source: tags/loci-tools-4.1.1/build.xml @ 5728

Revision 5728, 35.6 KB checked in by melissa, 11 years ago (diff)

4.1.1 release of LOCI Tools

Line 
1<!--
2build.xml
3
4Master ant build file for all Java software projects at LOCI.
5Download Apache Ant from http://ant.apache.org/.
6Type "ant -p" for a list of targets.
7
8===============================================================================
9This build file handles the following components.
10For more information on a component, see the
11build.properties file in that component's subtree.
12Run ./scan-deps.pl to programmatically generate this list.
13
14LOCI Common
15    A library containing common I/O and reflection classes
16    -=-
17    JAR file:      loci-common.jar
18    Path:          components/common
19    Project deps:  (none)
20    Library deps:  (none)
21    Optional:      (none)
22    License:       GPL
23
24OME-XML Java library
25    A library for working with OME-XML metadata structures
26    -=-
27    JAR file:      ome-xml.jar
28    Path:          components/ome-xml
29    Project deps:  (none)
30    Library deps:  (none)
31    Optional:      (none)
32    License:       GPL
33
34Bio-Formats
35    A library for reading and writing popular microscopy file formats
36    -=-
37    JAR file:      bio-formats.jar
38    Path:          components/bio-formats
39    Project deps:  LOCI Common, OME-XML Java library
40    Library deps:  JGoodies Forms
41    Optional:      OME I/O, OME Notes, Apache Jakarta POI,
42                   MDB Tools (Java port), JAI Image I/O Tools, NetCDF
43    License:       GPL
44
45LOCI code generator
46    Package for generating other code, including the Bio-Formats metadata API,
47    related documentation, Ice bindings, and Bio-Formats C++ bindings headers
48    -=-
49    JAR file:      loci-autogen.jar
50    Path:          components/autogen
51    Project deps:  LOCI Common, Bio-Formats
52    Library deps:  Apache Velocity
53    Optional:      (none)
54    License:       GPL
55
56Bio-Formats Ice framework
57    Bindings for Bio-Formats client/server communication enabling
58    cross-language interoperability
59    -=-
60    JAR file:      bf-ice.jar
61    Path:          components/bf-ice
62    Project deps:  LOCI Common, Bio-Formats
63    Library deps:  Ice
64    Optional:      (none)
65    License:       GPL
66
67LOCI Plugins for ImageJ
68    A collection of plugins for ImageJ, including the Bio-Formats Importer,
69    Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser, Stack
70    Colorizer and Stack Slicer
71    -=-
72    JAR file:      loci_plugins.jar
73    Path:          components/loci-plugins
74    Project deps:  LOCI Common, Bio-Formats
75    Library deps:  JGoodies Forms, ImageJ
76    Optional:      OME I/O, VisBio
77    License:       GPL
78
79OME I/O
80    A library for OME database import, upload and download
81    -=-
82    JAR file:      ome-io.jar
83    Path:          components/ome-io
84    Project deps:  LOCI Common, Bio-Formats
85    Library deps:  OMERO Client, OMERO Common
86    Optional:      OME-Java
87    License:       GPL
88
89OME Plugins for ImageJ
90    A collection of plugins for ImageJ, including the Download from OME and
91    Upload to OME plugins
92    -=-
93    JAR file:      ome_plugins.jar
94    Path:          components/ome-plugins
95    Project deps:  LOCI Common, Bio-Formats, LOCI Plugins for ImageJ, OME I/O
96    Library deps:  ImageJ
97    Optional:      (none)
98    License:       GPL
99
100VisBio
101    A multi-purpose biological analysis tool
102    -=-
103    JAR file:      visbio.jar
104    Path:          components/visbio
105    Project deps:  LOCI Common, OME-XML Java library, Bio-Formats, OME I/O,
106                   Apache Jakarta POI
107    Library deps:  Apple eAWT stubs, JGoodies Forms, ImageJ, JGoodies Looks,
108                   VisAD
109    Optional:      (none)
110    License:       GPL
111
112SLIM Plotter
113    An application and curve fitting library for visualization and analysis of
114    combined spectral lifetime data
115    -=-
116    JAR file:      SlimPlotter.jar
117    Path:          components/slim-plotter
118    Project deps:  LOCI Common, Bio-Formats, VisBio
119    Library deps:  L-M Fit, VisAD
120    Optional:      (none)
121    License:       GPL
122
123WiscScan Flow Cytometry
124    Server application for flow cytometry with WiscScan using JVMLink
125    -=-
126    JAR file:      flow-cytometry.jar
127    Path:          components/flow-cytometry
128    Project deps:  Bio-Formats
129    Library deps:  ImageJ, VisAD
130    Optional:      (none)
131    License:       BSD
132
133LOCI Checkstyle checks
134    LOCI's Checkstyle extensions, for checking source code style
135    -=-
136    JAR file:      loci-checks.jar
137    Path:          components/checkstyle
138    Project deps:  (none)
139    Library deps:  Checkstyle
140    Optional:      (none)
141    License:       Public domain
142
143LOCI testing framework
144    Framework for automated and manual testing of the LOCI software packages
145    -=-
146    JAR file:      loci-testing-framework.jar
147    Path:          components/test-suite
148    Project deps:  LOCI Common, Bio-Formats, OME I/O
149    Library deps:  TestNG
150    Optional:      (none)
151    License:       BSD
152
153===============================================================================
154The following components are considered "legacy" but still available:
155
156JVMLink
157    A library for communicating between a Java Virtual Machine and other
158    programs (e.g., C++ applications) via IP over localhost (or remotely)
159    -=-
160    JAR file:      jvmlink.jar
161    Path:          components/legacy/jvmlink
162    Project deps:  LOCI Common
163    Optional:      (none)
164    License:       BSD
165
166Multi-LUT
167    A demo application for visually exploring multi-spectral image data
168    -=-
169    JAR file:      MultiLUT.jar
170    Path:          components/legacy/multi-lut
171    Project deps:  (none)
172    Optional:      (none)
173    License:       Public domain
174
175OME Notes
176    A library for flexible organization and presentation of OME-XML metadata
177    within a graphical browser and editor interface
178    -=-
179    JAR file:      ome-notes.jar
180    Path:          components/legacy/ome-notes
181    Project deps:  LOCI Common, Bio-Formats
182    Optional:      (none)
183    License:       LGPL
184
185OME Metadata Editor
186    An application for exploration and editing of OME-XML and OME-TIFF metadata
187    -=-
188    JAR file:      ome-editor.jar
189    Path:          components/legacy/ome-editor
190    Project deps:  LOCI Common, OME-XML Java library, Bio-Formats
191    Optional:      (none)
192    License:       LGPL
193
194===============================================================================
195The following components are forks of third party projects:
196
197Apache Jakarta POI
198    Java API to handle Microsoft OLE 2 Compound Document format (Word, Excel)
199    -=-
200    JAR file:      poi-loci.jar
201    Path:          components/forks/poi
202    Project deps:  LOCI Common
203    Optional:      (none)
204    License:       Apache
205    Project URL:   http://jakarta.apache.org/poi/
206    Notes:         Based on poi-2.5.1-final-20040804.jar, with bugfixes for OLE
207                   v2 and memory efficiency improvements. Used by Bio-Formats
208                   for OLE support (cxd, ipw, oib, zvi). Used by VisBio
209                   overlays logic for XLS export feature.
210
211MDB Tools (Java port)
212    Java API to handle Microsoft MDB format (Access)
213    -=-
214    JAR file:      mdbtools-java.jar
215    Path:          components/forks/mdbtools
216    Project deps:  (none)
217    Optional:      (none)
218    License:       LGPL
219    Project URL:   http://sourceforge.net/forum/message.php?msg_id=2550619
220    Notes:         Used by Bio-Formats for Zeiss LSM metadata in MDB files.
221
222JAI Image I/O Tools
223    Java API to handle JPEG and JPEG2000 files
224    -=-
225    JAR file:      jai_imageio.jar
226    Path:          components/forks/jai
227    Project deps:  (none)
228    Optional:      (none)
229    License:       BSD
230    Project URL:   http://jai-imageio.dev.java.net/
231    Notes:         Used by Bio-Formats to read images compressed with JPEG2000
232                   and lossless JPEG. Modified from the 2008-10-14 source to
233                   include support for the YCbCr color space. Several files in
234                   the com.sun.media.jai packages were removed, as they are not
235                   needed by Bio-Formats, and created an additional dependency.
236                   This component will be removed once our changes have been
237                   added to the official JAI CVS repository.
238
239===============================================================================
240The following external dependencies (in the jar folder) may be required:
241Apple eAWT stubs
242    JAR file:  AppleJavaExtensions.jar
243    URL:       http://developer.apple.com/samplecode/AppleJavaExtensions/
244    Notes:     required to compile VisBio on non-Mac OS X machines
245    License:   BSD
246
247Ant-Contrib
248    JAR file:  ant-contrib-1.0b1.jar
249    URL:       http://ant-contrib.sourceforge.net/
250    Notes:     used by tools target to iterate over JAR files ("for" task)
251    License:   Apache
252
253Checkstyle
254    JAR file:  checkstyle-all-4.2.jar
255    URL:       http://checkstyle.sourceforge.net/
256    Notes:     used by style Ant target to check source code style conventions
257    License:   LGPL
258
259Apache Jakarta Commons HttpClient
260    JAR file:  commons-httpclient-2.0-rc2.jar
261    URL:       http://jakarta.apache.org/commons/httpclient/
262    Notes:     required for OME-Java to communicate with OME servers
263    License:   Apache
264
265Apache Jakarta Commons Logging
266    JAR file:  commons-logging.jar
267    URL:       http://jakarta.apache.org/commons/logging/
268    Notes:     used by OME-Java
269    License:   Apache
270
271FindBugs Ant task
272    JAR file:  findbugs-ant.jar
273    URL:       http://findbugs.sourceforge.net/
274    Notes:     used by findbugs Ant target to check for program bugs
275    License:   LGPL
276
277JGoodies Forms
278    JAR file:  forms-1.0.4.jar
279    URL:       http://www.jgoodies.com/freeware/forms/index.html
280    Notes:     used for layout by VisBio, Data Browser and OME Notes
281    License:   BSD
282
283Ice
284    JAR file:  Ice-3.3.1.jar
285    URL:       http://www.zeroc.com/ice.html
286    Notes:     used by Bio-Formats Ice framework
287    License:   GPL
288
289ImageJ
290    JAR file:  ij.jar
291    URL:       http://rsb.info.nih.gov/ij/
292    Notes:     used by LOCI plugins for ImageJ and OME plugins for ImageJ;
293               included with VisBio to achieve ImageJ interconnectivity
294    License:   Public domain
295
296JAI ImageIO wrapper
297    JAR file:  clibwrapper_jiio.jar
298    URL:       https://jai-imageio.dev.java.net/
299    Notes:     used by Bio-Formats via reflection for JPEG2000 support (ND2,
300               JP2) and lossless JPEG decompression (DICOM)
301    License:   BSD
302
303JUnit
304    JAR file:  junit.jar
305    URL:       http://www.junit.org/
306    Notes:     unit testing framework used for a few VisBio unit tests
307    License:   Common Public License
308
309L-M Fit
310    JAR file:  lma.jar
311    URL:       http://users.utu.fi/jaolho/
312    Notes:     Levenberg-Marquardt algorithm for exponential curve fitting,
313               used by SLIM Plotter
314    License:   LGPL
315
316JGoodies Looks
317    JAR file:  looks-1.2.2.jar
318    URL:       http://www.jgoodies.com/freeware/looks/index.html
319    Notes:     used for a nicer Look & Feel by VisBio and OME Metadata Editor
320    License:   BSD
321
322NetCDF
323    JAR file:  netcdf-4.0.jar
324    URL:       http://www.unidata.ucar.edu/software/netcdf-java/
325    Notes:     used by Bio-Formats via reflection for HDF support (Imaris 5.5)
326    License:   LGPL
327
328BUFR Java Decoder
329    JAR file:  bufr-1.1.00.jar
330    URL:       http://www.unidata.ucar.edu/software/netcdf-java/
331    Notes:     used by NetCDF library
332    License:   LGPL
333
334GRIB Java Decoder
335    JAR file:  grib-5.1.03.jar
336    URL:       http://www.unidata.ucar.edu/software/netcdf-java/
337    Notes:     used by NetCDF library
338    License:   LGPL
339
340Simple Logging Facade for Java
341    JAR file:  slf4j-jdk14.jar
342    URL:       http://www.slf4j.org/
343    Notes:     used by NetCDF library
344    License:   BSD
345
346OME-Java
347    JAR file:  ome-java.jar
348    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
349    Notes:     used by OME I/O to connect to OME servers
350    License:   LGPL
351
352OME-Java deprecated classes
353    JAR file:  ome-java-deprecated.jar
354    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
355    Notes:     used by OME Notes and OME Metadata Editor to work with OME-XML
356    License:   LGPL
357
358OMERO Client
359    JAR file:  omero-client-4.0.3.jar
360    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
361    Notes:     used by OME I/O to connect to OMERO servers
362    License:   GPL
363
364OMERO Common
365    JAR file:  omero-common-4.0.3.jar
366    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
367    Notes:     used by OME I/O to connect to OMERO servers
368    License:   GPL
369
370Skin Look and Feel
371    JAR file:  skinlf.jar
372    URL:       http://skinlf.l2fprod.com/
373    Notes:     not used (may be used in the future for flexible skinning)
374    License:   Custom (BSD-like)
375
376TestNG
377    JAR file:  testng-5.7-jdk14.jar
378    URL:       http://testng.org/
379    Notes:     testing framework used for LOCI software automated test suite
380    License:   Apache
381
382Apache Velocity
383    JAR file:  velocity-dep-1.5.jar
384    URL:       http://velocity.apache.org/
385    Notes:     used to autogenerate the loci.formats.meta and loci.formats.ome
386               Bio-Formats packages
387    License:   Apache
388
389VisAD
390    JAR file:  visad-lite.jar
391    URL:       http://www.ssec.wisc.edu/~billh/visad.html
392    Notes:     stripped down VisAD library used by VisBio and SLIM Plotter for
393               interactive visualization
394    License:   LGPL
395
396Apache XML-RPC
397    JAR file:  xmlrpc-1.2-b1.jar
398    URL:       http://ws.apache.org/xmlrpc/
399    Notes:     used by OME-Java library to communicate with OME servers
400    License:   Apache
401-->
402
403<project name="LOCI Software" default="jars" basedir=".">
404  <description>
405    Master build file for all Java software projects at LOCI
406  </description>
407
408  <property name="root.dir" location="${basedir}"/>
409  <import file="global.xml"/>
410  <property file="build.properties"/>
411
412  <!-- Global build targets -->
413
414  <target name="jars"
415    depends="copy-jars, jar-common, jar-ome-xml,
416      jar-jai, jar-poi-loci, jar-mdbtools,
417      jar-formats, jar-autogen, jar-bf-ice,
418      jar-loci-plugins, jar-ome-io, jar-ome-plugins,
419      jar-visbio, jar-slim, jar-flow,
420      jar-checks, jar-tests,
421      jar-jvmlink, jar-multi-lut,
422      jar-ome-notes, jar-ome-editor"
423    description="generate JAR files for LOCI software packages"/>
424
425  <!--
426  NB: Findbugs target does not test autogenerated code, forks and legacy:
427    findbugs-ome-xml
428    findbugs-jai
429    findbugs-poi-loci
430    findbugs-mdbtools
431    findbugs-bf-ice
432    findbugs-jvmlink
433    findbugs-multi-lut
434    findbugs-ome-notes
435    findbugs-ome-editor
436  -->
437  <target name="findbugs"
438    depends="findbugs-common,
439      findbugs-formats, findbugs-autogen,
440      findbugs-loci-plugins, findbugs-ome-io, findbugs-ome-plugins,
441      findbugs-visbio, findbugs-slim, findbugs-flow,
442      findbugs-checks, findbugs-tests"
443    description="run findbugs on most components"/>
444
445  <target name="clean"
446    depends="clean-common, clean-ome-xml,
447      clean-jai, clean-poi-loci, clean-mdbtools,
448      clean-formats, clean-autogen, clean-bf-ice,
449      clean-loci-plugins, clean-ome-io, clean-ome-plugins,
450      clean-visbio, clean-slim, clean-flow,
451      clean-checks, clean-tests,
452      clean-jvmlink, clean-multi-lut,
453      clean-ome-notes, clean-ome-editor"
454    description="remove all build files">
455    <delete dir="${artifact.dir}"/>
456    <delete dir="build"/>
457  </target>
458
459  <target name="utils"
460    depends="jars, utils-common, utils-formats, utils-loci-plugins"
461    description="compile all extra utilities">
462    <delete>
463      <fileset dir="${toplevel-utils.dir}" includes="*.class"/>
464    </delete>
465    <javac debug="true" deprecation="true" source="1.5" target="1.5"
466      srcdir="${toplevel-utils.dir}" includes="*.java">
467      <classpath>
468        <fileset dir="${artifact.dir}">
469          <include name="*.jar"/>
470        </fileset>
471      </classpath>
472    </javac>
473  </target>
474
475  <target name="docs" depends="jars"
476    description="generate javadocs for LOCI software packages">
477    <tstamp>
478      <format property="YEAR" pattern="yyyy"/>
479    </tstamp>
480    <javadoc sourcepath="${merged-docs.source}"
481      classpath="${merged-docs.classpath}"
482      destdir="${merged-docs.dir}/api"
483      maxmemory="${merged-docs.memory}"
484      failonerror="true" author="true" version="true" use="true"
485      nodeprecated="true" windowtitle="LOCI Software API">
486      <doctitle><![CDATA[<h1>LOCI Software</h1>]]></doctitle>
487      <bottom><![CDATA[${copyright.begin} ${YEAR} ${copyright.end}]]></bottom>
488      <link href="http://java.sun.com/j2se/1.5.0/docs/api/"/>
489      <link href="http://hudson.openmicroscopy.org.uk/job/OMEJAVA/javadoc/"/>
490      <link href="http://rsbweb.nih.gov/ij/developer/api/"/>
491      <link href="http://www.ssec.wisc.edu/visad-docs/javadoc/"/>
492      <!--<link href="http://www.jdocs.com/formlayout/1.0.4/api/"/>-->
493      <!--<link href="http://www.jdocs.com/looks/1.2.2/api/"/>-->
494    </javadoc>
495  </target>
496
497  <target name="copy-jars">
498    <!-- copy third party JARs into artifacts folder -->
499    <!-- necessary for runtime classpath dependencies to function properly -->
500    <copy todir="${artifact.dir}" preservelastmodified="true">
501      <fileset dir="${lib.dir}" includes="*.jar"/>
502    </copy>
503  </target>
504
505  <!-- LOCI common library -->
506
507  <target name="compile-common"
508    description="compile classes for LOCI common library">
509    <ant dir="components/common" target="common.compile"/>
510  </target>
511
512  <target name="jar-common"
513    description="generate JAR file for LOCI common library">
514    <ant dir="components/common" target="common.jar"/>
515  </target>
516
517  <target name="findbugs-common"
518    description="run findbugs on LOCI common library">
519    <ant dir="components/common" target="common.findbugs"/>
520  </target>
521
522  <target name="clean-common"
523    description="remove build files for LOCI common library">
524    <ant dir="components/common" target="common.clean"/>
525  </target>
526
527  <target name="utils-common" depends="jar-common"
528    description="compile extra utilities for LOCI common library">
529    <ant dir="components/common" target="common.utils"/>
530  </target>
531
532  <!-- JAI Image I/O Tools library -->
533
534  <target name="compile-jai"
535    description="compile classes for JAI Image I/O Tools library">
536    <ant dir="components/forks/jai" target="jai.compile"/>
537  </target>
538
539  <target name="jar-jai"
540    description="generate JAR file for JAI Image I/O Tools library">
541    <ant dir="components/forks/jai" target="jai.jar"/>
542  </target>
543
544  <target name="findbugs-jai"
545    description="run findbugs on JAI Image I/O Tools library">
546    <ant dir="components/forks/jai" target="jai.findbugs"/>
547  </target>
548
549  <target name="clean-jai"
550    description="remove build files for JAI Image I/O Tools library">
551    <ant dir="components/forks/jai" target="jai.clean"/>
552  </target>
553
554  <!-- Apache POI Java library -->
555
556  <target name="compile-poi-loci"
557    depends="compile-common"
558    description="compile classes for Apache POI library">
559    <ant dir="components/forks/poi" target="poi-loci.compile"/>
560  </target>
561
562  <target name="jar-poi-loci"
563    depends="jar-common"
564    description="generate JAR file for Apache POI library">
565    <ant dir="components/forks/poi" target="poi-loci.jar"/>
566  </target>
567
568  <target name="findbugs-poi-loci"
569    description="run findbugs on Apache POI library">
570    <ant dir="components/forks/poi" target="poi-loci.findbugs"/>
571  </target>
572
573  <target name="clean-poi-loci"
574    depends="clean-common"
575    description="remove build files for Apache POI library">
576    <ant dir="components/forks/poi" target="poi-loci.clean"/>
577  </target>
578
579  <!-- MDB Tools Java library -->
580
581  <target name="compile-mdbtools"
582    description="compile classes for MDB Tools Java library">
583    <ant dir="components/forks/mdbtools" target="mdbtools.compile"/>
584  </target>
585
586  <target name="jar-mdbtools"
587    description="generate JAR file for MDB Tools Java library">
588    <ant dir="components/forks/mdbtools" target="mdbtools.jar"/>
589  </target>
590
591  <target name="findbugs-mdbtools"
592    description="run findbugs on MDB Tools Java library">
593    <ant dir="components/forks/mdbtools" target="mdbtools.findbugs"/>
594  </target>
595
596  <target name="clean-mdbtools"
597    description="remove build files for MDB Tools Java library">
598    <ant dir="components/forks/mdbtools" target="mdbtools.clean"/>
599  </target>
600
601  <!-- OME-XML Java library -->
602
603  <target name="compile-ome-xml"
604    description="compile classes for OME-XML Java library">
605    <ant dir="components/ome-xml" target="ome-xml.compile"/>
606  </target>
607
608  <target name="jar-ome-xml"
609    description="generate JAR file for OME-XML Java library">
610    <ant dir="components/ome-xml" target="ome-xml.jar"/>
611  </target>
612
613  <target name="findbugs-ome-xml"
614    description="run findbugs on OME-XML Java library">
615    <ant dir="components/ome-xml" target="ome-xml.findbugs"/>
616  </target>
617
618  <target name="clean-ome-xml"
619    description="remove build files for OME-XML Java library">
620    <ant dir="components/ome-xml" target="ome-xml.clean"/>
621  </target>
622
623  <!-- Bio-Formats -->
624
625  <target name="compile-formats"
626    depends="compile-common, compile-ome-xml"
627    description="compile classes for Bio-Formats">
628    <ant dir="components/bio-formats" target="formats.compile"/>
629  </target>
630
631  <target name="jar-formats"
632    depends="jar-common, jar-ome-xml"
633    description="generate JAR file for Bio-Formats">
634    <ant dir="components/bio-formats" target="formats.jar"/>
635  </target>
636
637  <target name="findbugs-formats"
638    description="run findbugs on Bio-Formats">
639    <ant dir="components/bio-formats" target="formats.findbugs"/>
640  </target>
641
642  <target name="clean-formats"
643    depends="clean-common, clean-ome-xml"
644    description="remove build files for Bio-Formats">
645    <ant dir="components/bio-formats" target="formats.clean"/>
646  </target>
647
648  <target name="utils-formats" depends="jar-formats"
649    description="compile extra utilities for LOCI Plugins for ImageJ">
650    <ant dir="components/bio-formats" target="formats.utils"/>
651  </target>
652
653  <!-- LOCI autogen -->
654
655  <target name="compile-autogen"
656    depends="compile-common, compile-formats"
657    description="compile classes for LOCI autogen">
658    <ant dir="components/autogen" target="autogen.compile"/>
659  </target>
660
661  <target name="jar-autogen"
662    depends="jar-common, jar-formats"
663    description="generate JAR file for LOCI autogen">
664    <ant dir="components/autogen" target="autogen.jar"/>
665  </target>
666
667  <target name="findbugs-autogen"
668    description="run findbugs on LOCI autogen">
669    <ant dir="components/autogen" target="autogen.findbugs"/>
670  </target>
671
672  <target name="clean-autogen"
673    depends="clean-common, clean-formats"
674    description="remove build files for LOCI autogen">
675    <ant dir="components/autogen" target="autogen.clean"/>
676  </target>
677
678  <!-- Bio-Formats Ice framework -->
679
680  <target name="compile-bf-ice"
681    depends="compile-formats"
682    description="compile classes for Bio-Formats Ice framework">
683    <ant dir="components/bf-ice" target="bf-ice.compile"/>
684  </target>
685
686  <target name="jar-bf-ice"
687    depends="jar-formats"
688    description="generate JAR file for Bio-Formats Ice framework">
689    <ant dir="components/bf-ice" target="bf-ice.jar"/>
690  </target>
691
692  <target name="findbugs-bf-ice"
693    description="run findbugs on Bio-Formats Ice framework">
694    <ant dir="components/bf-ice" target="bf-ice.findbugs"/>
695  </target>
696
697  <target name="clean-bf-ice"
698    depends="clean-formats"
699    description="remove build files for Bio-Formats Ice framework">
700    <ant dir="components/bf-ice" target="bf-ice.clean"/>
701  </target>
702
703  <!-- LOCI Plugins for ImageJ -->
704
705  <target name="compile-loci-plugins"
706    depends="compile-common, compile-formats"
707    description="compile classes for LOCI Plugins for ImageJ">
708    <ant dir="components/loci-plugins" target="loci-plugins.compile"/>
709  </target>
710
711  <target name="jar-loci-plugins"
712    depends="jar-common, jar-formats"
713    description="generate JAR file for LOCI Plugins for ImageJ">
714    <ant dir="components/loci-plugins" target="loci-plugins.jar"/>
715  </target>
716
717  <target name="findbugs-loci-plugins"
718    description="run findbugs on LOCI Plugins for ImageJ">
719    <ant dir="components/loci-plugins" target="loci-plugins.findbugs"/>
720  </target>
721
722  <target name="clean-loci-plugins"
723    depends="clean-common, clean-formats"
724    description="remove build files for LOCI Plugins for ImageJ">
725    <ant dir="components/loci-plugins" target="loci-plugins.clean"/>
726  </target>
727
728  <target name="utils-loci-plugins" depends="jar-loci-plugins"
729    description="compile extra utilities for LOCI Plugins for ImageJ">
730    <ant dir="components/loci-plugins" target="loci-plugins.utils"/>
731  </target>
732
733  <!-- OME I/O -->
734
735  <target name="compile-ome-io"
736    depends="compile-common, compile-formats"
737    description="compile classes for OME I/O">
738    <ant dir="components/ome-io" target="ome-io.compile"/>
739  </target>
740
741  <target name="jar-ome-io"
742    depends="jar-common, jar-formats"
743    description="generate JAR file for OME I/O">
744    <ant dir="components/ome-io" target="ome-io.jar"/>
745  </target>
746
747  <target name="findbugs-ome-io"
748    description="run findbugs on OME I/O">
749    <ant dir="components/ome-io" target="ome-io.findbugs"/>
750  </target>
751
752  <target name="clean-ome-io"
753    depends="clean-common, clean-formats"
754    description="remove build files for OME I/O">
755    <ant dir="components/ome-io" target="ome-io.clean"/>
756  </target>
757
758  <!-- OME Plugins for ImageJ -->
759
760  <target name="compile-ome-plugins"
761    depends="compile-common, compile-formats,
762      compile-loci-plugins, compile-ome-io"
763    description="compile classes for OME Plugins for ImageJ">
764    <ant dir="components/ome-plugins" target="ome-plugins.compile"/>
765  </target>
766
767  <target name="jar-ome-plugins"
768    depends="jar-common, jar-formats, jar-loci-plugins, jar-ome-io"
769    description="generate JAR file for OME Plugins for ImageJ">
770    <ant dir="components/ome-plugins" target="ome-plugins.jar"/>
771  </target>
772
773  <target name="findbugs-ome-plugins"
774    description="run findbugs on OME Plugins for ImageJ">
775    <ant dir="components/ome-plugins" target="ome-plugins.findbugs"/>
776  </target>
777
778  <target name="clean-ome-plugins"
779    depends="clean-common, clean-formats, clean-loci-plugins, clean-ome-io"
780    description="remove build files for OME Plugins for ImageJ">
781    <ant dir="components/ome-plugins" target="ome-plugins.clean"/>
782  </target>
783
784  <!-- VisBio -->
785
786  <target name="compile-visbio"
787    depends="compile-common, compile-ome-xml, compile-formats,
788      compile-ome-io, compile-poi-loci"
789    description="compile classes for VisBio">
790    <ant dir="components/visbio" target="visbio.compile"/>
791  </target>
792
793  <target name="jar-visbio"
794    depends="jar-common, jar-ome-xml, jar-formats, jar-ome-io, jar-poi-loci"
795    description="generate JAR file for VisBio">
796    <ant dir="components/visbio" target="visbio.jar"/>
797  </target>
798
799  <target name="findbugs-visbio"
800    description="run findbugs on VisBio">
801    <ant dir="components/visbio" target="visbio.findbugs"/>
802  </target>
803
804  <target name="clean-visbio"
805    depends="clean-common, clean-ome-xml, clean-formats,
806      clean-ome-io, clean-poi-loci"
807    description="remove build files for VisBio">
808    <ant dir="components/visbio" target="visbio.clean"/>
809  </target>
810
811  <target name="dist-visbio"
812    description="create distribution archives for VisBio">
813    <ant dir="components/visbio" target="dist"/>
814  </target>
815
816  <target name="dist-visbio-win32"
817    description="create distribution archive for VisBio: Windows w/ JRE">
818    <ant dir="components/visbio" target="dist-win32"/>
819  </target>
820
821  <target name="dist-visbio-win32-nojre"
822    description="create distribution archive for VisBio: Windows no JRE">
823    <ant dir="components/visbio" target="dist-win32-nojre"/>
824  </target>
825
826  <target name="dist-visbio-macosx"
827    description="create distribution archive for VisBio: Mac OS X">
828    <ant dir="components/visbio" target="dist-macosx"/>
829  </target>
830
831  <target name="dist-visbio-linux"
832    description="create distribution archive for VisBio: Linux w/ JRE">
833    <ant dir="components/visbio" target="dist-linux"/>
834  </target>
835
836  <target name="dist-visbio-nojre"
837    description="create distribution archive for VisBio: cross-platform">
838    <ant dir="components/visbio" target="dist-nojre"/>
839  </target>
840
841  <!-- SLIM Plotter -->
842
843  <target name="compile-slim"
844    depends="compile-common, compile-formats, compile-visbio"
845    description="compile classes for SLIM Plotter">
846    <ant dir="components/slim-plotter" target="slim.compile"/>
847  </target>
848
849  <target name="jar-slim"
850    depends="jar-common, jar-formats, jar-visbio"
851    description="generate JAR file for SLIM Plotter">
852    <ant dir="components/slim-plotter" target="slim.jar"/>
853  </target>
854
855  <target name="findbugs-slim"
856    description="run findbugs on SLIM Plotter">
857    <ant dir="components/slim-plotter" target="slim.findbugs"/>
858  </target>
859
860  <target name="clean-slim"
861    depends="clean-common, clean-formats, clean-visbio"
862    description="remove build files for SLIM Plotter">
863    <ant dir="components/slim-plotter" target="slim.clean"/>
864  </target>
865
866  <target name="dist-slim"
867    description="create distribution archive for SLIM Plotter">
868    <ant dir="components/slim-plotter" target="dist"/>
869  </target>
870
871  <!-- WiscScan Flow Cytometry -->
872
873  <target name="compile-flow"
874    depends="compile-formats"
875    description="compile classes for WiscScan Flow Cytometry">
876    <ant dir="components/flow-cytometry" target="flow.compile"/>
877  </target>
878
879  <target name="jar-flow"
880    depends="jar-formats"
881    description="generate JAR file for WiscScan Flow Cytometry">
882    <ant dir="components/flow-cytometry" target="flow.jar"/>
883  </target>
884
885  <target name="findbugs-flow"
886    description="run findbugs on WiscScan Flow Cytometry">
887    <ant dir="components/flow-cytometry" target="flow.findbugs"/>
888  </target>
889
890  <target name="clean-flow"
891    depends="clean-formats"
892    description="remove build files for WiscScan Flow Cytometry">
893    <ant dir="components/flow-cytometry" target="flow.clean"/>
894  </target>
895
896  <target name="dist-flow"
897    description="create distribution archive for WiscScan Flow Cytometry">
898    <ant dir="components/flow-cytometry" target="dist"/>
899  </target>
900
901  <!-- LOCI Checkstyle checks -->
902
903  <target name="compile-checks"
904    description="compile classes for LOCI Checkstyle checks">
905    <ant dir="components/checkstyle" target="checks.compile"/>
906  </target>
907
908  <target name="jar-checks"
909    description="generate JAR file for LOCI Checkstyle checks">
910    <ant dir="components/checkstyle" target="checks.jar"/>
911  </target>
912
913  <target name="findbugs-checks"
914    description="run findbugs on LOCI Checkstyle checks">
915    <ant dir="components/checkstyle" target="checks.findbugs"/>
916  </target>
917
918  <target name="clean-checks"
919    description="remove build files for LOCI Checkstyle checks">
920    <ant dir="components/checkstyle" target="checks.clean"/>
921  </target>
922
923  <!-- LOCI testing framework -->
924
925  <target name="compile-tests"
926    depends="compile-common, compile-formats, compile-ome-io"
927    description="compile classes for LOCI testing framework">
928    <ant dir="components/test-suite" target="tests.compile"/>
929  </target>
930
931  <target name="jar-tests"
932    depends="jar-common, jar-formats, jar-ome-io"
933    description="generate JAR file for LOCI testing framework">
934    <ant dir="components/test-suite" target="tests.jar"/>
935  </target>
936
937  <target name="findbugs-tests"
938    description="run findbugs on LOCI testing framework">
939    <ant dir="components/test-suite" target="tests.findbugs"/>
940  </target>
941
942  <target name="clean-tests"
943    depends="clean-common, clean-formats, clean-ome-io"
944    description="remove build files for LOCI testing framework">
945    <ant dir="components/test-suite" target="tests.clean"/>
946  </target>
947
948  <!-- JVMLink -->
949
950  <target name="compile-jvmlink"
951    depends="compile-common"
952    description="compile classes for JVMLink">
953    <ant dir="components/legacy/jvmlink" target="jvmlink.compile"/>
954  </target>
955
956  <target name="jar-jvmlink"
957    depends="jar-common"
958    description="generate JAR file for JVMLink">
959    <ant dir="components/legacy/jvmlink" target="jvmlink.jar"/>
960  </target>
961
962  <target name="findbugs-jvmlink"
963    description="run findbugs on JVMLink">
964    <ant dir="components/legacy/jvmlink" target="jvmlink.findbugs"/>
965  </target>
966
967  <target name="clean-jvmlink"
968    depends="clean-common"
969    description="remove build files for JVMLink">
970    <ant dir="components/legacy/jvmlink" target="jvmlink.clean"/>
971  </target>
972
973  <!-- Multi LUT app -->
974
975  <target name="compile-multi-lut"
976    description="compile classes for Multi LUT app">
977    <ant dir="components/legacy/multi-lut" target="multi-lut.compile"/>
978  </target>
979
980  <target name="jar-multi-lut"
981    description="generate JAR file for Multi LUT app">
982    <ant dir="components/legacy/multi-lut" target="multi-lut.jar"/>
983  </target>
984
985  <target name="findbugs-multi-lut"
986    description="run findbugs on Multi LUT app">
987    <ant dir="components/legacy/multi-lut" target="multi-lut.findbugs"/>
988  </target>
989
990  <target name="clean-multi-lut"
991    description="remove build files for Multi LUT app">
992    <ant dir="components/legacy/multi-lut" target="multi-lut.clean"/>
993  </target>
994
995  <!-- OME Notes -->
996
997  <target name="compile-ome-notes"
998    depends="compile-common, compile-formats"
999    description="compile classes for OME Notes">
1000    <ant dir="components/legacy/ome-notes" target="ome-notes.compile"/>
1001  </target>
1002
1003  <target name="jar-ome-notes"
1004    depends="jar-common, jar-formats"
1005    description="generate JAR file for OME Notes">
1006    <ant dir="components/legacy/ome-notes" target="ome-notes.jar"/>
1007  </target>
1008
1009  <target name="findbugs-ome-notes"
1010    description="run findbugs for OME Notes">
1011    <ant dir="components/legacy/ome-notes" target="ome-notes.findbugs"/>
1012  </target>
1013
1014  <target name="clean-ome-notes"
1015    depends="clean-common, clean-formats"
1016    description="remove build files for OME Notes">
1017    <ant dir="components/legacy/ome-notes" target="ome-notes.clean"/>
1018  </target>
1019
1020  <!-- OME Metadata Editor -->
1021
1022  <target name="compile-ome-editor"
1023    depends="compile-common, compile-ome-xml, compile-formats"
1024    description="compile classes for OME Metadata Editor">
1025    <ant dir="components/legacy/ome-editor" target="ome-editor.compile"/>
1026  </target>
1027
1028  <target name="jar-ome-editor"
1029    depends="jar-common, jar-ome-xml, jar-formats"
1030    description="generate JAR file for OME Metadata Editor">
1031    <ant dir="components/legacy/ome-editor" target="ome-editor.jar"/>
1032  </target>
1033
1034  <target name="findbugs-ome-editor"
1035    description="run findbugs on OME Metadata Editor">
1036    <ant dir="components/legacy/ome-editor" target="ome-editor.findbugs"/>
1037  </target>
1038
1039  <target name="clean-ome-editor"
1040    depends="clean-common, clean-ome-xml, clean-formats"
1041    description="remove build files for OME Metadata Editor">
1042    <ant dir="components/legacy/ome-editor" target="ome-editor.clean"/>
1043  </target>
1044
1045  <!-- Tool collections -->
1046
1047  <target name="tools" depends="copy-jars, jar-common,
1048    jar-jai, jar-poi-loci, jar-mdbtools,
1049    jar-ome-xml, jar-formats, jar-loci-plugins"
1050    description="create JAR file encompassing several LOCI tools">
1051    <for list="${loci-tools.libraries}" param="jar" delimiter=" " trim="true">
1052      <sequential>
1053        <unjar src="${artifact.dir}/@{jar}" dest="${loci-tools.dir}">
1054          <patternset>
1055            <exclude name="META-INF/**"/>
1056          </patternset>
1057        </unjar>
1058      </sequential>
1059    </for>
1060    <jar jarfile="${loci-tools.jar}" basedir="${loci-tools.dir}">
1061      <manifest>
1062        <attribute name="Main-Class" value="${loci-tools.main}"/>
1063      </manifest>
1064    </jar>
1065    <delete dir="${loci-tools.dir}"/>
1066  </target>
1067
1068  <target name="tools-ome" depends="jar-ome-io, jar-ome-plugins"
1069    description="create JAR file encompassing several OME tools">
1070    <for list="${ome-tools.libraries}" param="jar" delimiter=" " trim="true">
1071      <sequential>
1072        <unjar src="${artifact.dir}/@{jar}" dest="${ome-tools.dir}">
1073          <patternset>
1074            <exclude name="META-INF/**"/>
1075          </patternset>
1076        </unjar>
1077      </sequential>
1078    </for>
1079    <jar jarfile="${ome-tools.jar}" basedir="${ome-tools.dir}">
1080      <manifest>
1081        <attribute name="Main-Class" value="${ome-tools.main}"/>
1082      </manifest>
1083    </jar>
1084    <delete dir="${ome-tools.dir}"/>
1085  </target>
1086
1087</project>
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