<!--
build.xml

Master ant build file for all Java software projects at LOCI.
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.
Run ./scan-deps.pl to programmatically generate this list.

LOCI Common
    A library containing common I/O and reflection classes
    -=-
    JAR file:      loci-common.jar
    Path:          components/common
    Project deps:  (none)
    Library deps:  (none)
    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:  (none)
    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:  LOCI Common, OME-XML Java library
    Library deps:  JGoodies Forms
    Optional:      OME I/O, OME Notes, Apache Jakarta POI,
                   MDB Tools (Java port), JAI Image I/O Tools, NetCDF
    License:       GPL

LOCI 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:      loci-autogen.jar
    Path:          components/autogen
    Project deps:  LOCI Common, Bio-Formats
    Library deps:  Apache Velocity
    Optional:      (none)
    License:       GPL

Bio-Formats Ice framework
    Bindings for Bio-Formats client/server communication enabling
    cross-language interoperability
    -=-
    JAR file:      bf-ice.jar
    Path:          components/bf-ice
    Project deps:  LOCI Common, Bio-Formats
    Library deps:  Ice
    Optional:      (none)
    License:       GPL

LOCI 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:      loci_plugins.jar
    Path:          components/loci-plugins
    Project deps:  LOCI Common, Bio-Formats
    Library deps:  JGoodies Forms, ImageJ
    Optional:      OME I/O, VisBio
    License:       GPL

OME I/O
    A library for OME database import, upload and download
    -=-
    JAR file:      ome-io.jar
    Path:          components/ome-io
    Project deps:  LOCI Common, Bio-Formats
    Library deps:  OMERO Client, OMERO Common
    Optional:      OME-Java
    License:       GPL

OME Plugins for ImageJ
    A collection of plugins for ImageJ, including the Download from OME and
    Upload to OME plugins
    -=-
    JAR file:      ome_plugins.jar
    Path:          components/ome-plugins
    Project deps:  LOCI Common, Bio-Formats, LOCI Plugins for ImageJ, OME I/O
    Library deps:  ImageJ
    Optional:      (none)
    License:       GPL

VisBio
    A multi-purpose biological analysis tool
    -=-
    JAR file:      visbio.jar
    Path:          components/visbio
    Project deps:  LOCI Common, OME-XML Java library, Bio-Formats, OME I/O,
                   Apache Jakarta POI
    Library deps:  Apple eAWT stubs, JGoodies Forms, ImageJ, JGoodies Looks,
                   VisAD
    Optional:      (none)
    License:       GPL

SLIM Plotter
    An application and curve fitting library for visualization and analysis of
    combined spectral lifetime data
    -=-
    JAR file:      SlimPlotter.jar
    Path:          components/slim-plotter
    Project deps:  LOCI Common, Bio-Formats, VisBio
    Library deps:  L-M Fit, VisAD
    Optional:      (none)
    License:       GPL

WiscScan Flow Cytometry
    Server application for flow cytometry with WiscScan using JVMLink
    -=-
    JAR file:      flow-cytometry.jar
    Path:          components/flow-cytometry
    Project deps:  Bio-Formats
    Library deps:  ImageJ, VisAD
    Optional:      (none)
    License:       BSD

LOCI Checkstyle checks
    LOCI's Checkstyle extensions, for checking source code style
    -=-
    JAR file:      loci-checks.jar
    Path:          components/checkstyle
    Project deps:  (none)
    Library deps:  Checkstyle
    Optional:      (none)
    License:       Public domain

LOCI testing framework
    Framework for automated and manual testing of the LOCI software packages
    -=-
    JAR file:      loci-testing-framework.jar
    Path:          components/test-suite
    Project deps:  LOCI Common, Bio-Formats, OME I/O
    Library deps:  TestNG
    Optional:      (none)
    License:       BSD

===============================================================================
The following components are considered "legacy" but still available:

JVMLink
    A library for communicating between a Java Virtual Machine and other
    programs (e.g., C++ applications) via IP over localhost (or remotely)
    -=-
    JAR file:      jvmlink.jar
    Path:          components/legacy/jvmlink
    Project deps:  LOCI Common
    Optional:      (none)
    License:       BSD

Multi-LUT
    A demo application for visually exploring multi-spectral image data
    -=-
    JAR file:      MultiLUT.jar
    Path:          components/legacy/multi-lut
    Project deps:  (none)
    Optional:      (none)
    License:       Public domain

OME Notes
    A library for flexible organization and presentation of OME-XML metadata
    within a graphical browser and editor interface
    -=-
    JAR file:      ome-notes.jar
    Path:          components/legacy/ome-notes
    Project deps:  LOCI Common, Bio-Formats
    Optional:      (none)
    License:       LGPL

OME Metadata Editor
    An application for exploration and editing of OME-XML and OME-TIFF metadata
    -=-
    JAR file:      ome-editor.jar
    Path:          components/legacy/ome-editor
    Project deps:  LOCI Common, OME-XML Java library, Bio-Formats
    Optional:      (none)
    License:       LGPL

===============================================================================
The following components are forks of third party projects:

Apache Jakarta POI
    Java API to handle Microsoft OLE 2 Compound Document format (Word, Excel)
    -=-
    JAR file:      poi-loci.jar
    Path:          components/forks/poi
    Project deps:  LOCI 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). Used by VisBio
                   overlays logic for XLS export feature.

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.

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.

===============================================================================
The following external dependencies (in the jar folder) may be required:
Apple eAWT stubs
    JAR file:  AppleJavaExtensions.jar
    URL:       http://developer.apple.com/samplecode/AppleJavaExtensions/
    Notes:     required to compile VisBio on non-Mac OS X machines
    License:   BSD

Ant-Contrib
    JAR file:  ant-contrib-1.0b1.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-4.2.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:  forms-1.0.4.jar
    URL:       http://www.jgoodies.com/freeware/forms/index.html
    Notes:     used for layout by VisBio, Data Browser and OME Notes
    License:   BSD

Ice
    JAR file:  Ice-3.3.1.jar
    URL:       http://www.zeroc.com/ice.html
    Notes:     used by Bio-Formats Ice framework
    License:   GPL

ImageJ
    JAR file:  ij.jar
    URL:       http://rsb.info.nih.gov/ij/
    Notes:     used by LOCI plugins for ImageJ and OME plugins for ImageJ;
               included with VisBio to achieve ImageJ interconnectivity
    License:   Public domain

JAI ImageIO wrapper
    JAR file:  clibwrapper_jiio.jar
    URL:       https://jai-imageio.dev.java.net/
    Notes:     used by Bio-Formats via reflection for JPEG2000 support (ND2,
               JP2) and lossless JPEG decompression (DICOM)
    License:   BSD

JUnit
    JAR file:  junit.jar
    URL:       http://www.junit.org/
    Notes:     unit testing framework used for a few VisBio unit tests
    License:   Common Public License

L-M Fit
    JAR file:  lma.jar
    URL:       http://users.utu.fi/jaolho/
    Notes:     Levenberg-Marquardt algorithm for exponential curve fitting,
               used by SLIM Plotter
    License:   LGPL

JGoodies Looks
    JAR file:  looks-1.2.2.jar
    URL:       http://www.jgoodies.com/freeware/looks/index.html
    Notes:     used for a nicer Look & Feel by VisBio and OME Metadata Editor
    License:   BSD

NetCDF
    JAR file:  netcdf-4.0.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

BUFR Java Decoder
    JAR file:  bufr-1.1.00.jar
    URL:       http://www.unidata.ucar.edu/software/netcdf-java/
    Notes:     used by NetCDF library
    License:   LGPL

GRIB Java Decoder
    JAR file:  grib-5.1.03.jar
    URL:       http://www.unidata.ucar.edu/software/netcdf-java/
    Notes:     used by NetCDF library
    License:   LGPL

Simple Logging Facade for Java
    JAR file:  slf4j-jdk14.jar
    URL:       http://www.slf4j.org/
    Notes:     used by NetCDF library
    License:   BSD

OME-Java
    JAR file:  ome-java.jar
    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
    Notes:     used by OME I/O to connect to OME servers
    License:   LGPL

OME-Java deprecated classes
    JAR file:  ome-java-deprecated.jar
    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
    Notes:     used by OME Notes and OME Metadata Editor to work with OME-XML
    License:   LGPL

OMERO Client
    JAR file:  omero-client-4.0.3.jar
    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
    Notes:     used by OME I/O to connect to OMERO servers
    License:   GPL

OMERO Common
    JAR file:  omero-common-4.0.3.jar
    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
    Notes:     used by OME I/O to connect to OMERO servers
    License:   GPL

Skin Look and Feel
    JAR file:  skinlf.jar
    URL:       http://skinlf.l2fprod.com/
    Notes:     not used (may be used in the future for flexible skinning)
    License:   Custom (BSD-like)

TestNG
    JAR file:  testng-5.7-jdk14.jar
    URL:       http://testng.org/
    Notes:     testing framework used for LOCI software automated test suite
    License:   Apache

Apache Velocity
    JAR file:  velocity-dep-1.5.jar
    URL:       http://velocity.apache.org/
    Notes:     used to autogenerate the loci.formats.meta and loci.formats.ome
               Bio-Formats packages
    License:   Apache

VisAD
    JAR file:  visad-lite.jar
    URL:       http://www.ssec.wisc.edu/~billh/visad.html
    Notes:     stripped down VisAD library used by VisBio and SLIM Plotter for
               interactive visualization
    License:   LGPL

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="LOCI Software" default="jars" basedir=".">
  <description>
    Master build file for all Java software projects at LOCI
  </description>

  <property name="root.dir" location="${basedir}"/>
  <import file="global.xml"/>
  <property file="build.properties"/>

  <!-- Global build targets -->

  <target name="jars"
    depends="copy-jars, jar-common, jar-ome-xml,
      jar-jai, jar-poi-loci, jar-mdbtools,
      jar-formats, jar-autogen, jar-bf-ice,
      jar-loci-plugins, jar-ome-io, jar-ome-plugins,
      jar-visbio, jar-slim, jar-flow,
      jar-checks, jar-tests,
      jar-jvmlink, jar-multi-lut,
      jar-ome-notes, jar-ome-editor"
    description="generate JAR files for LOCI software packages"/>

  <target name="osgi"
    depends="copy-jars, osgi-common, osgi-ome-xml,
      osgi-jai, osgi-poi-loci, osgi-mdbtools,
      osgi-formats, osgi-autogen, osgi-bf-ice,
      osgi-loci-plugins, osgi-ome-io, osgi-ome-plugins,
      osgi-visbio, osgi-slim, osgi-flow,
      osgi-checks, osgi-tests,
      osgi-jvmlink, osgi-multi-lut,
      osgi-ome-notes, osgi-ome-editor"
    description="generate OSGi bundles for LOCI software packages"/>

  <!--
  NB: Findbugs target does not test autogenerated code, forks and legacy:
    findbugs-ome-xml
    findbugs-jai
    findbugs-poi-loci
    findbugs-mdbtools
    findbugs-bf-ice
    findbugs-jvmlink
    findbugs-multi-lut
    findbugs-ome-notes
    findbugs-ome-editor
  -->
  <target name="findbugs"
    depends="findbugs-common,
      findbugs-formats, findbugs-autogen,
      findbugs-loci-plugins, findbugs-ome-io, findbugs-ome-plugins,
      findbugs-visbio, findbugs-slim, findbugs-flow,
      findbugs-checks, findbugs-tests"
    description="run findbugs on most components"/>

  <target name="clean"
    depends="clean-common, clean-ome-xml,
      clean-jai, clean-poi-loci, clean-mdbtools,
      clean-formats, clean-autogen, clean-bf-ice,
      clean-loci-plugins, clean-ome-io, clean-ome-plugins,
      clean-visbio, clean-slim, clean-flow,
      clean-checks, clean-tests,
      clean-jvmlink, clean-multi-lut,
      clean-ome-notes, clean-ome-editor"
    description="remove all build files">
    <delete dir="${artifact.dir}"/>
    <delete dir="build"/>
  </target>

  <target name="utils"
    depends="jars, utils-common, utils-formats, utils-loci-plugins"
    description="compile all extra utilities">
    <echo>----------=========== utils ===========----------</echo>
    <delete>
      <fileset dir="${toplevel-utils.dir}" includes="*.class"/>
    </delete>
    <javac debug="true" deprecation="true" source="1.5" target="1.5"
      srcdir="${toplevel-utils.dir}" includes="*.java">
      <classpath>
        <fileset dir="${artifact.dir}">
          <include name="*.jar"/>
        </fileset>
      </classpath>
    </javac>
  </target>

  <target name="docs" depends="jars"
    description="generate Javadocs for LOCI software packages">
    <echo>----------=========== Javadocs ===========----------</echo>
    <tstamp>
      <format property="YEAR" pattern="yyyy"/>
    </tstamp>
    <javadoc sourcepath="${merged-docs.source}"
      classpath="${merged-docs.classpath}"
      destdir="${merged-docs.dir}/api"
      maxmemory="${merged-docs.memory}"
      failonerror="true" author="true" version="true" use="true"
      nodeprecated="true" windowtitle="LOCI Software API">
      <doctitle><![CDATA[<h1>LOCI Software</h1>]]></doctitle>
      <bottom><![CDATA[${copyright.begin} ${YEAR} ${copyright.end}]]></bottom>
      <link href="http://java.sun.com/j2se/1.5.0/docs/api/"/>
      <link href="http://hudson.openmicroscopy.org.uk/job/OMEJAVA/javadoc/"/>
      <link href="http://rsbweb.nih.gov/ij/developer/api/"/>
      <link href="http://www.ssec.wisc.edu/visad-docs/javadoc/"/>
      <!--<link href="http://www.jdocs.com/formlayout/1.0.4/api/"/>-->
      <!--<link href="http://www.jdocs.com/looks/1.2.2/api/"/>-->
    </javadoc>
  </target>

  <target name="copy-jars">
    <!-- copy third party JARs into artifacts folder -->
    <!-- necessary for runtime classpath dependencies to function properly -->
    <copy todir="${artifact.dir}" preservelastmodified="true">
      <fileset dir="${lib.dir}" includes="*.jar"/>
    </copy>
  </target>

  <!-- LOCI common library -->

  <target name="compile-common"
    description="compile classes for LOCI common library">
    <ant dir="components/common" target="common.compile"/>
  </target>

  <target name="jar-common"
    description="generate JAR file for LOCI common library">
    <ant dir="components/common" target="common.jar"/>
  </target>

  <target name="osgi-common" depends="jar-common"
    description="generate OSGi bundle for LOCI common library">
    <ant dir="components/common" target="common.osgi"/>
  </target>

  <target name="findbugs-common"
    description="run findbugs on LOCI common library">
    <ant dir="components/common" target="common.findbugs"/>
  </target>

  <target name="clean-common"
    description="remove build files for LOCI common library">
    <ant dir="components/common" target="common.clean"/>
  </target>

  <target name="utils-common" depends="jar-common"
    description="compile extra utilities for LOCI common library">
    <ant dir="components/common" target="common.utils"/>
  </target>

  <!-- JAI Image I/O Tools library -->

  <target name="compile-jai"
    description="compile classes for JAI Image I/O Tools library">
    <ant dir="components/forks/jai" target="jai.compile"/>
  </target>

  <target name="jar-jai"
    description="generate JAR file for JAI Image I/O Tools library">
    <ant dir="components/forks/jai" target="jai.jar"/>
  </target>

  <target name="osgi-jai" depends="jar-jai"
    description="generate OSGi bundle for JAI Image I/O Tools library">
    <ant dir="components/forks/jai" target="jai.osgi"/>
  </target>

  <target name="findbugs-jai"
    description="run findbugs on JAI Image I/O Tools library">
    <ant dir="components/forks/jai" target="jai.findbugs"/>
  </target>

  <target name="clean-jai"
    description="remove build files for JAI Image I/O Tools library">
    <ant dir="components/forks/jai" target="jai.clean"/>
  </target>

  <!-- Apache POI Java library -->

  <target name="compile-poi-loci"
    depends="compile-common"
    description="compile classes for Apache POI library">
    <ant dir="components/forks/poi" target="poi-loci.compile"/>
  </target>

  <target name="jar-poi-loci"
    depends="jar-common"
    description="generate JAR file for Apache POI library">
    <ant dir="components/forks/poi" target="poi-loci.jar"/>
  </target>

  <target name="osgi-poi-loci" depends="jar-poi-loci"
    description="generate OSGi bundle for Apache POI library">
    <ant dir="components/forks/poi" target="poi-loci.osgi"/>
  </target>

  <target name="findbugs-poi-loci"
    description="run findbugs on Apache POI library">
    <ant dir="components/forks/poi" target="poi-loci.findbugs"/>
  </target>

  <target name="clean-poi-loci"
    depends="clean-common"
    description="remove build files for Apache POI library">
    <ant dir="components/forks/poi" target="poi-loci.clean"/>
  </target>

  <!-- MDB Tools Java library -->

  <target name="compile-mdbtools"
    description="compile classes for MDB Tools Java library">
    <ant dir="components/forks/mdbtools" target="mdbtools.compile"/>
  </target>

  <target name="jar-mdbtools"
    description="generate JAR file for MDB Tools Java library">
    <ant dir="components/forks/mdbtools" target="mdbtools.jar"/>
  </target>

  <target name="osgi-mdbtools" depends="jar-mdbtools"
    description="generate OSGi bundle for MDB Tools Java library">
    <ant dir="components/forks/mdbtools" target="mdbtools.osgi"/>
  </target>

  <target name="findbugs-mdbtools"
    description="run findbugs on MDB Tools Java library">
    <ant dir="components/forks/mdbtools" target="mdbtools.findbugs"/>
  </target>

  <target name="clean-mdbtools"
    description="remove build files for MDB Tools Java library">
    <ant dir="components/forks/mdbtools" target="mdbtools.clean"/>
  </target>

  <!-- OME-XML Java library -->

  <target name="compile-ome-xml"
    description="compile classes for OME-XML Java library">
    <ant dir="components/ome-xml" target="ome-xml.compile"/>
  </target>

  <target name="jar-ome-xml"
    description="generate JAR file for OME-XML Java library">
    <ant dir="components/ome-xml" target="ome-xml.jar"/>
  </target>

  <target name="osgi-ome-xml" depends="jar-ome-xml"
    description="generate OSGi bundle for OME-XML Java library">
    <ant dir="components/ome-xml" target="ome-xml.osgi"/>
  </target>

  <target name="findbugs-ome-xml"
    description="run findbugs on OME-XML Java library">
    <ant dir="components/ome-xml" target="ome-xml.findbugs"/>
  </target>

  <target name="clean-ome-xml"
    description="remove build files for OME-XML Java library">
    <ant dir="components/ome-xml" target="ome-xml.clean"/>
  </target>

  <!-- Bio-Formats -->

  <target name="compile-formats"
    depends="compile-common, compile-ome-xml"
    description="compile classes for Bio-Formats">
    <ant dir="components/bio-formats" target="formats.compile"/>
  </target>

  <target name="jar-formats"
    depends="jar-common, jar-ome-xml"
    description="generate JAR file for Bio-Formats">
    <ant dir="components/bio-formats" target="formats.jar"/>
  </target>

  <target name="osgi-formats" depends="jar-formats"
    description="generate OSGi bundle for Bio-Formats">
    <ant dir="components/bio-formats" target="formats.osgi"/>
  </target>

  <target name="findbugs-formats"
    description="run findbugs on Bio-Formats">
    <ant dir="components/bio-formats" target="formats.findbugs"/>
  </target>

  <target name="clean-formats"
    depends="clean-common, clean-ome-xml"
    description="remove build files for Bio-Formats">
    <ant dir="components/bio-formats" target="formats.clean"/>
  </target>

  <target name="utils-formats" depends="jar-formats"
    description="compile extra utilities for LOCI Plugins for ImageJ">
    <ant dir="components/bio-formats" target="formats.utils"/>
  </target>

  <!-- LOCI autogen -->

  <target name="compile-autogen"
    depends="compile-common, compile-formats"
    description="compile classes for LOCI autogen">
    <ant dir="components/autogen" target="autogen.compile"/>
  </target>

  <target name="jar-autogen"
    depends="jar-common, jar-formats"
    description="generate JAR file for LOCI autogen">
    <ant dir="components/autogen" target="autogen.jar"/>
  </target>

  <target name="osgi-autogen" depends="jar-autogen"
    description="generate OSGi bundle for LOCI autogen">
    <ant dir="components/autogen" target="autogen.osgi"/>
  </target>

  <target name="findbugs-autogen"
    description="run findbugs on LOCI autogen">
    <ant dir="components/autogen" target="autogen.findbugs"/>
  </target>

  <target name="clean-autogen"
    depends="clean-common, clean-formats"
    description="remove build files for LOCI autogen">
    <ant dir="components/autogen" target="autogen.clean"/>
  </target>

  <!-- Bio-Formats Ice framework -->

  <target name="compile-bf-ice"
    depends="compile-formats"
    description="compile classes for Bio-Formats Ice framework">
    <ant dir="components/bf-ice" target="bf-ice.compile"/>
  </target>

  <target name="jar-bf-ice"
    depends="jar-formats"
    description="generate JAR file for Bio-Formats Ice framework">
    <ant dir="components/bf-ice" target="bf-ice.jar"/>
  </target>

  <target name="osgi-bf-ice" depends="jar-bf-ice"
    description="generate OSGi bundle for Bio-Formats Ice framework">
    <ant dir="components/bf-ice" target="bf-ice.osgi"/>
  </target>

  <target name="findbugs-bf-ice"
    description="run findbugs on Bio-Formats Ice framework">
    <ant dir="components/bf-ice" target="bf-ice.findbugs"/>
  </target>

  <target name="clean-bf-ice"
    depends="clean-formats"
    description="remove build files for Bio-Formats Ice framework">
    <ant dir="components/bf-ice" target="bf-ice.clean"/>
  </target>

  <!-- LOCI Plugins for ImageJ -->

  <target name="compile-loci-plugins"
    depends="compile-common, compile-formats"
    description="compile classes for LOCI Plugins for ImageJ">
    <ant dir="components/loci-plugins" target="loci-plugins.compile"/>
  </target>

  <target name="jar-loci-plugins"
    depends="jar-common, jar-formats"
    description="generate JAR file for LOCI Plugins for ImageJ">
    <ant dir="components/loci-plugins" target="loci-plugins.jar"/>
  </target>

  <target name="osgi-loci-plugins" depends="jar-loci-plugins"
    description="generate OSGi bundle for LOCI Plugins for ImageJ">
    <ant dir="components/loci-plugins" target="loci-plugins.osgi"/>
  </target>

  <target name="findbugs-loci-plugins"
    description="run findbugs on LOCI Plugins for ImageJ">
    <ant dir="components/loci-plugins" target="loci-plugins.findbugs"/>
  </target>

  <target name="clean-loci-plugins"
    depends="clean-common, clean-formats"
    description="remove build files for LOCI Plugins for ImageJ">
    <ant dir="components/loci-plugins" target="loci-plugins.clean"/>
  </target>

  <target name="utils-loci-plugins" depends="jar-loci-plugins"
    description="compile extra utilities for LOCI Plugins for ImageJ">
    <ant dir="components/loci-plugins" target="loci-plugins.utils"/>
  </target>

  <!-- OME I/O -->

  <target name="compile-ome-io"
    depends="compile-common, compile-formats"
    description="compile classes for OME I/O">
    <ant dir="components/ome-io" target="ome-io.compile"/>
  </target>

  <target name="jar-ome-io"
    depends="jar-common, jar-formats"
    description="generate JAR file for OME I/O">
    <ant dir="components/ome-io" target="ome-io.jar"/>
  </target>

  <target name="osgi-ome-io" depends="jar-ome-io"
    description="generate OSGi bundle for OME I/O">
    <ant dir="components/ome-io" target="ome-io.osgi"/>
  </target>

  <target name="findbugs-ome-io"
    description="run findbugs on OME I/O">
    <ant dir="components/ome-io" target="ome-io.findbugs"/>
  </target>

  <target name="clean-ome-io"
    depends="clean-common, clean-formats"
    description="remove build files for OME I/O">
    <ant dir="components/ome-io" target="ome-io.clean"/>
  </target>

  <!-- OME Plugins for ImageJ -->

  <target name="compile-ome-plugins"
    depends="compile-common, compile-formats,
      compile-loci-plugins, compile-ome-io"
    description="compile classes for OME Plugins for ImageJ">
    <ant dir="components/ome-plugins" target="ome-plugins.compile"/>
  </target>

  <target name="jar-ome-plugins"
    depends="jar-common, jar-formats, jar-loci-plugins, jar-ome-io"
    description="generate JAR file for OME Plugins for ImageJ">
    <ant dir="components/ome-plugins" target="ome-plugins.jar"/>
  </target>

  <target name="osgi-ome-plugins" depends="jar-ome-plugins"
    description="generate OSGi bundle for OME Plugins for ImageJ">
    <ant dir="components/ome-plugins" target="ome-plugins.osgi"/>
  </target>

  <target name="findbugs-ome-plugins"
    description="run findbugs on OME Plugins for ImageJ">
    <ant dir="components/ome-plugins" target="ome-plugins.findbugs"/>
  </target>

  <target name="clean-ome-plugins"
    depends="clean-common, clean-formats, clean-loci-plugins, clean-ome-io"
    description="remove build files for OME Plugins for ImageJ">
    <ant dir="components/ome-plugins" target="ome-plugins.clean"/>
  </target>

  <!-- VisBio -->

  <target name="compile-visbio"
    depends="compile-common, compile-ome-xml, compile-formats,
      compile-ome-io, compile-poi-loci"
    description="compile classes for VisBio">
    <ant dir="components/visbio" target="visbio.compile"/>
  </target>

  <target name="jar-visbio"
    depends="jar-common, jar-ome-xml, jar-formats, jar-ome-io, jar-poi-loci"
    description="generate JAR file for VisBio">
    <ant dir="components/visbio" target="visbio.jar"/>
  </target>

  <target name="osgi-visbio" depends="jar-visbio"
    description="generate OSGi bundle for VisBio">
    <ant dir="components/visbio" target="visbio.osgi"/>
  </target>

  <target name="findbugs-visbio"
    description="run findbugs on VisBio">
    <ant dir="components/visbio" target="visbio.findbugs"/>
  </target>

  <target name="clean-visbio"
    depends="clean-common, clean-ome-xml, clean-formats,
      clean-ome-io, clean-poi-loci"
    description="remove build files for VisBio">
    <ant dir="components/visbio" target="visbio.clean"/>
  </target>

  <target name="dist-visbio"
    description="create distribution archives for VisBio">
    <ant dir="components/visbio" target="dist"/>
  </target>

  <target name="dist-visbio-win32"
    description="create distribution archive for VisBio: Windows w/ JRE">
    <ant dir="components/visbio" target="dist-win32"/>
  </target>

  <target name="dist-visbio-win32-nojre"
    description="create distribution archive for VisBio: Windows no JRE">
    <ant dir="components/visbio" target="dist-win32-nojre"/>
  </target>

  <target name="dist-visbio-macosx"
    description="create distribution archive for VisBio: Mac OS X">
    <ant dir="components/visbio" target="dist-macosx"/>
  </target>

  <target name="dist-visbio-linux"
    description="create distribution archive for VisBio: Linux w/ JRE">
    <ant dir="components/visbio" target="dist-linux"/>
  </target>

  <target name="dist-visbio-nojre"
    description="create distribution archive for VisBio: cross-platform">
    <ant dir="components/visbio" target="dist-nojre"/>
  </target>

  <!-- SLIM Plotter -->

  <target name="compile-slim"
    depends="compile-common, compile-formats, compile-visbio"
    description="compile classes for SLIM Plotter">
    <ant dir="components/slim-plotter" target="slim.compile"/>
  </target>

  <target name="jar-slim"
    depends="jar-common, jar-formats, jar-visbio"
    description="generate JAR file for SLIM Plotter">
    <ant dir="components/slim-plotter" target="slim.jar"/>
  </target>

  <target name="osgi-slim" depends="jar-slim"
    description="generate OSGi bundle for SLIM Plotter">
    <ant dir="components/slim-plotter" target="slim.osgi"/>
  </target>

  <target name="findbugs-slim"
    description="run findbugs on SLIM Plotter">
    <ant dir="components/slim-plotter" target="slim.findbugs"/>
  </target>

  <target name="clean-slim"
    depends="clean-common, clean-formats, clean-visbio"
    description="remove build files for SLIM Plotter">
    <ant dir="components/slim-plotter" target="slim.clean"/>
  </target>

  <target name="dist-slim"
    description="create distribution archive for SLIM Plotter">
    <ant dir="components/slim-plotter" target="dist"/>
  </target>

  <!-- WiscScan Flow Cytometry -->

  <target name="compile-flow"
    depends="compile-formats"
    description="compile classes for WiscScan Flow Cytometry">
    <ant dir="components/flow-cytometry" target="flow.compile"/>
  </target>

  <target name="jar-flow"
    depends="jar-formats"
    description="generate JAR file for WiscScan Flow Cytometry">
    <ant dir="components/flow-cytometry" target="flow.jar"/>
  </target>

  <target name="osgi-flow" depends="jar-flow"
    description="generate OSGi bundle for WiscScan Flow Cytometry">
    <ant dir="components/flow-cytometry" target="flow.osgi"/>
  </target>

  <target name="findbugs-flow"
    description="run findbugs on WiscScan Flow Cytometry">
    <ant dir="components/flow-cytometry" target="flow.findbugs"/>
  </target>

  <target name="clean-flow"
    depends="clean-formats"
    description="remove build files for WiscScan Flow Cytometry">
    <ant dir="components/flow-cytometry" target="flow.clean"/>
  </target>

  <target name="dist-flow"
    description="create distribution archive for WiscScan Flow Cytometry">
    <ant dir="components/flow-cytometry" target="dist"/>
  </target>

  <!-- LOCI Checkstyle checks -->

  <target name="compile-checks"
    description="compile classes for LOCI Checkstyle checks">
    <ant dir="components/checkstyle" target="checks.compile"/>
  </target>

  <target name="jar-checks"
    description="generate JAR file for LOCI Checkstyle checks">
    <ant dir="components/checkstyle" target="checks.jar"/>
  </target>

  <target name="osgi-checks" depends="jar-checks"
    description="generate OSGi bundle for LOCI Checkstyle checks">
    <ant dir="components/checkstyle" target="checks.osgi"/>
  </target>

  <target name="findbugs-checks"
    description="run findbugs on LOCI Checkstyle checks">
    <ant dir="components/checkstyle" target="checks.findbugs"/>
  </target>

  <target name="clean-checks"
    description="remove build files for LOCI Checkstyle checks">
    <ant dir="components/checkstyle" target="checks.clean"/>
  </target>

  <!-- LOCI testing framework -->

  <target name="compile-tests"
    depends="compile-common, compile-formats, compile-ome-io"
    description="compile classes for LOCI testing framework">
    <ant dir="components/test-suite" target="tests.compile"/>
  </target>

  <target name="jar-tests"
    depends="jar-common, jar-formats, jar-ome-io"
    description="generate JAR file for LOCI testing framework">
    <ant dir="components/test-suite" target="tests.jar"/>
  </target>

  <target name="osgi-tests" depends="jar-tests"
    description="generate OSGi bundle for LOCI testing framework">
    <ant dir="components/test-suite" target="tests.osgi"/>
  </target>

  <target name="findbugs-tests"
    description="run findbugs on LOCI testing framework">
    <ant dir="components/test-suite" target="tests.findbugs"/>
  </target>

  <target name="clean-tests"
    depends="clean-common, clean-formats, clean-ome-io"
    description="remove build files for LOCI testing framework">
    <ant dir="components/test-suite" target="tests.clean"/>
  </target>

  <!-- JVMLink -->

  <target name="compile-jvmlink"
    depends="compile-common"
    description="compile classes for JVMLink">
    <ant dir="components/legacy/jvmlink" target="jvmlink.compile"/>
  </target>

  <target name="jar-jvmlink"
    depends="jar-common"
    description="generate JAR file for JVMLink">
    <ant dir="components/legacy/jvmlink" target="jvmlink.jar"/>
  </target>

  <target name="osgi-jvmlink" depends="jar-jvmlink"
    description="generate OSGi bundle for JVMLink">
    <ant dir="components/legacy/jvmlink" target="jvmlink.osgi"/>
  </target>

  <target name="findbugs-jvmlink"
    description="run findbugs on JVMLink">
    <ant dir="components/legacy/jvmlink" target="jvmlink.findbugs"/>
  </target>

  <target name="clean-jvmlink"
    depends="clean-common"
    description="remove build files for JVMLink">
    <ant dir="components/legacy/jvmlink" target="jvmlink.clean"/>
  </target>

  <!-- Multi LUT app -->

  <target name="compile-multi-lut"
    description="compile classes for Multi LUT app">
    <ant dir="components/legacy/multi-lut" target="multi-lut.compile"/>
  </target>

  <target name="jar-multi-lut"
    description="generate JAR file for Multi LUT app">
    <ant dir="components/legacy/multi-lut" target="multi-lut.jar"/>
  </target>

  <target name="osgi-multi-lut" depends="jar-multi-lut"
    description="generate OSGi bundle for Multi LUT app">
    <ant dir="components/legacy/multi-lut" target="multi-lut.osgi"/>
  </target>

  <target name="findbugs-multi-lut"
    description="run findbugs on Multi LUT app">
    <ant dir="components/legacy/multi-lut" target="multi-lut.findbugs"/>
  </target>

  <target name="clean-multi-lut"
    description="remove build files for Multi LUT app">
    <ant dir="components/legacy/multi-lut" target="multi-lut.clean"/>
  </target>

  <!-- OME Notes -->

  <target name="compile-ome-notes"
    depends="compile-common, compile-formats"
    description="compile classes for OME Notes">
    <ant dir="components/legacy/ome-notes" target="ome-notes.compile"/>
  </target>

  <target name="jar-ome-notes"
    depends="jar-common, jar-formats"
    description="generate JAR file for OME Notes">
    <ant dir="components/legacy/ome-notes" target="ome-notes.jar"/>
  </target>

  <target name="osgi-ome-notes" depends="jar-ome-notes"
    description="generate OSGi bundle for OME Notes">
    <ant dir="components/legacy/ome-notes" target="ome-notes.osgi"/>
  </target>

  <target name="findbugs-ome-notes"
    description="run findbugs for OME Notes">
    <ant dir="components/legacy/ome-notes" target="ome-notes.findbugs"/>
  </target>

  <target name="clean-ome-notes"
    depends="clean-common, clean-formats"
    description="remove build files for OME Notes">
    <ant dir="components/legacy/ome-notes" target="ome-notes.clean"/>
  </target>

  <!-- OME Metadata Editor -->

  <target name="compile-ome-editor"
    depends="compile-common, compile-ome-xml, compile-formats"
    description="compile classes for OME Metadata Editor">
    <ant dir="components/legacy/ome-editor" target="ome-editor.compile"/>
  </target>

  <target name="jar-ome-editor"
    depends="jar-common, jar-ome-xml, jar-formats"
    description="generate JAR file for OME Metadata Editor">
    <ant dir="components/legacy/ome-editor" target="ome-editor.jar"/>
  </target>

  <target name="osgi-ome-editor" depends="jar-ome-editor"
    description="generate OSGi bundle for OME Metadata Editor">
    <ant dir="components/legacy/ome-editor" target="ome-editor.osgi"/>
  </target>

  <target name="findbugs-ome-editor"
    description="run findbugs on OME Metadata Editor">
    <ant dir="components/legacy/ome-editor" target="ome-editor.findbugs"/>
  </target>

  <target name="clean-ome-editor"
    depends="clean-common, clean-ome-xml, clean-formats"
    description="remove build files for OME Metadata Editor">
    <ant dir="components/legacy/ome-editor" target="ome-editor.clean"/>
  </target>

  <!-- Tool collections -->

  <target name="tools" depends="copy-jars, jar-common,
    jar-jai, jar-poi-loci, jar-mdbtools,
    jar-ome-xml, jar-formats, jar-loci-plugins"
    description="create JAR file encompassing several LOCI tools">
    <echo>----------=========== loci_tools ===========----------</echo>
    <for list="${loci-tools.libraries}" param="jar" delimiter=" " trim="true">
      <sequential>
        <unjar src="${artifact.dir}/@{jar}" dest="${loci-tools.dir}">
          <patternset>
            <exclude name="META-INF/**"/>
          </patternset>
        </unjar>
      </sequential>
    </for>
    <jar jarfile="${loci-tools.jar}" basedir="${loci-tools.dir}">
      <manifest>
        <attribute name="Main-Class" value="${loci-tools.main}"/>
      </manifest>
    </jar>
    <delete dir="${loci-tools.dir}"/>
  </target>

  <target name="tools-ome" depends="jar-ome-io, jar-ome-plugins"
    description="create JAR file encompassing several OME tools">
    <echo>----------=========== ome_tools ===========----------</echo>
    <for list="${ome-tools.libraries}" param="jar" delimiter=" " trim="true">
      <sequential>
        <unjar src="${artifact.dir}/@{jar}" dest="${ome-tools.dir}">
          <patternset>
            <exclude name="META-INF/**"/>
          </patternset>
        </unjar>
      </sequential>
    </for>
    <jar jarfile="${ome-tools.jar}" basedir="${ome-tools.dir}">
      <manifest>
        <attribute name="Main-Class" value="${ome-tools.main}"/>
      </manifest>
    </jar>
    <delete dir="${ome-tools.dir}"/>
  </target>

</project>