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From: Avilla R. E. <Eva...@us...> - 2021-03-25 19:23:28
|
Good evening, I'm trying to generate functional enrichment maps from proteomics data following the attached book chapter and I'm having an issue with JTree View. I have managed to generate a Tree with the JTreeView, using as input the .cdt file from Cluster 3.0 that contains the Log2FC values (I substituted the "1" in the output of GoMiner by the actual Log2FC between my 2 conditions as stated in the book chapter). However, it seems that JTreeView might have a problem reading my input file (?) since it's only depicting positive/0 values but not negative, and it's actually not able to generate a color scale, but all values have exactly the same color. Do you have an idea why this might be? Thanks a lot for the help in advance! Eva ____________________ Eva Avilla Royo PhD Student Laboratory for Cell and Tissue Engineering Department of Obstetrics UniversitätsSpital Zürich PATH G 67 Schmelzbergstrasse 12 8091 Zürich, Switzerland Phone: +41 44 255 32 85 Homepage: www.ehrbarlab.com<http://www.ehrbarlab.com/> |
From: Giblin, M. J <mer...@va...> - 2020-06-10 00:43:14
|
Hello, I have a dendogram generated in Cluster 3.0 that displays the % of the proteome for a particular protein. Because these are percentages, I only want positive values represented on the dendogram color scale bar. Even when I change the contrast value, it goes from say -5 to 5 but I just want it to go from 0 to 5. I know this is possible since a couple papers whose experiments and data analysis methods I am following have dendograms with scales of only positive numbers and say they used Cluster/JavaTree. I see other people have asked similar questions on here but I have not been able to find any answers. Its possible I am messing something up in Cluster, I am very new to these kinds of programs. If anyone is able to help out, that would be great! Thanks! Meredith Giblin |
From: Alok S. <alo...@gm...> - 2017-07-04 21:13:12
|
Hello, Have you tried installing the java JRE from the oracle website? http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html Hope this helps, Alok On Mon, Jun 19, 2017 at 4:14 PM, Rahim Ahmadvand <ahm...@gm...> wrote: > > Dear users, > I have installed the Java treeview-1.16r4 on my computer (64 bit- > operating system). I tried to open the software but I got the message " > windows is searching for javaw.exe. to locate the file yourself, click > Browse. " I clicked on browse and after opening javaw.exe, I got the second > error message " java(TM) webstart 10.21.2.11.fcs. I would like to know how > to solve the problem. > > Thank you in advance, > > -- > *Best regards, * > *Rahim Ahmadvand, Assistant professor, * > *Vegetable research department, Seed and Plant Improvement Institute, * > *Mahdasht Ave. 3185, P.O.Box 4119, Karaj, IRAN* > > *Tel: + 98-026-36703787 <+98%2026%203670%203787>* > > *Fax: + 98- 026-36703776 <+98%2026%203670%203776>* > > *Mobile: +98- 09127668505 <+98%20912%20766%208505>* > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > > |
From: Alok S. <alo...@gm...> - 2017-06-20 19:06:00
|
Hi Rahim, Unfortunately I don't have a lot of experience running JTV on recent windows machines. Have you tried installing a JRE directly from Oracle? Sometimes the version of java that comes preinstalled isn't fully compatible. http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html Hope this helps! Alok On Tue, Jun 20, 2017 at 1:30 PM, Rahim Ahmadvand <ahm...@gm...> wrote: > > Dear users, > I have installed the Java treeview-1.16r4 on my computer (64 bit- > operating system). I tried to open the software but I got the message " > windows is searching for javaw.exe. to locate the file yourself, click > Browse. " I clicked on browse and after opening javaw.exe, I got the second > error message " java(TM) webstart 10.21.2.11.fcs. I would like to know how > to solve the problem. > > Thank you in advance, > > > -- > *Best regards, * > *Rahim Ahmadvand, Assistant professor, * > *Vegetable research department, Seed and Plant Improvement Institute, * > *Mahdasht Ave. 3185, P.O.Box 4119, Karaj, IRAN* > > *Tel: + 98-026-36703787 <+98%2026%203670%203787>* > > *Fax: + 98- 026-36703776 <+98%2026%203670%203776>* > > *Mobile: +98- 09127668505 <+98%20912%20766%208505>* > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > > |
From: Rahim A. <ahm...@gm...> - 2017-06-20 17:30:54
|
Dear users, I have installed the Java treeview-1.16r4 on my computer (64 bit- operating system). I tried to open the software but I got the message " windows is searching for javaw.exe. to locate the file yourself, click Browse. " I clicked on browse and after opening javaw.exe, I got the second error message " java(TM) webstart 10.21.2.11.fcs. I would like to know how to solve the problem. Thank you in advance, -- *Best regards, * *Rahim Ahmadvand, Assistant professor, * *Vegetable research department, Seed and Plant Improvement Institute, * *Mahdasht Ave. 3185, P.O.Box 4119, Karaj, IRAN* *Tel: + 98-026-36703787* *Fax: + 98- 026-36703776* *Mobile: +98- 09127668505* |
From: Rahim A. <ahm...@gm...> - 2017-06-19 20:14:22
|
Dear users, I have installed the Java treeview-1.16r4 on my computer (64 bit- operating system). I tried to open the software but I got the message " windows is searching for javaw.exe. to locate the file yourself, click Browse. " I clicked on browse and after opening javaw.exe, I got the second error message " java(TM) webstart 10.21.2.11.fcs. I would like to know how to solve the problem. Thank you in advance, -- *Best regards, * *Rahim Ahmadvand, Assistant professor, * *Vegetable research department, Seed and Plant Improvement Institute, * *Mahdasht Ave. 3185, P.O.Box 4119, Karaj, IRAN* *Tel: + 98-026-36703787* *Fax: + 98- 026-36703776* *Mobile: +98- 09127668505* |
From: Alok S. <alo...@gm...> - 2017-03-22 10:43:46
|
Hi Mahesh, Did you install Java first? You may need to install a JRE, http://www.oracle.com/technetwork/java/javase/downloads/jre8-downloads-2133155.html On Wed, Mar 22, 2017 at 6:18 AM, Mahesh Appari <ap...@we...> wrote: > Dear Java tree users, > > > > I would like to install Javatree view on windows 7. It seems to me that > the program was installed. However, I am unable to open the program. > > > > Any suggestions or help would be highly appreciated. > > > > Thank you in advance. > > > > Best Regards, > > Mahesh Appari > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > > |
From: Mahesh A. <ap...@we...> - 2017-03-22 10:36:08
|
Dear Java tree users, I would like to install Javatree view on windows 7. It seems to me that the program was installed. However, I am unable to open the program. Any suggestions or help would be highly appreciated. Thank you in advance. Best Regards, Mahesh Appari |
From: Cherry, T. <Tim...@se...> - 2017-03-10 22:50:56
|
Hi, I would like to export the color bar to image or postscript. I am plotting the primary data log2 from purple (positive), to orange (zero), to pale orange (negative). The color bar, however, ranges from orange (1.00) to black (-1.00). I'm wondering how to match the color bar to the range and colors of the original heatmap. Thanks in advance for your help! -Tim Cherry CONFIDENTIALITY NOTICE: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information protected by law. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message. |
From: Alok S. <alo...@gm...> - 2016-12-09 10:40:47
|
Hi Jess, Sorry for the long delay in my reply. Do you want to extract a single list of genes at a particular correlation level containing a gene of interest, or find all lists of genes that are clustered at a certain correlation level? The first can be done fairly easily be selecting the gene of interest and using the up-arrow keyboard navigation to find the relevant parent node. The second would be tedious and error prone to do manually. I have done similar things in the past using custom perl scripts... the closest thing that's published is the colorByThreshold.pl available in the helper-scripts folder: https://sourceforge.net/p/jtreeview/git/ci/master/tree/helper-scripts/ You could run this on a mac with the following: # get the treeview source code git clone ssh://al...@gi.../p/jtreeview/git jtreeview-git # switch directories cd jtreeview-git/helper-scripts # unzip threshold.zip for an example unzip threshold.zip # add threshold coloring to some .gtr file (e.g. https://sourceforge.net/projects/jtreeview/files/examples/, look for threshold.zip) perl colorByThreshold.pl -t .5 threshold.gtr A couple of things to note: 1) The script will modify the .gtr file in place, so make sure you don't mind changing it. 2) If you call it multiple times, it will replace the colors 3) If you call the script with no args, it will print out a help message that tells you how to change the colors. Let me know if this is the kind of thing you wanted to do. If you find someone who is able to use this as a starting point to make a "splitByThreshold.pl" script, let me know and I would be happy to incorporate it into helper-scripts. Otherwise, I may be able to find time to make such a script myself, if you can be patient :) Best, Alok On Wed, Nov 30, 2016 at 7:05 PM, Jessica Schwaber <j.s...@uq...> wrote: > Hello, > > > I am using Java TreeView to look at the .cdt file output from Gene Cluster > 3.0. I do not use Java TreeView through the terminal - just the GUI > option. I want to create a sublist of genes that would cluster at a certain > correlation level. I see in the .gtr file that there may be X nodes of a > specific correlation level, but the nodes are embedded and > therefore finding a specific list of elements is manually exhausting. Also, > I can click manually on the hierarchical tree to see the correlation level > of certain clusters. How can I extract a sublist of genes at a certain > correlation level? (Obviously, I am not a programmer and have minimal to no > coding capacity). > > > Thanks! > > Jess > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > > |
From: Jessica S. <j.s...@uq...> - 2016-12-01 00:17:22
|
Hello, I am using Java TreeView to look at the .cdt file output from Gene Cluster 3.0. I do not use Java TreeView through the terminal - just the GUI option. I want to create a sublist of genes that would cluster at a certain correlation level. I see in the .gtr file that there may be X nodes of a specific correlation level, but the nodes are embedded and therefore finding a specific list of elements is manually exhausting. Also, I can click manually on the hierarchical tree to see the correlation level of certain clusters. How can I extract a sublist of genes at a certain correlation level? (Obviously, I am not a programmer and have minimal to no coding capacity). Thanks! Jess |
From: Alok S. <alo...@gm...> - 2015-10-03 02:03:56
|
Hi Vinicius, I'm still around, though mostly working on other things. I think your best bet is to make a ".jtv" file that has the same root as your cdt file (so, if it's "tree123.cdt", make a "tree123.jtv"). Java Treeview will (I think) load the settings before it renders the tree. The .jtv file is where it stores it's settings, it's simple XML, you are probably make one of your own just by editing the color settings in the GUI. Here's a example with a blue-yellow color scheme: <DocumentConfig><Views selected="0"><View type="Dendrogram" dock="1"><ColorExtractor><ColorSet up="#FEFF00" down="#1BB7E5"/></ColorExtractor></View></Views><UrlExtractor/><ArrayUrlExtractor/><MainView><ColorExtractor><ColorSet up="#0033FF" down="#FFFF00"/></ColorExtractor><ArrayDrawer/><GlobalXMap><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalXMap><GlobalYMap><FixedMap type="Fixed" scale="8.0"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalYMap><ZoomXMap><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomXMap><ZoomYMap><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomYMap><TextViewParent><TextView><GeneSummary/></TextView><TextView><GeneSummary/></TextView><TextView><GeneSummary/></TextView><TextView><GeneSummary/></TextView></TextViewParent><ArrayNameView><ArraySummary included="0"/></ArrayNameView></MainView></DocumentConfig> Please let me know if this works for you. Hope this helps, Alok On Fri, Oct 2, 2015 at 9:10 PM, Vinícius Bassaneze <vin...@ba...> wrote: > Hi, > > Is there somebody there? > I’m creating a large set of small-sized dendograms using Java TreeView > command line. > http://jtreeview.sourceforge.net/docs/JTVUserManual/single.html#ch2_flags > > But a couldn’t find an option to change up, down and zero colours. Is it > possible to do it in some alternative way? (automatically?) > > I'm currently using TreeView.jar -r $cdt -x Dendrogram -- -o $png -h 80 -w > 80 -s 36x20 -a0 -g 1,2-c 0.38 > It works, but only with give me the default colour > > best regards, > Vinicius > > > ------------------------------ > [image: Avast logo] <https://www.avast.com/antivirus> > > Este email foi escaneado pelo Avast antivírus. > www.avast.com <https://www.avast.com/antivirus> > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > > |
From: Donghun K. <kp...@gm...> - 2015-06-12 16:39:54
|
Hi, I am now generating heatmap of about 3,000 genes with k-Means by checking organized genes with 6k and 100 run. Could you help me how to order heatmap? Whenever I generate heatmap, the order of color is always changing. Please help me. Thank you very much in advance. Andy |
From: Alok S. <alo...@gm...> - 2013-08-17 08:21:18
|
Hi Fridtjof, I am having difficulty reproducing the problem. I have been able to open one file and then open a new window with "Window->New Window", then open another file in the new window. Are you using version 1.1.6r3? Does it only happen with specific files? Are able to open the file after restarting? Best, Alok On Aug 17, 2013, at 2:54, Fridtjof lund-johansen <fri...@gm...> wrote: > Hello, > > I have installed TreeView on several computers. Two have Windows7 one has XP. The program keeps crashing when I open new cdt files. It happens nearly every time I open a new window and load another file. I then have to use the task manager to end the program and start again. > > I love the program, so if there is any way to fix this problem I would be very grateful. > > Best regards, > > Fridtjof Lund-Johansen > Oslo University Hospital > Oslo, Norway > ------------------------------------------------------------------------------ > Get 100% visibility into Java/.NET code with AppDynamics Lite! > It's a free troubleshooting tool designed for production. > Get down to code-level detail for bottlenecks, with <2% overhead. > Download for free and get started troubleshooting in minutes. > http://pubads.g.doubleclick.net/gampad/clk?id=48897031&iu=/4140/ostg.clktrk > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users |
From: Fridtjof lund-j. <fri...@gm...> - 2013-08-17 06:54:32
|
Hello, I have installed TreeView on several computers. Two have Windows7 one has XP. The program keeps crashing when I open new cdt files. It happens nearly every time I open a new window and load another file. I then have to use the task manager to end the program and start again. I love the program, so if there is any way to fix this problem I would be very grateful. Best regards, Fridtjof Lund-Johansen Oslo University Hospital Oslo, Norway |
From: Alok S. <alo...@gm...> - 2013-01-07 12:19:20
|
Hi Varun, It appears that there are some bugs related to k-means heatmaps. As a fallback, your best bet may be to take screenshots. Could you send me an example file? I should be able to figure out what the issues are and whether I will have time to fix within the next week or so. Thanks, Alok On Wed, Jan 2, 2013 at 4:39 PM, varun gupta <gup...@ya...>wrote: > Hi Everyone > > I am using Java TreeView software for generating some heatmaps. I used > Cluster software on my list of 22000 genes and generated .cdt files which > are input for Java Treeview > > I run this command to open up the interface of treeview software > > > *java -jar -Xmx500m /apps1/treeview/1.1.6r2/TreeView.jar* > > * > * > > File ---> Open -->Selecting appropriate .cdt file ----> style as *kmeans* > > * > * > > Now here's the problem. When I do style as kmeans a heat map is generated. > I change the pixels and all so as to view it better and try to save the > image by going to Export---> Save Tree Image > > But nothing happens. When I use the style as *linked* I can save the > images. > > I am not sure but is it because I have around 22000 genes and around 50 > columns which is not letting me save the image of the heatmap on the kmeans > style. > > Hope to find solution at the earliest from you guys > > > Regards > > Varun > > > ------------------------------------------------------------------------------ > Master Java SE, Java EE, Eclipse, Spring, Hibernate, JavaScript, jQuery > and much more. Keep your Java skills current with LearnJavaNow - > 200+ hours of step-by-step video tutorials by Java experts. > SALE $49.99 this month only -- learn more at: > http://p.sf.net/sfu/learnmore_122612 > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > > |
From: varun g. <gup...@ya...> - 2013-01-02 21:39:57
|
Hi Everyone I am using Java TreeView software for generating some heatmaps. I used Cluster software on my list of 22000 genes and generated .cdt files which are input for Java Treeview I run this command to open up the interface of treeview software java -jar -Xmx500m /apps1/treeview/1.1.6r2/TreeView.jar File ---> Open -->Selecting appropriate .cdt file ----> style as kmeans Now here's the problem. When I do style as kmeans a heat map is generated. I change the pixels and all so as to view it better and try to save the image by going to Export---> Save Tree Image But nothing happens. When I use the style as linked I can save the images. I am not sure but is it because I have around 22000 genes and around 50 columns which is not letting me save the image of the heatmap on the kmeans style. Hope to find solution at the earliest from you guys Regards Varun |
From: Alok S. <alo...@gm...> - 2011-08-09 22:21:59
|
Hi John, 1) What exactly happens? 2) Have you tried installing java directly from oracle? Sometimes there are problems with the preinstalled java, here is a recent edition: http://www.oracle.com/technetwork/java/javase/downloads/jre-6u26-download-400751.html 3) Have you tried 1.1.5r2 ( http://sourceforge.net/projects/jtreeview/files/jtreeview/1.1.5r2/ )? Please let me know if any of these suggestions help. I believe java treeview has been worked on other windows 7 systems. Best, Alok On Tue, Aug 9, 2011 at 10:42 AM, John Rakus <jr...@ny...> wrote: > Hello, > > I recently purchased a Windows 7 Professional-operated computer and I can > no longer open Java TreeView. Are there any recommendations as to how to > overcome this problem? I assume there is a reasonably simple settings issue > that needs to be changed but I am at a loss as what to do. I use TreeView > quite frequently in my research. > > Regards, > > > -- > John F. Rakus, Ph.D. > Postdoctoral Fellow > Lara K. Mahal Laboratory > Department of Chemistry > New York University > 100 Washington Square East, Room 1001 > New York, NY 10003 > 212-992-6959 > jr...@ny... > > > ------------------------------------------------------------------------------ > uberSVN's rich system and user administration capabilities and model > configuration take the hassle out of deploying and managing Subversion and > the tools developers use with it. Learn more about uberSVN and get a free > download at: http://p.sf.net/sfu/wandisco-dev2dev > > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > > |
From: John R. <jr...@ny...> - 2011-08-09 14:42:52
|
Hello, I recently purchased a Windows 7 Professional-operated computer and I can no longer open Java TreeView. Are there any recommendations as to how to overcome this problem? I assume there is a reasonably simple settings issue that needs to be changed but I am at a loss as what to do. I use TreeView quite frequently in my research. Regards, -- John F. Rakus, Ph.D. Postdoctoral Fellow Lara K. Mahal Laboratory Department of Chemistry New York University 100 Washington Square East, Room 1001 New York, NY 10003 212-992-6959 jr...@ny... |
From: Alok S. <alo...@gm...> - 2011-04-16 23:41:35
|
This was a bug on the registration server, and is now fixed. On Mon, Mar 21, 2011 at 10:59 PM, Francismar Corrêa <fr...@gm...>wrote: > Hello Everybody > I am trying to install the version 1.5 r2 for mac of Tree view (green > tree in the application file), but the system never finished the > register! Always they return with message below: > > "Error reading response, could not complete registration > exception java.io.IOException: Server returned HTTP response code: 503 > for URL: http://jtreeview.sourceforge.net/reg/register.php > if problems persist please alert java treeview maintainers > (jtr...@li...). > > Would someone help me please? What is going on? > > Thank you ! > > > > > -- > Dra. Francismar Corrêa Marcelino > Genética Molecular de Plantas > Embrapa Soja > Rod. Carlos Strass, caixa postal 231 > Distrito de Warta > Londrina PR - 86001-970 > Tel: 55 43 3371 6265 > Fax: 55 43 3371 6100 > > > ------------------------------------------------------------------------------ > Enable your software for Intel(R) Active Management Technology to meet the > growing manageability and security demands of your customers. Businesses > are taking advantage of Intel(R) vPro (TM) technology - will your software > be a part of the solution? Download the Intel(R) Manageability Checker > today! http://p.sf.net/sfu/intel-dev2devmar > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > |
From: Cornet, M. <mc...@ch...> - 2011-04-15 15:46:15
|
Please, can you help mu I cannot registrer Thanks Dr Muriel Cornet Parasitologie-Mycologie. Institut de Biologie et de Pathologie CHU de Grenoble BP 217 38043 Grenoble cedex 9 France Tel: 33 4 76 76 54 90 / 53 50 Fax: 33 4 76 76 56 60 MC...@ch... TIMC-TheREx (UMR 5525 CNRS-UJF) Université Joseph Fourier Domaine de la Merci 38706 La Tronche France tel : 33 4 76 63 74 39 Fax: 33 4 76 63 75 59 |
From: Alok S. <al...@us...> - 2011-03-22 07:31:15
|
Hi Francismar, Thanks for this error report! It looks like there is an issue with registration. This should not affect the functionality of Java Treeview- for now you can just select "Do not register" and it should be fine - you can always register later by selecting "Help->Registration...". I will probably not have time to fix this until the weekend, will hopefully have a status update for you then. Best, Alok On Mon, Mar 21, 2011 at 10:59 PM, Francismar Corrêa <fr...@gm...>wrote: > Hello Everybody > I am trying to install the version 1.5 r2 for mac of Tree view (green > tree in the application file), but the system never finished the > register! Always they return with message below: > > "Error reading response, could not complete registration > exception java.io.IOException: Server returned HTTP response code: 503 > for URL: http://jtreeview.sourceforge.net/reg/register.php > if problems persist please alert java treeview maintainers > (jtr...@li...). > > Would someone help me please? What is going on? > > Thank you ! > > > > > -- > Dra. Francismar Corrêa Marcelino > Genética Molecular de Plantas > Embrapa Soja > Rod. Carlos Strass, caixa postal 231 > Distrito de Warta > Londrina PR - 86001-970 > Tel: 55 43 3371 6265 > Fax: 55 43 3371 6100 > > > ------------------------------------------------------------------------------ > Enable your software for Intel(R) Active Management Technology to meet the > growing manageability and security demands of your customers. Businesses > are taking advantage of Intel(R) vPro (TM) technology - will your software > be a part of the solution? Download the Intel(R) Manageability Checker > today! http://p.sf.net/sfu/intel-dev2devmar > _______________________________________________ > Jtreeview-users mailing list > Jtr...@li... > https://lists.sourceforge.net/lists/listinfo/jtreeview-users > |
From: Francismar C. <fr...@gm...> - 2011-03-22 02:59:37
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Hello Everybody I am trying to install the version 1.5 r2 for mac of Tree view (green tree in the application file), but the system never finished the register! Always they return with message below: "Error reading response, could not complete registration exception java.io.IOException: Server returned HTTP response code: 503 for URL: http://jtreeview.sourceforge.net/reg/register.php if problems persist please alert java treeview maintainers (jtr...@li...). Would someone help me please? What is going on? Thank you ! -- Dra. Francismar Corrêa Marcelino Genética Molecular de Plantas Embrapa Soja Rod. Carlos Strass, caixa postal 231 Distrito de Warta Londrina PR - 86001-970 Tel: 55 43 3371 6265 Fax: 55 43 3371 6100 |
From: Alok S. <al...@us...> - 2011-02-24 15:01:40
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If you type the following before the java command in your terminal, does the java command succeed? Xvfb :100 -ac export DISPLAY=100.0 If it does, then your server code needs to do the following before generating a PNG: 1) check if Xvfb is running and if not, start up a new process 2) set DISPLAY to 100.0 Regarding your questions, 1) I don't quite understand. The only way to generate an image is using a command similar to the one you have supplied. Would you like to have the images output to stdout instead to avoid writing them to disk? This would be pretty easy to add. 2a) It should be possible for perl to construct command lines similar to the one you have supplied and to generate PNG images that can be served to the client. 2b) It is not possible for java treeview to provide an interactive experience through a perl web application. 2c) However, you could run java treeview as an applet. The perl web application could create a .cdt file on disk, and then serve a page with the applet pointing at that new url. You can see the applet in action here: http://jtreeview.sourceforge.net/examples/applets.html Hope this helps, Alok On Thu, Feb 24, 2011 at 8:47 AM, brajendra kumar <bra...@gm...>wrote: > Hi Alok, > > Thank you for your quick response. > > I believe i did not convey the Treeview issue precisely in last mail. > > *Requirement* > > The plan is to integrate the Tree viewer in to our web application > (cgi-perl). > so as to > - generate a dendogram from *.cdt file (generated from Cluster 3.0) in the > backend (linux), - create a *.png file and > - finally display the image to the end-user via our front-end > > Currently, I run the command "*java -jar TreeView.jar -r > ~/Hclust_NGS/dlcl.cdt -x Dendrogram -- -o ./braj_image.png -s 10x1 -a 0 -c 1 > *" from my terminal and it fails with DISPLAY not set error "*(.:22914): > Gtk-WARNING **: cannot open display:*" > > 1. Is there any possibility of generating a PNG without 'export' option > from the command line? > > 2. Can treeview browser be integrated to perl code so that end-user can > view the treeview browser as part of our web application? > > > > Regards, > Brajendra Kumar > > > > > > > On 23 February 2011 22:07, Alok Saldanha <al...@us...>wrote: > >> I'm using AWT to render the image, and it most likely needs an x server on >> linux. I recommend running XVFB. Try doing the following before you run >> java: >> >> Xvfb :100 -ac >> export DISPLAY=100.0 >> >> Best, >> Alok >> >> >> On Wed, Feb 23, 2011 at 8:15 AM, brajendra kumar <bra...@gm...>wrote: >> >>> Hi Alok, >>> >>> I had downloaded the "TreeView-1.1.5r2-bin.tar.gz" file and want to run >>> it from command line on my *centos x86_64 server* with >>> *java version "1.4.2*" and gij (GNU libgcj) version 4.1.2 20080704 *(Red >>> Hat 4.1.2-44*) >>> >>> But while executing the command i am getting the error as below >>> >>> *###################################################* >>> -bash-3.1$ cd TreeView-1.1.5r2-bin >>> -bash-3.1$ ll >>> total 364 >>> drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 coordinates >>> -rw-r--r-- 1 brajcn brajcn 18009 Jun 26 2010 gpl.txt >>> drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 images >>> drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 lib >>> drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 META-INF >>> drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 plugins >>> -rw-r--r-- 1 brajcn brajcn 322184 Jun 26 2010 TreeView.jar >>> -rw-r--r-- 1 brajcn brajcn 32 Jun 26 2010 win32TreeView.bat >>> -bash-3.1$ *java -jar -Xmx500m TreeView.jar* >>> File not found, will try from URL >>> Making new configuration file /home/brajcn/.javaTreeViewXmlrc >>> Plugin Jar >>> jar:file:/home/brajcn/Hclust_NGS/JtreeView/TreeView-1.1.5r2-bin/./plugins/Dendrogram.jar!/ >>> >>> (.:15569): Gtk-WARNING **: cannot open display: >>> >>> >>> -bash-3.1$ *java -jar TreeView.jar -r ~/Hclust_NGS/dlcl.cdt -x >>> Dendrogram -- -o ./braj_image.png -s 10x1 -a 0 -c 1* >>> File not found, will try from URL >>> Making new configuration file /home/brajcn/.javaTreeViewXmlrc >>> Plugin Jar >>> jar:file:/home/brajcn/Hclust_NGS/JtreeView/TreeView-1.1.5r2-bin/./plugins/Dendrogram.jar!/ >>> >>> (.:15631): Gtk-WARNING **: cannot open display: >>> -bash-3.1$ >>> * >>> >>> #################################################################################### >>> * >>> >>> >>> My purpose is just to create the .png from the *.cdt file. >>> >>> >>> I wonder the same commands are working on my local machine with >>> Linux(fedora) GUI. >>> >>> Can you help me resolving the error i am getting on server, so that i can >>> successfully create the deprogram image. >>> >>> I will greatly appreciate your response in this concern. >>> >>> >>> Thanks, >>> Brajendra Kumar >>> +91-9884859121 >>> >>> India >>> >>> >>> >>> >>> >> > |
From: Alok S. <al...@us...> - 2011-02-23 16:37:16
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I'm using AWT to render the image, and it most likely needs an x server on linux. I recommend running XVFB. Try doing the following before you run java: Xvfb :100 -ac export DISPLAY=100.0 Best, Alok On Wed, Feb 23, 2011 at 8:15 AM, brajendra kumar <bra...@gm...>wrote: > Hi Alok, > > I had downloaded the "TreeView-1.1.5r2-bin.tar.gz" file and want to run it > from command line on my *centos x86_64 server* with > *java version "1.4.2*" and gij (GNU libgcj) version 4.1.2 20080704 *(Red > Hat 4.1.2-44*) > > But while executing the command i am getting the error as below > > *###################################################* > -bash-3.1$ cd TreeView-1.1.5r2-bin > -bash-3.1$ ll > total 364 > drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 coordinates > -rw-r--r-- 1 brajcn brajcn 18009 Jun 26 2010 gpl.txt > drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 images > drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 lib > drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 META-INF > drwxr-xr-x 2 brajcn brajcn 4096 Jun 26 2010 plugins > -rw-r--r-- 1 brajcn brajcn 322184 Jun 26 2010 TreeView.jar > -rw-r--r-- 1 brajcn brajcn 32 Jun 26 2010 win32TreeView.bat > -bash-3.1$ *java -jar -Xmx500m TreeView.jar* > File not found, will try from URL > Making new configuration file /home/brajcn/.javaTreeViewXmlrc > Plugin Jar > jar:file:/home/brajcn/Hclust_NGS/JtreeView/TreeView-1.1.5r2-bin/./plugins/Dendrogram.jar!/ > > (.:15569): Gtk-WARNING **: cannot open display: > > > -bash-3.1$ *java -jar TreeView.jar -r ~/Hclust_NGS/dlcl.cdt -x Dendrogram > -- -o ./braj_image.png -s 10x1 -a 0 -c 1* > File not found, will try from URL > Making new configuration file /home/brajcn/.javaTreeViewXmlrc > Plugin Jar > jar:file:/home/brajcn/Hclust_NGS/JtreeView/TreeView-1.1.5r2-bin/./plugins/Dendrogram.jar!/ > > (.:15631): Gtk-WARNING **: cannot open display: > -bash-3.1$ > * > > #################################################################################### > * > > > My purpose is just to create the .png from the *.cdt file. > > > I wonder the same commands are working on my local machine with > Linux(fedora) GUI. > > Can you help me resolving the error i am getting on server, so that i can > successfully create the deprogram image. > > I will greatly appreciate your response in this concern. > > > Thanks, > Brajendra Kumar > +91-9884859121 > > India > > > > > |