Can't find CyGroup/CyGroupFactory classes in latest release

[Omar Wagih]

I am trying to collapse nodes programatically with CyGroup. However, CyGroup does not seem to exist in the build I have: 3.0.0-beta3-SNAPSHOT

Any ideas? Were they removed? 

The functionality seems to be available through the GUI interface

Thanks,

Omar

[Omar Wagih]

Also, nested networks functionality does not seem to be in the CyNode class anymore.. 

[Scooter Morris]

On 08/28/2012 09:15 PM, Omar Wagih wrote:
> I am trying to collapse nodes programatically with CyGroup. However,
> CyGroup does not seem to exist in the build I have: 3.0.0-beta3-SNAPSHOT
>
> Any ideas? Were they removed?

No idea. They have certainly not been removed. Can you do a "list |
grep group" in the karaf console and let me know what you see?

-- scooter

>
> The functionality seems to be available through the GUI interface
>
> Thanks,
> Omar
>

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[Scooter Morris]

On 08/29/2012 08:57 AM, Omar Wagih wrote:

Also, nested networks functionality does not seem to be in the CyNode class anymore..

It is -- it's now called a "network pointer", so you can look for the getNetworkPointer/setNetworkPointer methods...

-- scooter

On Wednesday, 29 August 2012 00:15:02 UTC-4, Omar Wagih wrote:

I am trying to collapse nodes programatically with CyGroup. However, CyGroup does not seem to exist in the build I have: 3.0.0-beta3-SNAPSHOT

Any ideas? Were they removed? 

The functionality seems to be available through the GUI interface

Thanks,

Omar

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[Tim Hull]

That was actually a tad confusing to me when I first saw it - do you think we could look into making it clearer in the documentation that this is what the network pointer is for? I initially thought it was a pointer to the network (presumably the CyRootNetwork) containing the node.

Tim

[Tim Hull]

Does your project depend on the group-api project in the pom.xml file? This is needed if you want to do anything with groups...

Tim

On Wed, Aug 29, 2012 at 9:54 AM, Scooter Morris <sco...@cgl.ucsf.edu> wrote:

On 08/28/2012 09:15 PM, Omar Wagih wrote:

I am trying to collapse nodes programatically with CyGroup. However, CyGroup does not seem to exist in the build I have: 3.0.0-beta3-SNAPSHOT

Any ideas? Were they removed?

No idea.  They have certainly not been removed.  Can you do a "list | grep group" in the karaf console and let me know what you see?

-- scooter

The functionality seems to be available through the GUI interface

Thanks,
Omar

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[Scooter Morris]

On 08/29/2012 10:03 AM, Tim Hull wrote:

That was actually a tad confusing to me when I first saw it - do you think we could look into making it clearer in the documentation that this is what the network pointer is for? I initially thought it was a pointer to the network (presumably the CyRootNetwork) containing the node.

Well, it's used for multiple things -- nested networks as well as groups, but yes, it should be made clearer in the documentation.

-- scooter

[Omar Wagih]

Hi Scooter,

The grep results in:

[  91] [Active     ] [            ] [  110] Cytoscape Groups API (group-api) (3.0.0.beta2)

[ 121] [Active     ] [            ] [  125] Cytoscape Groups Impl (group-impl) (3.0.0.alpha9)

[ 136] [Active     ] [            ] [  160] Cytoscape Group Data Impl (group-data-impl) (3.0.0.alpha9)

[ 137] [Active     ] [            ] [  160] Cytoscape Group View Impl (group-view-impl) (3.0.0.alpha9)

[ 161] [Active     ] [            ] [  170] Cytoscape Group Session Restore Shim Impl (group-session-restore-shim-impl) (3.0.0.alpha9)

When I started my plugin I checked out sample2 as a maven project using from: http://chianti.ucsd.edu/svn/core3/samples/trunk/sample02

I am using the netbeans IDE

Omar

[Scooter Morris]

On 08/29/2012 04:29 PM, Omar Wagih wrote:

Hi Scooter,

The grep results in:

[  91] [Active     ] [            ] [  110] Cytoscape Groups API (group-api) (3.0.0.beta2)

[ 121] [Active     ] [            ] [  125] Cytoscape Groups Impl (group-impl) (3.0.0.alpha9)

[ 136] [Active     ] [            ] [  160] Cytoscape Group Data Impl (group-data-impl) (3.0.0.alpha9)

[ 137] [Active     ] [            ] [  160] Cytoscape Group View Impl (group-view-impl) (3.0.0.alpha9)

[ 161] [Active     ] [            ] [  170] Cytoscape Group Session Restore Shim Impl (group-session-restore-shim-impl) (3.0.0.alpha9)

When I started my plugin I checked out sample2 as a maven project using from: http://chianti.ucsd.edu/svn/core3/samples/trunk/sample02

I am using the netbeans IDE

OK, so the bundles are definitely being loaded.   You mention that you used sample02 -- did you modify the pom.xml to depend on group-api?  If not, you'll need to add:

   <dependency>
      <groupId>org.cytoscape</groupId>
      <artifactId>group-api</artifactId>
      <version>${cytoscape.api.version}</version>
    </dependency>

and I would be willing to bet you'll need model to:

   <dependency>
      <groupId>org.cytoscape</groupId>
      <artifactId>model-api</artifactId>
      <version>${cytoscape.api.version}</version>
    </dependency>


Then, in your CyActivator, you'll need to get the CyGroupFactory service:

    CyGroupFactory cyGroupFactory = getService(bc, CyGroupFactory.class);

Then you can create and manage groups...

-- scooter

Omar
On Wednesday, 29 August 2012 12:54:40 UTC-4, Scooter Morris wrote:

On 08/28/2012 09:15 PM, Omar Wagih wrote:
> I am trying to collapse nodes programatically with CyGroup. However,
> CyGroup does not seem to exist in the build I have: 3.0.0-beta3-SNAPSHOT
>
> Any ideas? Were they removed?
No idea.  They have certainly not been removed.  Can you do a "list |
grep group" in the karaf console and let me know what you see?

-- scooter
>
> The functionality seems to be available through the GUI interface
>
> Thanks,
> Omar
>
> --
> You received this message because you are subscribed to the Google
> Groups "cytoscape-discuss" group.
> To view this discussion on the web visit
> https://groups.google.com/d/msg/cytoscape-discuss/-/ZcbFDpPGRE0J.
> To post to this group, send email to cytoscap...@googlegroups.com.
> To unsubscribe from this group, send email to
> cytoscape-disc...@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/cytoscape-discuss?hl=en.

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