source: trunk/build.xml @ 6019

Revision 6019, 13.5 KB checked in by curtis, 10 years ago (diff)

Readd missing build.xml, and fix some javadoc 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 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  <import file="ant/toplevel.xml"/>
408</project>
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