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Message-ID: <504A20EA.9050009@cgl.ucsf.edu>
Date: Fri, 07 Sep 2012 09:29:30 -0700
From: Scooter Morris <scoo...@cgl.ucsf.edu>
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To: cytoscape-discuss@googlegroups.com
CC: Omar Wagih <omarwa...@gmail.com>
Subject: Re: [Cytoscape-discuss] Getting current network
References: <41bd2e06-4113-4e5a-985b-90643563af7d@googlegroups.com> <504850A9.20005@cgl.ucsf.edu> <a3669ca9-9362-4a7c-85e1-eb19d74ef26f@googlegroups.com>
In-Reply-To: <a3669ca9-9362-4a7c-85e1-eb19d74ef26f@googlegroups.com>
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Those are all bundles. CyAppAdapter is provided by app-api and
CySwingAppAdapter (which extends CyAppAdapter with some Swing
GUI-specific methods) is provided by swing-app-api. So all of the
bundles are starting as appropriate. So, in your pom.xml, you need to
depend on org.cytoscape.app:
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>app-api</artifactId>
<version>${cytoscape.api.version}</version>
</dependency>
-- scooter
On 09/06/2012 09:36 PM, Omar Wagih wrote:
> CyAppAdapter does not exist in the release I have...
>
> Did a grep on "app" in the karaf terminal:
> Cytoscape 3.0.0-M5> list | grep app
> [ 87] [Active ] [ ] [ 104] Molecular interaction
> cluster (OSGi wrapped version w/dependencies) (1.6)
> [ 97] [Active ] [ ] [ 110] Cytoscape Swing
> Application API (swing-application-api) (3.0.0.beta2)
> [ 99] [Active ] [ ] [ 110] Cytoscape App API
> (app-api) (3.0.0.beta2)
> [ 100] [Active ] [ ] [ 110] Cytoscape Swing App API
> (swing-app-api) (3.0.0.beta2)
> [ 109] [Active ] [ ] [ 110] Cytoscape Application API
> (application-api) (3.0.0.beta2)
> [ 128] [Active ] [ ] [ 135] Cytoscape Application Impl
> (application-impl) (3.0.0.alpha9)
> [ 135] [Active ] [ ] [ 160] Cytoscape Swing
> Application Impl (swing-application-impl) (3.0.0.alpha9)
> [ 162] [Active ] [ ] [ 175] Cytoscape App Impl
> (app-impl) (3.0.0.alpha9)
>
> The version I have (beta3) ..
> I have tired several dependencies in the list like
>
> <dependency>
> <groupId>org.cytoscape</groupId>
> <artifactId>application-api</artifactId>
> <version>${cytoscape.api.version}</version>
> </dependency>
>
> but the package org.cytoscape.app still isnt there.
>
> I also tried to search maven repositories for CyAppAdaptor... and
> nothing comes up
>
> Omar
>
> On Thursday, 6 September 2012 03:28:46 UTC-4, Scooter Morris wrote:
>
> On 09/05/2012 11:29 PM, Omar Wagih wrote:
>> How can you get the current network being looked at?
>> Online says use this through the CyAppAdapter, but this does not
>> seem to be available in the most recent release. Is there
>> something I'm missing?
>>
>> Cheers
>> --
>> 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/-/3EfTmmrtO9UJ
>> <https://groups.google.com/d/msg/cytoscape-discuss/-/3EfTmmrtO9UJ>.
>> To post to this group, send email to cytoscap...@googlegroups.com
>> <javascript:>.
>> To unsubscribe from this group, send email to
>> cytoscape-disc...@googlegroups.com <javascript:>.
>> For more options, visit this group at
>> http://groups.google.com/group/cytoscape-discuss?hl=en
>> <http://groups.google.com/group/cytoscape-discuss?hl=en>.
> Hi Omar,
> The current network is maintained by the
> CyApplicationManager. So, from your CyAppAdapter:
>
> CyNetwork currentNetwork =
> appAdapter.getCyApplicationManager().getCurrentNetwork();
>
> -- scooter
>
> --
> 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/-/VwKsbiZL8joJ.
> To post to this group, send email to cytoscape-discuss@googlegroups.com.
> To unsubscribe from this group, send email to
> cytoscape-discuss+unsubscribe@googlegroups.com.
> For more options, visit this group at
> http://groups.google.com/group/cytoscape-discuss?hl=en.
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<div class="moz-cite-prefix">Those are all bundles. CyAppAdapter is
provided by app-api and CySwingAppAdapter (which extends
CyAppAdapter with some Swing GUI-specific methods) is provided by
swing-app-api. So all of the bundles are starting as appropriate.
So, in your pom.xml, you need to depend on org.cytoscape.app:<br>
<br>
<dependency><br>
<groupId>org.cytoscape</groupId><br>
<artifactId>app-api</artifactId><br>
<version>${cytoscape.api.version}</version><br>
</dependency><br>
<br>
-- scooter<br>
<br>
On 09/06/2012 09:36 PM, Omar Wagih wrote:<br>
</div>
<blockquote
cite="mid:a3669ca9-9362-4a7c-85e1-eb19d74ef26f@googlegroups.com"
type="cite">CyAppAdapter does not exist in the release I have...
<div><br>
</div>
<div>Did a grep on "app" in the karaf terminal:</div>
<div>
<div>Cytoscape 3.0.0-M5> list | grep app</div>
<div>[ 87] [Active ] [ ] [ 104] Molecular
interaction cluster (OSGi wrapped version w/dependencies)
(1.6)</div>
<div>[ 97] [Active ] [ ] [ 110] Cytoscape Swing
Application API (swing-application-api) (3.0.0.beta2)</div>
<div>[ 99] [Active ] [ ] [ 110] Cytoscape App
API (app-api) (3.0.0.beta2)</div>
<div>[ 100] [Active ] [ ] [ 110] Cytoscape Swing
App API (swing-app-api) (3.0.0.beta2)</div>
<div>[ 109] [Active ] [ ] [ 110] Cytoscape
Application API (application-api) (3.0.0.beta2)</div>
<div>[ 128] [Active ] [ ] [ 135] Cytoscape
Application Impl (application-impl) (3.0.0.alpha9)</div>
<div>[ 135] [Active ] [ ] [ 160] Cytoscape Swing
Application Impl (swing-application-impl) (3.0.0.alpha9)</div>
<div>[ 162] [Active ] [ ] [ 175] Cytoscape App
Impl (app-impl) (3.0.0.alpha9)</div>
</div>
<div><br>
</div>
<div>The version I have (beta3) ..</div>
<div>I have tired several dependencies in the list like<br>
<br>
<div><dependency></div>
<div><groupId>org.cytoscape</groupId></div>
<div><artifactId>application-api</artifactId></div>
<div><version>${cytoscape.api.version}</version></div>
<div></dependency></div>
<div><br>
</div>
<div>but the package org.cytoscape.app still isnt there.<br>
<br>
I also tried to search maven repositories for CyAppAdaptor...
and nothing comes up</div>
<div><br>
</div>
<div>Omar</div>
<br>
On Thursday, 6 September 2012 03:28:46 UTC-4, Scooter Morris
wrote:
<blockquote class="gmail_quote" style="margin: 0;margin-left:
0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">
<div bgcolor="#FFFFFF" text="#000000">
<div>On 09/05/2012 11:29 PM, Omar Wagih wrote:<br>
</div>
<blockquote type="cite">How can you get the current network
being looked at?
<div>Online says use this through the <span
style="color:rgb(0,0,0);white-space:pre-wrap">CyAppAdapter,
but this does not seem to be available in the most
recent release. Is there something I'm missing? </span></div>
<div><span style="color:rgb(0,0,0);white-space:pre-wrap"><br>
</span></div>
<div><span style="color:rgb(0,0,0);white-space:pre-wrap">Cheers</span></div>
-- <br>
You received this message because you are subscribed to
the Google Groups "cytoscape-discuss" group.<br>
To view this discussion on the web visit <a
moz-do-not-send="true"
href="https://groups.google.com/d/msg/cytoscape-discuss/-/3EfTmmrtO9UJ"
target="_blank">https://groups.google.com/d/<wbr>msg/cytoscape-discuss/-/<wbr>3EfTmmrtO9UJ</a>.<br>
To post to this group, send email to <a
moz-do-not-send="true" href="javascript:"
target="_blank" gdf-obfuscated-mailto="mTNvJDfY2MwJ">cytoscap...@<wbr>googlegroups.com</a>.<br>
To unsubscribe from this group, send email to <a
moz-do-not-send="true" href="javascript:"
target="_blank" gdf-obfuscated-mailto="mTNvJDfY2MwJ">cytoscape-disc...@<wbr>googlegroups.com</a>.<br>
For more options, visit this group at <a
moz-do-not-send="true"
href="http://groups.google.com/group/cytoscape-discuss?hl=en"
target="_blank">http://groups.google.com/<wbr>group/cytoscape-discuss?hl=en</a>.<br>
</blockquote>
Hi Omar,<br>
The current network is maintained by the
CyApplicationManager. So, from your CyAppAdapter:<br>
<br>
CyNetwork currentNetwork = appAdapter.<wbr>getCyApplicationManager().<wbr>getCurrentNetwork();<br>
<br>
-- scooter<br>
<br>
</div>
</blockquote>
</div>
-- <br>
You received this message because you are subscribed to the Google
Groups "cytoscape-discuss" group.<br>
To view this discussion on the web visit <a
moz-do-not-send="true"
href="https://groups.google.com/d/msg/cytoscape-discuss/-/VwKsbiZL8joJ">https://groups.google.com/d/msg/cytoscape-discuss/-/VwKsbiZL8joJ</a>.<br>
To post to this group, send email to
<a class="moz-txt-link-abbreviated" href="mailto:cytoscape-discuss@googlegroups.com">cytoscape-discuss@googlegroups.com</a>.<br>
To unsubscribe from this group, send email to
<a class="moz-txt-link-abbreviated" href="mailto:cytoscape-discuss+unsubscribe@googlegroups.com">cytoscape-discuss+unsubscribe@googlegroups.com</a>.<br>
For more options, visit this group at
<a class="moz-txt-link-freetext" href="http://groups.google.com/group/cytoscape-discuss?hl=en">http://groups.google.com/group/cytoscape-discuss?hl=en</a>.<br>
</blockquote>
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