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File Date Author Commit
docs 2011-07-18 Paul Boddie Paul Boddie [2cdb01] The iRefScape 1.0 sources, imported from CVS on...
lib 2011-07-18 Paul Boddie Paul Boddie [2cdb01] The iRefScape 1.0 sources, imported from CVS on...
nbproject 2011-11-28 Paul Boddie Paul Boddie [0dc32e] Changes made by NetBeans 7.0.1 when handling th...
resources 2011-07-18 Paul Boddie Paul Boddie [2cdb01] The iRefScape 1.0 sources, imported from CVS on...
src 2012-09-07 Paul Boddie Paul Boddie [7e7f38] Introduced RandomAccessFile usage for a more ef...
tools 2011-11-28 Paul Boddie Paul Boddie [907d74] Added swing-layout details to the dependencies ...
.hgtags 2011-11-18 Paul Boddie Paul Boddie [2909d1] Added tag rel-1-18 for changeset e12f853c5951
README.txt 2011-11-28 Paul Boddie Paul Boddie [907d74] Added swing-layout details to the dependencies ...
build.xml 2011-07-18 Paul Boddie Paul Boddie [2cdb01] The iRefScape 1.0 sources, imported from CVS on...
manifest.mf 2011-07-18 Paul Boddie Paul Boddie [2cdb01] The iRefScape 1.0 sources, imported from CVS on...
minimal-build.xml 2011-11-18 Paul Boddie Paul Boddie [e12f85] Added documentation and licensing information t...

Read Me

iRefScape is a plugin for Cytoscape that exposes iRefIndex data as a navigable
graphical network. See the iRefScape page for documentation and installation
instructions:

http://irefindex.uio.no/wiki/iRefScape

Prerequisites
-------------

The following programs are required to use the plugin:

  * Cytoscape (tested with 2.8.2): http://www.cytoscape.org/
  * A Java virtual machine (tested with JDK 1.6): http://www.java.com/

Build Dependencies
------------------

In addition to the required programs mentioned in the section below, some
build dependencies are required to build the plugin:

  * cytoscape.jar
  * attribute-browser-2.8.0-jar-with-dependencies.jar

They can be obtained from the Cytoscape distribution:

http://www.cytoscape.org/

(These dependencies are required when compiling so that the compiler can be
satisfied that APIs referenced at run-time, when such libraries have been
loaded in the Cytoscape environment, are correctly used by the plugin.)

In a NetBeans environment, the following additional build dependency is
required:

  * org-netbeans-modules-java-j2seproject-copylibstask.jar

This library is provided as part of the NetBeans distribution:

http://www.netbeans.org/

(This dependency performs various operations during the build process.)

Obtaining the Build Dependencies
--------------------------------

With an unpacked Cytoscape distribution, it is possible to retrieve the
dependencies by running one of the supplied tools as follows:

python tools/get_build_dependencies.py <Cytoscape directory>

Here, you should replace <Cytoscape directory> with the actual location of the
Cytoscape software.

If you want to use NetBeans to build the software, specify the location of the
unpacked NetBeans distribution in addition to the Cytoscape directory:

python tools/get_build_dependencies.py <Cytoscape directory> <NetBeans directory>

Building the Plugin
-------------------

To build the plugin, one of the following programs is required:

  * Apache Ant (tested with 1.7.1): http://ant.apache.org/
  * NetBeans (tested with 6.8): http://www.netbeans.org/

The build dependencies appropriate to the program chosen must be copied into
the lib directory before proceeding, and this should have been done in the
section above.

Building the Plugin with Ant
----------------------------

With Apache Ant, a minimal-build.xml file is supplied that can be invoked as
follows to make an iRefScape.jar file suitable for deployment:

ant -f minimal-build.xml

Upon successful completion of the build process, the iRefScape.jar file will
be placed in the dist directory.

Building the Plugin with NetBeans
---------------------------------

In the NetBeans environment, the project file can be opened using the "File",
"Open Project..." menu item and navigating to the directory containing this
source distribution. It is then possible to build the project in the usual
fashion.

It is also possible to build the plugin from the command line by invoking ant
(with the build.xml file) as follows:

ant jar

Upon successful completion of the build process, the iRefScape.jar file will
be placed in the dist directory.

Updating the Help Texts
-----------------------

A Python program in the tools directory called tooltips.py is able to bundle
the different help texts found in the resources directory into a single file
that is then either built into the iRefScape.jar file or deployed on the
iRefScape FTP site for subsequent download by the deployed plugin.

Contact, Copyright and Licence Information
------------------------------------------

The current Web page for this software at the time of release is:

http://irefindex.uio.no/wiki/iRefScape

The current maintainer can be contacted at the following e-mail address:

paul.boddie@biotek.uio.no

Copyright and licence information can be found in the docs directory - see
docs/COPYING.txt and docs/gpl-3.0.txt for more information.