Java: Difference between revisions

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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.

==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==

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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.

**'''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].

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==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==

* [[Installing and enabling Java]]

* [[Using Java for Rendering Structures]]

* [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).

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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.
 ==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==
@@ Line 36: / Line 36: @@
 *'''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].
@@ Line 78: / Line 78: @@
 ==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==
+* [[Installing and enabling Java]]
+* [[Using Java for Rendering Structures]]
 * [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).