source: branches/4.2/build.xml @ 6517

Revision 6517, 14.3 KB checked in by melissa, 10 years ago (diff)

Fixed scan-deps.pl warnings.

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 code generator
15    Package for generating other code, including the Bio-Formats metadata API,
16    related documentation, Ice bindings, and Bio-Formats C++ bindings headers
17    -=-
18    JAR file:      loci-autogen.jar
19    Path:          components/autogen
20    Project deps:  Bio-Formats, LOCI Common
21    Library deps:  Apache Velocity
22    Optional:      (none)
23    License:       GPL
24
25Bio-Formats
26    A library for reading and writing popular microscopy file formats
27    -=-
28    JAR file:      bio-formats.jar
29    Path:          components/bio-formats
30    Project deps:  LOCI Common, OME-XML Java library, JAI Image I/O Tools,
31                   MDB Tools (Java port), Apache Jakarta POI,
32                   Luratech LuraWave stubs
33    Library deps:  JGoodies Forms, NetCDF, Simple Logging Facade for Java API,
34                   TestNG
35    Optional:      OME I/O, Apache log4j,
36                   Simple Logging Facade for Java log4j Binding,
37                   Xalan Serializer, Xalan
38    License:       GPL
39
40WiscScan Flow Cytometry
41    Server application for flow cytometry with WiscScan using JVMLink
42    -=-
43    JAR file:      flow-cytometry.jar
44    Path:          components/flow-cytometry
45    Project deps:  Bio-Formats, LOCI Common, OME-XML Java library
46    Library deps:  ImageJ, VisAD
47    Optional:      (none)
48    License:       BSD
49
50LOCI Checkstyle checks
51    LOCI's Checkstyle extensions, for checking source code style
52    -=-
53    JAR file:      loci-checks.jar
54    Path:          components/checkstyle
55    Project deps:  (none)
56    Library deps:  Checkstyle
57    Optional:      (none)
58    License:       Public domain
59
60LOCI Common
61    A library containing common I/O and reflection classes
62    -=-
63    JAR file:      loci-common.jar
64    Path:          components/common
65    Project deps:  (none)
66    Library deps:  Simple Logging Facade for Java API, TestNG
67    Optional:      Apache log4j, Simple Logging Facade for Java log4j Binding
68    License:       GPL
69
70LOCI Plugins for ImageJ
71    A collection of plugins for ImageJ, including the Bio-Formats Importer,
72    Bio-Formats Exporter, Bio-Formats Macro Extensions, Data Browser, Stack
73    Colorizer and Stack Slicer
74    -=-
75    JAR file:      loci_plugins.jar
76    Path:          components/loci-plugins
77    Project deps:  Bio-Formats, LOCI Common, OME-XML Java library
78    Library deps:  JGoodies Forms, ImageJ, JUnit, Apache log4j
79    Optional:      (none)
80    License:       GPL
81
82OME I/O
83    A library for OME database import, upload and download
84    -=-
85    JAR file:      ome-io.jar
86    Path:          components/ome-io
87    Project deps:  Bio-Formats, LOCI Common
88    Library deps:  Apache log4j, Simple Logging Facade for Java API,
89                   OMERO Client, OMERO Common, TestNG
90    Optional:      OME-Java
91    License:       GPL
92
93OME Plugins for ImageJ
94    A collection of plugins for ImageJ, including the Download from OME and
95    Upload to OME plugins
96    -=-
97    JAR file:      ome_plugins.jar
98    Path:          components/ome-plugins
99    Project deps:  Bio-Formats, LOCI Common, LOCI Plugins for ImageJ, OME I/O,
100                   OME-XML Java library
101    Library deps:  ImageJ
102    Optional:      (none)
103    License:       GPL
104
105OME-XML Java library
106    A library for working with OME-XML metadata structures
107    -=-
108    JAR file:      ome-xml.jar
109    Path:          components/ome-xml
110    Project deps:  (none)
111    Library deps:  Simple Logging Facade for Java API, TestNG
112    Optional:      (none)
113    License:       GPL
114
115SLIM Plotter
116    An application and curve fitting library for visualization and analysis of
117    combined spectral lifetime data
118    -=-
119    JAR file:      SlimPlotter.jar
120    Path:          components/slim-plotter
121    Project deps:  Bio-Formats, LOCI Common, VisBio
122    Library deps:  L-M Fit, VisAD
123    Optional:      (none)
124    License:       GPL
125
126LOCI testing framework
127    Framework for automated and manual testing of the LOCI software packages
128    -=-
129    JAR file:      loci-testing-framework.jar
130    Path:          components/test-suite
131    Project deps:  Bio-Formats, LOCI Common, OME I/O
132    Library deps:  Apache log4j, Simple Logging Facade for Java API, TestNG
133    Optional:      (none)
134    License:       BSD
135
136VisBio
137    A multi-purpose biological analysis tool
138    -=-
139    JAR file:      visbio.jar
140    Path:          components/visbio
141    Project deps:  Bio-Formats, LOCI Common, OME I/O, OME-XML Java library,
142                   Apache Jakarta POI
143    Library deps:  Apple eAWT stubs, JGoodies Forms, ImageJ, JUnit,
144                   JGoodies Looks, VisAD
145    Optional:      (none)
146    License:       GPL
147
148===============================================================================
149The following components are considered "legacy" but still available:
150
151JVMLink
152    A library for communicating between a Java Virtual Machine and other
153    programs (e.g., C++ applications) via IP over localhost (or remotely)
154    -=-
155    JAR file:      jvmlink.jar
156    Path:          components/legacy/jvmlink
157    Project deps:  LOCI Common
158    Optional:      (none)
159    License:       BSD
160
161Multi-LUT
162    A demo application for visually exploring multi-spectral image data
163    -=-
164    JAR file:      MultiLUT.jar
165    Path:          components/legacy/multi-lut
166    Project deps:  (none)
167    Optional:      (none)
168    License:       Public domain
169
170OME Metadata Editor
171    An application for exploration and editing of OME-XML and OME-TIFF metadata
172    -=-
173    JAR file:      ome-editor.jar
174    Path:          components/legacy/ome-editor
175    Project deps:  Bio-Formats, LOCI Common, OME-XML Java library
176    Optional:      (none)
177    License:       LGPL
178
179===============================================================================
180The following components are forks of third party projects:
181
182JAI Image I/O Tools
183    Java API to handle JPEG and JPEG2000 files
184    -=-
185    JAR file:      jai_imageio.jar
186    Path:          components/forks/jai
187    Project deps:  (none)
188    Optional:      (none)
189    License:       BSD
190    Project URL:   http://jai-imageio.dev.java.net/
191    Notes:         Used by Bio-Formats to read images compressed with JPEG2000
192                   and lossless JPEG. Modified from the 2008-10-14 source to
193                   include support for the YCbCr color space. Several files in
194                   the com.sun.media.jai packages were removed, as they are not
195                   needed by Bio-Formats, and created an additional dependency.
196                   This component will be removed once our changes have been
197                   added to the official JAI CVS repository.
198
199MDB Tools (Java port)
200    Java API to handle Microsoft MDB format (Access)
201    -=-
202    JAR file:      mdbtools-java.jar
203    Path:          components/forks/mdbtools
204    Project deps:  (none)
205    Optional:      (none)
206    License:       LGPL
207    Project URL:   http://sourceforge.net/forum/message.php?msg_id=2550619
208    Notes:         Used by Bio-Formats for Zeiss LSM metadata in MDB files.
209
210Apache Jakarta POI
211    Java API to handle Microsoft OLE 2 Compound Document format (Word, Excel)
212    -=-
213    JAR file:      poi-loci.jar
214    Path:          components/forks/poi
215    Project deps:  LOCI Common
216    Optional:      (none)
217    License:       Apache
218    Project URL:   http://jakarta.apache.org/poi/
219    Notes:         Based on poi-2.5.1-final-20040804.jar, with bugfixes for OLE
220                   v2 and memory efficiency improvements. Used by Bio-Formats
221                   for OLE support (cxd, ipw, oib, zvi). Used by VisBio
222                   overlays logic for XLS export feature.
223
224===============================================================================
225The following components are stubs of third party projects:
226
227Luratech LuraWave stubs
228    Stub of proprietary Java API to handle Luratech LWF compression
229    -=-
230    JAR file:      lwf-stubs.jar
231    Path:          components/stubs/lwf-stubs
232    Project deps:  (none)
233    Optional:      (none)
234    License:       BSD
235    Project URL:   http://www.luratech.com/
236    Notes:         required to compile Bio-Formats's support for Luratech LWF
237                   compression for the Opera Flex format
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 Mac-specific functionality on non-Mac OS X
245               machines
246    License:   BSD
247
248Ant-Contrib
249    JAR file:  ant-contrib-1.0b3.jar
250    URL:       http://ant-contrib.sourceforge.net/
251    Notes:     used by tools target to iterate over JAR files ("for" task)
252    License:   Apache
253
254Checkstyle
255    JAR file:  checkstyle-all-5.0.jar
256    URL:       http://checkstyle.sourceforge.net/
257    Notes:     used by style Ant target to check source code style conventions
258    License:   LGPL
259
260Apache Jakarta Commons HttpClient
261    JAR file:  commons-httpclient-2.0-rc2.jar
262    URL:       http://jakarta.apache.org/commons/httpclient/
263    Notes:     required for OME-Java to communicate with OME servers
264    License:   Apache
265
266Apache Jakarta Commons Logging
267    JAR file:  commons-logging.jar
268    URL:       http://jakarta.apache.org/commons/logging/
269    Notes:     used by OME-Java
270    License:   Apache
271
272FindBugs Ant task
273    JAR file:  findbugs-ant.jar
274    URL:       http://findbugs.sourceforge.net/
275    Notes:     used by findbugs Ant target to check for program bugs
276    License:   LGPL
277
278JGoodies Forms
279    JAR file:  forms-1.3.0.jar
280    URL:       http://www.jgoodies.com/freeware/forms/index.html
281    Notes:     used for layout by VisBio, Data Browser and OME Notes
282    License:   BSD
283
284Ice
285    JAR file:  Ice-3.3.1.jar
286    URL:       http://www.zeroc.com/ice.html
287    Notes:     used by Bio-Formats Ice framework
288    License:   GPL
289
290ImageJ
291    JAR file:  ij.jar
292    URL:       http://rsb.info.nih.gov/ij/
293    Notes:     used by LOCI plugins for ImageJ and OME plugins for ImageJ;
294               bundled with VisBio to achieve ImageJ interconnectivity
295    License:   Public domain
296
297JAI ImageIO wrapper
298    JAR file:  clibwrapper_jiio.jar
299    URL:       https://jai-imageio.dev.java.net/
300    Notes:     used by Bio-Formats via reflection for JPEG2000 support (ND2,
301               JP2) and lossless JPEG decompression (DICOM)
302    License:   BSD
303
304JUnit
305    JAR file:  junit.jar
306    URL:       http://www.junit.org/
307    Notes:     unit testing framework used for a few VisBio unit tests
308    License:   Common Public License
309
310L-M Fit
311    JAR file:  lma.jar
312    URL:       http://users.utu.fi/jaolho/
313    Notes:     Levenberg-Marquardt algorithm for exponential curve fitting,
314               used by SLIM Plotter
315    License:   LGPL
316
317Apache log4j
318    JAR file:  log4j-1.2.15.jar
319    URL:       http://logging.apache.org/log4j/
320    Notes:     required by SLF4J implementation
321    License:   Apache
322
323JGoodies Looks
324    JAR file:  looks-2.3.1.jar
325    URL:       http://www.jgoodies.com/freeware/looks/index.html
326    Notes:     used for a nicer Look & Feel by VisBio and OME Metadata Editor
327    License:   BSD
328
329NetCDF
330    JAR file:  netcdf-4.0.jar
331    URL:       http://www.unidata.ucar.edu/software/netcdf-java/
332    Notes:     used by Bio-Formats via reflection for HDF support (Imaris 5.5)
333    License:   LGPL
334
335Simple Logging Facade for Java API
336    JAR file:  slf4j-api-1.5.10.jar
337    URL:       http://www.slf4j.org/
338    Notes:     used for all logging in loci.*
339    License:   BSD
340
341Simple Logging Facade for Java log4j Binding
342    JAR file:  slf4j-log4j12-1.5.10.jar
343    URL:       http://www.slf4j.org/
344    Notes:     used for all logging in loci.*
345    License:   BSD
346
347OME-Java
348    JAR file:  ome-java.jar
349    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
350    Notes:     used by OME I/O to connect to OME servers
351    License:   LGPL
352
353OME-Java deprecated classes
354    JAR file:  ome-java-deprecated.jar
355    URL:       http://www.openmicroscopy.org/site/documents/data-management/ome-server/developer/java-api
356    Notes:     used by OME Notes and OME Metadata Editor to work with OME-XML
357    License:   LGPL
358
359OMERO Client
360    JAR file:  omero-client-4.1.1.jar
361    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
362    Notes:     used by OME I/O to connect to OMERO servers
363    License:   GPL
364
365OMERO Common
366    JAR file:  omero-common-4.1.1.jar
367    URL:       http://trac.openmicroscopy.org.uk/omero/wiki/MilestoneDownloads
368    Notes:     used by OME I/O to connect to OMERO servers
369    License:   GPL
370
371Xalan Serializer
372    JAR file:  serializer-2.7.1.jar
373    URL:       http://xml.apache.org/xalan-j/
374    Notes:     used for OME-XML transformations
375    License:   Apache
376
377Skin Look and Feel
378    JAR file:  skinlf.jar
379    URL:       http://skinlf.l2fprod.com/
380    Notes:     not used (may be used in the future for flexible skinning)
381    License:   Custom (BSD-like)
382
383TestNG
384    JAR file:  testng-5.11-jdk15.jar
385    URL:       http://testng.org/
386    Notes:     testing framework used for LOCI software automated test suite
387    License:   Apache
388
389Apache Velocity
390    JAR file:  velocity-1.6.3-dep.jar
391    URL:       http://velocity.apache.org/
392    Notes:     used to autogenerate the loci.formats.meta and loci.formats.ome
393               Bio-Formats packages
394    License:   Apache
395
396VisAD
397    JAR file:  visad-lite.jar
398    URL:       http://www.ssec.wisc.edu/~billh/visad.html
399    Notes:     stripped down VisAD library used by VisBio and SLIM Plotter for
400               interactive visualization
401    License:   LGPL
402
403Xalan
404    JAR file:  xalan-2.7.1.jar
405    URL:       http://xml.apache.org/xalan-j/
406    Notes:     used for OME-XML transformations
407    License:   Apache
408
409Apache XML-RPC
410    JAR file:  xmlrpc-1.2-b1.jar
411    URL:       http://ws.apache.org/xmlrpc/
412    Notes:     used by OME-Java library to communicate with OME servers
413    License:   Apache
414-->
415
416<project name="LOCI Software" default="jars" basedir=".">
417  <description>
418    Master build file for all Java software projects at LOCI
419  </description>
420  <import file="ant/toplevel.xml"/>
421</project>
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