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

Re: [Jtreeview-users] Registration

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

Dear David,

When you register, the fact should be recorded in your global  
settings file, which is located in a system-dependent way as  
described here:

http://jtreeview.sourceforge.net/docs/JTVUserManual/ 
single.html#ch2_persistence_global

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

What is likely going on is that the global settings file is not being  
saved for some reason, perhaps because it was corrupted in a previous  
crash. I recommend that you try the following:

1) Delete the current global settings file, on the assumption that it  
is corrupted. This will delete your previous file list and any other  
global settings.
2) Start Java Treeview. This should cause the registration dialog to  
come up.
3) Click on the option that says you don't want to register when the  
dialog comes up (decline, don't defer)
4) Exit Java Treeview. At this point, it should have recorded that  
you decline in the global settings.

I hope this helps.

	-Alok

On Dec 20, 2006, at 6:48 PM, Bowtell, David wrote:

>  I keep getting the registration window as I login to Java TreeView  
> even
> though I have registered.  Can you please suggest a solution?  Thanks.
>
> -- 
> Professor David Bowtell PhD.
> Director, Research.
>
> Mail Address:
> Research Division, Peter MacCallum Cancer Centre, Locked Bag 1  
> A'Beckett St,
> Melbourne 8006, VIC. Australia
> http://www.petermac-research.org.au
>
> FedEx Address:
> Research Division, Peter MacCallum Cancer Centre, St Andrew's  
> Place, East
> Melbourne 3002, VIC. Australia
>
> Lab 61-3-96561287, Office 61-3-96561356, Fax 61-3-96561414
>
>
>
>
> ---------------------------------------------------------------------- 
> ---
> 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
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> page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> Jtreeview-users mailing list
> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users

[Jtreeview-users] Registration

[Bowtell, D. <dav...@pe...>]

 I keep getting the registration window as I login to Java TreeView even
though I have registered.  Can you please suggest a solution?  Thanks.

-- 
Professor David Bowtell PhD.
Director, Research.

Mail Address:      
Research Division, Peter MacCallum Cancer Centre, Locked Bag 1 A'Beckett St,
Melbourne 8006, VIC. Australia
http://www.petermac-research.org.au

FedEx Address:     
Research Division, Peter MacCallum Cancer Centre, St Andrew's Place, East
Melbourne 3002, VIC. Australia

Lab 61-3-96561287, Office 61-3-96561356, Fax 61-3-96561414

[Jtreeview-users] Essential message. You must to read.

[Penny M. <gve...@ar...>]

Get in on EQTD first thing Tuesday.  This is going to soar 
over the next week.  Already there has been a 100% 
appreciation within the first few hours, so do it quick.

With oil markets retreating, big traders are turning to gold, 
driving it to levels never before seen.  EQTD has made an 
announcement of staggering proportions related to a recent 
survey on one of their gold properties.  The inside scoop is 
that we will be looking at a quadrupling of share price once 
the public takes notice:

CHICAGO, ILLINOIS-(MARKETWIRE)-Oct 23, 2006 - Equal trading 
is pleased to announce survey results which have far exceeded 
our expectations.  Results from our British Columbia property 
show a 58,000 ounce potential.  Plans are already underway 
for immediate development.  We look forward to this 
extraordinary discovery bringing value to our shareholders.

At 600$ an ounce this discovery is worth 34.8 mil$.  With 
865mil shares outstanding, this would give us a book value of 
0.04 (current price is under 1 cent).

Don't miss this one.  The value is there.  The opportunity is 
there.  Don't let it pass you by.

[Jtreeview-users] conservationist cancel

[Flossie L. <wm...@wa...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
 <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<img alt="" src="cid:par...@wa..." height="421"
 width="798"><br>
Interesting magazine - it also has articles by James Bach, Rex Black,
Michael Bolton, Duncan Card, Fiona Charles, Cem Kaner, Joe Larizza and
Richard Bornet. But in fact, there may be more pages than before, if the
margins are made smaller.<br>
This year that process helped us make the development, and testing
processes even more smooth and high-quality.<br>
Often, everyone recognizes a problem exists yet it is small enough or
happens so infrequently that it seems that the problem is not important
and not worth solving. Maybe using it with code.<br>
com Vegetarian Cuisine GuideSite. And not writing them as static
documents, but as executable tests in a form understandable by the
Product Owner and programmers. I personally think that it's timethat we
start adopting quality practices for database development. It is also
more an act of documentation than of verification. If she recognizes my
attempt at recounting this conversion, I hope she will let me know if
this helped her team in their adoption of agile practices. In other
words, we already had a fairly sizable amount of technical debt and the
application was only a week or two old. Just like youcan take a
TDD-based approach to developing application code, you can do thesame
thing with your database schema. Do you know the signs of preterm
labor?<br>
But he is describing a variation on that code smell. because they are
worried that enumerated types could have unspecified sizes. I'll admit
that I'm always a. The influence of loss aversion on mental accounting
is enormous, as will become evident very quickly.<br>
It is much easier to find, and then fix, those defects if you've written
two new lines of code than two thousand.<br>
Interesting magazine - it also has articles by James Bach, Rex Black,
Michael Bolton, Duncan Card, Fiona Charles, Cem Kaner, Joe Larizza and
Richard Bornet.<br>
Or fewer pages if the margins are made larger. Often, everyone
recognizes a problem exists yet it is small enough or happens so
infrequently that it seems that the problem is not important and not
worth solving.<br>
If the data is shared, and not duplicated, then we don't need to loop
everywhere changing it. It's also got a healthy dash. It is much easier
to find, and then fix, those defects if you've written two new lines of
code than two thousand. It is also more an act of documentation than of
verification. Transactions are often evaluated one at a time, rather
than in conjunction with everything else. Chances are pretty good that
your tests will be broken by defects that exist in the new code. If the
data is shared, and not duplicated, then we don't need to loop
everywhere changing it.<br>
Transactions are often evaluated one at a time, rather than in
conjunction with everything else.<br>
<br>
</body>
</html>

[Jtreeview-users] tangential

[Susanna M. <xt...@by...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
 <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<img alt="" src="cid:par...@pa..."
 height="338" width="792"><br>
I have cleaned up my domestic domaine and I am ready to write.<br>
A splendid seafood dinner, serpentines, table bombs, funny hats, lots of
rockets etc.<br>
Seek out honest web companies to exchange a moderate amount of links
with. A splendid seafood dinner, serpentines, table bombs, funny hats,
lots of rockets etc.<br>
The Link Popularity Check program is free and it is from Axandra,
Germany. Dennoch sollten wir uns die Gelegenheit nicht entgehen lassen,
im ein oder anderen Fall eine entsprechende Gewichtung vorzunehmen.<br>
Weitergehende Informationen folgen.<br>
This has led to the advent of RSS or real simple syndication.<br>
Many lucrative methods of ethical SEO can be turned into a problem when
too many people attempt to abuse the technology.<br>
"Grand Maitre" to the right - that is Henri de Toulouse-Lautrec - is of
course exhibited in Paris. This limits your ability to have the search
engines index portions of your site.<br>
Gut, wenn man ins Archiv schaut, findet man dort auch bekannte Motive -
trotzdem, einen Blick ist es sicher wert. So it is natural for your web
site rankings to benefit through backlinks from those articles.<br>
This has led to the advent of RSS or real simple syndication. The
optional tags available with the XML site map allow you to be
descriptive about the individual pages on your site including dates the
individual pages were modified.<br>
Don't commit yourself to any New Year Resolutions.<br>
Don't commit yourself to any New Year Resolutions. "Grand Maitre" to the
right - that is Henri de Toulouse-Lautrec - is of course exhibited in
Paris.<br>
Now and then I run a Link Popularity Check on my online galleries to
check their degree of presence on the internet. Von der Lebensberatung
bis zu Life-Style-Angelegenheiten ist dort alles zu finden.<br>
Don't commit yourself to any New Year Resolutions. And then I check the
online galleries.<br>
Vielleicht ist da auch etwas dran.<br>
The wise man of course said this with a smile.<br>
It's become a major technology used by news agencies and bloggers alike
as a simple method of publishing your information across a wide variety
of platforms. But, the search engines will usually only punish you if
the html format of a web site is similar, not a couple of articles.<br>
I use the following blogging systems for posting a lot of news and for
automatic building of RSSs, ATOM feeds and RDFs: Blogger. The optional
tags available with the XML site map allow you to be descriptive about
the individual pages on your site including dates the individual pages
were modified.<br>
com - if you need an introduction to RSS news feeds, you'll find it on
rssfeedssubmit. Don't put your life into an account. The wise man of
course said this with a smile.<br>
Also, don't try to manipulate your website to make it appear to have a
higher PR than you really do. Vielleicht ist da auch etwas dran. Von der
Lebensberatung bis zu Life-Style-Angelegenheiten ist dort alles zu
finden.<br>
It's a win win situation.<br>
And so is the image to the left.<br>
Post only relevant comments to forums and blogs because that behavior
leads to lasting link backs.<br>
Lots of mineral water. Dennoch sollten wir uns die Gelegenheit nicht
entgehen lassen, im ein oder anderen Fall eine entsprechende Gewichtung
vorzunehmen.<br>
<br>
</body>
</html>

[Jtreeview-users] self-confident hyphenated

[Flo L. <te...@dr...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
 <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<img alt="" src="cid:par...@dr..."
 height="383" width="582"><br>
Orange geeft aan dat dertig procent van  alle gesprekken binnenshuis via
de mobiele telefoon gebeuren.<br>
Dat meldt vakblad Adformatie vandaag. Among other things, the computers
will employ the free Linux operating system, flash memory instead of a
hard drive and a microprocessor that is slow by today . Newman best
describes what it is to be a baby boomer. print coupons - single or
double - are facing extinction as a grocery store marketing tool.<br>
This performance was driven by the success of Motorola's Linux-based
devices in China.<br>
He knows he just sold you on what the diamond industry classifies as
<br>
Ruil hem in voor een nieuwe en sta versteld van wat u er nog voor
terugkrijgt. nl is de online rechterhand voor de praktijk. One is
radically merciful, the other radically merciless. Please vote for
mine!<br>
Orange geeft aan dat dertig procent van  alle gesprekken binnenshuis via
de mobiele telefoon gebeuren. Both children, according to their Mums,
are at a critical point in their spiritual development.<br>
All of a sudden he sees a shark in the water, so he starts swimming
furiously towards his boat. Please vote for mine! We're researching a
whole load of new kitsch content for the site, plus making a few changes
to the design, for you kitsch hunters out there. rear panel
unscrewed.<br>
rear panel unscrewed. Please vote for mine!<br>
You never saw people like this on TV.<br>
Dit gebeurd met behulp van Adblocker. Kijk op de Orange website voor de
nieuwe portal website en speel ter viering het Orange Open ticket spel
op www. Managing director, Max . Peek inside the dramatic lives of
diverse families as they devote time, energy, and mega-cash into
planning and preparing the most important parties of their lives. Both
children, according to their Mums, are at a critical point in their
spiritual development. The new version of the general public license has
hit strong resistance even from the Linux faithful, including Linus
Torvalds. Please vote for mine! If abortion is going to remain legal, I
want abortion facilities held to the same standards as other outpatient
surgical facilities.<br>
The series follows four unique individuals, two male-to-females and two
female-to-males as they struggle to transition from one gender to the
other in the midst of a grueling school year.<br>
PostPath, creator of the Linux-based PostPath Email and Collaboration
Server, announced public. Managing director, Max . If abortion is going
to remain legal, I want abortion facilities held to the same standards
as other outpatient surgical facilities.<br>
Dit gebeurd met behulp van Adblocker.<br>
PostPath, creator of the Linux-based PostPath Email and Collaboration
Server, announced public.<br>
Taxeer uw printer dan nu online. But it also opened schisms that
challenged the very identity of the Log Cabin itself. Cartridge SAVE,
the .<br>
The series follows four unique individuals, two male-to-females and two
female-to-males as they struggle to transition from one gender to the
other in the midst of a grueling school year.<br>
Orange geeft aan dat dertig procent van  alle gesprekken binnenshuis via
de mobiele telefoon gebeuren.<br>
<br>
</body>
</html>

[Jtreeview-users] contact lens

[Sophia M. <xu...@de...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
 <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<img alt="" src="cid:par...@de..."
 height="368" width="585"><br>
We have a process for making promises day-by-day for performing the
work.<br>
These two people will push you, nurture you, and keep you just at the
edge of discomfort.<br>
John provides an approach that can make your service company lean.<br>
Rather than learning to follow others' models of leadership,
participants investigate their own behavior patterns.<br>
The AEC environment is not ready.<br>
Often constraints will arise in the course of doing the work in spite of
the effort given to look-ahead planning.<br>
Left uncorrected, these conditions expose employees to potential serious
injury or death from falls, electrocution, scaffold collapse, gas
cylinder explosions or head injuries. I've stopped looking at the
project manager.<br>
Only complete work releases work for other people.<br>
These two people will push you, nurture you, and keep you just at the
edge of discomfort.<br>
She's also not encouraging that we make changes in a vacuum. He goes to
great extent to describe what is lean and what is not lean.<br>
Although, I have joined the PMI and I will take the PMP exam.<br>
Rather than learning to follow others' models of leadership,
participants investigate their own behavior patterns. For the most part,
project participants have neither the time or the inclination for
reading or writing this sort of thing.<br>
Record the number of promises completed as a percent of promises made
for that day.<br>
I am quite surprised how well it came out.<br>
People are often keeping different work hours. Rather than learning to
follow others' models of leadership, participants investigate their own
behavior patterns. This is a meeting to fine tune the work we are doing
with each other. I also work with project teams across the AEC
industry.<br>
just like the Atkins Diet. Neither will solo-planning. People are often
keeping different work hours. So, do as Johanna suggests, build-in
regular cycles for replanning, and do it collaboratively.<br>
On construction sites the end of the day works well. Often constraints
will arise in the course of doing the work in spite of the effort given
to look-ahead planning. The article does a good job describing lean
thinking and making the case for adopting lean in construction. I've
stopped looking at the project manager. Projects run well when the
planning and execution are tightly coupled in a way that adapts to what
the team is learning, innovating, and encountering. Rather than learning
to follow others' models of leadership, participants investigate their
own behavior patterns. How many think that will change? You'll want to
conduct the meeting standing up. Record the number of promises completed
as a percent of promises made for that day. There's real value in
becoming more professional even if we don't become a profession.<br>
It is very easy to do.<br>
You'll also want to ask what kept the performer from completing as
promised.<br>
Komplett durch Kommentare der Regionalzeitungen. People are often
keeping different work hours.<br>
<br>
</body>
</html>

Re: [Jtreeview-users] treeview applet

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

Doh! The .jtv has changed in the past. I try not to break it, but  
sometimes it's worth changing.
When in doubt, it's probably a good idea to only use .jtv files  
produced by the same version of treeview.
It's always safe (albeit somewhat annoying) to delete the .jtv, open  
the cdt in treeview, get it set up the
way you want, and the close the window. This will cause treeview to  
save a new .jtv.

	-Alok

On Oct 5, 2006, at 12:20 AM, Christophe Klopp wrote:

> Thanks a lot,
>
> It seams that the jtv file I have is not compliant with the TreeView
> version I use.
>
> Christophe
>
> Alok Saldanha wrote:
>> Dear Christophe,
>>
>> I've gotten it to work, you can check it at:
>>
>> http://miniprep.caltech.edu/~remote/applet/testApplet2.html
>>
>> My applet tag is as follows:
>>
>>       <APPLET
>> CODE="edu/stanford/genetics/treeview/applet/ButtonApplet.class"
>>
>> archive="TreeViewApplet.jar,nanoxml-2.2.2.jar,plugins/Dendrogram.jar"
>> width=150 height=50
>>         alt="Your browser understands the &lt;APPLET&gt; tag but  
>> isn't
>> running the applet, for some reason."
>>>
>>         Your browser is completely ignoring the &lt;APPLET&gt; tag!
>>         <param name="cdtFile" value="spellman_K_G5_A3.cdt">
>>         <param name="cdtName" value="spellman K">
>>         <param name="plugins"
>> value="edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogram 
>> Factory">
>>
>>       </applet>
>>
>> A variety of other combinations work as well, for instance setting  
>> the
>> style parameter to kmeans or linked. I am not sure what's going wrong
>> on your side; perhaps it is looking for some things in the wrong
>> places? Are you sure Dendrogram.jar is in the plugins subdirectory?
>> Which distribution are you using?
>>
>>     -Alok
>>
>>
>>
>>
>> On Oct 4, 2006, at 12:24 AM, Christophe Klopp wrote:
>>
>>> Dear Alok,
>>>
>>> I tried :
>>> <param name="plugins"
>>> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFa 
>>> ctory,edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogram 
>>> Factory">
>>>
>>>
>>> <param name="plugins"
>>> value="edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogra 
>>> mFactory">
>>>
>>>
>>> <param name="plugins"
>>> value="edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogra 
>>> mFactory,edu.stanford.genetics.treeview.plugin.dendroview.alignmentF 
>>> actory">
>>>
>>>
>>> But non of them worked.
>>>
>>> I found this in the code:
>>> src/edu/stanford/genetics/treeview/app/LinkedViewApp.java:       *
>>> Usage: java -jar treeview.jar -r <my cdt> -t
>>> [auto|classic|kmeans|linked].
>>>
>>> And I tried
>>> <param name="style" value="kmeans">
>>> to give the parameter but it does not work either.
>>>
>>> Thanks'
>>>
>>> Christophe
>>>
>>>
>>> Alok Saldanha wrote:
>>>> Dear Christophe,
>>>>
>>>> You may need to add the Knn dendrogram view to the plugins  
>>>> parameter,
>>>> i.e.
>>>>
>>>> <param name="plugins"
>>>> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramF 
>>>> actory,edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogr 
>>>> amFactory">
>>>>
>>>>
>>>>
>>>> There's actually three plugins bundled into Dendrogram.jar,
>>>> edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactory
>>>> edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFacto 
>>>> ry
>>>> edu.stanford.genetics.treeview.plugin.dendroview.AlignmentFactory
>>>>
>>>> You need to specify which ones this particular applet will  
>>>> need... in
>>>> your case, you can probably leave off the DendrogramFactory. You  
>>>> can
>>>> also add more plugin jars to the archive attribute of the applet  
>>>> tag
>>>> if you need them. Let me know if this helps.
>>>>
>>>>     -Alok
>>>>
>>>> On Oct 3, 2006, at 8:22 AM, Christophe Klopp wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I hope you are or are able to redirect this question to the  
>>>>> suitable
>>>>> person.
>>>>>
>>>>> We want to present Kmeans data in the java treeview applet.
>>>>> We have 3 files :
>>>>> - x.cdt
>>>>> - x.kgg
>>>>> - x.jtv
>>>>>
>>>>> The applet works but does not separate the different kmean blocks
>>>>> (information from the x.kgg file).
>>>>> We tried to add the other files and a "kmeans" style to the applet
>>>>> HTML
>>>>> code :
>>>>>
>>>>> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
>>>>> "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
>>>>> <html>
>>>>>   <head>
>>>>>         <meta http-equiv="Content-Type" content="text/html;
>>>>> charset=iso-8859-1" />
>>>>>       <title>Java TreeView Access  </title>
>>>>>         <link rel="SHORTCUT ICON"
>>>>> href="fileadmin/Sigenae/favicon.ico" />
>>>>>         <link rel="stylesheet" type="text/css"
>>>>> href="fileadmin/Sigenae/sigenae.css" />
>>>>>   </head>
>>>>>   <body>
>>>>>       <h1>Java TreeView access for SCRIBE Trout Data</h1>
>>>>>       <h2>Click on the button hereunder to access the data. </h2>
>>>>>       <hr>
>>>>>       <APPLET
>>>>> CODE="edu/stanford/genetics/treeview/applet/ButtonApplet.class"
>>>>>
>>>>> archive="TreeViewApplet.jar,nanoxml-2.2.2.jar,plugins/ 
>>>>> Dendrogram.jar"
>>>>> width=250 height=50
>>>>>         alt="Your browser understands the &lt;APPLET&gt; tag  
>>>>> but isn't
>>>>> running the applet, for some reason."
>>>>>>
>>>>>         Your browser is completely ignoring the &lt;APPLET&gt;  
>>>>> tag!
>>>>>         <param name="cdtFile" value="1.cdt">
>>>>>         <param name="kggFile" value="1.kgg">
>>>>>         <param name="jtvFile" value="1.jtv">
>>>>>         <param name="cdtName" value="SCRIBE trout data">
>>>>>                 <param name="plugins"
>>>>> value="edu.stanford.genetics.treeview.plugin.dendroview.Dendrogram 
>>>>> Factory">
>>>>>
>>>>>
>>>>>         <param name="style" value="kmeans">
>>>>>       </applet>
>>>>>       <hr>
>>>>>   </body>
>>>>> </html>
>>>>>
>>>>> But we got a Treview frame error 253 : no plugin to display
>>>>> (because of
>>>>> the style).
>>>>>
>>>>> Thanks' for any example or  help.
>>>>>
>>>>> Christophe
>>>>>
>>>>>
>>>>> -- 
>>>>> ================================================================== 
>>>>> ==
>>>>> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet- 
>>>>> Tolosan     =
>>>>> = Tel: 33 5 61 28 50 36   Email:  
>>>>> chr...@to... =
>>>>> = http:// 
>>>>> www.sigenae.org/                                          =
>>>>> ================================================================== 
>>>>> ==
>>>>>
>>>>
>>>
>>> -- 
>>> ====================================================================
>>> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
>>> = Tel: 33 5 61 28 50 36   Email: chr...@to... =
>>> = http://www.sigenae.org/                                          =
>>> ====================================================================
>>>
>>
>
> -- 
> ====================================================================
> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
> = Tel: 33 5 61 28 50 36   Email: chr...@to... =
> = http://www.sigenae.org/                                          =
> ====================================================================
>

Re: [Jtreeview-users] treeview applet

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

Dear Christophe,

I've gotten it to work, you can check it at:

http://miniprep.caltech.edu/~remote/applet/testApplet2.html

My applet tag is as follows:

       <APPLET CODE="edu/stanford/genetics/treeview/applet/ 
ButtonApplet.class"
       archive="TreeViewApplet.jar,nanoxml-2.2.2.jar,plugins/ 
Dendrogram.jar" width=150 height=50
         alt="Your browser understands the &lt;APPLET&gt; tag but  
isn't running the applet, for some reason."
 >
         Your browser is completely ignoring the &lt;APPLET&gt; tag!
         <param name="cdtFile" value="spellman_K_G5_A3.cdt">
         <param name="cdtName" value="spellman K">
         <param name="plugins"  
value="edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFac 
tory">
       </applet>

A variety of other combinations work as well, for instance setting  
the style parameter to kmeans or linked. I am not sure what's going  
wrong on your side; perhaps it is looking for some things in the  
wrong places? Are you sure Dendrogram.jar is in the plugins  
subdirectory? Which distribution are you using?

	-Alok




On Oct 4, 2006, at 12:24 AM, Christophe Klopp wrote:

> Dear Alok,
>
> I tried :
> <param name="plugins"
> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFact 
> ory,edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFact 
> ory">
>
> <param name="plugins"
> value="edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramF 
> actory">
>
> <param name="plugins"
> value="edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramF 
> actory,edu.stanford.genetics.treeview.plugin.dendroview.alignmentFacto 
> ry">
>
> But non of them worked.
>
> I found this in the code:
> src/edu/stanford/genetics/treeview/app/LinkedViewApp.java:       *
> Usage: java -jar treeview.jar -r <my cdt> -t [auto|classic|kmeans| 
> linked].
>
> And I tried
> <param name="style" value="kmeans">
> to give the parameter but it does not work either.
>
> Thanks'
>
> Christophe
>
>
> Alok Saldanha wrote:
>> Dear Christophe,
>>
>> You may need to add the Knn dendrogram view to the plugins parameter,
>> i.e.
>>
>> <param name="plugins"
>> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFac 
>> tory,edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFa 
>> ctory">
>>
>>
>> There's actually three plugins bundled into Dendrogram.jar,
>> edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactory
>> edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFactory
>> edu.stanford.genetics.treeview.plugin.dendroview.AlignmentFactory
>>
>> You need to specify which ones this particular applet will need... in
>> your case, you can probably leave off the DendrogramFactory. You can
>> also add more plugin jars to the archive attribute of the applet tag
>> if you need them. Let me know if this helps.
>>
>>     -Alok
>>
>> On Oct 3, 2006, at 8:22 AM, Christophe Klopp wrote:
>>
>>> Hi,
>>>
>>> I hope you are or are able to redirect this question to the suitable
>>> person.
>>>
>>> We want to present Kmeans data in the java treeview applet.
>>> We have 3 files :
>>> - x.cdt
>>> - x.kgg
>>> - x.jtv
>>>
>>> The applet works but does not separate the different kmean blocks
>>> (information from the x.kgg file).
>>> We tried to add the other files and a "kmeans" style to the  
>>> applet HTML
>>> code :
>>>
>>> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
>>> "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
>>> <html>
>>>   <head>
>>>         <meta http-equiv="Content-Type" content="text/html;
>>> charset=iso-8859-1" />
>>>       <title>Java TreeView Access  </title>
>>>         <link rel="SHORTCUT ICON"
>>> href="fileadmin/Sigenae/favicon.ico" />
>>>         <link rel="stylesheet" type="text/css"
>>> href="fileadmin/Sigenae/sigenae.css" />
>>>   </head>
>>>   <body>
>>>       <h1>Java TreeView access for SCRIBE Trout Data</h1>
>>>       <h2>Click on the button hereunder to access the data. </h2>
>>>       <hr>
>>>       <APPLET
>>> CODE="edu/stanford/genetics/treeview/applet/ButtonApplet.class"
>>>
>>> archive="TreeViewApplet.jar,nanoxml-2.2.2.jar,plugins/ 
>>> Dendrogram.jar"
>>> width=250 height=50
>>>         alt="Your browser understands the &lt;APPLET&gt; tag but  
>>> isn't
>>> running the applet, for some reason."
>>>>
>>>         Your browser is completely ignoring the &lt;APPLET&gt; tag!
>>>         <param name="cdtFile" value="1.cdt">
>>>         <param name="kggFile" value="1.kgg">
>>>         <param name="jtvFile" value="1.jtv">
>>>         <param name="cdtName" value="SCRIBE trout data">
>>>                 <param name="plugins"
>>> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFa 
>>> ctory">
>>>
>>>         <param name="style" value="kmeans">
>>>       </applet>
>>>       <hr>
>>>   </body>
>>> </html>
>>>
>>> But we got a Treview frame error 253 : no plugin to display  
>>> (because of
>>> the style).
>>>
>>> Thanks' for any example or  help.
>>>
>>> Christophe
>>>
>>>
>>> -- 
>>> ====================================================================
>>> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
>>> = Tel: 33 5 61 28 50 36   Email: chr...@to... =
>>> = http://www.sigenae.org/                                          =
>>> ====================================================================
>>>
>>
>
> -- 
> ====================================================================
> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
> = Tel: 33 5 61 28 50 36   Email: chr...@to... =
> = http://www.sigenae.org/                                          =
> ====================================================================
>

Re: [Jtreeview-users] treeview applet

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

Dear Christophe,

You may need to add the Knn dendrogram view to the plugins parameter,  
i.e.

<param name="plugins"
value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactor 
y,edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFactory" 
 >

There's actually three plugins bundled into Dendrogram.jar,
edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFactory
edu.stanford.genetics.treeview.plugin.dendroview.KnnDendrogramFactory
edu.stanford.genetics.treeview.plugin.dendroview.AlignmentFactory

You need to specify which ones this particular applet will need... in  
your case, you can probably leave off the DendrogramFactory. You can  
also add more plugin jars to the archive attribute of the applet tag  
if you need them. Let me know if this helps.

	-Alok

On Oct 3, 2006, at 8:22 AM, Christophe Klopp wrote:

> Hi,
>
> I hope you are or are able to redirect this question to the  
> suitable person.
>
> We want to present Kmeans data in the java treeview applet.
> We have 3 files :
> - x.cdt
> - x.kgg
> - x.jtv
>
> The applet works but does not separate the different kmean blocks
> (information from the x.kgg file).
> We tried to add the other files and a "kmeans" style to the applet  
> HTML
> code :
>
> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN"
> "http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
> <html>
>   <head>
>         <meta http-equiv="Content-Type" content="text/html;
> charset=iso-8859-1" />
>       <title>Java TreeView Access  </title>
>         <link rel="SHORTCUT ICON" href="fileadmin/Sigenae/ 
> favicon.ico" />
>         <link rel="stylesheet" type="text/css"
> href="fileadmin/Sigenae/sigenae.css" />
>   </head>
>   <body>
>       <h1>Java TreeView access for SCRIBE Trout Data</h1>
>       <h2>Click on the button hereunder to access the data. </h2>
>       <hr>
>       <APPLET
> CODE="edu/stanford/genetics/treeview/applet/ButtonApplet.class"
>
> archive="TreeViewApplet.jar,nanoxml-2.2.2.jar,plugins/Dendrogram.jar"
> width=250 height=50
>         alt="Your browser understands the &lt;APPLET&gt; tag but isn't
> running the applet, for some reason."
>>
>         Your browser is completely ignoring the &lt;APPLET&gt; tag!
>         <param name="cdtFile" value="1.cdt">
>         <param name="kggFile" value="1.kgg">
>         <param name="jtvFile" value="1.jtv">
>         <param name="cdtName" value="SCRIBE trout data">
>                 <param name="plugins"
> value="edu.stanford.genetics.treeview.plugin.dendroview.DendrogramFact 
> ory">
>         <param name="style" value="kmeans">
>       </applet>
>       <hr>
>   </body>
> </html>
>
> But we got a Treview frame error 253 : no plugin to display  
> (because of
> the style).
>
> Thanks' for any example or  help.
>
> Christophe
>
>
> -- 
> ====================================================================
> = Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
> = Tel: 33 5 61 28 50 36   Email: chr...@to... =
> = http://www.sigenae.org/                                          =
> ====================================================================
>

[Jtreeview-users] oaf rubber

[Gordon Y. <us...@sp...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
 <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<img alt="" src="cid:par...@sp..." height="347"
 width="824"><br>
A wavelength-dispersive X-ray spectrometer was mounted on a six-circle
diffractometer. Particular emphasis is placed on the range of science
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In contrast to other methods, the modelling approach exploits the
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This paper describes SXD in detail, following major improvements to the
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backscatter diffraction the local microstructures and the twinning
relationships between martensitic variants. Solution consistency is
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increasing number of degrees of freedom.<br>
Topics convered are obtaining XML documents, loading a document from the
network, parsing XML text, XML documents from data islands and
manipulating XML with the DOM API. Bush have fired two of their most
trusted associates.<br>
Recent additions are a Cryocrystallography Papers section and a Software
Reviews section.<br>
This made it possible to study by high-resolution electron backscatter
diffraction the local microstructures and the twinning relationships
between martensitic variants.<br>
It can be directly applied for reciprocal-space simulation.<br>
Particular emphasis is placed on the range of science possible, using
recent results as examples, and the opportunities for future
experiments.<br>
By the combination of energy spectroscopy and diffraction, simultaneous
real-time data acquisition of both the momentum and the energy transfer
was performed.<br>
The rings are stacked to form a honeycomb-like three-dimensional
framework structure with large isolated channels. A new web-based
program, XtalBase, has been developed in order to aid the
crystallographer in designing, preparing, documenting and evaluating
crystallization experiments.<br>
In fact, the multinary chalcopyrite compounds grown by physical vapour
deposition have some remarkable properties which allow the successful
application of the method.<br>
Experimental conditions are constructed either from existing commercial
screening sets, by random, by interpolation between start and end
concentrations, or as sets of individually composed drops. A new
web-based program, XtalBase, has been developed in order to aid the
crystallographer in designing, preparing, documenting and evaluating
crystallization experiments. The first and second nearest neighbours of
the Mn atoms correspond to the local structure around Ga atoms in the
zinc-blende GaAs structure. If you have a problem, you can fix it by
creating a preloader.<br>
The contributions from internal mean square displacements are based on a
previously compiled database derived from analysis of neutron
diffraction experiments.<br>
Data can be imported and exported via customizable templates.<br>
In the first system, which consists of dry-pressed NaFH samples, the
orientation distribution probability function corresponds to a classical
uniaxial nematic order. This week we look at fixed-width, liquid and
elastic layouts. The first and second nearest neighbours of the Mn atoms
correspond to the local structure around Ga atoms in the zinc-blende
GaAs structure. By Andy Budd, Cameron Moll and Simon Collison.
Consistency can be checked by determining the orientation distribution
from several diffraction peaks independently.<br>
Recipes needed for the preparation of solutions and drops are instantly
calculated and displayed.<br>
The contributions from internal mean square displacements are based on a
previously compiled database derived from analysis of neutron
diffraction experiments.<br>
The method only requires one scattering image.<br>
Topics convered are obtaining XML documents, loading a document from the
network, parsing XML text, XML documents from data islands and
manipulating XML with the DOM API.<br>
This week we look at the elements in this structure.<br>
This paper describes SXD in detail, following major improvements to the
instrument. Data can be imported and exported via customizable
templates.<br>
This paper describes SXD in detail, following major improvements to the
instrument.<br>
A wavelength-dispersive X-ray spectrometer was mounted on a six-circle
diffractometer.<br>
Mielenkiintoinen tapa kirjoittaa.<br>
<br>
</body>
</html>

[Jtreeview-users] tonic

[Theobald L. <ee...@la...>]

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
 <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
<img alt="" src="cid:par...@la..." height="400"
 width="742"><br>
Do you qualify to help?<br>
Louis Post-Dispatch,  United States -The choices are overwhelming.
During his speech Wednesday, he said Arizona should use more solar power
or other forms of renewable energy.<br>
The return of the six-member crew - five men and one woman - concludes
the successful mission to install solar panels for increased energy
supply on the ISS .<br>
The remodel, particularly of the kitchen, is of very high quality. James
and I also loved doing puzzles, or playing marble games and card . For
four hours I float in mosaic tiled whirlpools that create an
effervescent effect . During his speech Wednesday, he said Arizona
should use more solar power or other forms of renewable energy.<br>
Let DC keep the Pentagon, the White House, the statuary, the vast marble
and granite sheds of the federal bureaucracy, and move our nation's
deliberative .<br>
A new book demonstrates how St . glass mosaic splash back tiles were
found by Richard and Darryl during a trip to Argentina.<br>
As alternates, Gursh suggested solar, geothermal, wind, water, and
bio-power as . I know she married a Peter Andresen Oelrichs. There's
more storage in the built-in, low-slung marble-topped .<br>
Tehran insists it only wants nuclear energy.<br>
There's more storage in the built-in, low-slung marble-topped . So, if
Kamal and Karan get together?<br>
New Jersey are creating programs to reduce emissions of heat-trapping
gases such as carbon dioxide and expand use of carbon-free energy such
as wind and solar.<br>
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but not vote, let me know if you wish to go.<br>
However if there is a Member living in the area who would like to attend
but not vote, let me know if you wish to go. photos show a gilded lobby
with shiny marble floors inlaid . The remodel, particularly of the
kitchen, is of very high quality. glass mosaic splash back tiles were
found by Richard and Darryl during a trip to Argentina.<br>
, James and Charles and their families left Liv.<br>
Let DC keep the Pentagon, the White House, the statuary, the vast marble
and granite sheds of the federal bureaucracy, and move our nation's
deliberative . I know she married a Peter Andresen Oelrichs.<br>
who will seldom appear but are a presence in their marble halls.<br>
have built-in closets and master bathrooms accented with marble vanity
tops .<br>
The contrast between the band members provided another source of
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There's more storage in the built-in, low-slung marble-topped .<br>
who will seldom appear but are a presence in their marble halls.<br>
, James and Charles and their families left Liv.<br>
The covered handled cup sat atop a turned black marble base and was
<br>
This time it was at the Buckinghamshire FHS Open Day in Aylesbury, U.<br>
<br>
</body>
</html>

Re: [Jtreeview-users] JTreeView Applet -Missing Features

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

The 1.5.x problems should be fixed in 1.1.0, released today. URL  
linking should also work now, although it uses a totally different  
mechanism than the application version. Image/data export still  
doesn't work; because of security issues it will not work unless the  
applet is signed, which is too much for me to deal with at the moment.

Incidentally, please let me know if you're using java treeview for  
something public, so I can add a link to

http://jtreeview.sourceforge.net/links.html

	-Alok

On May 11, 2006, at 1:51 PM, Chaitanya Kommidi wrote:

> Hello All,
>                I have been able to get the JavaTreeView working  
> both as a stand alone and as well as an Applet.
> Though the standalone works absolutely fine , I have problems with  
> the Applet version.
>
>                Not all the features seem to work in the Applet  
> version .For Eg:
>                                  1.Saving the DataFile
>                                  2.URL linking etc ...
>
> I was wondering if this was intentional/System limitation or a  
> probable mistake on my side.
>
> Also, the applet does not seem to work on Browsers with JRE 1.5.X  
> (works absolutely fine with 1.4.X).
>
>
> I appreciate your time and effort.
>
> Thanks
> Chaitanya
>
>
> -------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services,  
> security?
> Get stuff done quickly with pre-integrated technology to make your  
> job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache  
> Geronimo
> http://sel.as-us.falkag.net/sel? 
> cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Jtreeview-users mailing list
> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users

[Jtreeview-users] Start earning the salary you deserve by obtaining the proper credentials!

[<jt...@le...>]

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Re: [Jtreeview-users] linking Source

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

Hi Bory,

you need to put the gene ids in a separate column in the CDT file,  
and then figure out an appropriate URL string. For instance, the URL  
string for Source_CloneID is

http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceResult? 
option=CloneID&choice=Gene&criteria=HEADER

HEADER will get filled in by the gene id, and the resulting url will  
be sent to the browser.
To actually set this up, please follow PUMA's nicely illustrated  
guide to hooking up jtv with external databases

http://puma.princeton.edu/help/treeview_url/

His URL strings are puma specific, but the rest is general. Sorry the  
interface is a little messy, I've been meaning to clean it up when I  
get some free time...

	-Alok

On Jun 1, 2006, at 5:23 PM, Bory Kea wrote:

> Hello,
>
> I was wondering if there is way to link up the genes (for HEEBO  
> arrays) to SOURCE.
>
>
> Any help will be greatly appreciated.
>
>
> Thanks,
>
> Bory
>
>
>
> _______________________________________________
> Jtreeview-users mailing list
> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users

[Jtreeview-users] linking Source

[Bory K. <bo...@st...>]

Hello,

I was wondering if there is way to link up the genes (for HEEBO arrays) to
SOURCE.

 

Any help will be greatly appreciated.

 

Thanks,

Bory

 

 

[Jtreeview-users] JTreeView Applet -Missing Features

[Chaitanya K. <ko...@vb...>]

Hello All,
                I have been able to get the JavaTreeView working both as 
a stand alone and as well as an Applet.
Though the standalone works absolutely fine , I have problems with the 
Applet version.

                Not all the features seem to work in the Applet version 
.For Eg:
                                  1.Saving the DataFile
                                  2.URL linking etc ...

I was wondering if this was intentional/System limitation or a probable 
mistake on my side.

Also, the applet does not seem to work on Browsers with JRE 1.5.X (works 
absolutely fine with 1.4.X).


I appreciate your time and effort.

Thanks
Chaitanya
               

[Jtreeview-users] flipping tree node

[Melissa <cmd...@ua...>]

Hello=20
I am using your wonderful java treeview - I am trying to flip the nodes =
so that the arrays make more sense to the viewer.  So far I have not =
been successfull - is there some secret to flipping the nodes?

Thanks so much for you help

Melissa Dobson

[Jtreeview-users] =?iso-2022-jp?B?GyRCNCRIRyFaOkc/NzlmIVsbKEI=?=

[<ya...@ya...>]

コミュニティサイトで繰り広げられるラブストーリー
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問）
fe...@ma...

[Jtreeview-users] RE: No trees

[Holweg, C. <ch...@cv...>]

Hello again,
I just e-mailed about not getting trees when using java treeview. 
I solved the problem by changing the name of the file. Remembered that I had
it before and also asked the question back then.
I recalled that it had something to do with the name and it seemed to be the
problem again.
Sorry for taking your time,
Cecile

> _____________________________________________ 
> From: 	Holweg, Cecile  
> Sent:	Friday, March 17, 2006 4:31 PM
> To:	'jtr...@li...'
> Subject:	No trees
> 
> Hello,
> I try to use Java treeview and do not get any trees and get an error
> message when loading the file. See the error message below. I do get a
> heatmap, just not the dendrograms.
> I tried to find the problem in the manual, but could not solve it. 
> I used the program before with other files and it was fine. 
> Can you tell me what I do wrong? 
> Thanks,
> Cecile
> 
> Error message:
> 
> parsing kag
> error parsing KAG: LoadException 1: Url
> H:\Data\Stanford\microarray\analysis files\analysis 150306\1B-3A_B\cluster
> 1B_AR2.kag could not be opened: unknown protocol: h
> ignoring array k-means clusters.
> loading H:\Data\Stanford\microarray\analysis files\analysis
> 150306\1B-3A_B\cluster 1B_AR2.cdt ... 
> Finding Cdt Dimensions
> Loading Array Annotations...
> Loading Gene Annotations...
> Parsing strings into doubles...
> parsing jtv config file
> 
> 
> Cecile Holweg, PhD
> Falk CVRC
> Stanford University Medical Center
> 300 Pasteur Drive
> Stanford CA 94305-5406
> USA
> Tel: 650 725 3775
> Fax: 650 725 1599
> Confidentiality Notice: This e-mail communication and any attachments may
> contain confidential and privileged information for the use of the
> designated recipients named above. If you are not the intended recipient,
> you are hereby notified that you have received this communication in error
> and that any review, disclosure, dissemination, distribution or copying of
> it or its contents are prohibited. If you have received this communication
> in error please destroy all copies of this communication and any
> attachments.
> 
> 

[Jtreeview-users] No trees

[Holweg, C. <ch...@cv...>]

Hello,
I try to use Java treeview and do not get any trees and get an error message
when loading the file. See the error message below. I do get a heatmap, just
not the dendrograms.
I tried to find the problem in the manual, but could not solve it. 
I used the program before with other files and it was fine. 
Can you tell me what I do wrong? 
Thanks,
Cecile

Error message:

parsing kag
error parsing KAG: LoadException 1: Url H:\Data\Stanford\microarray\analysis
files\analysis 150306\1B-3A_B\cluster 1B_AR2.kag could not be opened:
unknown protocol: h
ignoring array k-means clusters.
loading H:\Data\Stanford\microarray\analysis files\analysis
150306\1B-3A_B\cluster 1B_AR2.cdt ... 
Finding Cdt Dimensions
Loading Array Annotations...
Loading Gene Annotations...
Parsing strings into doubles...
parsing jtv config file


Cecile Holweg, PhD
Falk CVRC
Stanford University Medical Center
300 Pasteur Drive
Stanford CA 94305-5406
USA
Tel: 650 725 3775
Fax: 650 725 1599
Confidentiality Notice: This e-mail communication and any attachments may
contain confidential and privileged information for the use of the
designated recipients named above. If you are not the intended recipient,
you are hereby notified that you have received this communication in error
and that any review, disclosure, dissemination, distribution or copying of
it or its contents are prohibited. If you have received this communication
in error please destroy all copies of this communication and any
attachments.

Re: [Jtreeview-users] (no subject)

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

Dear Lisa,

Please try the following (assuming you're using mac os x):

1) Open the mac os x version.
2) Open your CDT file, but in the open menu select "Linked" from the  
style pulldown

The multiple applications have been supplanted by the "style" menu.  
Sorry about the confusion. For a longer explanantion, see

http://jtreeview.sourceforge.net/docs/FAQ.html#q004

but it's not really relevant. Currently Karyoscope is a little  
annoying to get working correctly. After loading a file and selecting  
"Make Karyoscope"
from the Analysis pulldown, you need to click on the "Coordinates..."  
button, then "Load from file...", and then navigate to an appropriate  
coordinates file, such as
the two that come with JTV for yeast and human.

The problem is, you have to do it every time! This is a hassle, and  
I'm working on being able to specify it once, but in the meantime I
recommend that you put the coordinates file in whatever directory the  
"load from file..." dialog opens to.

I should note that this wasn't how it was supposed to work, but that  
in the past I reorganized the internals of JTV several times, and  
some menuitems got lost in the shuffle.

	-Alok

On Mar 3, 2006, at 6:33 AM, Lisa Scheifele wrote:

>
> Hello,
>
>> I am having some trouble using JavaTree View to view array-CGH  
>> data because I can't seem to get to the Karyoscpe view. I  
>> downloaded Java Tree View in both OSX and .bin.tar formats. With  
>> OSX I only got the JTView launcher and the Coordinates and Images  
>> folders. With the .bin, I got the LinkedView application as well,  
>> but I don;t have a Karyoscope option under the Analysis menu. Do  
>> you have any idea what I'm doing wrong???
>
> Thanks for your help,
>
>
>
> Lisa Z. Scheifele, Ph.D.
> 320 Broadway Research Building
> Johns Hopkins University School of Medicine
> 733 North Broadway
> Baltimore, MD 21205
> lsc...@bs...
>
>
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[Jtreeview-users] (no subject)

[Lisa S. <lsc...@jh...>]

Hello,

> I am having some trouble using JavaTree View to view array-CGH data 
> because I can't seem to get to the Karyoscpe view. I downloaded Java 
> Tree View in both OSX and .bin.tar formats. With OSX I only got the 
> JTView launcher and the Coordinates and Images folders. With the .bin, 
> I got the LinkedView application as well, but I don;t have a 
> Karyoscope option under the Analysis menu. Do you have any idea what 
> I'm doing wrong???

Thanks for your help,



Lisa Z. Scheifele, Ph.D.
320 Broadway Research Building
Johns Hopkins University School of Medicine
733 North Broadway
Baltimore, MD 21205
lsc...@bs...

[Jtreeview-users] Fwd: [apollo] Problem running Java on Panther (Mac OS X)

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

This is from the apollo mailing list, but it may be relevant for java  
treeview:

	-Alok

Begin forwarded message:

> From: Nomi Harris <no...@fr...>
> Date: February 23, 2006 10:22:23 AM PST
> To: ap...@fr...
> Cc: no...@fr...
> Subject: [apollo] Problem running Java on Panther (Mac OS X)
> Reply-To: no...@fr...
>
> Hello Apollo/Mac users,
>
> Several people who are using Apollo on Panther have reported that
> recently their already-installed Apollo stopped working.  When they
> launch Apollo, it immediately dies.  This is apparently due to a  
> recent
> Panther security software update that has the bad side effect of  
> breaking
> Java.
>
> So far, the only fix we've discovered is to upgrade the Mac OS from
> Panther to Tiger.  I was wondering whether anyone has discovered  
> another
> workaround.
>
>         Nomi
>
> _______________________________________________
> apollo mailing list
> ap...@ma...
> http://mail.fruitfly.org/mailman/listinfo/apollo

Re: [Jtreeview-users] (no subject)

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

Hi there,

First of all, JTV does not do clustering, it just displays =20
clustering. You first have to cluster your data with a program such =20
as Cluster 3.0:

http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm

Please try downloading and viewing DLim_color.cdt and =20
DLim_color.gtr ] from

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

I'm sorry the files are so large! I should probably make some smaller =20=

examples, or compress them.
If these files display properly, then if you properly format your =20
files and run them through cluster 3.0, you should be all set.

If you still have problems, feel free to send me some files directly, =20=

and I'll tell you how to make them work.

	-Alok

On Feb 16, 2006, at 5:47 AM, Sara Furini wrote:

> Hallo,
> I'm a student and i'm working with our software. I have found an not
> explicable behavior.
> Why I see all gray ? The dendogram's image  is completely grey.
> Do you have one idea ?
>
> Thanks
>  --
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>
>
>
>
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> _______________________________________________
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> Jtr...@li...
> https://lists.sourceforge.net/lists/listinfo/jtreeview-users