Jalview Readme
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The source is available as a tar file and comes complete with the GNU General Public License. 

To build the application you will need a J2SDK 1.7+. 

An Ant build file (build.xml) is provided, you will need to install Apache Ant first. 
Run ant to view usage which will display a list of useful build targets.

Jalview is primarily developed with eclipse, and a .project file is provided to simplify importing the source into your own eclipse workspace. A NetBeans nbbuild.xml file is also provided for developing Jalview with NetBeans - but this is not officially supported.

You may also be able to use Borland JBuilder to build Jalview. A JBuilder project file 
(JalviewX.jpx, JalviewApplet.jpx) for both application and applet is provided, 
but the library dependencies are almost certainly out of date. See the build.xml 
for current dependencies.

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Jalview-JS

To enable transpilation of Jalview's code:

1. Locate the 'dropins' directory in your eclipse installation and copy swingjs/net.sf.j2s.core.jar to it.
  - typically it is at the top of the Eclipse installation, or on OSX under Eclipse.app/Contents/Eclipse
  
2. Restart Eclipse

3. If all is well you should see the 'Java2Script' builder is listed as the primary builder for the Jalview project.
  if not, this is because your properties file needs to have the standard java builder replaced with the following:
  <name>net.sf.j2s.core.java2scriptbuilder</name>

- otherwise Javascript files will now be generated in the site/swingjs/j2s directory whenever a build occurs

4. Execute the 'unzip-to-site' task (if it isn't automatically run) to update the site directory with the latest versions of SwingJS, varna-js, JSmol and other dependencies required by Jalview.


  


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For more help, read the file doc/building.html


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To run application...
[ NOTE: when using the -classpath option with the '*' wildcard, the argument must be quoted to avoid shell expansion of the wildcard,
  ALSO, the wildcard MUST be as DIR/* and not DIR/*.jar etc or it will not be interpreted correctly ]

on Windows use:
  java -classpath "JALVIEW_HOME/lib/*;JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
and on MacOS or Linux:
  java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview

Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:

  java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview


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If you use a proxy server add 

-Dhttp.proxyServer=YOUR.SERVER -Dhttp.proxyPort=YOURPORT

If the proxy server requires authentication, add

-Dhttp.proxyUser=USERNAME -Dhttp.proxyPassword=PASSWORD