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build.xml
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build.xml
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<!--
build.xml
Master ant build file for Bio-Formats.
Download Apache Ant from http://ant.apache.org/.
Type "ant -p" for a list of targets.
===============================================================================
This build file handles the following components.
For more information on a component, see the
build.properties file in that component's subtree.
Formats code generator
Package for generating other code, including the Bio-Formats metadata API,
related documentation, Ice bindings, and Bio-Formats C++ bindings headers
-=-
JAR file: bf-autogen.jar
Path: components/autogen
Project deps: Bio-Formats, Formats Common
Library deps: Apache Velocity
Optional: (none)
License: GPL
Bio-Formats
A library for reading and writing popular microscopy file formats
-=-
JAR file: bio-formats.jar
Path: components/bio-formats
Project deps: Formats Common, OME-XML Java library, JAI Image I/O Tools,
MDB Tools (Java port), Apache Jakarta POI,
Luratech LuraWave stubs
Library deps: JGoodies Forms, Logback, NetCDF,
Simple Logging Facade for Java API, TestNG
Optional: Xalan Serializer, Xalan
License: GPL
Formats Common
A library containing common I/O and reflection classes
-=-
JAR file: formats-common.jar
Path: components/formats-common
Project deps: (none)
Library deps: Simple Logging Facade for Java API, TestNG
Optional: Logback
License: GPL
Plugins for ImageJ
A collection of plugins for ImageJ, including the Bio-Formats Importer,
Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser, Stack
Colorizer and Stack Slicer
-=-
JAR file: bio-formats_plugins.jar
Path: components/bio-formats-plugins
Project deps: Bio-Formats, Formats Common, OME-XML Java library
Library deps: JGoodies Forms, ImageJ, JUnit, Logback
Optional: (none)
License: GPL
OME-XML Java library
A library for working with OME-XML metadata structures
-=-
JAR file: ome-xml.jar
Path: components/ome-xml
Project deps: (none)
Library deps: Simple Logging Facade for Java API, TestNG
Optional: Logback
License: GPL
Testing framework
Framework for automated and manual testing of software components
-=-
JAR file: bio-formats-testing-framework.jar
Path: components/test-suite
Project deps: Bio-Formats, Formats Common, OME I/O
Library deps: Logback, Simple Logging Facade for Java API, TestNG
Optional: (none)
License: BSD
===============================================================================
The following components are forks of third party projects:
JAI Image I/O Tools
Java API to handle JPEG and JPEG2000 files
-=-
JAR file: jai_imageio.jar
Path: components/forks/jai
Project deps: (none)
Optional: (none)
License: BSD
Project URL: http://jai-imageio.dev.java.net/
Notes: Used by Bio-Formats to read images compressed with JPEG2000
and lossless JPEG. Modified from the 2008-10-14 source to
include support for the YCbCr color space. Several files in
the com.sun.media.jai packages were removed, as they are not
needed by Bio-Formats, and created an additional dependency.
This component will be removed once our changes have been
added to the official JAI CVS repository.
MDB Tools (Java port)
Java API to handle Microsoft MDB format (Access)
-=-
JAR file: mdbtools-java.jar
Path: components/forks/mdbtools
Project deps: (none)
Optional: (none)
License: LGPL
Project URL: http://sourceforge.net/forum/message.php?msg_id=2550619
Notes: Used by Bio-Formats for Zeiss LSM metadata in MDB files.
Apache Jakarta POI
Java API to handle Microsoft OLE 2 Compound Document format (Word, Excel)
-=-
JAR file: ome-poi.jar
Path: components/forks/poi
Project deps: Formats Common
Optional: (none)
License: Apache
Project URL: http://jakarta.apache.org/poi/
Notes: Based on poi-2.5.1-final-20040804.jar, with bugfixes for OLE
v2 and memory efficiency improvements. Used by Bio-Formats
for OLE support (cxd, ipw, oib, zvi).
===============================================================================
The following components are stubs of third party projects:
Luratech LuraWave stubs
Stub of proprietary Java API to handle Luratech LWF compression
-=-
JAR file: lwf-stubs.jar
Path: components/stubs/lwf-stubs
Project deps: (none)
Optional: (none)
License: BSD
Project URL: http://www.luratech.com/
Notes: required to compile Bio-Formats's support for Luratech LWF
compression for the Opera Flex format
===============================================================================
The following external dependencies (in the jar folder) may be required:
Ant-Contrib
JAR file: ant-contrib-1.0b3.jar
URL: http://ant-contrib.sourceforge.net/
Notes: used by tools target to iterate over JAR files ("for" task)
License: Apache
Checkstyle
JAR file: checkstyle-all-5.0.jar
URL: http://checkstyle.sourceforge.net/
Notes: used by style Ant target to check source code style conventions
License: LGPL
Apache Jakarta Commons HttpClient
JAR file: commons-httpclient-2.0-rc2.jar
URL: http://jakarta.apache.org/commons/httpclient/
Notes: required for OME-Java to communicate with OME servers
License: Apache
Apache Jakarta Commons Logging
JAR file: commons-logging.jar
URL: http://jakarta.apache.org/commons/logging/
Notes: used by OME-Java
License: Apache
FindBugs Ant task
JAR file: findbugs-ant.jar
URL: http://findbugs.sourceforge.net/
Notes: used by findbugs Ant target to check for program bugs
License: LGPL
JGoodies Forms
JAR file: jgoodies-forms-1.7.2.jar
URL: http://www.jgoodies.com/freeware/forms/index.html
Notes: used for layout by Data Browser and OME Notes
License: BSD
ImageJ
JAR file: ij.jar
URL: http://rsb.info.nih.gov/ij/
Notes: used by plugins for ImageJ and OME plugins for ImageJ
License: Public domain
JUnit
JAR file: junit-4.8.2.jar
URL: http://www.junit.org/
Notes: unit testing framework used for a few unit tests
License: Common Public License
Logback
JAR file: logback-core-1.1.1.jar, logback-classic-1.1.1.jar
URL: http://logback.qos.ch
Notes: (none)
License: EPL v1.0 and LGPL 2.1
Native library loader
JAR file: native-lib-loader-2.0.2.jar
URL: http://github.com/scijava/native-lib-loader
Notes: required for loading native libraries
License: BSD
NetCDF
JAR file: netcdf-4.3.19.jar
URL: http://www.unidata.ucar.edu/software/netcdf-java/
Notes: used by Bio-Formats via reflection for HDF support (Imaris 5.5)
License: LGPL
Simple Logging Facade for Java API
JAR file: slf4j-api-1.7.6.jar
URL: http://www.slf4j.org/
Notes: used for all logging in loci.*
License: BSD
Xalan Serializer
JAR file: serializer-2.7.1.jar
URL: http://xml.apache.org/xalan-j/
Notes: used for OME-XML transformations
License: Apache
TestNG
JAR file: testng-6.8.jar
URL: http://testng.org/
Notes: testing framework used for the automated test suite
License: Apache
Apache Velocity
JAR file: velocity-1.6.3-dep.jar
URL: http://velocity.apache.org/
Notes: used to autogenerate the loci.formats.meta and loci.formats.ome
Bio-Formats packages
License: Apache
Xalan
JAR file: xalan-2.7.1.jar
URL: http://xml.apache.org/xalan-j/
Notes: used for OME-XML transformations
License: Apache
Apache XML-RPC
JAR file: xmlrpc-1.2-b1.jar
URL: http://ws.apache.org/xmlrpc/
Notes: used by OME-Java library to communicate with OME servers
License: Apache
-->
<project name="Bio-Formats" default="jars" basedir=".">
<description>
Master build file for all Bio-Formats software components
</description>
<import file="ant/toplevel.xml"/>
<!-- OME-compatibility layer -->
<target name="dist" description="OME hook: build and publish Bio-Formats dist">
<ant target="tools"/>
<ant target="tools-ome"/>
<ant target="jar-formats-bsd-tests"/>
<ant antfile="ome.xml" inheritRefs="false" inheritAll="false"/>
</target>
<target name="eclipse" description="OME hook: create eclipse .classpath file">
<ant target="eclipse" antfile="ome.xml" inheritRefs="false" inheritAll="false"/>
</target>
<target name="test-compile" depends="compile-tests" description="OME hook: compile all tests"/>
<target name="integration" description="No-op"/>
</project>