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''Java'' (or more specifically the ''Java virtual machine'') is software that enables programs written in the ''Java language'' to operate essentially identically on multiple computer platforms, such as Microsoft Windows, Apple Mac OS X, and linux, without special adaptation to each platform. [[Jmol]] is one such program. Jmol will not operate unless Java is installed on the host computer. Since interactive molecular visualizations in [[Proteopedia]] depend upon Jmol, both Proteopedia and Jmol require Java.
''Java'' (or more specifically the ''Java virtual machine'') is software that enables programs written in the ''Java language'' to operate essentially identically on multiple computer platforms, such as Microsoft Windows, Apple Mac OS X, and linux, without special adaptation to each platform. [[Jmol]] can operate using Java or HTML5/Javascript. Jmol cannot operate in Java-mode unless Java is installed on the host computer. '''Interactive molecular visualizations in [[Proteopedia]] are computationally demanding and will perform best in Java-mode at this time'''.
* See [[Installing and enabling Java]] to make sure Java is up to date, and enabled in your favorite web browser.
* See [[Using Java for Rendering Structures]] for how to opt in to Java mode in Proteopedia.


Java is bundled with Mac OS X (10.6 and earlier), and the Apple ''Software Update'' on Macs upgrades Java as new versions are released. (For Mac OS 10.7 Lion, Java must be installed by the user.) Microsoft Windows does not provide Java, but it can easily be installed or updated by visiting [http://java.com Java.Com]. The original (and still most widely used) Java is developed by Sun Microsystems (a subsidiary of Oracle Corporation), and [http://en.wikipedia.org/wiki/Java_(software_platform)#Licensing since mid-2007, has been open-source software].
The original (and still most widely used) Java is developed by Sun Microsystems (a subsidiary of Oracle Corporation), and [http://en.wikipedia.org/wiki/Java_(software_platform)#Licensing since mid-2007, has been open-source software].


Apple adapted Java to work efficiently on OS 10.6 and earlier OS versions (citation needed). Apple Java is typically many versions behind Sun Java. For example, in March, 2011, the current Apple Java is 1.5.0_28 while Sun Java (e.g. installed on MS Windows) is 1.6.0_22. Beginning with OS 10.7 Lion, Apple is managing Java differently (details needed).
Occasionally bugs in current java releases affect the performance of Proteopedia or Jmol. These are generally resolved in subsequent releases. You should be able to bypass these problems now by running Jmol withing Proteopedia in HTML5/Javascript mode.
 
Occasionally bugs in current java releases affect the performance of Proteopedia or Jmol. These are generally resolved in subsequent releases.  


==Enable Java on your computer==
==Enable Java on your computer==
Besides any Preferences setup, you might need to go to [http://www.java.com/en/download/installed.jsp?detect=jre ''Do I Have Java?''] and enable Java by clicking on the ''inactive plugin'' statement, if present.  
Please see [[Installing and enabling Java]] for detailed instructions.


==Detecting your Java version==
==Detecting your Java version==
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In January, 2013, the [http://www.us-cert.gov/cas/techalerts/TA13-032A.html US Department of Homeland Security issued a warning recommending that Java be disabled in web browsers]. For a few days at the end of January, 2013, Apple blocked the use of java in web browsers on Mac computers worldwide. This was a major inconvenience to some, but clearly Apple felt the security risks were quite serious. Oracle, the company providing Java, subsequently fixed some of the vulnerabilities in Java (and Apple re-enabled Java on Macs), but most likely other security risks remain.
In January, 2013, the [http://www.us-cert.gov/cas/techalerts/TA13-032A.html US Department of Homeland Security issued a warning recommending that Java be disabled in web browsers]. For a few days at the end of January, 2013, Apple blocked the use of java in web browsers on Mac computers worldwide. This was a major inconvenience to some, but clearly Apple felt the security risks were quite serious. Oracle, the company providing Java, subsequently fixed some of the vulnerabilities in Java (and Apple re-enabled Java on Macs), but most likely other security risks remain.
In January 2014, Proteopedia moved to using a signed Java applet certified by the Jmol developers. Jmol is developed in the open by trustworthy developers and users can now easily opt to accept to run the Java code from these developers.


==How to be as safe as possible with Java==
==How to be as safe as possible with Java==


Assuming that you wish to use Proteopedia and other Jmol-based resources, such as [[FirstGlance in Jmol]], you will need java. (If you don't, simply uninstall Java.) How can you minimize your risk?
Assuming that you wish to use Proteopedia and other Jmol-based resources, such as [[FirstGlance in Jmol]], at their optimum ability you will need java. (If you don't, simply uninstall Java.) How can you minimize your risk?


*Whenever an '''update''' for Java is available, install it. To confirm that you have the latest Java, visit [http://java.com/ java.com], click on the link "Do I have Java?" and then on the button "Verify Java".
*Whenever an '''update''' for Java is available, install it. To confirm that you have the latest Java, visit [http://java.com/ java.com], click on the link "Do I have Java?" and then on the button "Verify Java".
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*'''Disable java''' in the web browser that you use for general-purpose browsing, email, google searches, etc. Here are instructions for [http://www.java.com/en/download/help/disable_browser.xml disabling java in a particular browser]. Use a '''different browser''' for resources that require Java.
*'''Disable java''' in the web browser that you use for general-purpose browsing, email, google searches, etc. Here are instructions for [http://www.java.com/en/download/help/disable_browser.xml disabling java in a particular browser]. Use a '''different browser''' for resources that require Java.
**'''Windows users''': Due to a limitation in Internet Explorer, you should '''use Internet Explorer for java'''. Use a different browser such as Firefox or Chrome for general web browsing, and disable java in that browser.
**'''Windows users''': Due to a limitation in Internet Explorer, you should '''use Internet Explorer for java'''. Use a different browser such as Firefox or Chrome for general web browsing. [[Installing_and_enabling_Java#Java_Applets_Do_Not_Work_In_Chrome|Chrome no longer supports Java]], but you should disable Java in Firefox for general web browsing.


These recommendations were made by Michael Horowitz in his Defensive Computing Blog in his January 2013 post [http://blogs.computerworld.com/cybercrime-and-hacking/21626/how-be-safe-possible-java How to be as safe as possible with Java].
These recommendations were made by Michael Horowitz in his Defensive Computing Blog in his January 2013 post [http://blogs.computerworld.com/cybercrime-and-hacking/21626/how-be-safe-possible-java How to be as safe as possible with Java].


==Adding Proteopedia to the Java Exceptions list==
==Jmol is now a signed Java applet==
In the quest to make Java less of a security risk Oracle has made it so that after January 15th, 2014, Java will no longer work with unsigned Java applets. The current version of Jmol in Proteopedia runs on such an applet.  We are addressing this but in the meantime to make Jmol work within Proteopedia End-users will have to add the Proteopedia site to a list of allow exceptions on their own computers. Here is how to do this:
In the quest to make Java less of a security risk Oracle has made it so that after January 15th, 2014, Java will no longer work with unsigned Java applets. Jmol on Proteopedia now runs with a signed applet and so you should be able to run Jmol in Java mode with no problem if you have an up to date installation of Java.
 
Recently with the changes users had to add Proteopedia to a trusted list of applets. We are leaving these oboselete directions on how to do that below in case you have issues while this transition is still new.
 
The version of the [[Jmol]] structure viewer previously utilized by Proteopedia ran on an unsigned applet.  If you are having problems because you have not updated your Java and are unable to at the present time, you may be able to add the Proteopedia site to a list of allow exceptions on your computer and get past security warnings. The following is how to do this:


* Copy the below URL to your clipboard by highlighting the text and select '''copy''' from under your browsers edit menu.
* Copy the below URL to your clipboard by highlighting the text and select '''copy''' from under your browsers '''edit''' menu.
     <code><nowiki>http://proteopedia.org/wiki/</nowiki></code>
     <code><nowiki>http://proteopedia.org/wiki/</nowiki></code>
      
      
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     Linux/Solaris - Run the jcontrol command.
     Linux/Solaris - Run the jcontrol command.


* Choose the Security tab.
* Choose the '''Security tab'''.
* Click the '''Edit Site List''' button near the bottom left.
* Click the '''Edit Site List''' button near the bottom left.
*Click the '''Add''' button and paste in the text you copied earlier.
*Click the '''Add''' button and paste in the text you copied earlier.
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*Open or reload the page on Proteopedia in your browser and you should get prompts you can now allow to activate Java again..
*Open or reload the page on Proteopedia in your browser and you should get prompts you can now allow to activate Java again..


The technical version of above with some images that may help can be found [https://blogs.oracle.com/java-platform-group/entry/upcoming_exception_site_list_in?msgid=3-9509477622 here] under '''Adding a site to the Exception Site List''''.  
The technical version of above with some images that may help can be found [https://blogs.oracle.com/java-platform-group/entry/upcoming_exception_site_list_in?msgid=3-9509477622 here], under '''Adding a site to the Exception Site List'''.
 
At present Proteopedia uses a signed applet and adding Proteopedia to the exceptions list '''should not be needed'''.
 
==An alternative to Java has been implemented in Proteopedia==
 
The solely Java-based [[Jmol]] has been phased out of Jmol development in favor of a version of Jmol that does not absolutely require Java, see [http://wiki.jmol.org/index.php/JSmol JSmol object in the Jmol wiki]). It has the ability to either run in Java or use HTML5/Javascript on devices or machines not running Java.
 
Proteopedia is now using this new version of [[Jmol]]. This offers users a way to use Proteopedia without the need for Java. Another big advantage is that even tablets and mobile devices can now use Proteopedia. It is now even possible to author on your favorite tablet an entire page that includes 3D Proteopedia scenes.


Soon Proteopedia will use a signed applet that will have the option of allowing people to also work completely without Java, meaning mobile devices such as tablets should then be able to use Proteopedia. However, making all of Proteopedia work with the new version will take some time. We are hoping to have it working before the end of January. We advise you to take advantage of this above workaround in the interim.
Java-based [[Jmol]] has significant performance advantages over running in the HTML5/Javascript and power users may wish to keep using Java-based Jmol. Registered Proteopedia users wishing to still use Java-based [[Jmol]] still have that ability. It just needs to be on your machine and enabled in your Proteopedia preferences. Non-registered users can simply append <code>?_USE=SIGNED</code> to the URL of any Proteopedia page. For more about these options, see [[Using Java for Rendering Structures|here]].  


==Long term solution==
For those wishing to see how the performance differs, we have [[Testing PDB File Sizes|a benchmarking page testing various structures operating on different platforms in different modes]].


It appears likely that Java-based Jmol will eventually be phased out in favor of a version of Jmol that does not require Java, called [http://sourceforge.net/projects/jsmol/ JSmol] (see also [http://wiki.jmol.org/index.php/JSmol JSmol in the Jmol wiki]).
==Controlling if Proteopedia scenes are rendered with Java==
See [[Using Java for Rendering Structures]] for how to opt in to Java mode. Otherwise, the default is the HMTL5/Javascript mode that has slower performance.


==See Also==
==See Also==
* [[Installing and enabling Java]]
* [[Using Java for Rendering Structures]]
* [http://en.wikipedia.org/wiki/Java_(software_platform) Java (software platform)] at Wikipedia.
* [http://en.wikipedia.org/wiki/Java_(software_platform) Java (software platform)] at Wikipedia.
* [http://www.apple.com/pr/library/2010/11/12openjdk.html Oracle and Apple Announce OpenJDK Project for Mac OS X] (November, 2010).
* [http://www.apple.com/pr/library/2010/11/12openjdk.html Oracle and Apple Announce OpenJDK Project for Mac OS X] (November, 2010).
Retrieved from "https://proteopedia.org/Java"