Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:
-
Story Points:2.5
-
Epic Link:
-
Sprint:Spring 2 : 20 Jan to 31 Jan, Spring 3 : 3 Feb to 14 Feb
Description
IGB uses the Genoviz Software Development Kit (SDK), a Swing-based library that implements animated, one-dimensional zooming and many other useful features for genome visualization.
App developers need better documentation for the Genoviz SDK so that they can make use of its features in Apps. Also, IGB platform developers need better documentation so that they can improve the core IGB infrastructure.
When Genoviz was first released as a commercial product, developer Eric Blossom created an interactive tutorial for Genoviz features that used Java applets. The tutorial consists of several interlinked Web pages with embedded java applets.
However, to run the tutorial, users need to configure their Web browser to enable java applets. Also, the java applet tags within the pages may need to be updated with new classpaths, as we changed how the library is getting built when we moved from ant to maven based build system.
For this task, look into the code base and figure out how to get the applets to run properly in the tutorial.
Note: This paper gives a high-level overview of Genoviz SDK https://www.ncbi.nlm.nih.gov/pubmed/19706180
Attachments
Issue Links
Activity
This is good - thanks Pawan Bole
Please can you also give step-by-step instructions explaining to a user what they must do to run the applets in the tutorial?
Some basic information of applets and how to run applets using Appletviewer can be found on the link below.
https://www.geeksforgeeks.org/java-applet-basics/
Thanks Pawan Bole
Please provide detailed step-by-step instructions on how to run the applets using appletviewer.
Applets are no longer supported/deprecated by all major browsers as they do not support the Netscape Plugin API(NPAPI).
The only browser that supports is Internet explorer.
However, I tried an example by building a simple applet.
For example, http://journals.ecs.soton.ac.uk/java/tutorial/getStarted/applet/index.html
I tried loading in Internet Explorer and it failed to load the applet.
Also, using the Appletviewer I was able to load the applet.
The Appletviewer and applet tags are no longer supported from Java 9 and above versions.
https://docs.oracle.com/javase/9/docs/api/java/applet/package-summary.html
https://www.oracle.com/technetwork/java/javase/9-deprecated-features-3745636.html
Pawan Bole - thanks for the summary yesterday about applet tags. Please document same here.
Please test to determine this fix works for MacOS Chrome not just Windows Chrome.
Following is the link to enable Java in web browsers.
https://www.digitalcitizen.life/how-enable-java-all-major-web-browsers
Please fork this https://bitbucket.org/lorainelab/genoviz-sdk-demos for next steps.
Hi, Dr. [~aloraine]:
Following are the steps to load the site
1. Build the Genoviz project
2. Open the local repository and navigate to \src\main\resources\html and open index.html
To load the applet.
1. Inspect element for the applet in the web browser.
For example :
<applet codebase="../demo" archive="genoviz.jar" code="genoviz.tutorial.SimpleMap1" height="150" width="570">
2. From the code, attribute select the class you want to load. In the above example, it is SimpleMap1.
3. Using NetBeans load the genoviz tutorial project.
4. In the projects, section click on Source Packages and then click on com.affymetrix.genoviz.tutorial
5. Right-click on the respective class to execute, for example, right-click on "SimpleMap1.java" and click run.
6. The applet is loaded for the class.
If you are using an older version of Netbeans you will not have an option on right-click on the class to run.
Instead, you can use the following command in the command line.
java -Dfile.encoding=UTF-8 -classpath "target classes path;Genoviz jar path" com.affymetrix.genoviz.tutorial.SimpleMap1
For example:
java -Dfile.encoding=UTF-8 -classpath "G:\LoraineLab\genoviz-sdk-demos\target\classes;C:\Users\pawan\.m2\repository\com\affymetrix\genoviz\1.1.8\genoviz-1.1.8.jar" com.affymetrix.genoviz.tutorial.SimpleMap1