scaffoldhunter-devel — Discussion list for Scaffold Hunter developers

Re: [Scaffoldhunter-devel] GSoC 2014 participation and Command Line Support project

[Check N. <che...@gm...>]

Hi Till,

first of all: please ask your questions over the developer mailing list, so
> we do not need to repeat our self and the other participants can also
> profit from the discussion.
>
>
My mistake forgot completely.

> > I need some assistance with compiling and installing scaffold. I've tried
> > running shell script install.sh.template but it can't find the Jar file.
> As far as i know there is no install.sh.template file in the repository.
> Therefore, i am not sure what you are referencing here.
>
> Well there is an "install.sh.template" file in the
"scaffoldhunter/scripts" directory. Executing this script returns an error
" File "@SH_JAR_FILE@" not found!" So I don't really understand what to do
here. I do all this from the terminal.


> > So
> > I don't if i'll have to compile the entire source code and I'll need some
> > assistance with this.
> You do not need to "install" the scaffold hunter software. As a developer,
> it is recommended to use the eclipse project and run the software from
> within eclipse. If you use another IDE or want to build your project for a
> distribution, we have also an ant build.xml directly in the projects root
> folder. The targets of the ant file should be self explaining.
>
>
Well since I'm working on this code as a developer, I'll like to know the
manual steps on the terminal for compiling the code with ant. I've ran
"ant; ant build" and it returns an error "BUILD FAILED
Target "build" does not exist in the project "ScaffoldHunter"". So i'll
like to get some directives in this case on how to compile the complete
source code.

Thanks,
Nyah

Re: [Scaffoldhunter-devel] GSOC 2014 Java Test

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

Hi Aly,

You first need to submit your proposal. After that tasks will be 
submitted in comments to proposal.

Regards,
Andrew

On 03/17/2014 11:17 PM, Aly Osama wrote:
> Hi ,
>
> Could anyone tell me about the java test ? how can i do this now ?
>
> Thanks
> Aly

Re: [Scaffoldhunter-devel] GSOC 2014 Java Test

[Werner S. <wer...@gm...>]

Hi,

On 03/17/2014 09:17 PM, Aly Osama wrote:
> Hi ,
>
> Could anyone tell me about the java test ? how can i do this now ?
You will receive further information about the test after submitting 
your proposal.

Regards,
Werner

[Scaffoldhunter-devel] GSOC 2014 Java Test

[Aly O. <aly...@ho...>]

Hi , 

Could anyone tell me about the java test ? how can i do this now ? 
Thanks
Aly 		 	   		  

[Scaffoldhunter-devel] GSoC 2014 SH Test

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

Hi Till,

I am finishing the SH task now so I would like to know one more
essential thing which is how big can property values can be?

Regards,
Andrew

Re: [Scaffoldhunter-devel] GSoC 2014 Molecule Clouds: Prefuse vsPiccolo

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

Hi again, Nils,
First of all, thank for the sources of the algorithm. I will probably stick to the idea of creating new layout just need some time to look through the Piccolo functionality.

Regards,
Andrew

(officially: Andrey Zhylka)

-----Original Message-----
From: "nl...@us..." <nl...@us...>
Sent: ‎17/‎03/‎2014 13:36
To: "sca...@li..." <sca...@li...>
Cc: "Anjenson" <hot...@gm...>
Subject: Re: [Scaffoldhunter-devel] GSoC 2014 Molecule Clouds: Prefuse vsPiccolo

Hi Andrew,

Piccolo2D is a great library for structured graphics, but does not provide the 
required layout functionality. You may have a look at their tutorial and the 
code examples contained in the library. This will give you an idea what can be 
done with Piccolo2D. I really like the idea of a force-based layout algorithm. 
I think using Piccolo and implementing your own force-based layout, e.g., as 
an alternative to the static layout provided, should be doable. We would like 
all views to be as consistent as possible (Zooming, Panning, Shortcuts etc.). 
Adjusting a view based on Prefuse to the same "look and feel" might be even 
more time-consuming (and less fun) than using Piccolo and implementing your 
own layout algorithm specially designed for molecule clouds.


Regards,
  Nils

On Sunday 16 March 2014 00:11:28 Anjenson wrote:
> I decided to share some more of my thoughts about the case.
> I went into some more details about how force is used in Prefuse and how
> nodes are created and attached in Piccolo2D. Combining seems
> non-trivial, however, my first thought was that creation of custom class
> which extends PNode and depends on Prefuse will probably solve the
> problem. But still there some kind of layer used in Prefuse for the
> purpose. Thus it involves creating other custom classes.
> 
> So, all together although we may provide less friendly and maybe ( I am
> still not sure as I feel lack of knowledge about Piccolo and hope for
> advice) dynamic, it will result in less complicated implementation.
> 
> And one more point, probably against Prefuse, is that if really all the
> customization I mentioned really needed then molecule-clod view will be
> a lot different from other views which may seem confusing later. Stil, I
> may be wrong in my judgment.
> 
> Regards,
> Andrew
> 
> ----------------------------------------------------------------------------
> -- 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/13534_NeoTech
> _______________________________________________
> Scaffoldhunter-devel mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel

Re: [Scaffoldhunter-devel] GSOC 2014 - Sub graph network

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

Hi, 
 
Am Samstag, 15. März 2014, 21:57:53 schrieb Aly Osama:
> Hello, I am a pr-junior student at Computer Engineering and Software Systems  .i have good experience with java and GUI with Swing library for 2 years , i have worked on a research project at AinShames university and develop a graphical tool that will used in VLSI industry using swing for 5 months . i am also interested in problem solving  and participate in Local ACM competition ACM ECPC . i have also some experience with image processing using MATLAB and Sci-kit library with python in Scanning Electron Microscopy Image Analysis software .
thank you for your introduction.

> I am really interested in Scaffold Hunter project as want to contribute in this field  so i will participate in this project for GSOC 2014 , i have got an overview of the user side in addition to getting in touch with the code , and i start learning Piccolo2D for 3 days . i think that  i can participate at Sub-graph Network or Molecule Clouds , 
As we have some Molecule Cloud proposals already, it will improve your chances to get accepted if you go for the subgraph network.


> I will work further on these ideas to choose one of them , but could you give me more details about sub-graph network ? 
The scaffold principle is a classification of molecules based on their (ring) graph structure. If you cut all the side chains (that means paths and trees, which are not part of a circle) of a molecule you get a so called murcko scaffold. As different Molecules might have the same murcko scaffold, you can think of a class of molecules with the same murcko scaffold. This scaffold itself serves as a descriptor of this class.

To take this approach a step further, one can select a rings of the scaffold and remove this ring. Therefore, you get a smaller parent scaffold. If you select the this ring with some strategy, you get a hierarchy of scaffolds and a hierarchical classification scheme for your molecules. This is what the scaffold tree view visualizes. 

Now, one can imagine, the the selection of the ring to remove can be done in various ways. That means with different ring selection strategies, you will get different classification hierarchies. 

The scaffold / subgraph network, is a DAG, where each scaffold has as many parents as there exists rings. That means for each ring, there exist one parent (the one which is created by removing this ring). All possible scaffold hierarchies can be embedded into this graph. 
The goal here is to find a layout for this DAG and also some filter techniques, because the DAG can be dense / huge. 

The provided papers are describing this in more detail. 

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] GSoC 2014 Molecule Clouds: Prefuse vs Piccolo

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

Hi Andrew,

Piccolo2D is a great library for structured graphics, but does not provide the 
required layout functionality. You may have a look at their tutorial and the 
code examples contained in the library. This will give you an idea what can be 
done with Piccolo2D. I really like the idea of a force-based layout algorithm. 
I think using Piccolo and implementing your own force-based layout, e.g., as 
an alternative to the static layout provided, should be doable. We would like 
all views to be as consistent as possible (Zooming, Panning, Shortcuts etc.). 
Adjusting a view based on Prefuse to the same "look and feel" might be even 
more time-consuming (and less fun) than using Piccolo and implementing your 
own layout algorithm specially designed for molecule clouds.


Regards,
  Nils

On Sunday 16 March 2014 00:11:28 Anjenson wrote:
> I decided to share some more of my thoughts about the case.
> I went into some more details about how force is used in Prefuse and how
> nodes are created and attached in Piccolo2D. Combining seems
> non-trivial, however, my first thought was that creation of custom class
> which extends PNode and depends on Prefuse will probably solve the
> problem. But still there some kind of layer used in Prefuse for the
> purpose. Thus it involves creating other custom classes.
> 
> So, all together although we may provide less friendly and maybe ( I am
> still not sure as I feel lack of knowledge about Piccolo and hope for
> advice) dynamic, it will result in less complicated implementation.
> 
> And one more point, probably against Prefuse, is that if really all the
> customization I mentioned really needed then molecule-clod view will be
> a lot different from other views which may seem confusing later. Stil, I
> may be wrong in my judgment.
> 
> Regards,
> Andrew
> 
> ----------------------------------------------------------------------------
> -- 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/13534_NeoTech
> _______________________________________________
> Scaffoldhunter-devel mailing list
> Sca...@li...
> https://lists.sourceforge.net/lists/listinfo/scaffoldhunter-devel

Re: [Scaffoldhunter-devel] GSoC 2014 Molecule Clouds

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

Hi Andrew,

On Saturday 15 March 2014 23:20:33 Anjenson wrote:
> I wish to make use of prefuse.util.force package, that will enable user
> to move molecules after the cloud is rendered in order to see more
> details as the intersaction area may vary depending on the size of the
> dataset.

what does "intersection area" mean here? The overlap between the cloud 
elements? The position of cloud elements may also dynamically change when the 
user moves the mouse, e.g., in a way that the element the mouse pointer is 
over becomes completely visible. I have send you a mail with the author's code 
attached. You can also use their static layout algorithm or plan to provide 
multiple layouts. For large clouds simple force-based approaches may be too 
slow.

> I also would like to implement zooming of molecules separately as it
> seems to me that due to the number of molecules in the cloud some of
> them may be really small. However, I think that I will be able to
> implement this feature with Piccolo2D pretty easily. How do you like
> this idea?
> I am currently studying the Piccolo2D so I may not know if it provides
> functionality I intend to achieve by using Prefuse, so I would be
> greatful if you could give me any advice.

Piccolo2D provides zooming and panning, but no appropriate layout 
functionality. There is a good tutorial at their website [1].


Regards,
  Nils

[1] http://piccolo2d.org/learn/index.html 

[Scaffoldhunter-devel] GSoC 2014 Molecule Clouds: Prefuse vs Piccolo

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

Nils,

I decided to share some more of my thoughts about the case.
I went into some more details about how force is used in Prefuse and how 
nodes are created and attached in Piccolo2D. Combining seems 
non-trivial, however, my first thought was that creation of custom class 
which extends PNode and depends on Prefuse will probably solve the 
problem. But still there some kind of layer used in Prefuse for the 
purpose. Thus it involves creating other custom classes.

So, all together although we may provide less friendly and maybe ( I am 
still not sure as I feel lack of knowledge about Piccolo and hope for 
advice) dynamic, it will result in less complicated implementation.

And one more point, probably against Prefuse, is that if really all the 
customization I mentioned really needed then molecule-clod view will be 
a lot different from other views which may seem confusing later. Stil, I 
may be wrong in my judgment.

Regards,
Andrew

Re: [Scaffoldhunter-devel] GSoC 2014 Molecule Clouds

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

Hi Nils,

I wish to make use of prefuse.util.force package, that will enable user 
to move molecules after the cloud is rendered in order to see more 
details as the intersaction area may vary depending on the size of the 
dataset.

I also would like to implement zooming of molecules separately as it 
seems to me that due to the number of molecules in the cloud some of 
them may be really small. However, I think that I will be able to 
implement this feature with Piccolo2D pretty easily. How do you like 
this idea?

I am currently studying the Piccolo2D so I may not know if it provides 
functionality I intend to achieve by using Prefuse, so I would be 
greatful if you could give me any advice.

Regards,
Andrew

[Scaffoldhunter-devel] GSOC 2014 - Sub graph network

[Aly O. <aly...@ho...>]

Hello, I am a pr-junior student at Computer Engineering and Software Systems  .i have good experience with java and GUI with Swing library for 2 years , i have worked on a research project at AinShames university and develop a graphical tool that will used in VLSI industry using swing for 5 months . i am also interested in problem solving  and participate in Local ACM competition ACM ECPC . i have also some experience with image processing using MATLAB and Sci-kit library with python in Scanning Electron Microscopy Image Analysis software .I am really interested in Scaffold Hunter project as want to contribute in this field  so i will participate in this project for GSOC 2014 , i have got an overview of the user side in addition to getting in touch with the code , and i start learning Piccolo2D for 3 days . i think that  i can participate at Sub-graph Network or Molecule Clouds , I will work further on these ideas to choose one of them , but could you give me more details about sub-graph network ? 
Regards,Aly 
 		 	   		  

Re: [Scaffoldhunter-devel] GSoC 2014 Molecule Clouds

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

Hi Andrew,

of course you may use additional libraries for implementing the project. 
Prefuse is a great toolkit for information visualization. However, it is very 
powerful and we will most likely only need a specific functionality that must 
be integrated in the existing code. Currently we are using Piccolo2D [1] for 
most views and Batik to depict SVGs within the Piccolo2D scenegraph. This 
works quite well and it may be non-trivial to do the same with Prefuse. 
Therefore, I think this should be well thought out before deciding to use 
Prefuse. Can you give us more details on the functionality provided by Prefuse 
you want to use for implementing the project?


Regards,
  Nils 

[1] http://www.piccolo2d.org/

On Saturday 15 March 2014 10:32:21 Andrew Zhilka wrote:
> Hi again, Till,
> 
> I have been searching for the ways to implement a dynamic cloud and came
> across Prefuse <http://prefuse.org/> visualisation toolkit. So, I just
> wander whether it can be used for the goals of the project?
> 
> Regards,
> Andrew

Re: [Scaffoldhunter-devel] [gsoc] GSOC 2014 - Parallel Coordinate Plots

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

Hello Sonia,

thanks for your interest in Scaffold Hunter. 

On Friday 14 March 2014 21:26:20 sonia castelo wrote:
> I like to get more information about the Project, for example: What is the
> kind and size of the data base? 

Data sets may contain of a few hundred or millions of molecules. The views 
currently implemented work smoothly with about 50.000 molecules. For very 
larger data sets the user can use filtering techniques to reduce the number of 
molecules that must be displayed. For each molecule various properties are 
stored in the data base. You may have a look at the data sets available at 
PubChem [1] to get an idea what kind of properties are typically associated 
with a molecule.

> Will user be able to interact with the visualization?

Yes, we want to support interactive visualization.

Regards,
  Nils

[1] https://pubchem.ncbi.nlm.nih.gov/

[Scaffoldhunter-devel] GSoC 2014 Molecule Clouds

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

Hi again, Till,

I have been searching for the ways to implement a dynamic cloud and came 
across Prefuse <http://prefuse.org/> visualisation toolkit. So, I just 
wander whether it can be used for the goals of the project?

Regards,
Andrew

[Scaffoldhunter-devel] [gsoc] GSOC 2014 - Parallel Coordinate Plots

[sonia c. <sca...@gm...>]

Hello,


My name is Sonia Castelo Quispe. I'm currently a Computer Science master's
student at  University of Sao Paulo (USP) - Brazil. I work at the
laboratory of Information Visualization and Computer Graphics (VICG).


I was working at Research and Software Development Center (Catedra Concytec
- Perú) for 2 years, in this time, I was responsible of research and
development of the Automation of Classification Process based on Computer
Vision Techniques with a strong focus on Pattern Recognition and Machine
Vision on real-time applications. These projects were programmed in C++ and
OpenCV.


Currently, I work at the laboratory of Information Visualization and
Computer Graphics (VICG). All of the tools we developed at the research
group are coded using Java and Swing (http://vicg.icmc.usp.br/infovis2/Tools).
 I have 4 years' experience working in java. Currently, I work in my master
with high dimensional data visualization. I am using visualization
techniques as TreeMap, Coordinate Parallel, Local Affine Multidimensional
Projection, NeighborJoin Tree, and another.


I'm very interested on the Information Visualization, and I think that
Coordinate Parallel Projection could help to find patterns and correlations
in the compound properties'interplay, and discover new information about
the data.


I like to get more information about the Project, for example: What is the
kind and size of the data base? Will user be able to interact with the
visualization?


Looking forward to hearing from you,


Sonia.

Re: [Scaffoldhunter-devel] [Java test] Simple Calculation Plugin

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

Hi, 

Am Freitag, 14. März 2014, 15:58:28 schrieb Werner Sturm:
> Hello,
> 
> I have almost finished the provided java test. My simple calculation 
> plugin already runs but I am not completely sure what "undefined value" 
> means in that context. According to the plugin examples, numerical 
> values should be casted to Double. So the object itself can be null or 
> the value could be Double.NaN. Is there any uniform way to represent 
> undefined (numerical) values for molecules? Of course I can also check 
> for both cases.
it can happen that a property is not defined for each structure in a dataset. 

Think of an IAtomContainer mol and a PropertyDefinition propDef. 
The IAtomContainer is a molecule. We use this class here rather than the Molecule class from the db package, because the IAtomContainer also contains structural informations (the graph) about the molecule and that can be helpful to compute some structure dependent property. The PropertyDefinitions define which properties are available for the dataset. 

If you want to know if the propDef is defined for mol you can use:
mol.getProperties().containsKey(propDef)


> 
> Do I miss further technical information somewhere? I just noticed there 
> is limited access to the internal Wiki.
calc plugin example 5 should explain everything (also see the implementation in SVN). The internal wiki does not contain any documentation about the code.


> 
> Moreover, as I understand I have to send my solution to _all_ mentors, 
> right?
Yes, please send it to the mentors, which are listed for the specific project. 

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] [Java test] Simple Calculation Plugin

[Werner S. <wer...@gm...>]

Hello,

I have almost finished the provided java test. My simple calculation 
plugin already runs but I am not completely sure what "undefined value" 
means in that context. According to the plugin examples, numerical 
values should be casted to Double. So the object itself can be null or 
the value could be Double.NaN. Is there any uniform way to represent 
undefined (numerical) values for molecules? Of course I can also check 
for both cases.

Do I miss further technical information somewhere? I just noticed there 
is limited access to the internal Wiki.

Moreover, as I understand I have to send my solution to _all_ mentors, 
right?

Regards,
Werner

Re: [Scaffoldhunter-devel] GSoC 2014 participation and Command Line Support project

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

Hi, 
first of all: please ask your questions over the developer mailing list, so we do not need to repeat our self and the other participants can also profit from the discussion.

Am Freitag, 14. März 2014, 11:22:02 schrieb Check Nyah:
> I need some assistance with compiling and installing scaffold. I've tried
> running shell script install.sh.template but it can't find the Jar file. 
As far as i know there is no install.sh.template file in the repository. Therefore, i am not sure what you are referencing here. 

> So
> I don't if i'll have to compile the entire source code and I'll need some
> assistance with this.
You do not need to "install" the scaffold hunter software. As a developer, it is recommended to use the eclipse project and run the software from within eclipse. If you use another IDE or want to build your project for a distribution, we have also an ant build.xml directly in the projects root folder. The targets of the ant file should be self explaining.

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] GSoC 2014 Molecule Clouds

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

Hi, 


Am Mittwoch, 12. März 2014, 22:49:06 schrieb Anjenson:
> Hi,
> I have several questions about the code for now:
> 1. Should I always use DBExceptionHandler if I need to refer to the 
> database?
good question!
short answer: Yes
long answer: All database communication is handled by DbManager. All other POJO classes for Hibernate object-relational mapping are only loaded/ saved over this single class. Whenever there is a database access, the GUI must handle errors that can happen in this circumstances (e.g  connection loss). This is what the DBExceptionHandler is for. It handles the errors automatically in easy situations (such as reconnecting to the database and retry).Furthermore, For consistency, it should be used for every DbManager call. 

> 2. What is Banner exactly for? Now it seems to me as we use it simply to 
> store trees with different access level.
A Banner is simply a quick annotation (in the GUI it is called flag), which can be turned on or off.   It is used for quickly identifying important structures. For example, you can toggle that flag in the scaffold tree view by right click and selecting the flag option. 
> 3. GenericView contains method getExportActions(). What are this actions 
> can be? Is it something like exporting to image?
Yes, see the scaffold tree view for an example. 
> 
> And also the question concerning clouds. Should the export of them to 
> image or some other special format be implemented? I personally think 
> that export to image must be implemented. However, I am not sure about 
> other options.
svg and pixel image would be perfect. svg is more important in my opinion. 


Greetings, 
Till 
> 
> Andrew Zhylka
> 
> ------------------------------------------------------------------------------
> 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/13534_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

Re: [Scaffoldhunter-devel] P.S. Application Template

[Werner S. <wer...@gm...>]

Hello,

On 03/12/2014 08:55 PM, Anjenson wrote:
> Just one thing I forgot to ask.
>
> Is there a special template for application?
Yes, you can find it in the form where you submit your proposal for 
Scaffold Hunter.

[Scaffoldhunter-devel] P.S. Application Template

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

Just one thing I forgot to ask.

Is there a special template for application?

Regards,
Andrew

[Scaffoldhunter-devel] GSoC 2014 Molecule Clouds

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

Hi,
I have several questions about the code for now:
1. Should I always use DBExceptionHandler if I need to refer to the 
database?
2. What is Banner exactly for? Now it seems to me as we use it simply to 
store trees with different access level.
3. GenericView contains method getExportActions(). What are this actions 
can be? Is it something like exporting to image?

And also the question concerning clouds. Should the export of them to 
image or some other special format be implemented? I personally think 
that export to image must be implemented. However, I am not sure about 
other options.

Andrew Zhylka

Re: [Scaffoldhunter-devel] GSoC 2014 participation and Command Line Support project

[Check N. <che...@gm...>]

Hi Till,

Thanks, would upload ASAP.

Cheers!
Nyah

Re: [Scaffoldhunter-devel] GSoC 2014 participation and Command Line Support project

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

Hi, 
i am sorry, but there is no IRC channel. You have to use E-Mail. 

Regarding the Proposal: AFAIK you can update your proposal in Melange. Therefore it does not need to be perfect the first time. 

Regards 
Till


Am Mittwoch, 12. März 2014, 00:12:08 schrieb Check Nyah:
> Hi,
> 
> I am currently writing my proposal, so I'll like to know the IRC
> freenode channel where I could directly ask for my review and pressing
> questions. I'll also love to know how I can create wiki pages on the
> project website where I could post my proposal before applying
> directly.
> 
> Cheers!
> Nyah
> 
> _______________________________________________
> 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
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