jtreeview-users — List for users to post to for help. The project administrator will read it.

[Jtreeview-users] Heat plot only one colour

[H. M. <hm...@ca...>]

Hi,

I have just installed Cluster and Java TreeView to analyse some microarray 
data. Everything appears to be working fine apart from the heat plot, which 
I can only get to be the colour of positive residues. Do you know how I 
could solve this problem?

Best regards,
Helga

[Jtreeview-users] Cluster 3 and TreeView 1.1.0 for finding cluster alternatives with "average linkage"-method

[Thorsten O. <t.o...@gm...>]

Hello,

we would like to work with cluster 3.0 and treeview 1.1.0  for =
generating=20
consistent alternatives of an evaluation of a triangle matrix. The rows=20
and columns have got the same signification/variables.
My question is how to get a choosen number of alternatives with the=20
average linkage method and if i have to modify something in the cluster =
or=20
the treeview program.
Regarding the evaluation of the connections/relation there has to be=20
processed a clustering process looking for connection each other=20
supporting. For instance, if variable "a" is connected with "b" by a 5 =
(5=20
means very good support), but "a" to "c" by a 3 (more or less/or=20
independent), and "b" to "c" by 5 the process has to figure out that "a" =

is supporting "c" through its very support with "b". The only difference =

should be that the 2nd degree connection has another weight, means that=20
there is considered less value than for a direct connection.

We do need this kind process concluding a number of alternatives to be=20
choosen. The values we=B4re using are 1 to 5, but they may change. It=20
doesn=B4t matter!
1 =3D completly inconsistent influence
2 =3D probably inconsistent influence
3 =3D not influencing each other / independent
4 =3D probably consistent influence
5 =3D completly consistent influence

It would be great if i might get in touch with somebody of capacity=20
personally.
Thank a lot for your effort applied in advance!

Best regards!

Thorsten

Thorsten Ortjohann
Hans-Humpert-Str. 9a
33102 Paderborn
+49 5251 778504
+49 179 9090511
t.o...@gm...

[Jtreeview-users] consistent alternatives of triangle matirx with average linkage method

[Thorsten O. <tho...@ly...>]

Hello,

we would like to work with cluster 3.0 and treeview 1.1.0  for generating=20
consistent alternatives of an evaluation of a triangle matrix. The rows=20
and columns have got the same signification/variables.
My question is how to get a choosen number of alternatives with the=20
average linkage method and if i have to modify something in the cluster or=
=20
the treeview program.
Regarding the evaluation of the connections/relation there has to be=20
processed a clustering process looking for connection each other=20
supporting. For instance, if variable "a" is connected with "b" by a 5 (5=20
means very good support), but "a" to "c" by a 3 (more or less/or=20
independent), and "b" to "c" by 5 the process has to figure out that "a"=20
is supporting "c" through its very support with "b". The only difference=20
should be that the 2nd degree connection has another weight, means that=20
there is considered less value than for a direct connection.

We do need this kind process concluding a number of alternatives to be=20
choosen. The values we=B4re using are 1 to 5, but they may change. It=20
doesn=B4t matter!
1 =3D completly inconsistent influence
2 =3D probably inconsistent influence
3 =3D not influencing each other / independent
4 =3D probably consistent influence
5 =3D completly consistent influence

It would be great if i might get in touch with somebody of capacity=20
personally.
Thank a lot for your effort applied in advance!

Best regards!

Thorsten


Thorsten Ortjohann
Consultant Business Process Management
Lynx-Consulting AG
Johanniskirchplatz 6
D-33615 Bielefeld
Fon: +49 521 5247-0
Fax: +49 521 5247-250
Mobil: +49 175 22 85 490


Company and Management Headquarters:
Lynx-Consulting AG, Johanniskirchplatz 6, D-33615 Bielefeld
Fon: +49 521 5247-0, Fax: +49 521 5247-250, www.lynx.de

Court Registration: Amtsgericht Bielefeld HRB 35946
Members of the Management Board authorised to represent: Peter H=FCsener
Chairman of the Supervisory Board: Hans-Joachim Rosowski

---------------------------------------------------------------------------=
-------------------------
This e-mail may contain trade secrets or privileged, undisclosed, or otherw=
ise confidential information. If you have received this e-mail in error, yo=
u are hereby notified that any review, copying, or distribution of it is st=
rictly prohibited. Please inform us immediately and destroy the original tr=
ansmittal. Thank you for your cooperation.=20
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[Jtreeview-users] Problem with "open"

[Daniel S L. (<dl...@Pr...>]

Hi,
  I've been using Java Treeview with no problem for the past couple of months. Then Java automatically updated something on my computer and the program stopped working in that it would take a looong time to open the dialog box after i clicked "open" and when i select a file I get this error:

C:\Documents and Settings\dlieber\Desktop\TreeView-1.1.1-win>java -jar -Xmx500m
TreeView.jar
Plugin Jar jar:file:/C:/Documents and Settings/dlieber/Desktop/TreeView-1.1.1-wi
n/plugins/Dendrogram.jar!/
Registering Plugin Dendrogram
Registering Plugin Alignment
Registering Plugin KnnDendrogram
Plugin Jar jar:file:/C:/Documents and Settings/dlieber/Desktop/TreeView-1.1.1-wi
n/plugins/Karyoscope.jar!/
Registering Plugin Karyoscope
Plugin Jar jar:file:/C:/Documents and Settings/dlieber/Desktop/TreeView-1.1.1-wi
n/plugins/Scatterplot.jar!/
Registering Plugin Scatterplot
Plugin Jar jar:file:/C:/Documents and Settings/dlieber/Desktop/TreeView-1.1.1-wi
n/plugins/Treeanno.jar!/
Registering Plugin ArrayTreeAnno
Registering Plugin GeneTreeAnno
initial style kmeans
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
        at edu.stanford.genetics.treeview.model.KnnModelLoader.<init>(Unknown So
urce)
        at edu.stanford.genetics.treeview.model.KnnModel.loadNew(Unknown Source)

        at edu.stanford.genetics.treeview.LinkedViewFrame.loadKnnModel(Unknown S
ource)
        at edu.stanford.genetics.treeview.LinkedViewFrame.loadFileSet(Unknown So
urce)
        at edu.stanford.genetics.treeview.TreeViewFrame$FileMenuListener$1.run(U
nknown Source)
        at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
        at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
ad.java:273)
        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
java:183)
        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
ad.java:173)
        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)





I tried reinstalling java, and using older and newer versions of the program but those did not seem to work. Do you know what's wrong or have any suggestions?

thanks,

-Danny Lieber

dl...@pr...

[Jtreeview-users] Thank you No Hassle Quotes

[Russell B. <dok...@qu...>]

Thank you for your loan request, which we recieved yesterday. We'd like to 
inform you that we are accepting your application. We are ready to give you=
 a 
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Re: [Jtreeview-users] Save a gene list or data etc in JTV (applet)?

[Alok S. <alo...@gm...>]

Thanks Min! I wish I had more time to spend on it... I really need to  
put out a new version as there are several bug fixes that I need to  
release.

The short answer is that the JTV applet cannot access the hard drive  
because of
Java security restrictions. Technically, we could sign the applet so  
it is trusted, but it's a hassle.

You can still export gene lists from the applet using cut-and-paste.  
First open the applet and select some genes of interest, then use  
export->save list or export->save data. In the dialog, just select  
all (ctrl-a or apple-a) and then copy (ctrl-c or apple-c).

Incidentally, you can open any applet-based jtv file using the  
desktop application just by entering the url for the .cdt file. For  
instance, if you start up the desktop version of java treeview, go to  
"File->open url..." and enter

http://jtreeview.sourceforge.net/examples/spellman.cdt

it will open the spellman example file. In my experience,  firefox on  
mac os x does not display the menu bar, but it does work in safari,  
and I think in both firefox and ie on windows (although I haven't  
tried Vista yet)

-Alok


On May 21, 2007, at 1:06 PM, Min Li wrote:

> Dear Alok,
>
> Thanks for your generosity of sharing the JTV. We are enjoying  
> using the program. I am wondering if you can tell us how to save or  
> export the result from JTreeview. I am using the JTV applet. it  
> works great. the problem is that I couldn't do anyting to deal with  
> the menu bar function such as save and export...
>
> any suggestion will be appreciated.
>
>
> Min

Re: [Jtreeview-users] Could not find main class

[Alok S. <alo...@gm...>]

Thanks for sorting this out Omar! Numerous strange problems have been  
fixed by reinstalling java. The fact that no one else reported this  
problem should have tipped me off.

	-Alok

On May 18, 2007, at 10:45 AM, OMA...@co...  
wrote:

> The fix for this was installing Java version 6 update 1.
>
> Omar Andrade
>
>  -----Original Message-----
> From: 	JENNIFER.WITT@BCBS
> Sent:	Friday, May 18, 2007 8:06 AM
> To:	Alok.Saldanha[aloksaldanha]@gmail.com.CDS
> Cc:	OMAR.ANDRADE
> Subject:	RE:Re: [Jtreeview-users] Could not find main class
>
> Can you please tell me how to change the main class to LinkedView?   
> I am not
> java trained
>
> Thanks very much!
> ------------------( Forwarded letter 1 follows )--------------------
> cc: jtr...@li...
> From: Alok.Saldanha[aloksaldanha]@gmail.com.CDS
> Subject: Re: [Jtreeview-users] Could not find main class
> Date: Thu, 17 May 2007 23:25:29 -0400
> To: JENNIFER.WITT
> X-HDT-HopCount: 1
>
> Interesting. Please try changing the Main-Class to LinkedView.
> Probably it should really be
> edu.stanford.genetics.treeview.app.LinkedViewApp
> I'll look into this more for the next release.
>
> 	-Alok
>
> On May 17, 2007, at 6:16 PM, JEN...@co...
> wrote:
>
>> Hello,
>> I am a support tech trying to install some programs for a doctor
>> and I'm
>> having a problem with Treeview. I downloaded, unzipped and installed
>> Treeview.  When we run it the java launcher error Could not find
>> main class.
>>
>> I am not trained in java, I've researched on the web and tried some
>> changes
>> to the location of the jar files and changes in the manifest. The
>> manifest
>> contains -        Class-Path: . nanoxml-2.1.jar GIFEncoder.jar
>> Main-Class:
>> TreeView
>>
>> There is a file nanoxml-2.2.2.jar - I tried changing the manifest
>> to this
>> jar, but still getting the error.  Any help will be much appreciated!
>>
>> Thanks, Jen
>>
>> Jennifer Witt
>> Manager, Companion Data Services
>> Work 410-683-2531
>> Cell 410-258-8804
>>
>>
>

Re: [Jtreeview-users] Could not find main class

[Alok S. <alo...@gm...>]

Interesting. Please try changing the Main-Class to LinkedView.
Probably it should really be  
edu.stanford.genetics.treeview.app.LinkedViewApp
I'll look into this more for the next release.

	-Alok

On May 17, 2007, at 6:16 PM, JEN...@co...  
wrote:

> Hello,
> I am a support tech trying to install some programs for a doctor  
> and I'm
> having a problem with Treeview. I downloaded, unzipped and installed
> Treeview.  When we run it the java launcher error Could not find  
> main class.
>
> I am not trained in java, I've researched on the web and tried some  
> changes
> to the location of the jar files and changes in the manifest. The  
> manifest
> contains -        Class-Path: . nanoxml-2.1.jar GIFEncoder.jar   
> Main-Class:
> TreeView
>
> There is a file nanoxml-2.2.2.jar - I tried changing the manifest  
> to this
> jar, but still getting the error.  Any help will be much appreciated!
>
> Thanks, Jen
>
> Jennifer Witt
> Manager, Companion Data Services
> Work 410-683-2531
> Cell 410-258-8804
>
>
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[Jtreeview-users] Could not find main class

[<JEN...@co...>]

Hello,
I am a support tech trying to install some programs for a doctor and I'm
having a problem with Treeview. I downloaded, unzipped and installed
Treeview.  When we run it the java launcher error Could not find main class.

I am not trained in java, I've researched on the web and tried some changes
to the location of the jar files and changes in the manifest. The manifest
contains -        Class-Path: . nanoxml-2.1.jar GIFEncoder.jar  Main-Class:
TreeView

There is a file nanoxml-2.2.2.jar - I tried changing the manifest to this
jar, but still getting the error.  Any help will be much appreciated!

Thanks, Jen

Jennifer Witt
Manager, Companion Data Services
Work 410-683-2531
Cell 410-258-8804


CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
and privileged information.  Any unauthorized review, use, disclosure or
distribution is prohibited.  If you are not the intended recipient, please
contact the sender by reply e-mail and destroy all copies of the original
message.

Re: [Jtreeview-users] dendrogram colorbar - number of decimal places?

[Alok S. <alo...@gm...>]

It is not possible at this time. It would not be too difficult to  
add, but I am not sure when I will have time. For the time being, you  
could try to work around it somehow, perhaps multiplying your data  
values by a constant.

	-Alok

On May 9, 2007, at 8:36 AM, Gordon Robertson wrote:

> Is it possible to increase the number of decimal places displayed  
> with an exported colorbar graphic? Rather than a colorbar cell  
> being labeled as 0.01, I'd like to see, say, 0.015 (or whatever the  
> program reports, given a particular loaded dataset). I don't see  
> this as a setting within JTV 1.1.0 (on OSX 10.4.9), and don't see  
> it discussed in the online documentation.
>
> Thank you.
>
> Gordon
> --
> Gordon Robertson
> Canada's Michael Smith Genome Sciences Centre
> Vancouver BC Canada
>
>
>
> ---------------------------------------------------------------------- 
> ---
> This SF.net email is sponsored by DB2 Express
> Download DB2 Express C - the FREE version of DB2 express and take
> control of your XML. No limits. Just data. Click to get it now.
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> _______________________________________________
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> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users

[Jtreeview-users] dendrogram colorbar - number of decimal places?

[Gordon R. <agr...@te...>]

Is it possible to increase the number of decimal places displayed  
with an exported colorbar graphic? Rather than a colorbar cell being  
labeled as 0.01, I'd like to see, say, 0.015 (or whatever the program  
reports, given a particular loaded dataset). I don't see this as a  
setting within JTV 1.1.0 (on OSX 10.4.9), and don't see it discussed  
in the online documentation.

Thank you.

Gordon
--
Gordon Robertson
Canada's Michael Smith Genome Sciences Centre
Vancouver BC Canada

Re: [Jtreeview-users] question for selection of different genes using the dendogram

[Alok S. <alo...@gm...>]

The behavior is expected. However, if you open the CDT file in excel  
you can add a common annotation to all the genes that you wish to see  
placed together.  You don't need to enter a complete gene name, you  
can enter a substring of any annotation. It would probably be better  
if there were an "add to selection" option or something, instead of  
it always replacing the current selection.

Incidentally, you can append to current selection in the scatterplot  
view if you hold down the control key. But that doesn't work anywhere  
else. You can scatterplot index against index to get the idea- index  
is just the distance of the gene from the top of the dendrogram. To  
use the scatterplot, you may need to select "linked" from the style  
menu when you open a new, and then select "Analysis->scatterplot".

	-Alok

On Mar 16, 2007, at 12:01 PM, jeremie poschmann wrote:

> Hi Alok
> thanks for taking the time to answer me. You answered exactly my  
> questions,
> However I cant accumulate genes in the find genes dialog. Each time
> the previously searched gene is gone, only the currently selected gene
> is shown. Is this normal or do I have a problem with the program ?
> thank you
> cheers
> jeremie
>
> 2007/3/16, Alok Saldanha <alo...@gm...>:
>> I'm not entirely sure what you're asking.
>> If you can give the genes similar annotations, you can view them in a
>> separate window using the following:
>>
>> 1) Open Analysis->Find Genes... dialog
>> 2) Type in the relevant annotation
>> 3) Press return to initiate search
>> 4) Click "All" to select all
>> 5) Click "Summary Popup"
>>
>> At any time, you can click "Analysis->Summary popup" to get  a
>> summary popup of the currently selected genes. There's currently no
>> way to select discontinuous ranges manually, however- the only way in
>> dendrogram view is by searching for annotation. The other way
>> currently to select discontinuous ranges is selecting points in a
>> scatterplot. This is entirely a UI issue.
>>
>> Hope this helps,
>> Alok
>>
>> On Mar 15, 2007, at 3:54 PM, jeremie poschmann wrote:
>>
>> > HI,
>> > I have a dendrogram with several hundred genes which are ordered by
>> > hirarchical clustering.  I would like to know if its possible to
>> > choose some different genes which arent related and then put them
>> > below each other in the dendrogram, so that I can compare them  
>> to the
>> > total set of genes
>> > Please help me
>> > thank you very much
>> > all the best
>> >
>> > --
>> > Jeremie Poschmann
>> > PhD student
>> > Centre de Recherche Guy Bernier
>> > Hopital Rosemont-Maissonneuve
>> > 5415 Boul. de l'Assomption
>> > Montreal Quebec
>> > H1T 2M4
>> > Tel 514 252 3400 ext. 3349
>> >
>> >  
>> --------------------------------------------------------------------- 
>> -
>> > ---
>> > Take Surveys. Earn Cash. Influence the Future of IT
>> > Join SourceForge.net's Techsay panel and you'll get the chance to
>> > share your
>> > opinions on IT & business topics through brief surveys-and earn  
>> cash
>> > http://www.techsay.com/default.php?
>> > page=join.php&p=sourceforge&CID=DEVDEV
>> > _______________________________________________
>> > Jtreeview-users mailing list
>> > Jtr...@li...
>> > https://lists.sourceforge.net/lists/listinfo/jtreeview-users
>>
>>
>
>
> -- 
> Jeremie Poschmann
> PhD student
> Centre de Recherche Guy Bernier
> Hopital Rosemont-Maissonneuve
> 5415 Boul. de l'Assomption
> Montreal Quebec
> H1T 2M4
> Tel 514 252 3400 ext. 3349

Re: [Jtreeview-users] question for selection of different genes using the dendogram

[Alok S. <alo...@gm...>]

I'm not entirely sure what you're asking.
If you can give the genes similar annotations, you can view them in a  
separate window using the following:

1) Open Analysis->Find Genes... dialog
2) Type in the relevant annotation
3) Press return to initiate search
4) Click "All" to select all
5) Click "Summary Popup"

At any time, you can click "Analysis->Summary popup" to get  a  
summary popup of the currently selected genes. There's currently no  
way to select discontinuous ranges manually, however- the only way in  
dendrogram view is by searching for annotation. The other way  
currently to select discontinuous ranges is selecting points in a  
scatterplot. This is entirely a UI issue.

Hope this helps,
Alok

On Mar 15, 2007, at 3:54 PM, jeremie poschmann wrote:

> HI,
> I have a dendrogram with several hundred genes which are ordered by
> hirarchical clustering.  I would like to know if its possible to
> choose some different genes which arent related and then put them
> below each other in the dendrogram, so that I can compare them to the
> total set of genes
> Please help me
> thank you very much
> all the best
>
> -- 
> Jeremie Poschmann
> PhD student
> Centre de Recherche Guy Bernier
> Hopital Rosemont-Maissonneuve
> 5415 Boul. de l'Assomption
> Montreal Quebec
> H1T 2M4
> Tel 514 252 3400 ext. 3349
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> Jtreeview-users mailing list
> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users

[Jtreeview-users] question for selection of different genes using the dendogram

[jeremie p. <jpo...@gm...>]

HI,
I have a dendrogram with several hundred genes which are ordered by
hirarchical clustering.  I would like to know if its possible to
choose some different genes which arent related and then put them
below each other in the dendrogram, so that I can compare them to the
total set of genes
Please help me
thank you very much
all the best

-- 
Jeremie Poschmann
PhD student
Centre de Recherche Guy Bernier
Hopital Rosemont-Maissonneuve
5415 Boul. de l'Assomption
Montreal Quebec
H1T 2M4
Tel 514 252 3400 ext. 3349

Re: [Jtreeview-users] JTV as a browser plugin

[Alok S. <alo...@gm...>]

that's odd! do the plugins work on the example page?

http://jtreeview.sourceforge.net/examples/applets.html

if those work, then there's probably something to fix with your  
applet page. If those don't work, then there's some issue with your  
browser's java setup. Which browser are you using? Can you tell which  
java it's using? try going to this page:

http://www.javatester.org/version.html

	-Alok

On Mar 7, 2007, at 9:34 AM, Charles, Peter wrote:

> Alok-
>
> also- I am running JAVA 2 Platform Standard Edition Version 1.5.0  
> (build 1.5.0_10-b03), Sun, etc.
>
> Best regards-
>
> peter
>
> Peter C. Charles, PhD
> Director,
> Cardiovascular Functional Genomics Laboratory
> Carolina Cardiovascular Biology Center
> Department of Medicine
> 2312B Molecular Biomedical Research Building, CB 7126
> UNC-CH
> Chapel Hill, NC 27599-7126
> Office: 919.843.1610
> Lab: 919.843.4587
> Mobile: 919.308.3839
> Pager: 919.216.5726
>
> From: Alok Saldanha [mailto:alo...@gm...]
> Sent: Wed 3/7/2007 12:16 PM
> To: jtr...@li...
> Cc: Charles, Peter
> Subject: JTV as a browser plugin
>
> Peter Charles asked:
>
> > Hello  Gentlepeople-
> >
> > I am a long time user of JTV and have = what might  be a stoopid
> > question...
> >
> > Has anyone implemented JTV as a plugin = for a  browser (Mozilla/
> > FireFox or IE)?  We are interested in sharing our = heatmap
> > images, but also want to allow the users to brows the clusters as
> > one = does with  JTV.  We have so many widespread users that I
> > really don't want to = set up  TreeView on all of their
> > systems...Anyone know of a good = solution?
> >
> > Best regards
> > -peter
>
> You should have a look at the "applet" version:
>
> http://jtreeview.sourceforge.net/examples/applets.html
>
> That particular page can take a few moments to load because there are
> a lot of applets on it. It displays using version 1.1.0. I just
> noticed that the menu items don't show up on firefox on mac os x, but
> they do on safari.
>
>         -Alok
>
>

[Jtreeview-users] JTV as a browser plugin

[Alok S. <alo...@gm...>]

Peter Charles asked:

> Hello  Gentlepeople-
>
> I am a long time user of JTV and have = what might  be a stoopid  
> question...
>
> Has anyone implemented JTV as a plugin = for a  browser (Mozilla/ 
> FireFox or IE)?  We are interested in sharing our = heatmap   
> images, but also want to allow the users to brows the clusters as  
> one = does with  JTV.  We have so many widespread users that I  
> really don't want to = set up  TreeView on all of their  
> systems...Anyone know of a good = solution?
>
> Best regards
> -peter

You should have a look at the "applet" version:

http://jtreeview.sourceforge.net/examples/applets.html

That particular page can take a few moments to load because there are  
a lot of applets on it. It displays using version 1.1.0. I just  
noticed that the menu items don't show up on firefox on mac os x, but  
they do on safari.

	-Alok

Re: [Jtreeview-users] Java issue with OSX 10.4.8?

[Leonard F. <ljf...@in...>]

Thanks for the quick reply Alok. Here's my version info:

java version "1.5.0_07"
Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_07-164)
Java HotSpot(TM) Client VM (build 1.5.0_07-87, mixed mode, sharing)

Thanks

Leonard


On 21-Feb-07, at 7:55 PM, Alok Saldanha wrote:

> Dear Leonard,
>
> The error typically indicates some java version incompatibility.
> If you open Terminal (In Applications->Utilities) and type:
>
>> java -version
>
> you should get something like:
>
>> java version "1.5.0_06"
>> Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-113)
>> Java HotSpot(TM) Client VM (build 1.5.0_06-68, mixed mode, sharing)
>
> Could you cut and paste your version info?
>
> Thanks,
> Alok
>
> On Feb 21, 2007, at 7:41 PM, Leonard Foster wrote:
>
>> Hello,
>>
>> I tried installing JTV (both the universal binary and the Mac
>> Universal versions) on a Mac Book Pro with 10.4.8 installed and I get
>> the following error in the Console:
>>
>> [JavaAppLauncher Error] CallStaticVoidMethod() threw an exception
>> Exception in thread "main" java.lang.UnsupportedClassVersionError:
>> edu/stanford/genetics/treeview/app/LinkedViewApp (Unsupported
>> major.minor version 49.0)
>> 	at java.lang.ClassLoader.defineClass0(Native Method)
>> 	at java.lang.ClassLoader.defineClass(ClassLoader.java:539)
>> 	at java.security.SecureClassLoader.defineClass
>> (SecureClassLoader.java:123)
>> 	at java.net.URLClassLoader.defineClass(URLClassLoader.java:251)
>> 	at java.net.URLClassLoader.access$100(URLClassLoader.java:55)
>> 	at java.net.URLClassLoader$1.run(URLClassLoader.java:194)
>> 	at java.security.AccessController.doPrivileged(Native Method)
>> 	at java.net.URLClassLoader.findClass(URLClassLoader.java:187)
>> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:289)
>> 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:274)
>> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:235)
>> 	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:302)
>> 	at java.lang.Class.forName0(Native Method)
>> 	at java.lang.Class.forName(Class.java:219)
>> 	at apple.launcher.LaunchRunner.loadMainMethod(LaunchRunner.java:55)
>> 	at apple.launcher.LaunchRunner.run(LaunchRunner.java:84)
>> 	at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:50)
>> 	at apple.launcher.JavaApplicationLauncher.launch
>> (JavaApplicationLauncher.java:52)
>>
>> I have the latest Java update. Am I missing something?
>>
>> Thanks
>>
>> Leonard
>>
>> --------------------------------------------------------------------- 
>> ----
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to  
>> share your
>> opinions on IT & business topics through brief surveys-and earn cash
>> http://www.techsay.com/default.php? 
>> page=join.php&p=sourceforge&CID=DEVDEV
>> _______________________________________________
>> Jtreeview-users mailing list
>> Jtr...@li...
>> https://lists.sourceforge.net/lists/listinfo/jtreeview-users
>

Re: [Jtreeview-users] Java issue with OSX 10.4.8?

[Alok S. <al...@ca...>]

Dear Leonard,

The error typically indicates some java version incompatibility.
If you open Terminal (In Applications->Utilities) and type:

> java -version

you should get something like:

> java version "1.5.0_06"
> Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-113)
> Java HotSpot(TM) Client VM (build 1.5.0_06-68, mixed mode, sharing)

Could you cut and paste your version info?

Thanks,
Alok

On Feb 21, 2007, at 7:41 PM, Leonard Foster wrote:

> Hello,
>
> I tried installing JTV (both the universal binary and the Mac
> Universal versions) on a Mac Book Pro with 10.4.8 installed and I get
> the following error in the Console:
>
> [JavaAppLauncher Error] CallStaticVoidMethod() threw an exception
> Exception in thread "main" java.lang.UnsupportedClassVersionError:
> edu/stanford/genetics/treeview/app/LinkedViewApp (Unsupported
> major.minor version 49.0)
> 	at java.lang.ClassLoader.defineClass0(Native Method)
> 	at java.lang.ClassLoader.defineClass(ClassLoader.java:539)
> 	at java.security.SecureClassLoader.defineClass
> (SecureClassLoader.java:123)
> 	at java.net.URLClassLoader.defineClass(URLClassLoader.java:251)
> 	at java.net.URLClassLoader.access$100(URLClassLoader.java:55)
> 	at java.net.URLClassLoader$1.run(URLClassLoader.java:194)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at java.net.URLClassLoader.findClass(URLClassLoader.java:187)
> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:289)
> 	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:274)
> 	at java.lang.ClassLoader.loadClass(ClassLoader.java:235)
> 	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:302)
> 	at java.lang.Class.forName0(Native Method)
> 	at java.lang.Class.forName(Class.java:219)
> 	at apple.launcher.LaunchRunner.loadMainMethod(LaunchRunner.java:55)
> 	at apple.launcher.LaunchRunner.run(LaunchRunner.java:84)
> 	at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:50)
> 	at apple.launcher.JavaApplicationLauncher.launch
> (JavaApplicationLauncher.java:52)
>
> I have the latest Java update. Am I missing something?
>
> Thanks
>
> Leonard
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> Jtreeview-users mailing list
> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users

[Jtreeview-users] Java issue with OSX 10.4.8?

[Leonard F. <ljf...@in...>]

Hello,

I tried installing JTV (both the universal binary and the Mac  
Universal versions) on a Mac Book Pro with 10.4.8 installed and I get  
the following error in the Console:

[JavaAppLauncher Error] CallStaticVoidMethod() threw an exception
Exception in thread "main" java.lang.UnsupportedClassVersionError:  
edu/stanford/genetics/treeview/app/LinkedViewApp (Unsupported  
major.minor version 49.0)
	at java.lang.ClassLoader.defineClass0(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:539)
	at java.security.SecureClassLoader.defineClass 
(SecureClassLoader.java:123)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:251)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:55)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:194)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:187)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:289)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:274)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:235)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:302)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:219)
	at apple.launcher.LaunchRunner.loadMainMethod(LaunchRunner.java:55)
	at apple.launcher.LaunchRunner.run(LaunchRunner.java:84)
	at apple.launcher.LaunchRunner.callMain(LaunchRunner.java:50)
	at apple.launcher.JavaApplicationLauncher.launch 
(JavaApplicationLauncher.java:52)

I have the latest Java update. Am I missing something?

Thanks

Leonard

Re: [Jtreeview-users] Highlighting specific edges in JTV

[Alok S. <al...@ca...>]

Ah, it seems I misunderstood your question. Currently, there is no =20
way to represent relationships between pairs of nodes in java =20
treeview. I can think of two ways to do it:

1) The hard way to do it that would be in keeping with the java =20
treeview design would be to introduce some interface like HeaderInfo =20
that would capture the pairwise relationships on the nodes, add a =20
method to DataModel that makes it possible to retrieve the data =20
structure, and then modify the TreeDrawer to make use of it. You =20
would also have to introduce a new file format to keep track of =20
pairwise node relationships.

2) A much easier solution would be to add "LEFTCOLOR" and =20
"RIGHTCOLOR" columns to the GTR/ATR files, and then hack TreeColorer =20
and TreeDrawer to make use of those columns when "NODECOLOR" is not =20
present. You would also need to add two fields to TreeDrawerNode to =20
hold the left and right colors. If all three colors are present, you =20
could color the base of the node with NODECOLOR and the two branches =20
with the left and right.

I would recommend #2, unless you plan on doing a lot with pairwise =20
node relationships, in which case #1 may pay off eventually. Let me =20
know if you plan to implement one of these, or something rather =20
different. #2 has the advantage that it could be implemented entirely =20=

as a standalone plugin- just copy over the plugin/dendrogram source =20
tree and subclass TreeDrawerNode in the plugin, and use it when you =20
build the tree in TreeDrawer.setData(). If/when I adsorb it back into =20=

the main source tree, I should be able to just overwrite the base =20
class with your TreeDrawerNode, and update the relevant classes in =20
plugin/dendrogram. Changing colors on the fly would work as described =20=

in my previous email.

	-Alok

On Feb 20, 2007, at 7:20 AM, Itamar Cohen wrote:

> Hi Alok,
> First of all, thanks for the quick response.  As I understood from =20
> your response the only way to change colors is by changing the =20
> color of both edges coming out of the node (changing the color of =20
> A  B  C will change both the edges AB and AC).  Is there a way to =20
> only change the color of one of them?
>
> Thanks,
> Itamar Cohen
>
> CC: jtr...@li...
> From: al...@ca...
> Subject: Re: Highlighting specific edges in JTV
> Date: Tue, 13 Feb 2007 15:21:28 -0800
> To: co...@ho...
>
> Hi Itamar,
>
> First of all, you should look at this example:
>
> http://jtreeview.sourceforge.net/examples/index.html#ex5
>
> You can probably achieve the display that you want by actually hard-=20=

> coding the colors in the GTR (gene tree) file. For example,
>
> NODEID LEFT RIGHT CORRELATION NODECOLOR
> NODE1X GENE2268X GENE2269X 0.989404 #9900FF
>
> This indicates that the node named "NODE1X" which is formed by =20
> joining "GENE2268X" and "GENE2269X" should be colored "#9900FF" or =20
> bright purple.
>
> However, rather than preprocessing the GTR files and adding a =20
> column, you may want to add functionality to do this on the fly. =20
> The best way to do this is to write a plugin. I have written an =20
> example plugin that you should be able to read through as it is =20
> under 200 lines of code:
>
> https://sourceforge.net/docman/display_doc.php?=20
> docid=3D35149&group_id=3D84593
>
> Your plugin shouldn't be too hard, depending on how exactly the =20
> coloring works. Here's one scheme that could work:
>
> 1) Write a class that extends PluginFactory. Look at the code for =20
> DataTableFactory from the example plugin to see how easy it can be. =20=

> There are two ways you could make it work:
> 1a) The selection of the file and coloring of the tree can happen =20
> within dialogs triggered by restorePlugin, which would then return =20
> null, or
> 1b) restorePlugin returns a MainPanel that has a button that opens =20
> a file search dialog to locate the file with the color info, and a =20
> second button that loads it.
> The advantage of 1b is that you can then have a list of common =20
> presets, if there are particular sorts of colorings you use often
>
> 2) Your write a method either in the PluginFactory or MainPanel =20
> that gets called with two parameters, 1) the name of the file with =20
> the coloring info, and 2) The viewFrame reference that was passed =20
> in to restorePlugin. It loads up the coloring info, and then calls =20
> viewFrame.getDataModel().getGtrHeaderInfo() to get the HeaderInfo =20
> representing the headers for the gene tree.
>
> 3) Call HeaderInfo.getHeaderIndex("NODECOLOR") to see if column =20
> exists, if not call HeaderInfo.addName("NODECOLOR", getNumHeaders=20
> ()), and check to make sure it returns true.
>
> 4) Traverse the gene tree headers to figure out which nodes to =20
> color what, and then call HeaderInfo.setHeader(nodeNumber, =20
> "NODECOLOR", "#9900FF"), with the appropriate node number and color =20=

> of course.
>
> This may or may not work as planned... in particular, the updates =20
> from calling setHeader may not propagate all the way, as I don't =20
> have a plugin that works in quite this way yet. If you think it =20
> would be helpful, I could write up a quick test plugin that =20
> implements the above four steps and colors the nodes using a user-=20
> specified correlation threshold on the fly- i have been meaning to =20
> do this at some point anyways.
>
> I should also mention that you can get access to the state and data =20=

> structures of the dendrogram (and in particular its in-memory tree =20
> of TreeDrawerNodes) by calling viewFrame.getMainPanelsByName=20
> ("Dendrogram"). it's straightforward, but a little more coding =20
> (although less coding than building your own tree of TreeDrawerNodes).
>
> All of the above only applies to the version of the code checked =20
> into CVS, there are a number of fixes made since the last =20
> release... in fact, I was planning to do a new release soon, since =20
> there are a few big problems in the last release. If there are any =20
> issues that need to be addressed for your plugin, it would be nice =20
> to do it before then.
>
> -Alok
>
>
> On Feb 13, 2007, at 12:53 PM, Itamar Cohen wrote:
>
> Hi Alok,
>
> First of all, thanks for your response about height of subtrees, it =20=

> was very helpful.  We have a project now in which we are trying to =20
> highlight specific edges in a tree.  I'm trying to alter the JTV =20
> code so it would read a list of node pairs and would show these =20
> edges in a different color.  Could you suggest a simple way to =20
> enable this?
>
> Thanks,
> Itamar
>
> Live Search: New search found Try it!
>
>
> Find a local pizza place, movie theater, and more=85.then map the =20
> best route! Try it!

Re: [Jtreeview-users] Highlighting specific edges in JTV

[Alok S. <al...@ca...>]

Hi Itamar,

First of all, you should look at this example:

http://jtreeview.sourceforge.net/examples/index.html#ex5

You can probably achieve the display that you want by actually hard- 
coding the colors in the GTR (gene tree) file. For example,

> NODEID	LEFT	RIGHT	CORRELATION	NODECOLOR
> NODE1X	GENE2268X	GENE2269X	0.989404	#9900FF

This indicates that the node named "NODE1X" which is formed by  
joining "GENE2268X" and "GENE2269X" should be colored "#9900FF" or  
bright purple.

However, rather than preprocessing the GTR files and adding a column,  
you may want to add functionality to do this on the fly. The best way  
to do this is to write a plugin. I have written an example plugin  
that you should be able to read through as it is under 200 lines of  
code:

https://sourceforge.net/docman/display_doc.php? 
docid=35149&group_id=84593

Your plugin shouldn't be too hard, depending on how exactly the  
coloring works. Here's one scheme that could work:

1) Write a class that extends PluginFactory. Look at the code for  
DataTableFactory from the example plugin to see how easy it can be.  
There are two ways you could make it work:
1a) The selection of the file and coloring of the tree can happen  
within dialogs triggered by restorePlugin, which would then return  
null, or
1b) restorePlugin returns a MainPanel that has a button that opens a  
file search dialog to locate the file with the color info, and a  
second button that loads it.
The advantage of 1b is that you can then have a list of common  
presets, if there are particular sorts of colorings you use often

2) Your write a method either in the PluginFactory or MainPanel that  
gets called with two parameters, 1) the name of the file with the  
coloring info, and 2) The viewFrame reference that was passed in to  
restorePlugin. It loads up the coloring info, and then calls  
viewFrame.getDataModel().getGtrHeaderInfo() to get the HeaderInfo  
representing the headers for the gene tree.

3) Call HeaderInfo.getHeaderIndex("NODECOLOR") to see if column  
exists, if not call HeaderInfo.addName("NODECOLOR", getNumHeaders()),  
and check to make sure it returns true.

4) Traverse the gene tree headers to figure out which nodes to color  
what, and then call HeaderInfo.setHeader(nodeNumber, "NODECOLOR",  
"#9900FF"), with the appropriate node number and color of course.

This may or may not work as planned... in particular, the updates  
from calling setHeader may not propagate all the way, as I don't have  
a plugin that works in quite this way yet. If you think it would be  
helpful, I could write up a quick test plugin that implements the  
above four steps and colors the nodes using a user-specified  
correlation threshold on the fly- i have been meaning to do this at  
some point anyways.

I should also mention that you can get access to the state and data  
structures of the dendrogram (and in particular its in-memory tree of  
TreeDrawerNodes) by calling viewFrame.getMainPanelsByName 
("Dendrogram"). it's straightforward, but a little more coding  
(although less coding than building your own tree of TreeDrawerNodes).

All of the above only applies to the version of the code checked into  
CVS, there are a number of fixes made since the last release... in  
fact, I was planning to do a new release soon, since there are a few  
big problems in the last release. If there are any issues that need  
to be addressed for your plugin, it would be nice to do it before then.

	-Alok


On Feb 13, 2007, at 12:53 PM, Itamar Cohen wrote:

> Hi Alok,
>
> First of all, thanks for your response about height of subtrees, it  
> was very helpful.  We have a project now in which we are trying to  
> highlight specific edges in a tree.  I'm trying to alter the JTV  
> code so it would read a list of node pairs and would show these  
> edges in a different color.  Could you suggest a simple way to  
> enable this?
>
> Thanks,
> Itamar
>
> Live Search: New search found Try it!

Re: [Jtreeview-users] height of subtrees

[Alok S. <al...@ca...>]

Dear Itamar,

By height of subtree, I will assume you mean the x axis offset for  
the horizontal (i.e. gene) tree, or the y-axis offset for the  
vertical (i.e. array) tree. The height of each subtree is given by  
the correlation of the node that corresponds to that subtree, so the  
problem of calculating the height of subtrees is fairly trivial. In  
JTV, the interval from the minimum correlation to 1.0 correlation is  
mapped onto the interval of pixels that are available, so once you  
know the minimum correlation in the tree (typically the correlation  
of the root node) and the number of available pixels, you can  
calculate subtree height in pixels.

Did I misunderstand the question?

	-Alok

On Jan 10, 2007, at 1:46 PM, Itamar Cohen wrote:

> Hi all,
>
> I have been working with trees in the same format as the ones used  
> in jtreeview (cdt & gtr files).  I have recently been trying to  
> calculate height  of subtrees.  I'm sure that's a problem addressed  
> in the treeview, do you have a specific method for this calculation?
>
> Thanks
> Itamar Cohen
>
> Get the Live.com Holiday Page for recipes, gift-giving ideas, and  
> more. Check it out!
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV________________________________ 
> _______________
> Jtreeview-users mailing list
> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users

[Jtreeview-users] height of subtrees

[Itamar C. <co...@ho...>]

Hi all,
=20
I have been working with trees in the same format as the ones used in jtree=
view (cdt & gtr files).  I have recently been trying to calculate height  o=
f subtrees.  I'm sure that's a problem addressed in the treeview, do you ha=
ve a specific method for this calculation?
=20
Thanks
Itamar Cohen =20
_________________________________________________________________
Get the Live.com Holiday Page for recipes, gift-giving ideas, and more.
www.live.com/?addtemplate=3Dholiday=

Re: [Jtreeview-users] Program crashing

[Alok J. S. <al...@ca...>]

Dear Raj,

That's odd! I haven't heard of anything similar happening, much less
something as reproducible as what you're seeming. I'm at a loss to
explain it... which version of Java and JTV are you using (type "java
-version" at the command line)?  I have two suggestions:

1) On mac os x, open the Console application (Found in
Applications/Utilities). When you try to open java treeview and nothing
happens, it's probably running into an error on startup that should be
printed to the console. Cutting and pasting the error message complete
with source code line numbers would be very helpful to me.
2) Since the problem occurs during subsequent startup, there's probably
something with your file/directory naming is giving java treeview
problems. it might name the file something boring and put it in a boring
place.

It might help to delete the global config file, which is located in a
system-dependent way as =20
described here:

http://jtreeview.sourceforge.net/docs/JTVUserManual/single.html#ch2_persist=
ence_global

On unix, this resolves to a .javaTreeViewXmlrc file in your home =20
directory. On OSX, it resolves to a JavaTreeView Config in your =20
home directory. On PC, it resolves to a jtview.xml file, although =20
I'm not sure where windows considers your home directory to be.

Deleting the global file should allow JTV to run in a similar fashion as
the first time, but will probably not solve the problem given how
reproducible it is.

The console output would be most informative.=20

-Alok

> Hello,
>=20
> We ran TreeView initially, and it worked great, on all the machines we ra=
n
> it on. We then took a break, closed the programs, and tried starting them
> again. This Time, however, the pogram refuses to start at all. One of the
> Macs gave an error code saying:
>=20
> Cannot Launch Java application
> java.lang.ArrayIndexOutOfBoundsException: 2
>=20
> The other mac and the Windows machine didn't do anything at all, and just
> seemed to act like as if I didn't try to run the program at all.
> Program won't start, both on a Windows machine, and two Macs
>=20
> A prompt reply would be appreciated, as we have a paper to publish and ar=
e
> extremely excited to run this really cool program :).
>=20
> Thanks,
> --=20
> Raj Srikrishnan
> rsr...@uc...
> (281) 748-0619
>=20

[Jtreeview-users] Program crashing

[Raj S. <ra...@gm...>]

Hello,

We ran TreeView initially, and it worked great, on all the machines we ran
it on. We then took a break, closed the programs, and tried starting them
again. This Time, however, the pogram refuses to start at all. One of the
Macs gave an error code saying:

Cannot Launch Java application
java.lang.ArrayIndexOutOfBoundsException: 2

The other mac and the Windows machine didn't do anything at all, and just
seemed to act like as if I didn't try to run the program at all.
Program won't start, both on a Windows machine, and two Macs

A prompt reply would be appreciated, as we have a paper to publish and are
extremely excited to run this really cool program :).

Thanks,
-- 
Raj Srikrishnan
rsr...@uc...
(281) 748-0619