Java - Revision history

Eric Martz: /* How to be as safe as possible with Java */

2015-09-03T17:20:04Z

How to be as safe as possible with Java

← Older revision		Revision as of 17:20, 3 September 2015
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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].

Eric Martz at 04:46, 27 April 2014

2014-04-27T04:46:09Z

← Older revision		Revision as of 04:46, 27 April 2014
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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]] 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 [[Using Java for Rendering Structures~~\|here~~]] for how to opt in to Java mode.		''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. You should be able to bypass these problems now by running Jmol withing Proteopedia in HTML5/Javascript mode.

	==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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	==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).

Eric Martz: /* Controlling if Proteopedia scenes are rendered with Java */

2014-04-25T16:05:37Z

Controlling if Proteopedia scenes are rendered with Java

← Older revision		Revision as of 16:05, 25 April 2014
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	==Controlling if Proteopedia scenes are rendered with Java==		==Controlling if Proteopedia scenes are rendered with Java==
	See [[Using Java for Rendering Structures~~\|here~~]] for how to opt in to Java mode. Otherwise, the default is ~~for~~ the HMTL5/Javascript mode that has ~~slightly weaker~~ performance.		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==
	* [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).

Wayne Decatur: /* Controlling if Proteopedia scenes are rendered with Java */

2014-01-29T05:30:51Z

Controlling if Proteopedia scenes are rendered with Java

← Older revision		Revision as of 05:30, 29 January 2014
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	==Controlling if Proteopedia scenes are rendered with Java==		==Controlling if Proteopedia scenes are rendered with Java==
	See [[Using Java for Rendering Structures\|here]] for how to opt in to Java mode. Otherwise the default is for the HMTL5/Javascript mode that has slightly weaker performance.		See [[Using Java for Rendering Structures\|here]] for how to opt in to Java mode. Otherwise, the default is for the HMTL5/Javascript mode that has slightly weaker performance.


	==See Also==		==See Also==
	* [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).

Wayne Decatur at 04:52, 29 January 2014

2014-01-29T04:52:56Z

← Older revision		Revision as of 04:52, 29 January 2014
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	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]].		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]].

			==Controlling if Proteopedia scenes are rendered with Java==
			See [[Using Java for Rendering Structures\|here]] for how to opt in to Java mode. Otherwise the default is for the HMTL5/Javascript mode that has slightly weaker performance.


	==See Also==		==See Also==
	* [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).

Wayne Decatur at 04:51, 29 January 2014

2014-01-29T04:51:04Z

← Older revision		Revision as of 04:51, 29 January 2014
Line 1:		Line 1:
	''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'''.		''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 [[Using Java for Rendering Structures\|here]] for how to opt in to Java mode.

	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].		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].

Wayne Decatur: /* An alternative to Java has been implemented in Proteopedia */

2014-01-29T03:36:39Z

An alternative to Java has been implemented in Proteopedia

← Older revision		Revision as of 03:36, 29 January 2014
Line 73:		Line 73:
	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.		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.

	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]].		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]].

	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]].		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]].

Wayne Decatur: /* An alternative to Java has been implemented in Proteopedia */

2014-01-29T03:36:00Z

An alternative to Java has been implemented in Proteopedia

← Older revision		Revision as of 03:36, 29 January 2014
Line 73:		Line 73:
	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.		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.

	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 [[~~here\|~~Using Java for Rendering Structures]].		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]].

	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]].		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]].

Wayne Decatur at 03:33, 29 January 2014

2014-01-29T03:33:54Z

← Older revision		Revision as of 03:33, 29 January 2014
Line 67:		Line 67:
	At present Proteopedia uses a signed applet and adding Proteopedia to the exceptions list '''should not be needed'''.		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==		==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.		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]] ~~on Proteopedia~~. 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 possible to author an entire page ~~and make~~ Proteopedia scenes ~~on your favorite tablet~~.		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.

	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 preferences. ~~Java~~-~~based~~ [[~~Jmol~~]] ~~has significant performance advantages over running in the HTML5/Javascript and power users may wish to keep using Java-based Jmol~~.		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 [[here\|Using Java for Rendering Structures]].

	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]].		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]].

Wayne Decatur: /* An alternative to Java has been implemented */

2014-01-28T16:01:10Z

An alternative to Java has been implemented

← Older revision		Revision as of 16:01, 28 January 2014
Line 74:		Line 74:

	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 preferences. 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 preferences. Java-based [[Jmol]] has significant performance advantages over running in the HTML5/Javascript and power users may wish to keep using Java-based Jmol.

			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]].

	==See Also==		==See Also==
	* [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).