jtreeview-users Mailing List for Java Treeview (Page 5)
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From: Sara F. <sf...@em...> - 2006-02-16 13:47:45
|
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=20 -- Email.it, the professional e-mail, gratis per te: http://www.email.it/f =20 Sponsor: DVD vergini: acquista online a prezzi vantaggiosi! Clicca qui: http://adv.email.it/cgi-bin/foclick.cgi?mid=3D4589&d=3D20060= 216 |
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From: Michel M. <mic...@gm...> - 2006-02-12 00:15:31
|
Java TreeView not run correctly on Debian Alpha, at least not with sablevm or kaffe. In SableVM, of all best, trying to visualize a tree, happen programs exit. Thanks |
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From: Alok S. <al...@ca...> - 2006-01-24 17:56:40
|
try setting the contrast, under Settings->Pixel Settings... The contrast is the value at which the colors saturate. The default contrast is 3 (8 fold on a log2 scale). If you data has small values, then it will appear black. Let me know if this doesn't help. -Alok On Jan 24, 2006, at 9:17 AM, Holly K Dressman wrote: > > I have used Cluster program to generate CDT file and then loaded > this into > the javatreeview, but see no color, figure is all black. What do I > need to > do to get some color? > > Thanks for your help, > Holly > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through > log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD > SPLUNK! > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users |
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From: Holly K D. <dre...@mc...> - 2006-01-24 17:15:27
|
I have used Cluster program to generate CDT file and then loaded this into the javatreeview, but see no color, figure is all black. What do I need to do to get some color? Thanks for your help, Holly |
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From: Jin M. <ha...@ya...> - 2005-12-19 08:43:05
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Hi! I followed your suggestion and solved the problem. Thanks! and Happy Christmas! __________________________________________________ 赶快注册雅虎超大容量免费邮箱? http://cn.mail.yahoo.com |
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From: Alok S. <al...@ca...> - 2005-12-19 08:27:16
|
JTV doesn't know how to use proxies. Have you tried clicking on "No" =20 or "Cancel" when the registration pops up? I appreciate your desire to register, but skip it if it's giving you =20 problems. Also, try > java -Xmx400m -jar TreeViewLauncher.jar The Xmx argument tell java how much RAM it can use, you need to =20 adjust it so the number is not bigger than your physical RAM. here, 400m means 400 megabytes, which should leave 80 MB for windows. -Alok On Dec 18, 2005, at 11:33 PM, Jin Miao wrote: > Dear Sir or Madam: > My Treeview 1.0.12 has some problem with registration > and 'allocating RAM'. Because I have to use proxy > server to access to website abroad, I think TreeView > might have some problem with proxy server. The 'out of > memory' problem seems dependent on registration, > everytime I run 'java -Xmx800m -jar > TreeViewLauncher.jar' as the trouble shooting > suggested, the registration window pop-up. (I use Win > XP professional sp2. 480 M RAM) > Please reply at your earliest convenience. > > regards > > Miao Jin > 191205 > > __________________________________________________ > =E8=B5=B6=E5=BF=AB=E6=B3=A8=E5=86=8C=E9=9B=85=E8=99=8E=E8=B6=85=E5=A4=A7= =E5=AE=B9=E9=87=8F=E5=85=8D=E8=B4=B9=E9=82=AE=E7=AE=B1? > http://cn.mail.yahoo.com > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through =20 > log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD =20 > SPLUNK! > http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users |
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From: Jin M. <ha...@ya...> - 2005-12-19 08:00:51
|
Dear Sir or Madam: My Treeview 1.0.12 has some problem with registration and 'allocating RAM'. Because I have to use proxy server to access to website abroad, I think TreeView might have some problem with proxy server. The 'out of memory' problem seems dependent on registration, everytime I run 'java -Xmx800m -jar TreeViewLauncher.jar' as the trouble shooting suggested, the registration window pop-up. (I use Win XP professional sp2. 480 M RAM) Please reply at your earliest convenience. regards Miao Jin 191205 __________________________________________________ 赶快注册雅虎超大容量免费邮箱? http://cn.mail.yahoo.com |
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From: Alok S. <al...@ca...> - 2005-11-16 18:37:21
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This is a heads up, in case anyone's been having trouble with JTV on
OSX 10.4.3 after upgrading. Apparently, upgrading java too can help.
-Alok
Begin forwarded message:
> From: Gavin Sherlock <she...@ge...>
> Date: November 16, 2005 10:10:43 AM PST
> To: Alok Saldanha <al...@ca...>
> Subject: Re: JavaTreeView problem
>
>
> Hey Alok,
>
> Just to let you know that after upgrading my Java on Tiger this
> morning, that JavaTreeview works again - yay!
>
> Cheers,
> Gavin
>
> On Nov 3, 2005, at 12:58 PM, Gavin Sherlock wrote:
>
>
>> Hi Alok,
>>
>> I just today that I can no longer launch JavaTreeView on OSX since
>> I upgraded to 10.4.3 the other day. The crash log (attached) has
>> in part the following:
>>
>> Thread 1 Crashed:
>> 0 libjvm.dylib 0x965cd428
>> JNI_GetCreatedJavaVMs_Impl + 146676
>> 1 libjvm.dylib 0x9646fdc0 jio_snprintf +
>> 165976
>> 2 libjvm.dylib 0x96479600 jio_snprintf +
>> 204952
>> 3 libjvm.dylib 0x96479194 jio_snprintf +
>> 203820
>> 4 libjvm.dylib 0x96470088 jio_snprintf +
>> 166688
>> 5 libjvm.dylib 0x9646f248 jio_snprintf +
>> 163040
>> 6 libjvm.dylib 0x9646edc4 jio_snprintf +
>> 161884
>> 7 libjvm.dylib 0x9646eb48 jio_snprintf +
>> 161248
>> 8 libjvm.dylib 0x9646e1a0 jio_snprintf +
>> 158776
>> 9 libjvm.dylib 0x9646e13c jio_snprintf +
>> 158676
>> 10 libjvm.dylib 0x96464754 jio_snprintf +
>> 119276
>> 11 libjvm.dylib 0x9646428c jio_snprintf +
>> 118052
>> 12 libjvm.dylib 0x9643df18 operator new
>> (unsigned long) + 8072
>> 13 libjvm.dylib 0x9643623c
>> JNI_CreateJavaVM_Impl + 1584
>> 14 libjvm.dylib 0x96435cc0
>> JNI_CreateJavaVM_Impl + 180
>> 15 ...ple.JavaApplicationLauncher 0x94fe3874
>> startJavaApplication + 336
>> 16 ...ple.JavaApplicationLauncher 0x94fe36ec java_main_stub
>> (void*) + 16
>> 17 libSystem.B.dylib 0x9002b200 _pthread_body + 96
>>
>> I don't know if you have the same problem, or any inclination to
>> take a look at it, but I thought I'd let you know in case there's
>> a chance you may be able to put together a fix. I also filed a
>> bug with Apple, in case it's their problem,
>>
>> Cheers,
>> Gavin
>>
>> <JavaApplicationStub.crash.log>
>>
>
>
|
|
From: Alok S. <al...@ca...> - 2005-11-09 23:06:43
|
The problem is the _A in the file name. For reasons that are not worth
going into right now, this causes Java Treeview to treat the file as
a k-means
clustered file instead of a hierarchical clustered file. This behavior
will hopefully go away later.
There are two solutions to this problem right now:
1) When you open the file, select "Linked" or "Classic" in the style
pulldown of the "Open.." dialog. You may not have noticed it, but it's
there.
Also, treeview will remember what you picked if you select it from the
recent files list.
2) Don't use "_G" or "_A" in your file names.
-Alok
On Nov 9, 2005, at 2:25 PM, Holweg, Cecile wrote:
> Dear Sir, Madam,
> I tried to visualize a cluster in Java Treeview and get the error
> message copied below. I did the clustering with the Eisen cluster
> program. I used this before with other datasets and had no problems
> to visualize it in Java Treeview. The file I used now to cluster my
> data is similar in format, but gives the error massage when I load
> the file. When I do dismiss, I do get the heatmap, but the trees
> are not there.
>
> Can you tell me what goes wrong? I tried to find it in the manual
> but was unable to find it.
> Thank you,
> Cecile
>
>
> parsing kag
> error parsing KAG: LoadException 1: Url H:\Data\Stanford\microarray
> \analysis files\analysis 102605\median clustering genes\cluster
> common genes 0_1B_AR.kag could not be opened: unknown protocol: h
>
> ignoring array k-means clusters.
> loading H:\Data\Stanford\microarray\analysis files\analysis 102605
> \median clustering genes\cluster common genes 0_1B_AR.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.
>
>
|
|
From: Holweg, C. <ch...@cv...> - 2005-11-09 22:26:03
|
Dear Sir, Madam, I tried to visualize a cluster in Java Treeview and get the error message copied below. I did the clustering with the Eisen cluster program. I used this before with other datasets and had no problems to visualize it in Java Treeview. The file I used now to cluster my data is similar in format, but gives the error massage when I load the file. When I do dismiss, I do get the heatmap, but the trees are not there. Can you tell me what goes wrong? I tried to find it in the manual but was unable to find it. Thank you, Cecile parsing kag error parsing KAG: LoadException 1: Url H:\Data\Stanford\microarray\analysis files\analysis 102605\median clustering genes\cluster common genes 0_1B_AR.kag could not be opened: unknown protocol: h ignoring array k-means clusters. loading H:\Data\Stanford\microarray\analysis files\analysis 102605\median clustering genes\cluster common genes 0_1B_AR.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. |
|
From: suryadevara v. <sur...@ya...> - 2005-10-28 18:47:53
|
Hi There, I am using java treeview to visualise the clustered data of my protein experiments. I would like to know is there a way if I want to color a perticular mutation with a different color intensity . I mean a perticular column in the .cdt file with different colors rather than the rest of the columns. Thank you very much. Regards, Vijay ___________________________________________________________ How much free photo storage do you get? Store your holiday snaps for FREE with Yahoo! Photos http://uk.photos.yahoo.com |
|
From: Alok S. <al...@ca...> - 2005-10-12 16:34:55
|
At a minimum, duplicate the first column. The better thing would be to add a "GWEIGHT" column after your gene ids, and an "EWEIGHT" row below your array ids. Please view the online file format documentation at http://jtreeview.sourceforge.net/docs/JTVUserManual/ch02s11.html in particular the section on the CDT file. -Alok On Oct 12, 2005, at 9:10 AM, ses...@ut... wrote: > > > Hi There, > I am using Java Treeview to view my cluster. > I have 21 columns of data. > the first column is unique ID and the rest are the data for 20 > amino acids. > For some reason I can view the data for 19 amino acids. I am > wondering what's > going on. > I could not find the reason though I spent a couple of hours. > I appreciate for your help. > Thank you very much. > Regards, > Seshu > > |
|
From: Alok S. <al...@ca...> - 2005-09-01 00:03:10
|
Dear Hrishi,
There is currently no PCA-specific view in java treeview. Hopefully,
this will change at some point in the future, but I unfortunately
don't have time to add a PCA viewer. I will be adding a plugin
interface to the next version, this should make it somewhat easier to
add new views, but the PCA data is really quite different from the
other ways of clustering, and will still take some work before it is
ready to go.
I will give you some ideas on what you can do in the meantime. There
should be an "svu.txt" file and an "svv.txt" file. I will describe
them separately:
SVU:
To open this file, you must go to file->open Java Treeview, and then
select the "All Files" option from the file format pulldown.
When the file opens, most likely you will see a black rectangle. This
is because the values in are normalized to between 0 and 1, and
typically have values around 1/N, where N is the number of genes in
the dataset, which just shows up as black in java treeview. To fix
this, go to "Settings->Pixel Settings..." and set the contrast to 1/
N, more or less, and you should be able to see things. The gene names
should be as expected, and the array names will be replaced with the
eigen values of the corresponding eigen arrays.
SVV:
This is tricker, since the format of the _svv.txt files does not
correspond with what JTV expects. You must do the following:
1) open in Excel or other spreadsheet program
2) duplicate the EIGVALUE column. The first two columns in java
treeview are supposed to be identifiers; doubling this column will
just make an extra column for each eigen gene. The "names" of the
eigen genes will be the associated eigenvalues.
3) Save the file as "tab delimitted text".
Now, you should be able to open and view the data in java treeview.
As a quick fix, I could add some detection code to java treeview to
do these manipulations automatically when it sees a EIGVALUE first
column, and no GWEIGHT column. Do you think this would be useful?
Take care,
Alok
On Aug 31, 2005, at 7:07 AM, Hrishikesh Deshmukh wrote:
> Hi All,
>
> I have used Cluster 3.0 to calculate PCA results but how does one
> use TreeView to visualize results?!
>
> Thanks,
> Hrishi
|
|
From: Hrishikesh D. <hde...@gm...> - 2005-08-31 14:07:50
|
Hi All, I have used Cluster 3.0 to calculate PCA results but how does one use=20 TreeView to visualize results?! Thanks, Hrishi |
|
From: T <tsh...@nc...> - 2005-06-27 11:38:53
|
Dear Alok I enjoy using your Java TreeView programme and I"ll be very grateful if you could help me with the following problem: I want to export image file of my clustering results in PNG and JPEG format. But, PNG files cannot open using any software including Photoshop. JPAG files can open but images are all red and can not be read. Thanks a lot for any suggestions to fix this problem. Best wishes, Tatsu |
|
From: Alok S. <al...@ca...> - 2005-06-21 19:19:43
|
Not currently. It wouldn't be too hard to throw together a command-
line exporter; the main annoyance would be figuring out what the
image should look like, since it can't steal the settings from the
GUI. I might be willing to put something together, if you think it
would get used heavily by yourself or others. Do you have specific
plans for it?
-Alok
On Jun 15, 2005, at 11:49 AM, Timur Shtatland wrote:
> I would like to export the dendrogram/heatmap and save it as a png
> or ps file for many input files. This can be done using the Java
> TreeView GUI, one file at a time. Can this be done from the command
> line on Mac OS X or on Linux?
> Thank you.
>
> Timur Shtatland
>
>
>
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> https://lists.sourceforge.net/lists/listinfo/jtreeview-users
>
>
|
|
From: Timur S. <tsh...@pa...> - 2005-06-15 18:50:16
|
I would like to export the dendrogram/heatmap and save it as a png or ps file for many input files. This can be done using the Java TreeView GUI, one file at a time. Can this be done from the command line on Mac OS X or on Linux? Thank you. Timur Shtatland |
|
From: Xiaoqing Z. <xia...@cg...> - 2005-05-06 15:36:06
|
Hi Alok, Thank you for your previous reply. It helped me a lot. I have few more questions now: I just wonder what class is used to read the data such as .cdt .gtr, = into TreeView application. If I want to let the new application I am writing = to read a new format file such a matrix file and make it available to some panels, what is the best way to do it? Second, I did not understand what is the function of MapContainer, can I = just use the TreeSelection class to represent the object which is current selected? Thanks for your help. Xiaoqing -----Original Message----- From: Alok Saldanha [mailto:al...@ca...]=20 Sent: Tuesday, March 15, 2005 6:28 PM To: Xiaoqing Zhang Cc: jtr...@li... Subject: Re: [Jtreeview-users] How to do alignment view? You need to select "Linked" from the style pulldown on the=20 "File->Open..." dialog. Sorry about the confusion; at some point, I=20 hope to get rid of the style pulldown and make everything Linked. -Alok On Mar 15, 2005, at 2:17 PM, Xiaoqing Zhang wrote: > Hi Alok, > > =A0 > > I downloaded the human fgf files from samples. There are two files:=20 > fgf.cpt and fgf.gtr. But I noticed that when I start JTV, there is no=20 > menu item under Analysis and Export. So I can only open the file=20 > fgf.cpt from File menu. Then I only saw tree structure at the geneTree = > panel, the Global pixels and Zoom pixels panel are gray colored. How=20 > can I see the nice image posted in the samples? > > =A0 > > After I load the file, I can see some menu items under "Analysis". So=20 > I tried to do "analysis-> align to tree" , there is no "Alignment"=20 > menu item, then I opened the .cpt or .gtr file but no effect at all. > > =A0 > > Do I miss something here? I can open other sample .cpt files without=20 > any problem. > > =A0 > > =A0 > > =A0 > > Xiaoqing > > =A0 > > =A0 > > =A0 > > =A0 > > =A0 |
|
From: gangshi w. <gan...@ya...> - 2005-05-03 13:09:45
|
Dear Alok, I used TreeView very well last year and am trying to continue using it. Unfortunately, I have problems when I install TreeView on my PC. My PC system is Windows 2000. Cluster 3.0 is intalled. I downloaded Treeview 1.0.12. When the installation goes at the step of Adding Java TreeView to the start menu, a pop-up window shows Access is denied. The next window shows the installation is completed. I can not find the TreeView icon in the start menu, I also can not find TreeView in the default destination directory C:\program files\Stanford university\java TreeView. But I can see a TreeView icon under C:\. I guess it might be the Cluster 3.0 integration problem. I followed the TreeView readme file like this: 2) Cluster-3.0-OSX-Integration The following is a brief description of how to get the "Launch Treeview" button of cluster 3.0 (see http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/software.htm) to work nicely on Mac OSX. 1) download the TreeView-X.X.X-bin.tar.gz file. This should unpack to make a TreeView-X.X.X-bin folder. Be sure not to get the TreeView-X.X.X-osx.dmg file by mistake. 2) Rename the TreeView-X.X.X-bin folder to TreeView 3) Move the TreeView folder to the Applications folder in the finder Double-clicking "Cluster" in the Applications folder, and then clicking the java treeview button should now work The problem is still there. I dont understand what the Applications folder means. Could you please kindly show me step-by-step how to solve the problem? Thank you very much. I look forward to your reply. Best wishes, Gangshi __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
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From: Neateye <nit...@ao...> - 2005-04-20 19:35:44
|
Call out Gouranga be happy!!! Gouranga Gouranga Gouranga .... That which brings the highest happiness!! |
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From: Alok S. <al...@ca...> - 2005-04-20 18:32:48
|
Also, there's this: http://docs.info.apple.com/article.html?artnum=301380 -Alok On Apr 20, 2005, at 5:15 AM, Patrick Fleming wrote: > Hello, > > Just updated the OSX and jtree crashes now. Here is the crash report - > any advice? > > 33% more JavaApplicationStub.crash.log > ********** > > Host Name: resolute.local > Date/Time: 2005-04-20 08:11:08 -0400 > OS Version: 10.3.9 (Build 7W98) > Report Version: 2 > > Command: JavaApplicationStub > Path: /Applications/TreeView-1.0.12-osx/TreeView/Java > TreeView.app/Contents/MacOS/JavaA > pplicationStub > Version: ??? (???) > PID: 667 > Thread: 1 > > Exception: EXC_BAD_ACCESS (0x0001) > Codes: KERN_INVALID_ADDRESS (0x0001) at 0xa7531d54 > > Thread 0: > 0 libSystem.B.dylib 0x90007878 mach_msg_trap + 0x8 > 1 libSystem.B.dylib 0x900073f8 mach_msg + 0x38 > 2 com.apple.CoreFoundation 0x901c16e0 __CFRunLoopRun + > 0x350 > 3 com.apple.CoreFoundation 0x901c5e6c > CFRunLoopRunSpecific + 0x148 > 4 ...ple.JavaApplicationLauncher 0x850318b4 startupJava(int, > int, char const**, __C > FDictionary const*, BuilderVersion, char const*, char const**) + 0x128 > 5 ??? 0x00009574 0x1000 + 0x8574 > 6 ??? 0x000093e8 0x1000 + 0x83e8 > > Thread 1 Crashed: > 0 libjvm.dylib 0x936b33f8 JVM_Timeout + 0x1018 > 1 libjvm.dylib 0x936bab04 JVM_DoPrivileged + > 0x2ea4 > 2 libjvm.dylib 0x936c7220 > JVM_MonitorNotifyAll + 0xf50 > 3 libjvm.dylib 0x93674d14 > JVM_GetClassAccessFlags + 0xab4 > 4 libjvm.dylib 0x93677544 JVM_MonitorWait + > 0x1da4 > 5 libjvm.dylib 0x936772bc JVM_MonitorWait + > 0x1b1c > 6 libjvm.dylib 0x9373345c > JVM_GetClassDeclaredFields + 0x161c > 7 libjvm.dylib 0x93762d70 > JVM_GetInterfaceVersion + 0x15330 > 8 libjvm.dylib 0x9375daa8 > JVM_GetInterfaceVersion + 0x10068 > 9 libjvm.dylib 0x9375d5dc > JVM_GetInterfaceVersion + 0xfb9c > 10 libjvm.dylib 0x9373e47c > JVM_IsPrimitiveClass + 0x1fcc > 11 libjvm.dylib 0x9372e3b0 > JVM_GetClassDeclaredMethods + 0x8c0 > 12 libjvm.dylib 0x93748d6c > JNI_CreateJavaVM_Impl + 0x7c > 13 ...ple.JavaApplicationLauncher 0x85031a6c > startJavaApplication + 0x150 > 14 ...ple.JavaApplicationLauncher 0x850318e4 > java_main_stub(void*) + 0x10 > 15 libSystem.B.dylib 0x90024910 _pthread_body + 0x28 > > Thread 2: > 0 libSystem.B.dylib 0x90007878 mach_msg_trap + 0x8 > 1 libSystem.B.dylib 0x900073f8 mach_msg + 0x38 > 2 libjvm.dylib 0x9374d1dc > JNI_CreateJavaVM_Impl + 0x44ec > 3 libjvm.dylib 0x9374d170 > JNI_CreateJavaVM_Impl + 0x4480 > 4 libjvm.dylib 0x9383f90c JVM_UnloadLibrary + > 0xb0fec > 5 libSystem.B.dylib 0x90024910 _pthread_body + 0x28 > > PPC Thread State: > srr0: 0x936b33f8 srr1: 0x0200f030 vrsave: 0x00000000 > cr: 0x24004222 xer: 0x00000004 lr: 0x936b3300 ctr: 0x900019c0 > r0: 0x00000112 r1: 0xf0800500 r2: 0x6e800230 r3: 0x6e800238 > r4: 0x00000000 r5: 0xa7531cd0 r6: 0x036ffef5 r7: 0x0000df45 > r8: 0x01be8a8b r9: 0x000d150f r10: 0x01b1757c r11: 0x0362eaf8 > r12: 0x03ce0000 r13: 0x00000000 r14: 0x00000000 r15: 0xa366d638 > r16: 0xa366f06c r17: 0xa366d638 r18: 0x00000000 r19: 0x00000000 > r20: 0x00000000 r21: 0xf0800860 r22: 0xa36748c4 r23: 0x00000000 > r24: 0x00000000 r25: 0x003012d0 r26: 0x00000000 r27: 0x6e0000e0 > r28: 0x00000000 r29: 0x6e0000e0 r30: 0x00304b70 r31: 0x936b3300 > > Binary Images Description: > 0x1000 - 0xafff ??? ??? (1.0.12) > /Applications/TreeView-1.0.12-osx/TreeView > /Java TreeView.app/Contents/MacOS/JavaApplicationStub > 0x80830000 - 0x8090efff libxml2.2.dylib > /usr/lib/libxml2.2.dylib > 0x85030000 - 0x85043fff com.apple.JavaApplicationLauncher 2.0.2 > /System/Library/PrivateFra > meworks/JavaApplicationLauncher.framework/Versions/A/ > JavaApplicationLauncher > 0x86180000 - 0x8618bfff libzip.jnilib > /System/Library/Frameworks/JavaVM.framework/Versio > ns/1.4.2/Libraries/libzip.jnilib > 0x8fe00000 - 0x8fe4ffff dyld /usr/lib/dyld > 0x90000000 - 0x9014ffff libSystem.B.dylib > /usr/lib/libSystem.B.dylib > 0x901c0000 - 0x9026dfff com.apple.CoreFoundation 6.3.7 (299.35) > /System/Library/Frameworks > /CoreFoundation.framework/Versions/A/CoreFoundation > 0x902b0000 - 0x90529fff com.apple.CoreServices.CarbonCore 10.3.7 > /System/Library/Fr > ameworks/CoreServices.framework/Versions/A/Frameworks/ > CarbonCore.framework/Versions/A/Carb > onCore > 0x90584000 - 0x905d4fff com.apple.HIServices 1.4.1 (0.0.1d1) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > HIServices.framework/Versions/A/HISer > vices > 0x90610000 - 0x9069afff com.apple.CoreServices.OSServices 3.0.1 > /System/Library/Frameworks > /CoreServices.framework/Versions/A/Frameworks/OSServices.framework/ > Versions/A/OSServices > 0x90700000 - 0x90700fff com.apple.CoreServices 10.3 (???) > /System/Library/Frameworks > /CoreServices.framework/Versions/A/CoreServices > 0x90720000 - 0x90787fff com.apple.audio.CoreAudio 2.1.2 > /System/Library/Frameworks/CoreAud > io.framework/Versions/A/CoreAudio > 0x907f0000 - 0x907f9fff com.apple.DiskArbitration 2.0.5 > /System/Library/PrivateFrameworks/ > DiskArbitration.framework/Versions/A/DiskArbitration > 0x90810000 - 0x90810fff com.apple.ApplicationServices 1.0 (???) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/ApplicationServices > 0x90830000 - 0x9089ffff libobjc.A.dylib > /usr/lib/libobjc.A.dylib > 0x90940000 - 0x909b3fff com.apple.DesktopServices 1.2.4 > /System/Library/PrivateFrameworks/ > DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv > 0x909f0000 - 0x90a04fff libCGATS.A.dylib > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/ > A/Resources/libCGATS. > A.dylib > 0x90a20000 - 0x90b7bfff com.apple.Foundation 6.3.6 (500.58) > /System/Library/Frameworks > /Foundation.framework/Versions/C/Foundation > 0x90d00000 - 0x90d1bfff com.apple.SystemConfiguration 1.7.1 (???) > /System/Library/Fr > ameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration > 0x90ec2000 - 0x90f7bfff com.apple.QD 3.4.67 (???) > /System/Library/Frameworks/Applica > tionServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD > 0x90fce000 - 0x90fe9fff libjava.jnilib > /System/Library/Frameworks/JavaVM.framework/Versio > ns/1.4.2/Libraries/libjava.jnilib > 0x91002000 - 0x9100dfff libCSync.A.dylib > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/ > A/Resources/libCSync. > A.dylib > 0x910b0000 - 0x91101fff com.apple.bom 1.2.5 (63.2) > /System/Library/PrivateFrameworks/ > Bom.framework/Versions/A/Bom > 0x9110d000 - 0x91176fff com.apple.htmlrendering 1.1.2 > /System/Library/Frameworks/Carbon. > framework/Versions/A/Frameworks/HTMLRendering.framework/Versions/A/ > HTMLRendering > 0x916ec000 - 0x9177ffff com.apple.print.framework.PrintCore 3.3 > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > PrintCore.framework/Versions/A/PrintC > ore > 0x917e0000 - 0x917f0fff com.apple.speech.recognition.framework 3.3 > /System/Library/Fr > ameworks/Carbon.framework/Versions/A/Frameworks/ > SpeechRecognition.framework/Versions/A/Spe > echRecognition > 0x91810000 - 0x9182afff com.apple.openscripting 1.2.1 (???) > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/ > Versions/A/OpenScripting > 0x91850000 - 0x91860fff com.apple.ImageCapture 2.1.5 > /System/Library/Frameworks/Carbon. > framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ > ImageCapture > 0x91890000 - 0x9189cfff com.apple.help 1.0.1 > /System/Library/Frameworks/Carbon.framewor > k/Versions/A/Frameworks/Help.framework/Versions/A/Help > 0x918c0000 - 0x918cdfff com.apple.CommonPanels 1.2.1 (1.0) > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/ > Versions/A/CommonPanels > 0x918f0000 - 0x9193efff com.apple.print.framework.Print 3.3 > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/ > Print > 0x91990000 - 0x9199bfff com.apple.securityhi 1.2 (90) > /System/Library/Frameworks/Carbon. > framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/ > SecurityHI > 0x919a3000 - 0x91a12fff com.apple.framework.IOKit 1.3.6 (???) > /System/Library/Frameworks > /IOKit.framework/Versions/A/IOKit > 0x91a40000 - 0x91ab3fff com.apple.NavigationServices 3.3.3 > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/ > Versions/A/Navigation > Services > 0x91b10000 - 0x91b2afff libPDFRIP.A.dylib > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/ > A/Resources/libPDFRIP > .A.dylib > 0x91b50000 - 0x91b5ffff libPSRIP.A.dylib > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/ > A/Resources/libPSRIP. > A.dylib > 0x91b80000 - 0x91b93fff libRIP.A.dylib > /System/Library/Frameworks/ApplicationServices.fra > mework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/ > Resources/libRIP.A.dylib > 0x91b9a000 - 0x91d2ffff com.apple.QuickTime 6.5.2 > /System/Library/Frameworks/QuickTi > me.framework/Versions/A/QuickTime > 0x91dcc000 - 0x91dd0fff com.apple.JavaVM 2.0.0 > /System/Library/Frameworks/JavaVM.framewor > k/Versions/A/JavaVM > 0x91dd4000 - 0x91ddefff libverify.dylib > /System/Library/Frameworks/JavaVM.framewor > k/Versions/1.4.2/Libraries/libverify.dylib > 0x91ebd000 - 0x91ebdfff com.apple.Carbon 10.3 (???) > /System/Library/Frameworks/Carbon. > framework/Versions/A/Carbon > 0x92070000 - 0x92096fff com.apple.FindByContent 1.4 (1.2) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > FindByContent.framework/Versions/A/Fi > ndByContent > 0x920c0000 - 0x922a7fff com.apple.security 2.4 (177) > /System/Library/Frameworks/Securit > y.framework/Versions/A/Security > 0x92430000 - 0x92468fff com.apple.LaunchServices 10.3.5 (98.4) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > LaunchServices.framework/Versions/A/L > aunchServices > 0x92727000 - 0x9275ffff com.apple.AE 1.4 > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE > 0x927f0000 - 0x92827fff com.apple.CFNetwork 1.2.1 (7) > /System/Library/Frameworks/CoreSer > vices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/ > CFNetwork > 0x92880000 - 0x92c05fff com.apple.HIToolbox 1.3.6 (???) > /System/Library/Frameworks/Carbon. > framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/ > HIToolbox > 0x92e70000 - 0x9336ffff com.apple.AppKit 6.3.7 (743.36) > /System/Library/Frameworks/AppKit. > framework/Versions/C/AppKit > 0x9366d000 - 0x938bbfff libjvm.dylib > /System/Library/Frameworks/JavaVM.framework/Versio > ns/1.4.2/Libraries/libjvm.dylib > 0x93920000 - 0x93933fff com.apple.speech.synthesis.framework 3.2 > /System/Library/Fr > ameworks/ApplicationServices.framework/Versions/A/Frameworks/ > SpeechSynthesis.framework/Ver > sions/A/SpeechSynthesis > 0x939a0000 - 0x939b4fff libcups.2.dylib > /usr/lib/libcups.2.dylib > 0x939d0000 - 0x939d4fff libmathCommon.A.dylib > /usr/lib/system/libmathCommon.A.dylib > 0x93b50000 - 0x93bf3fff com.apple.audio.toolbox.AudioToolbox 1.3.2 > /System/Library/Fr > ameworks/AudioToolbox.framework/Versions/A/AudioToolbox > 0x93c3c000 - 0x93c53fff com.apple.LangAnalysis 1.5.4 > /System/Library/Frameworks/Applica > tionServices.framework/Versions/A/Frameworks/LangAnalysis.framework/ > Versions/A/LangAnalysi > s > 0x944c0000 - 0x944ddfff com.apple.audio.SoundManager 3.8 > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/CarbonSound.framework/ > Versions/A/CarbonSound > 0x944ef000 - 0x9451dfff libssl.0.9.7.dylib > /usr/lib/libssl.0.9.7.dylib > 0x945b0000 - 0x945b9fff libz.1.dylib /usr/lib/libz.1.dylib > 0x94610000 - 0x9462afff libresolv.9.dylib > /usr/lib/libresolv.9.dylib > 0x94650000 - 0x946affff com.apple.SearchKit 1.0.2 > /System/Library/Frameworks/CoreSer > vices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/ > SearchKit > 0x94800000 - 0x9488cfff com.apple.ink.framework 101.1.4 (55.12) > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink > 0x94eaf000 - 0x94f6efff ColorSync > /System/Library/Frameworks/ApplicationServices.fra > mework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync > 0x95ec2000 - 0x95edafff com.apple.WebServices 1.1.1 (1.1.0) > /System/Library/Frameworks > /CoreServices.framework/Versions/A/Frameworks/ > WebServicesCore.framework/Versions/A/WebServ > icesCore > 0x968d0000 - 0x969b2fff libicucore.A.dylib > /usr/lib/libicucore.A.dylib > 0x96a20000 - 0x96ae2fff libcrypto.0.9.7.dylib > /usr/lib/libcrypto.0.9.7.dylib > 0x96b30000 - 0x96b30fff com.apple.audio.units.AudioUnit 1.3.2 > /System/Library/Frameworks > /AudioUnit.framework/Versions/A/AudioUnit > 0x96b43000 - 0x96b4bfff libbsm.dylib /usr/lib/libbsm.dylib > 0x96b50000 - 0x96bdffff ATS > /System/Library/Frameworks/ApplicationServices.framework/V > ersions/A/Frameworks/ATS.framework/Versions/A/ATS > 0x96cb0000 - 0x96d9efff libiconv.2.dylib > /usr/lib/libiconv.2.dylib > 0x98b82000 - 0x98e5afff com.apple.CoreGraphics 1.203.30 (???) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > CoreGraphics.framework/Versions/A/Cor > eGraphics > > -- > Patrick Fleming, Ph.D. > The Johns Hopkins University Department of Biophysics > 201 Jenkins Hall 3400 North Charles Street Baltimore, MD 21218 Tel: > 410-516-7654 > Fax: 410-516-4118 > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: New Crystal Reports XI. > Version 11 adds new functionality designed to reduce time involved in > creating, integrating, and deploying reporting solutions. Free runtime > info, > new features, or free trial, at: > http://www.businessobjects.com/devxi/728 > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > |
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From: Alok S. <al...@ca...> - 2005-04-20 18:26:29
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That's pretty scary. It is consistent? Have you tried rebooting since you updated? It looks like it's happening very early in the boot process - does the main screen even come up? In particular, it's happening in libjvm.dylib, which is part of java, not part of JTV. I googled your stack trace, and it appears that matlab has a similar problem with 10.2.9: http://newsreader.mathworks.com/WebX?14@747.Jr8baFhrRZb.0@.ef03043 They say it was fixed by applying this patch: http://www.apple.com/support/downloads/ securityupdate2005002macosx1034orlater.html A key indication for this patch is that java itself won't run from the terminal: > The backtrace that Matlab was giving when started from a terminal > window indicated Java was broken. Trying to run Java by itself from the > command line resulted in a segmentation fault, which indicated that in > fact Java was probably broken, not Matlab. I searched for references to > broken Java after applying 10.3.9 and found a reference to the 2005-002 > update. That update fixes a previous Java issue, I believe, and in fact > fixed this one. Please let me know if this fixes your problem, and I'll add a flashy link to the JTV homepage. -Alok On Apr 20, 2005, at 5:15 AM, Patrick Fleming wrote: > Hello, > > Just updated the OSX and jtree crashes now. Here is the crash report - > any advice? > > 33% more JavaApplicationStub.crash.log > ********** > > Host Name: resolute.local > Date/Time: 2005-04-20 08:11:08 -0400 > OS Version: 10.3.9 (Build 7W98) > Report Version: 2 > > Command: JavaApplicationStub > Path: /Applications/TreeView-1.0.12-osx/TreeView/Java > TreeView.app/Contents/MacOS/JavaA > pplicationStub > Version: ??? (???) > PID: 667 > Thread: 1 > > Exception: EXC_BAD_ACCESS (0x0001) > Codes: KERN_INVALID_ADDRESS (0x0001) at 0xa7531d54 > > Thread 0: > 0 libSystem.B.dylib 0x90007878 mach_msg_trap + 0x8 > 1 libSystem.B.dylib 0x900073f8 mach_msg + 0x38 > 2 com.apple.CoreFoundation 0x901c16e0 __CFRunLoopRun + > 0x350 > 3 com.apple.CoreFoundation 0x901c5e6c > CFRunLoopRunSpecific + 0x148 > 4 ...ple.JavaApplicationLauncher 0x850318b4 startupJava(int, > int, char const**, __C > FDictionary const*, BuilderVersion, char const*, char const**) + 0x128 > 5 ??? 0x00009574 0x1000 + 0x8574 > 6 ??? 0x000093e8 0x1000 + 0x83e8 > > Thread 1 Crashed: > 0 libjvm.dylib 0x936b33f8 JVM_Timeout + 0x1018 > 1 libjvm.dylib 0x936bab04 JVM_DoPrivileged + > 0x2ea4 > 2 libjvm.dylib 0x936c7220 > JVM_MonitorNotifyAll + 0xf50 > 3 libjvm.dylib 0x93674d14 > JVM_GetClassAccessFlags + 0xab4 > 4 libjvm.dylib 0x93677544 JVM_MonitorWait + > 0x1da4 > 5 libjvm.dylib 0x936772bc JVM_MonitorWait + > 0x1b1c > 6 libjvm.dylib 0x9373345c > JVM_GetClassDeclaredFields + 0x161c > 7 libjvm.dylib 0x93762d70 > JVM_GetInterfaceVersion + 0x15330 > 8 libjvm.dylib 0x9375daa8 > JVM_GetInterfaceVersion + 0x10068 > 9 libjvm.dylib 0x9375d5dc > JVM_GetInterfaceVersion + 0xfb9c > 10 libjvm.dylib 0x9373e47c > JVM_IsPrimitiveClass + 0x1fcc > 11 libjvm.dylib 0x9372e3b0 > JVM_GetClassDeclaredMethods + 0x8c0 > 12 libjvm.dylib 0x93748d6c > JNI_CreateJavaVM_Impl + 0x7c > 13 ...ple.JavaApplicationLauncher 0x85031a6c > startJavaApplication + 0x150 > 14 ...ple.JavaApplicationLauncher 0x850318e4 > java_main_stub(void*) + 0x10 > 15 libSystem.B.dylib 0x90024910 _pthread_body + 0x28 > > Thread 2: > 0 libSystem.B.dylib 0x90007878 mach_msg_trap + 0x8 > 1 libSystem.B.dylib 0x900073f8 mach_msg + 0x38 > 2 libjvm.dylib 0x9374d1dc > JNI_CreateJavaVM_Impl + 0x44ec > 3 libjvm.dylib 0x9374d170 > JNI_CreateJavaVM_Impl + 0x4480 > 4 libjvm.dylib 0x9383f90c JVM_UnloadLibrary + > 0xb0fec > 5 libSystem.B.dylib 0x90024910 _pthread_body + 0x28 > > PPC Thread State: > srr0: 0x936b33f8 srr1: 0x0200f030 vrsave: 0x00000000 > cr: 0x24004222 xer: 0x00000004 lr: 0x936b3300 ctr: 0x900019c0 > r0: 0x00000112 r1: 0xf0800500 r2: 0x6e800230 r3: 0x6e800238 > r4: 0x00000000 r5: 0xa7531cd0 r6: 0x036ffef5 r7: 0x0000df45 > r8: 0x01be8a8b r9: 0x000d150f r10: 0x01b1757c r11: 0x0362eaf8 > r12: 0x03ce0000 r13: 0x00000000 r14: 0x00000000 r15: 0xa366d638 > r16: 0xa366f06c r17: 0xa366d638 r18: 0x00000000 r19: 0x00000000 > r20: 0x00000000 r21: 0xf0800860 r22: 0xa36748c4 r23: 0x00000000 > r24: 0x00000000 r25: 0x003012d0 r26: 0x00000000 r27: 0x6e0000e0 > r28: 0x00000000 r29: 0x6e0000e0 r30: 0x00304b70 r31: 0x936b3300 > > Binary Images Description: > 0x1000 - 0xafff ??? ??? (1.0.12) > /Applications/TreeView-1.0.12-osx/TreeView > /Java TreeView.app/Contents/MacOS/JavaApplicationStub > 0x80830000 - 0x8090efff libxml2.2.dylib > /usr/lib/libxml2.2.dylib > 0x85030000 - 0x85043fff com.apple.JavaApplicationLauncher 2.0.2 > /System/Library/PrivateFra > meworks/JavaApplicationLauncher.framework/Versions/A/ > JavaApplicationLauncher > 0x86180000 - 0x8618bfff libzip.jnilib > /System/Library/Frameworks/JavaVM.framework/Versio > ns/1.4.2/Libraries/libzip.jnilib > 0x8fe00000 - 0x8fe4ffff dyld /usr/lib/dyld > 0x90000000 - 0x9014ffff libSystem.B.dylib > /usr/lib/libSystem.B.dylib > 0x901c0000 - 0x9026dfff com.apple.CoreFoundation 6.3.7 (299.35) > /System/Library/Frameworks > /CoreFoundation.framework/Versions/A/CoreFoundation > 0x902b0000 - 0x90529fff com.apple.CoreServices.CarbonCore 10.3.7 > /System/Library/Fr > ameworks/CoreServices.framework/Versions/A/Frameworks/ > CarbonCore.framework/Versions/A/Carb > onCore > 0x90584000 - 0x905d4fff com.apple.HIServices 1.4.1 (0.0.1d1) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > HIServices.framework/Versions/A/HISer > vices > 0x90610000 - 0x9069afff com.apple.CoreServices.OSServices 3.0.1 > /System/Library/Frameworks > /CoreServices.framework/Versions/A/Frameworks/OSServices.framework/ > Versions/A/OSServices > 0x90700000 - 0x90700fff com.apple.CoreServices 10.3 (???) > /System/Library/Frameworks > /CoreServices.framework/Versions/A/CoreServices > 0x90720000 - 0x90787fff com.apple.audio.CoreAudio 2.1.2 > /System/Library/Frameworks/CoreAud > io.framework/Versions/A/CoreAudio > 0x907f0000 - 0x907f9fff com.apple.DiskArbitration 2.0.5 > /System/Library/PrivateFrameworks/ > DiskArbitration.framework/Versions/A/DiskArbitration > 0x90810000 - 0x90810fff com.apple.ApplicationServices 1.0 (???) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/ApplicationServices > 0x90830000 - 0x9089ffff libobjc.A.dylib > /usr/lib/libobjc.A.dylib > 0x90940000 - 0x909b3fff com.apple.DesktopServices 1.2.4 > /System/Library/PrivateFrameworks/ > DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv > 0x909f0000 - 0x90a04fff libCGATS.A.dylib > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/ > A/Resources/libCGATS. > A.dylib > 0x90a20000 - 0x90b7bfff com.apple.Foundation 6.3.6 (500.58) > /System/Library/Frameworks > /Foundation.framework/Versions/C/Foundation > 0x90d00000 - 0x90d1bfff com.apple.SystemConfiguration 1.7.1 (???) > /System/Library/Fr > ameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration > 0x90ec2000 - 0x90f7bfff com.apple.QD 3.4.67 (???) > /System/Library/Frameworks/Applica > tionServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD > 0x90fce000 - 0x90fe9fff libjava.jnilib > /System/Library/Frameworks/JavaVM.framework/Versio > ns/1.4.2/Libraries/libjava.jnilib > 0x91002000 - 0x9100dfff libCSync.A.dylib > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/ > A/Resources/libCSync. > A.dylib > 0x910b0000 - 0x91101fff com.apple.bom 1.2.5 (63.2) > /System/Library/PrivateFrameworks/ > Bom.framework/Versions/A/Bom > 0x9110d000 - 0x91176fff com.apple.htmlrendering 1.1.2 > /System/Library/Frameworks/Carbon. > framework/Versions/A/Frameworks/HTMLRendering.framework/Versions/A/ > HTMLRendering > 0x916ec000 - 0x9177ffff com.apple.print.framework.PrintCore 3.3 > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > PrintCore.framework/Versions/A/PrintC > ore > 0x917e0000 - 0x917f0fff com.apple.speech.recognition.framework 3.3 > /System/Library/Fr > ameworks/Carbon.framework/Versions/A/Frameworks/ > SpeechRecognition.framework/Versions/A/Spe > echRecognition > 0x91810000 - 0x9182afff com.apple.openscripting 1.2.1 (???) > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/ > Versions/A/OpenScripting > 0x91850000 - 0x91860fff com.apple.ImageCapture 2.1.5 > /System/Library/Frameworks/Carbon. > framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ > ImageCapture > 0x91890000 - 0x9189cfff com.apple.help 1.0.1 > /System/Library/Frameworks/Carbon.framewor > k/Versions/A/Frameworks/Help.framework/Versions/A/Help > 0x918c0000 - 0x918cdfff com.apple.CommonPanels 1.2.1 (1.0) > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/ > Versions/A/CommonPanels > 0x918f0000 - 0x9193efff com.apple.print.framework.Print 3.3 > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/ > Print > 0x91990000 - 0x9199bfff com.apple.securityhi 1.2 (90) > /System/Library/Frameworks/Carbon. > framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/ > SecurityHI > 0x919a3000 - 0x91a12fff com.apple.framework.IOKit 1.3.6 (???) > /System/Library/Frameworks > /IOKit.framework/Versions/A/IOKit > 0x91a40000 - 0x91ab3fff com.apple.NavigationServices 3.3.3 > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/ > Versions/A/Navigation > Services > 0x91b10000 - 0x91b2afff libPDFRIP.A.dylib > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/ > A/Resources/libPDFRIP > .A.dylib > 0x91b50000 - 0x91b5ffff libPSRIP.A.dylib > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/ > A/Resources/libPSRIP. > A.dylib > 0x91b80000 - 0x91b93fff libRIP.A.dylib > /System/Library/Frameworks/ApplicationServices.fra > mework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/ > Resources/libRIP.A.dylib > 0x91b9a000 - 0x91d2ffff com.apple.QuickTime 6.5.2 > /System/Library/Frameworks/QuickTi > me.framework/Versions/A/QuickTime > 0x91dcc000 - 0x91dd0fff com.apple.JavaVM 2.0.0 > /System/Library/Frameworks/JavaVM.framewor > k/Versions/A/JavaVM > 0x91dd4000 - 0x91ddefff libverify.dylib > /System/Library/Frameworks/JavaVM.framewor > k/Versions/1.4.2/Libraries/libverify.dylib > 0x91ebd000 - 0x91ebdfff com.apple.Carbon 10.3 (???) > /System/Library/Frameworks/Carbon. > framework/Versions/A/Carbon > 0x92070000 - 0x92096fff com.apple.FindByContent 1.4 (1.2) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > FindByContent.framework/Versions/A/Fi > ndByContent > 0x920c0000 - 0x922a7fff com.apple.security 2.4 (177) > /System/Library/Frameworks/Securit > y.framework/Versions/A/Security > 0x92430000 - 0x92468fff com.apple.LaunchServices 10.3.5 (98.4) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > LaunchServices.framework/Versions/A/L > aunchServices > 0x92727000 - 0x9275ffff com.apple.AE 1.4 > /System/Library/Frameworks/ApplicationServ > ices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE > 0x927f0000 - 0x92827fff com.apple.CFNetwork 1.2.1 (7) > /System/Library/Frameworks/CoreSer > vices.framework/Versions/A/Frameworks/CFNetwork.framework/Versions/A/ > CFNetwork > 0x92880000 - 0x92c05fff com.apple.HIToolbox 1.3.6 (???) > /System/Library/Frameworks/Carbon. > framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/ > HIToolbox > 0x92e70000 - 0x9336ffff com.apple.AppKit 6.3.7 (743.36) > /System/Library/Frameworks/AppKit. > framework/Versions/C/AppKit > 0x9366d000 - 0x938bbfff libjvm.dylib > /System/Library/Frameworks/JavaVM.framework/Versio > ns/1.4.2/Libraries/libjvm.dylib > 0x93920000 - 0x93933fff com.apple.speech.synthesis.framework 3.2 > /System/Library/Fr > ameworks/ApplicationServices.framework/Versions/A/Frameworks/ > SpeechSynthesis.framework/Ver > sions/A/SpeechSynthesis > 0x939a0000 - 0x939b4fff libcups.2.dylib > /usr/lib/libcups.2.dylib > 0x939d0000 - 0x939d4fff libmathCommon.A.dylib > /usr/lib/system/libmathCommon.A.dylib > 0x93b50000 - 0x93bf3fff com.apple.audio.toolbox.AudioToolbox 1.3.2 > /System/Library/Fr > ameworks/AudioToolbox.framework/Versions/A/AudioToolbox > 0x93c3c000 - 0x93c53fff com.apple.LangAnalysis 1.5.4 > /System/Library/Frameworks/Applica > tionServices.framework/Versions/A/Frameworks/LangAnalysis.framework/ > Versions/A/LangAnalysi > s > 0x944c0000 - 0x944ddfff com.apple.audio.SoundManager 3.8 > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/CarbonSound.framework/ > Versions/A/CarbonSound > 0x944ef000 - 0x9451dfff libssl.0.9.7.dylib > /usr/lib/libssl.0.9.7.dylib > 0x945b0000 - 0x945b9fff libz.1.dylib /usr/lib/libz.1.dylib > 0x94610000 - 0x9462afff libresolv.9.dylib > /usr/lib/libresolv.9.dylib > 0x94650000 - 0x946affff com.apple.SearchKit 1.0.2 > /System/Library/Frameworks/CoreSer > vices.framework/Versions/A/Frameworks/SearchKit.framework/Versions/A/ > SearchKit > 0x94800000 - 0x9488cfff com.apple.ink.framework 101.1.4 (55.12) > /System/Library/Frameworks > /Carbon.framework/Versions/A/Frameworks/Ink.framework/Versions/A/Ink > 0x94eaf000 - 0x94f6efff ColorSync > /System/Library/Frameworks/ApplicationServices.fra > mework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync > 0x95ec2000 - 0x95edafff com.apple.WebServices 1.1.1 (1.1.0) > /System/Library/Frameworks > /CoreServices.framework/Versions/A/Frameworks/ > WebServicesCore.framework/Versions/A/WebServ > icesCore > 0x968d0000 - 0x969b2fff libicucore.A.dylib > /usr/lib/libicucore.A.dylib > 0x96a20000 - 0x96ae2fff libcrypto.0.9.7.dylib > /usr/lib/libcrypto.0.9.7.dylib > 0x96b30000 - 0x96b30fff com.apple.audio.units.AudioUnit 1.3.2 > /System/Library/Frameworks > /AudioUnit.framework/Versions/A/AudioUnit > 0x96b43000 - 0x96b4bfff libbsm.dylib /usr/lib/libbsm.dylib > 0x96b50000 - 0x96bdffff ATS > /System/Library/Frameworks/ApplicationServices.framework/V > ersions/A/Frameworks/ATS.framework/Versions/A/ATS > 0x96cb0000 - 0x96d9efff libiconv.2.dylib > /usr/lib/libiconv.2.dylib > 0x98b82000 - 0x98e5afff com.apple.CoreGraphics 1.203.30 (???) > /System/Library/Frameworks > /ApplicationServices.framework/Versions/A/Frameworks/ > CoreGraphics.framework/Versions/A/Cor > eGraphics > > -- > Patrick Fleming, Ph.D. > The Johns Hopkins University Department of Biophysics > 201 Jenkins Hall 3400 North Charles Street Baltimore, MD 21218 Tel: > 410-516-7654 > Fax: 410-516-4118 > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: New Crystal Reports XI. > Version 11 adds new functionality designed to reduce time involved in > creating, integrating, and deploying reporting solutions. Free runtime > info, > new features, or free trial, at: > http://www.businessobjects.com/devxi/728 > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > |
|
From: Patrick F. <pat...@jh...> - 2005-04-20 12:15:46
|
Hello,
Just updated the OSX and jtree crashes now. Here is the crash report -
any advice?
33% more JavaApplicationStub.crash.log
**********
Host Name: resolute.local
Date/Time: 2005-04-20 08:11:08 -0400
OS Version: 10.3.9 (Build 7W98)
Report Version: 2
Command: JavaApplicationStub
Path: /Applications/TreeView-1.0.12-osx/TreeView/Java
TreeView.app/Contents/MacOS/JavaA
pplicationStub
Version: ??? (???)
PID: 667
Thread: 1
Exception: EXC_BAD_ACCESS (0x0001)
Codes: KERN_INVALID_ADDRESS (0x0001) at 0xa7531d54
Thread 0:
0 libSystem.B.dylib 0x90007878 mach_msg_trap + 0x8
1 libSystem.B.dylib 0x900073f8 mach_msg + 0x38
2 com.apple.CoreFoundation 0x901c16e0 __CFRunLoopRun + 0x350
3 com.apple.CoreFoundation 0x901c5e6c CFRunLoopRunSpecific
+ 0x148
4 ...ple.JavaApplicationLauncher 0x850318b4 startupJava(int, int,
char const**, __C
FDictionary const*, BuilderVersion, char const*, char const**) + 0x128
5 ??? 0x00009574 0x1000 + 0x8574
6 ??? 0x000093e8 0x1000 + 0x83e8
Thread 1 Crashed:
0 libjvm.dylib 0x936b33f8 JVM_Timeout + 0x1018
1 libjvm.dylib 0x936bab04 JVM_DoPrivileged + 0x2ea4
2 libjvm.dylib 0x936c7220 JVM_MonitorNotifyAll
+ 0xf50
3 libjvm.dylib 0x93674d14
JVM_GetClassAccessFlags + 0xab4
4 libjvm.dylib 0x93677544 JVM_MonitorWait + 0x1da4
5 libjvm.dylib 0x936772bc JVM_MonitorWait + 0x1b1c
6 libjvm.dylib 0x9373345c
JVM_GetClassDeclaredFields + 0x161c
7 libjvm.dylib 0x93762d70
JVM_GetInterfaceVersion + 0x15330
8 libjvm.dylib 0x9375daa8
JVM_GetInterfaceVersion + 0x10068
9 libjvm.dylib 0x9375d5dc
JVM_GetInterfaceVersion + 0xfb9c
10 libjvm.dylib 0x9373e47c JVM_IsPrimitiveClass
+ 0x1fcc
11 libjvm.dylib 0x9372e3b0
JVM_GetClassDeclaredMethods + 0x8c0
12 libjvm.dylib 0x93748d6c JNI_CreateJavaVM_Impl
+ 0x7c
13 ...ple.JavaApplicationLauncher 0x85031a6c startJavaApplication
+ 0x150
14 ...ple.JavaApplicationLauncher 0x850318e4 java_main_stub(void*)
+ 0x10
15 libSystem.B.dylib 0x90024910 _pthread_body + 0x28
Thread 2:
0 libSystem.B.dylib 0x90007878 mach_msg_trap + 0x8
1 libSystem.B.dylib 0x900073f8 mach_msg + 0x38
2 libjvm.dylib 0x9374d1dc JNI_CreateJavaVM_Impl
+ 0x44ec
3 libjvm.dylib 0x9374d170 JNI_CreateJavaVM_Impl
+ 0x4480
4 libjvm.dylib 0x9383f90c JVM_UnloadLibrary +
0xb0fec
5 libSystem.B.dylib 0x90024910 _pthread_body + 0x28
PPC Thread State:
srr0: 0x936b33f8 srr1: 0x0200f030 vrsave: 0x00000000
cr: 0x24004222 xer: 0x00000004 lr: 0x936b3300 ctr: 0x900019c0
r0: 0x00000112 r1: 0xf0800500 r2: 0x6e800230 r3: 0x6e800238
r4: 0x00000000 r5: 0xa7531cd0 r6: 0x036ffef5 r7: 0x0000df45
r8: 0x01be8a8b r9: 0x000d150f r10: 0x01b1757c r11: 0x0362eaf8
r12: 0x03ce0000 r13: 0x00000000 r14: 0x00000000 r15: 0xa366d638
r16: 0xa366f06c r17: 0xa366d638 r18: 0x00000000 r19: 0x00000000
r20: 0x00000000 r21: 0xf0800860 r22: 0xa36748c4 r23: 0x00000000
r24: 0x00000000 r25: 0x003012d0 r26: 0x00000000 r27: 0x6e0000e0
r28: 0x00000000 r29: 0x6e0000e0 r30: 0x00304b70 r31: 0x936b3300
Binary Images Description:
0x1000 - 0xafff ??? ??? (1.0.12)
/Applications/TreeView-1.0.12-osx/TreeView
/Java TreeView.app/Contents/MacOS/JavaApplicationStub
0x80830000 - 0x8090efff libxml2.2.dylib /usr/lib/libxml2.2.dylib
0x85030000 - 0x85043fff com.apple.JavaApplicationLauncher 2.0.2
/System/Library/PrivateFra
meworks/JavaApplicationLauncher.framework/Versions/A/JavaApplicationLauncher
0x86180000 - 0x8618bfff libzip.jnilib
/System/Library/Frameworks/JavaVM.framework/Versio
ns/1.4.2/Libraries/libzip.jnilib
0x8fe00000 - 0x8fe4ffff dyld /usr/lib/dyld
0x90000000 - 0x9014ffff libSystem.B.dylib /usr/lib/libSystem.B.dylib
0x901c0000 - 0x9026dfff com.apple.CoreFoundation 6.3.7 (299.35)
/System/Library/Frameworks
/CoreFoundation.framework/Versions/A/CoreFoundation
0x902b0000 - 0x90529fff com.apple.CoreServices.CarbonCore 10.3.7
/System/Library/Fr
ameworks/CoreServices.framework/Versions/A/Frameworks/CarbonCore.framework/Versions/A/Carb
onCore
0x90584000 - 0x905d4fff com.apple.HIServices 1.4.1 (0.0.1d1)
/System/Library/Frameworks
/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HISer
vices
0x90610000 - 0x9069afff com.apple.CoreServices.OSServices 3.0.1
/System/Library/Frameworks
/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
0x90700000 - 0x90700fff com.apple.CoreServices 10.3 (???)
/System/Library/Frameworks
/CoreServices.framework/Versions/A/CoreServices
0x90720000 - 0x90787fff com.apple.audio.CoreAudio 2.1.2
/System/Library/Frameworks/CoreAud
io.framework/Versions/A/CoreAudio
0x907f0000 - 0x907f9fff com.apple.DiskArbitration 2.0.5
/System/Library/PrivateFrameworks/
DiskArbitration.framework/Versions/A/DiskArbitration
0x90810000 - 0x90810fff com.apple.ApplicationServices 1.0 (???)
/System/Library/Frameworks
/ApplicationServices.framework/Versions/A/ApplicationServices
0x90830000 - 0x9089ffff libobjc.A.dylib /usr/lib/libobjc.A.dylib
0x90940000 - 0x909b3fff com.apple.DesktopServices 1.2.4
/System/Library/PrivateFrameworks/
DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
0x909f0000 - 0x90a04fff libCGATS.A.dylib
/System/Library/Frameworks/ApplicationServ
ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCGATS.
A.dylib
0x90a20000 - 0x90b7bfff com.apple.Foundation 6.3.6 (500.58)
/System/Library/Frameworks
/Foundation.framework/Versions/C/Foundation
0x90d00000 - 0x90d1bfff com.apple.SystemConfiguration 1.7.1 (???)
/System/Library/Fr
ameworks/SystemConfiguration.framework/Versions/A/SystemConfiguration
0x90ec2000 - 0x90f7bfff com.apple.QD 3.4.67 (???)
/System/Library/Frameworks/Applica
tionServices.framework/Versions/A/Frameworks/QD.framework/Versions/A/QD
0x90fce000 - 0x90fe9fff libjava.jnilib
/System/Library/Frameworks/JavaVM.framework/Versio
ns/1.4.2/Libraries/libjava.jnilib
0x91002000 - 0x9100dfff libCSync.A.dylib
/System/Library/Frameworks/ApplicationServ
ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libCSync.
A.dylib
0x910b0000 - 0x91101fff com.apple.bom 1.2.5 (63.2)
/System/Library/PrivateFrameworks/
Bom.framework/Versions/A/Bom
0x9110d000 - 0x91176fff com.apple.htmlrendering 1.1.2
/System/Library/Frameworks/Carbon.
framework/Versions/A/Frameworks/HTMLRendering.framework/Versions/A/HTMLRendering
0x916ec000 - 0x9177ffff com.apple.print.framework.PrintCore 3.3
/System/Library/Frameworks
/ApplicationServices.framework/Versions/A/Frameworks/PrintCore.framework/Versions/A/PrintC
ore
0x917e0000 - 0x917f0fff com.apple.speech.recognition.framework 3.3
/System/Library/Fr
ameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/Spe
echRecognition
0x91810000 - 0x9182afff com.apple.openscripting 1.2.1 (???)
/System/Library/Frameworks
/Carbon.framework/Versions/A/Frameworks/OpenScripting.framework/Versions/A/OpenScripting
0x91850000 - 0x91860fff com.apple.ImageCapture 2.1.5
/System/Library/Frameworks/Carbon.
framework/Versions/A/Frameworks/ImageCapture.framework/Versions/A/ImageCapture
0x91890000 - 0x9189cfff com.apple.help 1.0.1
/System/Library/Frameworks/Carbon.framewor
k/Versions/A/Frameworks/Help.framework/Versions/A/Help
0x918c0000 - 0x918cdfff com.apple.CommonPanels 1.2.1 (1.0)
/System/Library/Frameworks
/Carbon.framework/Versions/A/Frameworks/CommonPanels.framework/Versions/A/CommonPanels
0x918f0000 - 0x9193efff com.apple.print.framework.Print 3.3
/System/Library/Frameworks
/Carbon.framework/Versions/A/Frameworks/Print.framework/Versions/A/Print
0x91990000 - 0x9199bfff com.apple.securityhi 1.2 (90)
/System/Library/Frameworks/Carbon.
framework/Versions/A/Frameworks/SecurityHI.framework/Versions/A/SecurityHI
0x919a3000 - 0x91a12fff com.apple.framework.IOKit 1.3.6 (???)
/System/Library/Frameworks
/IOKit.framework/Versions/A/IOKit
0x91a40000 - 0x91ab3fff com.apple.NavigationServices 3.3.3
/System/Library/Frameworks
/Carbon.framework/Versions/A/Frameworks/NavigationServices.framework/Versions/A/Navigation
Services
0x91b10000 - 0x91b2afff libPDFRIP.A.dylib
/System/Library/Frameworks/ApplicationServ
ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libPDFRIP
.A.dylib
0x91b50000 - 0x91b5ffff libPSRIP.A.dylib
/System/Library/Frameworks/ApplicationServ
ices.framework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libPSRIP.
A.dylib
0x91b80000 - 0x91b93fff libRIP.A.dylib
/System/Library/Frameworks/ApplicationServices.fra
mework/Versions/A/Frameworks/CoreGraphics.framework/Versions/A/Resources/libRIP.A.dylib
0x91b9a000 - 0x91d2ffff com.apple.QuickTime 6.5.2
/System/Library/Frameworks/QuickTi
me.framework/Versions/A/QuickTime
0x91dcc000 - 0x91dd0fff com.apple.JavaVM 2.0.0
/System/Library/Frameworks/JavaVM.framewor
k/Versions/A/JavaVM
0x91dd4000 - 0x91ddefff libverify.dylib
/System/Library/Frameworks/JavaVM.framewor
k/Versions/1.4.2/Libraries/libverify.dylib
0x91ebd000 - 0x91ebdfff com.apple.Carbon 10.3 (???)
/System/Library/Frameworks/Carbon.
framework/Versions/A/Carbon
0x92070000 - 0x92096fff com.apple.FindByContent 1.4 (1.2)
/System/Library/Frameworks
/ApplicationServices.framework/Versions/A/Frameworks/FindByContent.framework/Versions/A/Fi
ndByContent
0x920c0000 - 0x922a7fff com.apple.security 2.4 (177)
/System/Library/Frameworks/Securit
y.framework/Versions/A/Security
0x92430000 - 0x92468fff com.apple.LaunchServices 10.3.5 (98.4)
/System/Library/Frameworks
/ApplicationServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/L
aunchServices
0x92727000 - 0x9275ffff com.apple.AE 1.4
/System/Library/Frameworks/ApplicationServ
ices.framework/Versions/A/Frameworks/AE.framework/Versions/A/AE
0x927f0000 - 0x92827fff com.apple.CFNetwork 1.2.1 (7)
/System/Library/Frameworks/CoreSer
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--
Patrick Fleming, Ph.D.
The Johns Hopkins University
Department of Biophysics
201 Jenkins Hall
3400 North Charles Street
Baltimore, MD 21218
Tel: 410-516-7654
Fax: 410-516-4118
|
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From: Alok S. <al...@ca...> - 2005-03-15 23:28:20
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You need to select "Linked" from the style pulldown on the=20 "File->Open..." dialog. Sorry about the confusion; at some point, I=20 hope to get rid of the style pulldown and make everything Linked. -Alok On Mar 15, 2005, at 2:17 PM, Xiaoqing Zhang wrote: > Hi Alok, > > =A0 > > I downloaded the human fgf files from samples. There are two files:=20 > fgf.cpt and fgf.gtr. But I noticed that when I start JTV, there is no=20= > menu item under Analysis and Export. So I can only open the file=20 > fgf.cpt from File menu. Then I only saw tree structure at the geneTree=20= > panel, the Global pixels and Zoom pixels panel are gray colored. How=20= > can I see the nice image posted in the samples? > > =A0 > > After I load the file, I can see some menu items under =93Analysis=94. = So=20 > I tried to do =93analysis-> align to tree=94 , there is no =93Alignment=94= =20 > menu item, then I opened the .cpt or .gtr file but no effect at all. > > =A0 > > Do I miss something here? I can open other sample .cpt files without=20= > any problem. > > =A0 > > =A0 > > =A0 > > Xiaoqing > > =A0 > > =A0 > > =A0 > > =A0 > > =A0 |
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From: Xiaoqing Z. <xia...@cg...> - 2005-03-15 22:17:14
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Hi Alok, =20 I downloaded the human fgf files from samples. There are two files: = fgf.cpt and fgf.gtr. But I noticed that when I start JTV, there is no menu item = under Analysis and Export. So I can only open the file fgf.cpt from File menu. = Then I only saw tree structure at the geneTree panel, the Global pixels and = Zoom pixels panel are gray colored. How can I see the nice image posted in = the samples? =20 After I load the file, I can see some menu items under "Analysis". So I = tried to do "analysis-> align to tree" , there is no "Alignment" menu item, = then I opened the .cpt or .gtr file but no effect at all.=20 =20 Do I miss something here? I can open other sample .cpt files without any problem. =20 =20 =20 Xiaoqing =20 =20 =20 =20 =20 |
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