jtreeview-devel — List for developers, to coordinate coding

Re: [Jtreeview-devel] Signed applets anyone?

[vkj <ve...@gm...>]

Hi Alok,

Thanks again for your attention!

> I have not tried signing the applet. Does the unsigned version crash
> the browser, or just the signed one? Which browser with which JVM?

Only the signed version crashes the browser. Unsigned version works
perfectly. I have tested this on the following combinations:

1. IE6 on WinXP, JDK 1.5

2. Firefox 2.0.5 on opensuse linux, JDK 1.5 as well as 1.6

3. Mozilla on solaris, JDK 1.5.

4. Seamonkey on opensuse linux, JDK 1.5.

Applet launches fine and behaves perfectly until I close it. At that
point it closes the browser from which it was launched. Xterm from
which I launch browser shows the following message after browser
closes:

<start>
INTERNAL ERROR on Browser End: Plugin instance index out of bounds -17409

System error?:: Success
<end>

Numeric value in the end of first statement varies across occurrences.
It is not the process ID of either the browser process of java_vm
process.

Occasionally I also get a slightly different error:
<start>
 INTERNAL ERROR on Browser End: Pipe closed during read? State may be corrupt
System error?:: Resource temporarily unavailable
<end>

Few more details:
---
I am creating a new dialog box which causes a browser window to open.
This not possible in unsigned applets because of applet sandbox
security model. Hence I am creating a signed applet.

I first noticed the error I mentioned in this modified JTreeView. Then
I went back and signed the original applet and that too had the same
behavior. To be sure, I created a "Hello World" applet and signed it.
This does not crash the browser.

I have googled for this error message but nothing relevant is
available. Sun has fixed a bug related to this error message
("http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4935740"). That
was in Oct 2003: I am sure it must have gone into JDK distributions
(at least in 1.6), though I must admit that the information on that
bug report is teasingly similar to the error message I get.

At this point I am clueless and any pointers will be deeply
appreciated. The next step for me would be to try to attach a debugger
to the running jvm. I was hoping to learn from others' experience if
possible.

Vineet

Re: [Jtreeview-devel] Signed applets anyone?

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

I have not tried signing the applet. Does the unsigned version crash  
the browser, or just the signed one? Which browser with which JVM?

On Jan 23, 2008, at 9:16 PM, vineet joshi wrote:

> Hello,
>
> Has anyone tried to signing this applet before serving on the web? I
> need to sign this applet for a very different reason. When the user
> launches this signed applet and then closes it, the applet crashes the
> browser.
>
> I was wondering if someone has any experience with this.
>
> Vineet
>
> ---------------------------------------------------------------------- 
> ---
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[Jtreeview-devel] Signed applets anyone?

[vineet j. <ve...@gm...>]

Hello,

Has anyone tried to signing this applet before serving on the web? I
need to sign this applet for a very different reason. When the user
launches this signed applet and then closes it, the applet crashes the
browser.

I was wondering if someone has any experience with this.

Vineet

Re: [Jtreeview-devel] What is the best way to add more functions/panels?

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

Hi Xiaoqing,

First, let me say that I don't really understand what you want to do-=20
it is hard to get a sense for it over email. In general, I recommend=20
that you write a new "View". There are already several views, such as=20
dendroview, karyoview, scatterview, and treeanno. Each view is defined=20=

in it's own package. The main class for each view implements MainPanel,=20=

i.e.

Dendroview: edu.stanford.genetics.treeview.dendroview.Dendroview.java
Karyoview: edu.stanford.genetics.treeview.karyoview.KaryoPanel.java
Scatterview:=20
edu.stanford.genetics.treeview.scatterview.ScatterPanel.java
Tree Annotation:=20
edu.stanford.genetics.treeview.treeanno.TreeAnnoPanel.java


I recommend that you define a new view in a new package. The package=20
need not begin with edu.stanford.genetics.treeview, but the main class=20=

of your view must implement MainPanel. Since your view is likely very=20
similar to the dendroview, you can either copy over the classes into=20
your package, or just reference the relevant parts. If you find that=20
you must modify something, just copy the code over.
I recommend that you add new annotation columns or rows in the CDT file=20=

with special column/row names that only your View uses, and that you=20
put all specific data for your view in those columns or rows. This will=20=

ensure that the standard DataModel can load your data and make it=20
available to your View.

Once you have defined your main class, you just need to add an option=20
for it to edu.stanford.genetics.treeview.LinkedPanel. It should be=20
straightforward, as there are only a few parts of LinkedPanel that=20
depend upon knowing what views exist. After you have done this, you can=20=

open up your custom view using "Analysis->Your view". Alternatively,=20
you can make your view the one that is loaded by default by=20
LinkedPanel, by editing the setupRunning method or one of the functions=20=

it calls.

I am sorry that this is so complicated. By the end of the year, I hope=20=

to transition to a plugin-style architecture. In the new architecture,=20=

Java Treeview will be split into a small kernel and a variety of=20
plugins, one plugin for each View. Each plugin will be distributed as a=20=

separate jar file, and Java Treeview will load all the plugins at=20
startup. The user will be able to change the plugin that is used by=20
default, so they won't have to continually select "Analysis->Your=20
View".  Once that transition is complete, you will be able to make your=20=

View available as a jar file plugin that people can download and use=20
with the standard Treeview distribution simply by copying it to the=20
"plugins" folder. The user will also be able to delete the jar files=20
for plugins that they seldom use. Until then, I recommend that you=20
maintain a separate source tree for your organization, and distribute=20
your modified version to whoever needs it.

I am willing to consider adding your functionality to the main=20
Dendroview component. However, I would prefer that you implement it=20
first, with maximum freedom to add the features you want, and then=20
later on we can consider whether to add it to Dendroview or keep it as=20=

a separate plugin.

I hope that this is enough to get you started.

	-Alok

On Mar 15, 2005, at 2:30 PM, Xiaoqing Zhang wrote:

> Hi Alok,
>
> =A0
>
> This is Xiaoqing Zhang from Columbia University. I am a Java=20
> programmer and work for Dr. Christina Leslie. We want to add some=20
> functions in the JTV. The idea is after it opens a .cpt file, we hope=20=

> JVT can load some additional files which contain upstream regulatory=20=

> motif of each probe or such information can be included in the .cpt=20
> file too. An additional Gene Panel will be created. =A0Then when the=20=

> mouse moves over some probes, in the gene panel, it will display a=20
> line with colored motif in it for each selected gene. =A0I did not see=20=

> any similar thing in the current JTV. I just wonder whether you can=20
> give me some suggestions about how to do it. I know I may change the=20=

> GUI of your JTV and I do not want to disrupt more things than=20
> absolutely necessary.
>
> =A0
>
> =A0
>
> Thanks a lot for your attention.
>
> =A0
>
> =A0
>
> =A0
>
> =A0
>
> Xiaoqing

[Jtreeview-devel] What is the best way to add more functions/panels?

[Xiaoqing Z. <xia...@cg...>]

Hi Alok,

=20

This is Xiaoqing Zhang from Columbia University. I am a Java programmer =
and
work for Dr. Christina Leslie. We want to add some functions in the JTV. =
The
idea is after it opens a .cpt file, we hope JVT can load some additional
files which contain upstream regulatory motif of each probe or such
information can be included in the .cpt file too. An additional Gene =
Panel
will be created.  Then when the mouse moves over some probes, in the =
gene
panel, it will display a line with colored motif in it for each selected
gene.  I did not see any similar thing in the current JTV. I just wonder
whether you can give me some suggestions about how to do it. I know I =
may
change the GUI of your JTV and I do not want to disrupt more things than
absolutely necessary.

=20

=20

Thanks a lot for your attention.

=20

=20

=20

=20

Xiaoqing

[Jtreeview-devel] The Future of Java Treeview development

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

Hello all,

I thank you all for your contributions, and I think Java Treeview is a 
useful piece of software with a bright future because of them. However, 
as java treeview becomes more mature, you are using it in very 
different ways. There seems to be increasing opportunity for changes to 
conflict. Imposing some order to minimize conflicts is the purpose of 
this email.

In particular,

1) I would like to put everyone that this email is addressed to on the 
jtreeview-devel list (except those already on it) and keep most of the 
development talk on that list so that you can keep abreast  of changes 
that may impact you. I realize that we all get way too much email 
already, but you can always delete them when they are irrelevant. also, 
it will all be archived. I would like to be clear that unless I hear 
otherwise, I plan to sign you up for this list.

2) I think we should try to come up with a fairly comprehensive set of 
test cases. This can simply be driven by things that go wrong, and 
slowly accrete as time goes by. Here's what I currently do before each 
build:

- ensure that all examples from the website load and display all views 
properly
- ensure that the applet version loads and displays files properly
- ensure that k-means files load properly.
- try doing a find, and then generating a summary view.

I don't want to drag anyone's feet over the coals, but the above was 
sufficient to catch notable bugs in code that was submitted to me. For 
instance, the TextView was redone so that each column of annotations 
gets its own frame and scrollbar  by adding a TextViewManager, which is 
a subclass of ModelView. Unfortunately, TextViewManager that didn't not 
propagate setViewFrame() to all the TextViews it manages, and so was a 
badly flawed implementation of ModelView that led to some weird 
behavior in the test suite. As a second example, when the file loading 
was redone to reduce memory load,  a row count bug was introduced that 
caused off-by-one errors in the display of certain, but not all files.

It's impossible to read through 1000 lines of code and find these bugs, 
we need a good, hopefully automated, test suite. The current test suite 
is far from comprehensive (for instance, I don't test export at all), 
so you may want to think of some new tests to add that are specific to 
functionality that is important to you. I had to do all above testing 
by hand, which is really tedious, and will get even more so as more 
tests are added. We should probably try to find ways to automate 
testing. Anyone do this before? Is JUnit any good? Automated test 
suggestions accompanied by code would be ideal. In the meantime, I will 
just put together a web page of tests that we can run, most likely, 
we'll just run tests by hand that seem relevant to the subsection we 
messed with until we get automated testing worked out.

I'm going to close with some of the ideas I have for upcoming 
development.

	Take care,
	Alok

Alok's Plans:

Things to add in next few months:

	karyoscope: add postscript output						karyoscope: change "pixel per 
value" to y-zoom, add zoom in, out buttcons	karyoscope: change "pixel 
per map" to x-zoom, add zoom in, out buttcons	karyoscope: add overlay  
of multiple graphs in karyoscope	scatterplot: add postscript 
output						registration: add check to see that global xml config can 
be parsed/written, warn user if there is problem.	dendrogram: make sure 
that "compare with..." works
	dendrogram: document node-flipping and compare with... 
functionality	url linking: add note about escaping chars in windows 
URLs (Davin Townley-Tilson)	RAM: switch data model to floats instead of 
doubles to save RAM.	RAM: remove all refs to (String []) 
RectData.elementAt(i), use getString() instead.	general: change to MIT 
Open Source License				general: add check in makeTars that checks 
version in build.xml and TreeViewApp.	website: make web page with links 
to projects that use java treeview (GMOD, TAIR)	website: add k-means 
example to examples page			website: read over documentation to ensure 
that it is consistent with current application	

Bugs to fix in next few months:

	dendrogram: resolve node-flipping inconsistency
	dendrogram: fix selection triggered by opening "Find..." when no genes 
selected
	dendrogram: find doesn't always let you pop up summary.
	karyoscope: fix bug in export - yeast chr 16
	knnview: rename to kmeansview. Eclipse makes it easy!
	javadoc: during html generation, there are many (well, 73) warnings 
which should be looked at.

Things to do later:

	plugin architecture. make all views plugins, even dendrogram.
	add plugin for the SGT (http://www.epic.noaa.gov/java/sgt/index.html)
	use the SGT to allow arbitrary plots on karyoscope
	plugin for fuzzy clustering display
	implement GEO cluster browser helper application
	redo "knn" (actually k-means) so it uses normal tvmodel, dendroview, 
add group-by feature to dendroview
	try out new version of Your Kit Java Memory Profiler on JTV to find 
RAM leaks.

[Jtreeview-devel] JTV 1.0.9 released!

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

It's been a while, but there's a new version of java treeview. Main 
features:

- less memory consumption. ~50% of RAM for the same size files
- more stability. A lot of weirdness went away when I cleaned up the 
code to gear up for "The Future"
- optional registration.

As some of you know, we have submitted a grant, and it would be helpful 
to have some statistics on users. Click "No" if for any reason you 
don't want to register, and you should not be bothered until you 
download a new version. There's also a new Help->Registration... menu 
item where you can go and register if you change your mind. Or even 
register multiple times, but please don't do that, as it may confuse us 
and cause the reviewers to become suspicious.

For those who are curious, I will present here a rough, non-binding 
sketch of what might happen in the future. Please feel free to suggest 
any changes or additions, although I can't guarantee high priority.

Things to add in next few months:

	karyoscope: add postscript output						karyoscope: change "pixel per 
value" to y-zoom, add zoom in, out buttcons	karyoscope: change "pixel 
per map" to x-zoom, add zoom in, out buttcons	karyoscope: add overlay  
of multiple graphs in karyoscope	scatterplot: add postscript 
output						registration: add check to see that global xml config can 
be parsed/written, warn user if there is problem.	dendrogram: make sure 
that "compare with..." works
	dendrogram: document node-flipping and compare with... 
functionality	url linking: add note about escaping chars in windows 
URLs (Davin Townley-Tilson)	RAM: switch data model to floats instead of 
doubles to save RAM.	RAM: remove all refs to (String []) 
RectData.elementAt(i), use getString() instead.	general: change to MIT 
Open Source License				general: add check in makeTars that checks 
version in build.xml and TreeViewApp.	website: make web page with links 
to projects that use java treeview (GMOD, TAIR)	website: add k-means 
example to examples page			website: read over documentation to ensure 
that it is consistent with current application	

Bugs to fix in next few months:

	dendrogram: resolve node-flipping inconsistency
	dendrogram: fix selection triggered by opening "Find..." when no genes 
selected
	dendrogram: find doesn't always let you pop up summary.
	karyoscope: fix bug in export - yeast chr 16
	knnview: rename to kmeansview. Eclipse makes it easy!
	javadoc: during html generation, there are many (well, 73) warnings 
which should be looked at.

Things to do later:

	plugin architecture. make all views plugins, even dendrogram.
	add plugin for the SGT (http://www.epic.noaa.gov/java/sgt/index.html)
	use the SGT to allow arbitrary plots on karyoscope
	plugin for fuzzy clustering display
	implement GEO cluster browser helper application
	redo "knn" (actually k-means) so it uses normal tvmodel, dendroview, 
add group-by feature to dendroview
	try out new version of Your Kit Java Memory Profiler on JTV to find 
RAM leaks.

[Jtreeview-devel] Fwd: Mail delivery failed: returning message to sender

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

Dear Bogdan,

The PCL format is used as the input to Gavin Sherlock's cluster,
described at
http://genetics.stanford.edu/~sherlock/cluster.html#formats . There is
also some discussion of the PCL format at
http://jtreeview.sourceforge.net/docs/JTVUserManual/ch02s11.html which
should help you figure out what your PCL file's contents mean.

With Java Treeview one can load a PCL file and then export the
resulting image to postscript. This can then be converted to PDF with
Adobe Illustrator or a similar tool. If you are interested in coding
direct pdf export, I recommend that you write a PdfExportPanel class
based on either the
edu.stanford.genetics.treeview.dendroview.BitmapExportPanel or
edu.stanford.genetics.treeview.dendroview.PostscriptExportPanel. I
recommend that you start by reading over the text of
BitmapExportPanel.save() and PostscriptExportPanel.save(), as this is
the method you would need to modify in order to make a PdfExportPanel.
Note that the BitmapExportPanel delegates all drawing to standard Java
Treeview components using "drawAll(g, 1.0);" wherease the
PostscriptExportPanel has to output actual postscript for each part of
the image. That's why the BitmapExportPanel has 154 lines whereas the
PostscriptExportPanel has 452.

If you really want to do all the rendering yourself, you can borrow
edu.stanford.genetics.treeview.model.FlatFileParser and interpret the
pcl yourself. Slightly less work would be to use the
edu.stanford.genetics.treeview.model.TVModelLoader class to load the
pcl into a TVModel object, and then render from that. But if you ask
me, it's much easier to write a subclass of ExportPanel as described
above.

How are you going to do PDF export in java? I wanted to add PDF export
to java treeview back in the day, but I couldn't find a high-quality
PDF writer.

	-Alok

On Sep 13, 2004, at 9:02 AM, BOGDAN wrote:

> Message body follows:
>
> Hello!
> I wanted to ask you about small consultation.
> In my education Ive a task of converting a pcl file  into pdf.
> Its necessary to write  on JAVA.
> I could not find the precise description of structure of a file pcl
> and system of commands pcl.
> But Ive found your project in which you parse pcl file
> (pcl-analysis
> and TreeView).
> Could you  help me: whether you know any references to the
> documentation about pcl file format, or ready pcl file parsers?
>
>
>
> -- 
> Best regards
>  Bogdan                          mailto:bn...@ya...
>
> --
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