
> >> > > Thanks
> >> > > Shamshad
> >> > > 
> >> > > 
> >> > > 
> >> > > On Wed, Apr 16, 2014 at 3:21 PM, Till Schäfer <
> >> 
> >> til...@tu...
> >> 
> >> > > > wrote:
> >> > > > 
> >> > > > Hi,
> >> > > > lets go back to mailing list communication ;).
> >> > > > 
> >> > > > Am Mittwoch, 16. April 2014, 14:57:34 schrieb Shamshad Alam:
> >> > > > > Hi,
> >> > > > > 
> >> > > > > While working on this feature as you suggested I found that for a
> >> 
> >> large
> >> 
> >> > > > > dataset there are more than a hundred scaffolds at a given ring
> >> 
> >> level and
> >> 
> >> > > > > many of them contain a few (usually 1-10) molecules. So, after
> >> 
> >> split up
> >> 
> >> > > > > hundred of subsets which merely contain a few molecules are
> >> 
> >> created. It
> >> 
> >> > > > > makes Subset Manager Panel a little bit chaotic [Please refer to
> >> 
> >> the
> >> 
> >> > > > image
> >> > > > 
> >> > > > > attached to understand the situation well].
> >> > > > 
> >> > > > The features purpose is to be able to handle dataset of very large
> >> 
> >> size
> >> 
> >> > > > (i.e. about a million molecules). In this case one is not able to
> >> 
> >> show all
> >> 
> >> > > > molecules in a view, because of performance limitations. Therefore
> >> 
> >> the
> >> 
> >> > > > split is a way to handle the dataset step by step and it is a
> >> 
> >> natural split
> >> 
> >> > > > by the structure of the molecules (at least for a chemist ;-) ).
> >> > > > 
> >> > > > As the number of molecules on level 1 ore 2 does not increase that
> >> 
> >> much,
> >> 
> >> > > > for larger datasets, this splitting makes sense for large datasets,
> >> 
> >> but not
> >> 
> >> > > > for small ones.
> >> > > > 
> >> > > > To conclude: It is totally fine, that you create so many small
> >> 
> >> datasets.
> >> 
> >> > > > Regards,
> >> > > > Till
> >> > > > 
> >> > > > > Should I go ahead to and create a patch for this implementation?
> >> > > > > 
> >> > > > > 
> >> > > > > Or, we should include some further criteria such as subsets for
> >> 
> >> only
> >> 
> >> > > > those
> >> > > > 
> >> > > > > scaffolds which have more than n (a number specified by user)
> >> 
> >> molecules
> >> 
> >> > > > are
> >> > > > 
> >> > > > > created.
> >> > > > > 
> >> > > > > Have you any other idea which makes this feature more usable?
> >> > > > > 
> >> > > > > Thanks
> >> > > > > Shamshad
> >> > > > > 
> >> > > > > 
> >> > > > > On Tue, Apr 15, 2014 at 10:18 PM, Till Schäfer <
> >> > > > > 
> >> > > > > til...@tu...> wrote:
> >> > > > > > Hi,
> >> > > > > > 
> >> > > > > > Am Dienstag, 15. April 2014, 21:30:29 schrieb Shamshad Alam:
> >> > > > > > > Hi,
> >> > > > > > > 
> >> > > > > > > Thanks for feedback, and sorry for misunderstanding.
> >> > > > > > > 
> >> > > > > > > You mean that n subsets will be created if there are n
> >> 
> >> scaffolds at
> >> 
> >> > > > ring
> >> > > > 
> >> > > > > > > level x. In this case, it will be tedious task to enter name
> >> 
> >> of the
> >> 
> >> > > > each
> >> > > > 
> >> > > > > > > subset to be created. So, what naming convention should I
> >> 
> >> use? I
> >> 
> >> > > > have an
> >> > > > 
> >> > > > > > > idea:
> >> > > > > > > 
> >> > > > > > > --> User will enter the name of the subset which will act as
> >> > > > > > > a
> >> > > > 
> >> > > > prefix and
> >> > > > 
> >> > > > > > > we will add suffix 1 for first subset, 2 for second
> >> 
> >> subset..., and n
> >> 
> >> > > > for
> >> > > > 
> >> > > > > > > nth subset, to the name for each subset to be created (You
> >> 
> >> may get
> >> 
> >> > > > the
> >> > > > 
> >> > > > > > > better picture of idea in the image attached) .
> >> > > > > > 
> >> > > > > > Sounds good. The default name should be orientated towards the
> >> 
> >> default
> >> 
> >> > > > > > name schema of filters and random subset creation.
> >> > > > > > 
> >> > > > > > Something like: "Split(Level 3) - n"
> >> > > > > > 
> >> > > > > > where n refers to the counter.
> >> > > > > > 
> >> > > > > > Regards,
> >> > > > > > Till
> >> > > > > > 
> >> > > > > > > --> Please tell me if you have any better idea regarding
> >> > > > > > > this.
> >> > > > > > > 
> >> > > > > > > Thanks
> >> > > > > > > Shamshad
> >> > > > > > > 
> >> > > > > > > 
> >> > > > > > > On Tue, Apr 15, 2014 at 5:36 PM, Till Schäfer <
> >> > > > > > 
> >> > > > > > til...@tu...
> >> > > > > > 
> >> > > > > > > > wrote:
> >> > > > > > > > 
> >> > > > > > > > Hi,
> >> > > > > > > > your patch just creates a single subset, where the top
> >> 
> >> rings are
> >> 
> >> > > > > > filtered
> >> > > > > > 
> >> > > > > > > > out. It does not SPLIT the subset.
> >> > > > > > > > See section "misunderstanding" in my previous mail.
> >> > > > > > > > 
> >> > > > > > > > Greetings,
> >> > > > > > > > Till
> >> > > > > > > > 
> >> > > > > > > > Am Montag, 14. April 2014, 09:10:46 schrieb Shamshad Alam:
> >> > > > > > > > > Hi,
> >> > > > > > > > > 
> >> > > > > > > > > I have made the changes you suggested. You can find
> >> 
> >> patches in
> >> 
> >> > > > > > attached
> >> > > > > > 
> >> > > > > > > > > file with this mail.
> >> > > > > > > > > 
> >> > > > > > > > > Thanks
> >> > > > > > > > > Shamshad
> >> > > > > > > > > 
> >> > > > > > > > > 
> >> > > > > > > > > On Fri, Apr 11, 2014 at 9:58 PM, Till Schäfer <
> >> > > > > > > > 
> >> > > > > > > > til...@tu...
> >> > > > > > > > 
> >> > > > > > > > > > wrote:
> >> > > > > > > > > > 
> >> > > > > > > > > > Hi,
> >> > > > > > > > > > thx for the patch.
> >> > > > > > > > > > I just looked through the code and there was some
> >> > > > 
> >> > > > misunderstanding
> >> > > > 
> >> > > > > > > > > > regarding the task:
> >> > > > > > > > > > - You selected the molecules of all scaffolds on ring
> >> 
> >> level x
> >> 
> >> > > > and
> >> > > > 
> >> > > > > > > > created
> >> > > > > > > > 
> >> > > > > > > > > > a single subset from this.
> >> > > > > > > > > > 
> >> > > > > > > > > > - The feature request 38 asked for something diferent:
> >> > > > > > > > > >  -> for each of the scaffolds on level x, select the
> >> 
> >> molecules
> >> 
> >> > > > > > from the
> >> > > > > > 
> >> > > > > > > > > > scaffold and his subtree and create a new subset.
> >> > > > > > > > > > 
> >> > > > > > > > > >  -> that means we will have n subsets if there are n
> >> 
> >> scaffolds
> >> 
> >> > > > on
> >> > > > 
> >> > > > > > > > level x.
> >> > > > > > > > 
> >> > > > > > > > > >  -> that means we partition the subset (minus the
> >> 
> >> molecules
> >> 
> >> > > > from
> >> > > > 
> >> > > > > > lower
> >> > > > > > 
> >> > > > > > > > > > rings)
> >> > > > > > > > > > 
> >> > > > > > > > > > The good message is, that your dialog seems to be
> >> 
> >> reusable for
> >> 
> >> > > > this
> >> > > > 
> >> > > > > > > > task.
> >> > > > > > > > 
> >> > > > > > > > > > We just need to change the description.
> >> > > > > > > > > > One small bug in the dialog: Only the visible rings are
> >> > > > > > 
> >> > > > > > selectable, not
> >> > > > > > 
> >> > > > > > > > > > the complete tree levels
> >> > > > > > > > > > 
> >> > > > > > > > > > One further note: The action should be located in the
> >> 
> >> subset
> >> 
> >> > > > menu
> >> > > > 
> >> > > > > > and
> >> > > > > > 
> >> > > > > > > > > > therefore should be implemented at the same place,
> >> 
> >> where also
> >> 
> >> > > > the
> >> > > > 
> >> > > > > > patch
> >> > > > > > 
> >> > > > > > > > > > from najenson was imlemented (SubssetManager /
> >> 
> >> SubsetActions).
> >> 
> >> > > > > > > > > > You can access the complete tree for a subset over
> >> > > > > > > > 
> >> > > > > > > > DbManager.getScaffolds.
> >> > > > > > > > 
> >> > > > > > > > > > Please wrap each of the DbManager calls in a
> >> 
> >> DbExceptionHandler
> >> 
> >> > > > > > (you
> >> > > > > > 
> >> > > > > > > > will
> >> > > > > > > > 
> >> > > > > > > > > > find some examples in the SubsetManger).
> >> > > > > > > > > > 
> >> > > > > > > > > > Regards,
> >> > > > > > > > > > Till
> >> > > > > > > > > > 
> >> > > > > > > > > > Am Mittwoch, 9. April 2014, 15:19:28 schrieb Shamshad
> >> 
> >> Alam:
> >> > > > > > > > > > > Hi,
> >> > > > > > > > > > > 
> >> > > > > > > > > > > Feature Request #38 has been implemented, and you can
> >> 
> >> find
> >> 
> >> > > > > > related
> >> > > > > > 
> >> > > > > > > > > > patches
> >> > > > > > > > > > 
> >> > > > > > > > > > > in attachment.
> >> > > > > > > > > > > 
> >> > > > > > > > > > > When you will execute the application after applying
> >> > > > 
> >> > > > patches, a
> >> > > > 
> >> > > > > > tool
> >> > > > > > 
> >> > > > > > > > bar
> >> > > > > > > > 
> >> > > > > > > > > > > button (to make subset from ring) will appear at the
> >> 
> >> right
> >> 
> >> > > > side
> >> > > > 
> >> > > > > > of
> >> > > > > > 
> >> > > > > > > > export
> >> > > > > > > > 
> >> > > > > > > > > > > toolbar button. Follow that button to create a new
> >> 
> >> subset at
> >> 
> >> > > > > > > > specified
> >> > > > > > > > 
> >> > > > > > > > > > ring
> >> > > > > > > > > > 
> >> > > > > > > > > > > level.
> >> > > > > > > > > > > 
> >> > > > > > > > > > > Thanks
> >> > > > > > > > > > > Shamshad
> >> > > > > > > > > > 
> >> > > > > > > > > > --
> >> > > > > > > > > > Dipl.-Inf. Till Schäfer
> >> > > > > > > > > > TU Dortmund University
> >> > > > > > > > > > Chair 11 - Algorithm Engineering
> >> > > > > > > > > > Otto-Hahn-Str. 14 / Room 237
> >> > > > > > > > > > 44227 Dortmund, Germany
> >> > > > > > > > > > 
> >> > > > > > > > > > e-mail: til...@cs...
> >> > > > > > > > > > phone: +49(231)755-7706
> >> > > > > > > > > > fax: +49(231)755-7740
> >> > > > > > > > > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> >> 
> >> > > > > > > > > > pgp:
> >> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84D
> >> ED79>> 
> >> > > > > > > > --
> >> > > > > > > > Dipl.-Inf. Till Schäfer
> >> > > > > > > > TU Dortmund University
> >> > > > > > > > Chair 11 - Algorithm Engineering
> >> > > > > > > > Otto-Hahn-Str. 14 / Room 237
> >> > > > > > > > 44227 Dortmund, Germany
> >> > > > > > > > 
> >> > > > > > > > e-mail: til...@cs...
> >> > > > > > > > phone: +49(231)755-7706
> >> > > > > > > > fax: +49(231)755-7740
> >> > > > > > > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> >> 
> >> > > > > > > > pgp:
> >> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84D
> >> ED79>> 
> >> > > > > > --
> >> > > > > > Dipl.-Inf. Till Schäfer
> >> > > > > > TU Dortmund University
> >> > > > > > Chair 11 - Algorithm Engineering
> >> > > > > > Otto-Hahn-Str. 14 / Room 237
> >> > > > > > 44227 Dortmund, Germany
> >> > > > > > 
> >> > > > > > e-mail: til...@cs...
> >> > > > > > phone: +49(231)755-7706
> >> > > > > > fax: +49(231)755-7740
> >> > > > > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> >> 
> >> > > > > > pgp:
> >> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84D
> >> ED79>> 
> >> > > > --
> >> > > > Dipl.-Inf. Till Schäfer
> >> > > > TU Dortmund University
> >> > > > Chair 11 - Algorithm Engineering
> >> > > > Otto-Hahn-Str. 14 / Room 237
> >> > > > 44227 Dortmund, Germany
> >> > > > 
> >> > > > e-mail: til...@cs...
> >> > > > phone: +49(231)755-7706
> >> > > > fax: +49(231)755-7740
> >> > > > web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> >> 
> >> > > > pgp:
> >> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84D
> >> ED79
> >> 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> --
> >> Dipl.-Inf. Till Schäfer
> >> TU Dortmund University
> >> Chair 11 - Algorithm Engineering
> >> Otto-Hahn-Str. 14 / Room 237
> >> 44227 Dortmund, Germany
> >> 
> >> e-mail: til...@cs...
> >> phone: +49(231)755-7706
> >> fax: +49(231)755-7740
> >> web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
> >> pgp:
> >> https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84D
> >> ED79> 
> > --
> > -Shamshad Alam
> > 
> > +91 9911631198
> > 
> > LinkedIn : in.linkedin.com/pub/shamshad-alam/58/939/70
> > GitHub: @shamshad-npti
> > Facbook: @shamshad.saralindia

Re: [Scaffoldhunter-devel] Zoom Browsing

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

Hi Andrew,

zooming is implemented using Piccolo2D. The methods in VCanvas just provide  
convenient zooming function that are then realized by Piccolo methods. The 
library uses a scene graph model and zooming and panning works by modifying 
the PCamera [1] object associated with the canvas. There is a useful tutorial 
on the Piccolo2D website [2]. 


Regards,
  Nils

[1] 
http://piccolo2d.org/doc/piccolo2d.java/release-1.3.2/core/edu/umd/cs/piccolo/PCamera.html
[2] http://piccolo2d.org/learn/index.html



On Tuesday 22 April 2014 22:24:45 Anjenson wrote:
> Hi Till,
> 
> Well as I understand whenever I want to zoom a selected set or anything
> else it is done with help of /vcanvas/ field. If it is really so I don't
> quite understand how its content is changed as it seems to me that
> operations are applied to /selectio//n//field/. I have already found
> listeners but that are attached to /vcanvas/ in ScaffoldTreeView,
> however I am not sure that it is done through them.
> 
> Regards,
> Andrew "Anjenson" Zhilka
> 
> On 04/22/2014 05:25 PM, Till Schäfer wrote:
> > Hi,
> > i do not understand the context here. Can you explain your idea in more
> > detail?
> > 
> > Greetings,
> > Till

Re: [Scaffoldhunter-devel] Zoom Browsing

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

Hi Till,

Well as I understand whenever I want to zoom a selected set or anything 
else it is done with help of /vcanvas/ field. If it is really so I don't 
quite understand how its content is changed as it seems to me that 
operations are applied to /selectio//n//field/. I have already found 
listeners but that are attached to /vcanvas/ in ScaffoldTreeView, 
however I am not sure that it is done through them.

Regards,
Andrew "Anjenson" Zhilka

On 04/22/2014 05:25 PM, Till Schäfer wrote:
> Hi,
> i do not understand the context here. Can you explain your idea in more detail?
>
> Greetings,
> Till

Re: [Scaffoldhunter-devel] Zoom Browsing

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

Hi, 
i do not understand the context here. Can you explain your idea in more detail?

Greetings,
Till

Am Donnerstag, 17. April 2014, 22:57:33 schrieb Anjenson:
> Hi,
> 
> I decided that it will much more useful to implement Zoom Browsing.
> And after looking into code I would be grateful if someone could explain 
> me how vcanvas formed each time when we apply different actions to it in 
> ScaffoldTreeView? Where is it updated?
> 
> Thanks in advance,
> Andrew "Anjenson" Zhilka
> 
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
> _______________________________________________
> 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

[Scaffoldhunter-devel] Bonding Period

[Andrew Z. <hot...@gm...>]

Hi,

First of all, thank you for accepting my proposal very much.

Secondly, well it seems like time to solve some questions concerning 
workflow, etc.
So, considering VCS I suggest that I create a GitHub repo, so that I 
have a place to comfortably store my project without influencing main 
SVN trunk.

I also plan to create a UML diagram so that it will make implementation 
of the feature faster.

I will be glad to hear your opinion and suggestions.
Looking forward to receiving your reply.

Many thanks,
Andrew "Anjenson" Zhilka

[Scaffoldhunter-devel] Zoom Browsing

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

Hi,

I decided that it will much more useful to implement Zoom Browsing.
And after looking into code I would be grateful if someone could explain 
me how vcanvas formed each time when we apply different actions to it in 
ScaffoldTreeView? Where is it updated?

Thanks in advance,
Andrew "Anjenson" Zhilka

Re: [Scaffoldhunter-devel] More Improvements for Random Subset

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

Hi Till,

On 04/17/2014 05:20 PM, Till Schäfer wrote:
>  However i have another problem with that look and feel, and that is: 
> the background color is not drawn for (qt / kde look and feel), 
It's quite strange because I am using openSUSE KDE and everything is OK.
> but i have integrated your other fix.
Great! Thanks!

Regards,
Andrew "Anjenson" Zhilka

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

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

Hi,

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

Thanks
Shamshad


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

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



-- 
-Shamshad Alam

+91 9911631198

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

Re: [Scaffoldhunter-devel] More Improvements for Random Subset

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

Hi, 

Am Donnerstag, 17. April 2014, 12:41:35 schrieb Andrew Zhilka:
> 
> -----Original Message-----
> From: "Anjenson" <hot...@gm...>
> Sent: ‎15/‎04/‎2014 21:00
> To: "Till Schäfer" <til...@tu...>
> Subject: More Improvements for Random Subset
> 
> Hi Till,
> 
> I have noticed you fixed my bug about resetting background. In your fixes you used border, so I wanted to explain why I have chosen background: when resetting border to red numbers are aligned to new border and it's like weird animation. 
> I also noticed that if I delete default text letter by letter NumberFormatException is thrown (when you're setting value variable. So I added changes that assume that field is empty while it is empty or it contains text.
> 
> I attached the improvements. Hope they help.
Good to now! I can reproduce the jumping behaviour. it seems to be a problem of the native look and feel, that we are using for the swing components (borderfactory borders do not respect this look and feel settings). However i have another problem with that look and feel, and that is: the background color is not drawn for (qt / kde look and feel), therefore i will stick with the borders, but i have integrated your other fix. 


Greetings, 
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] Solved [Feature Request #38 : Split Subsets by Scaffolds On a Specified Level]

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

Hi, 
i just updated the menu and added some categories as comments and also changed the ordering a little bit. 
-> your action should now go to "single subset filters" category. 

Viele Grüße 
Till

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

e-mail: til...@cs...
phone: +49(231)755-7706
fax: +49(231)755-7740
web: http://ls11-www.cs.uni-dortmund.de/staff/schaefer
pgp: https://keyserver2.pgp.com/vkd/SubmitSearch.event?&&SearchCriteria=0xD84DED79