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7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
1 <project name="CDK" default="dist" basedir=".">
3d221c1 Added additional PDBReader tests.
yeldar authored
2
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
3 <property name="version" value="20040604-CVS" />
4
3a26de3 Made compilation with debug=on customizable.
egonw authored
5 <!-- compile options -->
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
6 <property name="build.sysclasspath" value="ignore" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
7 <property name="build.compiler" value="modern" />
3a26de3 Made compilation with debug=on customizable.
egonw authored
8 <property name="debug" value="on" />
460ea79 Detect deprecated methods
egonw authored
9 <property name="deprecation" value="on" />
3a26de3 Made compilation with debug=on customizable.
egonw authored
10 <property name="optimization" value="off" />
11
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
12 <!-- patches to apply -->
13
3a26de3 Made compilation with debug=on customizable.
egonw authored
14 <!-- where to find Java3D -->
15 <property name="pathtojava3d" value="" />
16 <property name="pathtojoelib" value="../../JoeLib/joelib/" />
17
18 <!-- directories -->
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
19 <property name="build" value="build" />
20 <property name="sourcedist" value="sourcedist" />
21 <property name="dist" value="dist" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
22 <property name="doc" value="doc" />
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
23 <property name="src" value="src" />
24 <property name="lib" value="jar" />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
25 <property name="src.tests" value="${src}/org/openscience/cdk/test" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
26 <property name="reports.tests" value="reports" />
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
27 <property name="appjars.dir" value="${dist}/appjars" />
f7be51f Removed alternative core classes patch offering more detailed debug info
egonw authored
28
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar which ...
egonw authored
29 <!-- class to run for testing-->
30 <property name="testclass" value="CDKTests" />
31 <property name="runclass" value="applications.Viewer" />
32 <property name="arg1" value="" />
33 <property name="arg2" value="" />
34 <property name="arg3" value="" />
35 <property name="arg4" value="" />
58425b9 Added use of properties to run target
steinbeck authored
36
6fa86d2 Added task dist core-debug which will create a cdk-core-debug.jar which ...
egonw authored
37 <!-- CLASSPATH -->
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
38 <path id="project.class.path">
0c049c7 Further work on new build system: all packages compile, but target test-...
egonw authored
39 <pathelement location="${java.ext.dirs}/rt.jar" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
40
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
41 <fileset dir="${lib}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
42 <include name="batik-awt-util.jar" />
43 <include name="batik-dom.jar" />
9bcb948 Updated Xerces and Batik libraries to current versions
egonw authored
44 <include name="batik-svggen.jar" />
327694a Uploaded two required batik libs, and new version of castor
egonw authored
45 <include name="batik-util.jar" />
46 <include name="batik-xml.jar" />
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
47 <include name="baysmith-io.jar" />
48 <include name="dadml.jar" />
49 <include name="gnujaxp.jar" />
50 <include name="junit.jar" />
51 <include name="log4j-core.jar" />
52 <include name="log4j.jar" />
53 <include name="mysql-2.0.4.jar" />
54 <include name="postgresql7.0-1.2.jar" />
55 <include name="printf.jar" />
56 <include name="vecmath1.2-1.14.jar" />
21491b7 Updated for new Xerces lib
egonw authored
57 <include name="xerces-2.6.2.jar" />
58 <include name="xmlApis-2.6.2.jar" />
8658001 Added libraries for XindiceReader
yz237 authored
59 <include name="xindice.jar" />
60 <include name="xmldb.jar" />
4ac3d10 Add patches to sourcedist
egonw authored
61 <include name="stmml.jar" />
327694a Uploaded two required batik libs, and new version of castor
egonw authored
62 <include name="castor-0.9.5-xml.jar" />
482731a Extended classpath to include cml stuff
shk3 authored
63 <include name="cmlAll.jar" />
64 <include name="base.jar" />
65 <include name="pmrlib.jar" />
7f7ea85 Have the experimental JME reader actually compile
egonw authored
66 <include name="jmolApis.jar" />
67 <include name="jmolIO.jar" />
5569297 Updated FileConvertor: all options are now implemented, and the app now ...
egonw authored
68 <include name="commons-cli-1.0.jar" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
69 </fileset>
943daec Location of Java3D classes is now settable. If Java3D is not installed i...
egonw authored
70 <fileset dir="${pathtojava3d}">
71 <include name="*.jar" />
72 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
73 </path>
74
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
75 <target id="info" name="info" depends="check">
76 <!-- Gives information about the building process. -->
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
77 <echo message="Environment:" />
78 <echo message=" Ant version: ${ant.version}" />
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_HOM...
egonw authored
79 <echo message=" ${ANT_HOME}: ${ant.home}" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
80 <echo message=" Java version: ${java.version}" />
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_HOM...
egonw authored
81 <echo message=" Java ext dir: ${java.ext.dirs}" />
cc7da6f Report on found 'requirements'
egonw authored
82 <echo message=" JOELib found: ${joelib.present}" />
0bbc7aa Fixed compiling without CMLDOM libraries (for some reason it does not de...
egonw authored
83 <echo message=" CMLDOM found: ${cmllibs.present}" />
f3efa88 Add string resources for IUPAC name generator to jar
egonw authored
84 <echo message=" Java3D found: ${java3D.present}" />
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_HOM...
egonw authored
85 <echo message=" Junit found: ${junit.present}" />
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
86 <echo message="" />
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
87 <echo message="Compiling:" />
88 <echo message=" for: ${build.compiler}" />
89 <echo message=" debug: ${debug}" />
90 <echo message=" deprecation: ${deprecation}" />
91 <echo message=" optimization: ${optimization}" />
2f3eee0 Adapted to provide for a customizable patch scheme
egonw authored
92 <echo message="" />
93 <echo message="Patches to apply" />
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
94 </target>
95
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
96 <target id="check" name="check">
97 <!-- Checks which parts of CDK can be build. -->
bd7054c Don't try to build libio if lib jars are not available
egonw authored
98 <available classname="joelib.molecule.JOEAtom"
99 classpath="${lib}/libio/joelib.jar"
100 property="joelib.present"/>
cbfa2fa Fixed building of CMLDom libio
egonw authored
101 <available file="${lib}/cmlAll.jar"
0bbc7aa Fixed compiling without CMLDOM libraries (for some reason it does not de...
egonw authored
102 property="cmllibs.present"/>
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
103 <available classname="javax.media.j3d.Canvas3D"
104 classpathref="project.class.path"
105 property="java3D.present"/>
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_HOM...
egonw authored
106 <available classname="junit.framework.TestCase"
107 classpath="${ant.home}/lib/junit.jar"
108 property="junit.present"/>
1dca8cc Optionalized IUPAC parser compilation depending on Ant 1.6 availability
egonw authored
109 <condition property="hasAnt16">
110 <contains string="${ant.version}" substring="1.6"/>
111 </condition>
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
112 <condition property="isJava13">
113 <contains string="${java.version}" substring="1.3"/>
114 </condition>
8a8b889 Don't redo javacc if not necessary (closes #888925), and fixed uptodaten...
egonw authored
115 <uptodate property="dotjavafiles.uptodate"
116 targetfile="${src}/core.javafiles">
1449de7 Added test to see if *.javafiles are up to date
egonw authored
117 <srcfiles dir="${src}" includes="**/*.java" />
118 </uptodate>
2fa9ba9 Forgot to upload the updated build.xml
egonw authored
119 <condition property="dotjjfiles.uptodate">
120 <and>
121 <uptodate property="NomParserJavafiles.uptodate"
122 targetfile="${src}/org/openscience/cdk/iupac/parser/NomParser.java">
123 <srcfiles dir="${src}" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
124 </uptodate>
125 <uptodate property="SMARTSParserJavafiles.uptodate"
126 targetfile="${src}/org/openscience/cdk/smiles/smarts/SMARTSParser.java">
127 <srcfiles dir="${src}" includes="org/openscience/cdk/smiles/smarts/SMARTSParser.jj" />
128 </uptodate>
129 </and>
130 </condition>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
131 </target>
132
d2ed020 Reworked dependencies
egonw authored
133 <target id="init" name="init" depends="check, setupBuildDir"/>
2b69107 Ok, reworked build process that now also build restrictions can be given...
egonw authored
134 <target id="customize" name="customize" depends="javacc"/>
44a4466 Now detects Java1.3 and makes changes to have it succesfully compile
egonw authored
135
136 <target id="setupBuildDir" name="setupBuildDir">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
137 <tstamp />
138 <mkdir dir="${build}" />
139 <mkdir dir="${sourcedist}" />
140 <mkdir dir="${dist}" />
141 <mkdir dir="${reports.tests}" />
142 </target>
143
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
144 <target id="clean" name="clean" description="Removes autogenerated files.">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
145 <delete>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
146 <fileset dir="." includes="**/*~" />
147 <fileset dir="." includes="*.tar.gz" />
148 <fileset dir="." includes="*.zip" />
149 <fileset dir="${src}" includes="*.classes" />
df95df5 Don't delete the *.javafiles from CVS
egonw authored
150 <fileset dir="${src}" includes="*.javafiles">
151 <exclude name="jmol*.javafiles" />
152 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
153 </delete>
154
155 <delete dir="${build}" />
156 <delete dir="${sourcedist}" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
157 <delete dir="${dist}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
158 <delete dir="${reports.tests}" />
159 </target>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
160
ca98ea5 Refactored build process (closes #883519)
egonw authored
161 <target name="compileDoclet" id="compileDoclet">
162 <javac srcdir="doc/javadoc/source" destdir="doc/javadoc"
163 includes="MakeJavaFilesFilesDoclet.java">
164 <classpath>
165 <fileset dir="${java.ext.dirs}">
166 <include name="tools.jar" />
167 </fileset>
5a62197 Fixed compileDoclet target
egonw authored
168 <fileset dir="${java.ext.dirs}/../../../lib">
169 <include name="tools.jar" />
170 </fileset>
ca98ea5 Refactored build process (closes #883519)
egonw authored
171 </classpath>
172 </javac>
173 </target>
174
2583a62 Added better output about missing src/*.javafiles
egonw authored
175 <target name="runDoclet" id="runDoclet" depends="reallyRunDoclet, failIfNoDocletResults"/>
176
177 <target name="checkDocletResults">
178 <condition property="dotjavafiles.uptodate">
179 <and>
180 <available file="${src}/core.javafiles" />
181 <available file="${src}/standard.javafiles" />
182 <available file="${src}/extra.javafiles" />
183 <available file="${src}/io.javafiles" />
184 </and>
185 </condition>
186 </target>
187
188 <target name="failIfNoDocletResults" depends="checkDocletResults" unless="dotjavafiles.uptodate">
189 <fail>
190 There seems to be a problem with building the cdk/src/*.javafiles.
191 Please report this to cdk-devel@lists.sf.net and send the output of
192 this command: ant -v info runDoclet.
193 </fail>
194 </target>
195
196 <target name="reallyRunDoclet" depends="compileDoclet" unless="dotjavafiles.uptodate">
ca98ea5 Refactored build process (closes #883519)
egonw authored
197 <javadoc private="false" public="true">
198 <classpath refid="project.class.path" />
199 <doclet name="MakeJavaFilesFilesDoclet" path="${doc}/javadoc"/>
24af772 Delete autogenerated .javafiles in clean target
egonw authored
200
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
201 <packageset dir="${src}">
ca98ea5 Refactored build process (closes #883519)
egonw authored
202 <include name="org/openscience/cdk/**"/>
203 </packageset>
204 </javadoc>
0bbfc90 Removed Viewer application. Use JChemPaint (jchempaint.sf.net) or Jmol (...
egonw authored
205 <move todir="${src}" failonerror="true">
ca98ea5 Refactored build process (closes #883519)
egonw authored
206 <fileset dir=".">
207 <include name="*.javafiles"/>
0c049c7 Further work on new build system: all packages compile, but target test-...
egonw authored
208 <include name="*.classes"/>
ca98ea5 Refactored build process (closes #883519)
egonw authored
209 </fileset>
210 </move>
211 </target>
212
1449de7 Added test to see if *.javafiles are up to date
egonw authored
213 <target name="compile.init" id="compile.init"
214 depends="init, customize, compileDoclet, runDoclet"/>
215
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
216 <target id="compile" name="compile"
217 description="Compiles the CDK."
d2ed020 Reworked dependencies
egonw authored
218 depends="compile-core, compile-standard, compile-extra, compile-io,
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
219 compile-render, compile-render-with-java3d, compile-libio">
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
220 </target>
221
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
222 <target id="compile-all" name="compile-all" depends="compile, compile-experimental, compile-apps"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
223 description="Compiles the CDK, including experimental classes.">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
224 </target>
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
225
0bbc7aa Fixed compiling without CMLDOM libraries (for some reason it does not de...
egonw authored
226 <target id="compile-libio" name="compile-libio" depends="dist-standard,
227 compile-libio-joelib, compile-libio-cml" />
bd7054c Don't try to build libio if lib jars are not available
egonw authored
228
229 <target name="dont-compile-libio-joelib" unless="joelib.present">
230 <echo message="Not compiling libio for JOELib, jar/libio/joelib.jar is not present" />
231 </target>
232
0bbc7aa Fixed compiling without CMLDOM libraries (for some reason it does not de...
egonw authored
233 <target name="dont-compile-libio-cml" unless="cmllibs.present">
234 <echo message="Not compiling libio for CMLDOM, jar/cmlAll.jar is not present" />
235 </target>
236
237 <target name="compile-libio-joelib" if="joelib.present" depends="dont-compile-libio-joelib">
bd7054c Don't try to build libio if lib jars are not available
egonw authored
238 <!-- Task to build the libio classes for JOELib. -->
239 <echo message="Compiling libio for JOELib" />
7ce93c7 Added cdk.Atom <-> joelib.molecule.JOEAtom Convertor procedure.
egonw authored
240
bd7054c Don't try to build libio if lib jars are not available
egonw authored
241 <javac destdir="${build}" optimize="${optimization}"
242 debug="${debug}" deprecation="${deprecation}">
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
243 <src path="${src}/org/openscience/cdk/libio/joelib" />
244 <src path="${src}/org/openscience/cdk/test/libio/joelib" />
bd7054c Don't try to build libio if lib jars are not available
egonw authored
245
246 <classpath refid="project.class.path" />
247 <classpath>
248 <fileset dir="${lib}/libio">
249 <include name="*.jar" />
250 </fileset>
251 </classpath>
252 </javac>
253 </target>
7ce93c7 Added cdk.Atom <-> joelib.molecule.JOEAtom Convertor procedure.
egonw authored
254
0bbc7aa Fixed compiling without CMLDOM libraries (for some reason it does not de...
egonw authored
255 <target name="compile-libio-cml" if="cmllibs.present" depends="dont-compile-libio-cml">
256 <!-- Task to build the libio classes for CMLDOM. -->
257 <echo message="Compiling libio for CMLDOM" />
258
259 <javac destdir="${build}" optimize="${optimization}"
260 debug="${debug}" deprecation="${deprecation}">
261 <src path="${src}/org/openscience/cdk/libio/cml" />
262
263 <classpath refid="project.class.path" />
264 <classpath>
265 <fileset dir="${lib}">
266 <include name="base.jar" />
267 <include name="cmlAll.jar" />
268 <include name="pmrlib.jar" />
269 </fileset>
270 </classpath>
271 </javac>
272 </target>
273
4b8b4e6 Added shell variant of test.bat
egonw authored
274 <target id="compile-apps" name="compile-apps"
0bbfc90 Removed Viewer application. Use JChemPaint (jchempaint.sf.net) or Jmol (...
egonw authored
275 depends="dist-libio, dist-experimental, dist-render-with-java3d">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
276 <!-- Task to build the applications classes. Some require extra
277 jars, like those in ${lib}/libio -->
278 <echo message="Compiling classes defined in ${src}/applications.javafiles." />
38401bd Put applications in separate jar.
egonw authored
279
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
280 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be given...
egonw authored
281 debug="${debug}" deprecation="${deprecation}">
282 <includesfile name="${src}/applications.javafiles"/>
283 <excludesfile name="${src}/java1.4.javafiles" if="isJava13"/>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
284 <classpath refid="project.class.path" />
285 <classpath>
286 <fileset dir="${dist}/jar">
287 <include name="cdk-core.jar" />
288 <include name="cdk-standard.jar" />
289 <include name="cdk-render.jar" />
290 <include name="cdk-io.jar" />
291 <include name="cdk-extra.jar" />
292 <include name="cdk-libio.jar" />
293 <include name="cdk-experimental.jar" />
294 </fileset>
295 </classpath>
296 <classpath>
297 <fileset dir="${lib}/libio">
298 <include name="*.jar" />
299 </fileset>
300 </classpath>
301 </javac>
38401bd Put applications in separate jar.
egonw authored
302 </target>
303
d2ed020 Reworked dependencies
egonw authored
304 <target id="compile-core" name="compile-core" depends="compile.init">
36b733d Adding cdk-standard module.
egonw authored
305 <echo message="Compiling classes for cdk-core module." />
20ba54a Simplifying the build proces.
egonw authored
306
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
307 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
3a26de3 Made compilation with debug=on customizable.
egonw authored
308 debug="${debug}" deprecation="${deprecation}"
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
309 includesfile="${src}/core.javafiles">
20ba54a Simplifying the build proces.
egonw authored
310 <classpath refid="project.class.path" />
311 </javac>
312 </target>
313
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
314 <target id="compile-standard" name="compile-standard" depends="dist-core">
36b733d Adding cdk-standard module.
egonw authored
315 <echo message="Compiling classes for cdk-standard module." />
316
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
317 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be given...
egonw authored
318 debug="${debug}" deprecation="${deprecation}">
319 <includesfile name="${src}/standard.javafiles"/>
320 <excludesfile name="${src}/java1.4.javafiles" if="isJava13"/>
36b733d Adding cdk-standard module.
egonw authored
321 <classpath>
322 <fileset dir="${lib}">
db10183 Moving general code out of ShelX reader.
egonw authored
323 <include name="vecmath1.2-1.14.jar" />
015e9b3 Fixed bug #649013.
egonw authored
324 <include name="log4j-core.jar" />
325 <include name="log4j.jar" />
4c55e18 Added missing jar files required for cdk-standard
egonw authored
326 <include name="gnujaxp.jar" />
9bcb948 Updated Xerces and Batik libraries to current versions
egonw authored
327 <include name="xerces-2.5.0.jar" />
36b733d Adding cdk-standard module.
egonw authored
328 </fileset>
329 <fileset dir="${dist}/jar">
330 <include name="cdk-core.jar" />
331 </fileset>
332 </classpath>
333 </javac>
334 </target>
335
a34eb22 More @cdkPackage completed: cdk-io now also compiles with kaffe
egonw authored
336 <target id="compile-io" name="compile-io" depends="init, dist-core, dist-standard">
36b733d Adding cdk-standard module.
egonw authored
337 <echo message="Compiling classes for cdk-io module." />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
338
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
339 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be given...
egonw authored
340 debug="${debug}" deprecation="${deprecation}">
341 <includesfile name="${src}/io.javafiles"/>
342 <excludesfile name="${src}/java1.4.javafiles" if="isJava13"/>
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
343 <classpath refid="project.class.path" />
344 <classpath>
345 <fileset dir="${dist}/jar">
346 <include name="cdk-core.jar" />
36b733d Adding cdk-standard module.
egonw authored
347 <include name="cdk-standard.jar" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
348 </fileset>
349 </classpath>
350 </javac>
351 </target>
352
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
353 <target id="compile-render" name="compile-render" depends="init, dist-core, dist-standard">
8095921 Added rendering of wedged bonds.
egonw authored
354 <echo message="Compiling classes for cdk-render module." />
355
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
356 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
94396d9 More @cdkPackage completed: cdk-render now also compiles with kaffe
egonw authored
357 debug="${debug}" deprecation="${deprecation}"
358 includesfile="${src}/render.javafiles">
8095921 Added rendering of wedged bonds.
egonw authored
359
360 <classpath refid="project.class.path" />
361 <classpath>
362 <fileset dir="${dist}/jar">
363 <include name="cdk-core.jar" />
364 <include name="cdk-standard.jar" />
365 </fileset>
366 </classpath>
367 </javac>
368 </target>
1dd9647 Added IUPAC name parser
stomkinson authored
369
370 <!-- Convert the JavaCC .jj file to the correct .java files for the IUPAC parser -->
62f2673 Don't delete everything in cdk.iupac.parser
egonw authored
371 <target id="javacc" name="javacc" depends="init, check" if="hasAnt16" unless="dotjjfiles.uptodate">
cd49d3a A bit of comment
egonw authored
372 <!-- the IUPAC name parser -->
1dd9647 Added IUPAC name parser
stomkinson authored
373 <delete>
374 <fileset id="javacc-generated"
cd49d3a A bit of comment
egonw authored
375 dir="${src}/org/openscience/cdk/iupac/parser/"
376 includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
1dd9647 Added IUPAC name parser
stomkinson authored
377 </delete>
378 <javacc target="${src}/org/openscience/cdk/iupac/parser/NomParser.jj"
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
379 outputdirectory="${src}/org/openscience/cdk/iupac/parser/"
1dd9647 Added IUPAC name parser
stomkinson authored
380 javacchome="${lib}"/>
2fa9ba9 Forgot to upload the updated build.xml
egonw authored
381 <delete>
382 <fileset id="javacc-generated"
383 dir="${src}/org/openscience/cdk/smiles/smarts/"
384 includes="*.java"/>
385 </delete>
386 <javacc target="${src}/org/openscience/cdk/smiles/smarts/SMARTSParser.jj"
387 outputdirectory="${src}/org/openscience/cdk/smiles/smarts/"
388 javacchome="${lib}"/>
1dd9647 Added IUPAC name parser
stomkinson authored
389 </target>
8095921 Added rendering of wedged bonds.
egonw authored
390
d2ed020 Reworked dependencies
egonw authored
391 <target id="compile-extra" name="compile-extra" depends="dist-standard, dist-io, dist-render">
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
392 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be given...
egonw authored
393 debug="${debug}" deprecation="${deprecation}">
394 <includesfile name="${src}/extra.javafiles"/>
395 <excludesfile name="${src}/java1.4.javafiles" if="isJava13"/>
62f2673 Don't delete everything in cdk.iupac.parser
egonw authored
396 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
72d1834 Explicitily state which cdk jars to use for compile-extra
egonw authored
397
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
398 <classpath refid="project.class.path" />
72d1834 Explicitily state which cdk jars to use for compile-extra
egonw authored
399 <classpath>
400 <fileset dir="${dist}/jar">
401 <include name="cdk-core.jar" />
402 <include name="cdk-standard.jar" />
0386767 More @cdkPackage completed for test classes
egonw authored
403 <include name="cdk-render.jar" />
404 <include name="cdk-io.jar" />
72d1834 Explicitily state which cdk jars to use for compile-extra
egonw authored
405 </fileset>
406 </classpath>
9f4ce4f Added patch for RFC #20
egonw authored
407 </javac>
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
408 </target>
f095e4e Fixed dist.extra target. Not all classes were added to the jar: it did
egonw authored
409
0386767 More @cdkPackage completed for test classes
egonw authored
410 <target id="compile-experimental" name="compile-experimental"
411 depends="dist-extra">
412 <echo message="Compiling classes for cdk-experimental module." />
0ef4af6 Added cdk-experimental package
egonw authored
413
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
414 <javac srcdir="${src}" destdir="${build}" optimize="${optimization}"
0386767 More @cdkPackage completed for test classes
egonw authored
415 debug="${debug}" deprecation="${deprecation}"
416 includesfile="${src}/experimental.javafiles">
417 <classpath refid="project.class.path" />
418 <classpath>
419 <fileset dir="${dist}/jar">
420 <include name="cdk-core.jar" />
421 <include name="cdk-standard.jar" />
422 <include name="cdk-render.jar" />
423 <include name="cdk-io.jar" />
424 <include name="cdk-extra.jar" />
425 </fileset>
426 </classpath>
427 </javac>
0ef4af6 Added cdk-experimental package
egonw authored
428 </target>
429
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
430 <target id="compile-test" name="compile-test"
431 depends="dist-all">
0386767 More @cdkPackage completed for test classes
egonw authored
432 <!-- Task to build the test classes. -->
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
433 <javac srcdir="${src}"
0386767 More @cdkPackage completed for test classes
egonw authored
434 destdir="${build}" optimize="${optimization}"
2b69107 Ok, reworked build process that now also build restrictions can be given...
egonw authored
435 debug="${debug}" deprecation="${deprecation}">
436 <includesfile name="${src}/test.javafiles"/>
437 <excludesfile name="${src}/java1.4.javafiles" if="isJava13"/>
62f2673 Don't delete everything in cdk.iupac.parser
egonw authored
438 <excludesfile name="${src}/ant1.6.javafiles" unless="hasAnt16"/>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
439
0386767 More @cdkPackage completed for test classes
egonw authored
440 <classpath refid="project.class.path" />
441 <classpath>
442 <fileset dir="${dist}/jar">
443 <include name="cdk-core.jar" />
444 <include name="cdk-standard.jar" />
445 <include name="cdk-render.jar" />
446 <include name="cdk-io.jar" />
447 <include name="cdk-extra.jar" />
448 <include name="cdk-libio.jar" />
449 <include name="cdk-experimental.jar" />
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
450 <include name="cdk-apps.jar" />
0386767 More @cdkPackage completed for test classes
egonw authored
451 </fileset>
452 </classpath>
453 </javac>
bfe9294 Some changes to make a CML lib jar for Jmol.
egonw authored
454 </target>
455
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
456
457 <target name="compile-render-with-java3d"
458 depends="dont-compile-render-with-java3d, do-compile-render-with-java3d"/>
459
460 <target name="dont-compile-render-with-java3d" depends="compile-render"
461 unless="java3D.present">
462 <echo message="Cannot compile Java3D based viewer classes. Java3D is not present" />
463 </target>
464
465 <target name="do-compile-render-with-java3d" depends="compile-render"
466 if="java3D.present">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
467 <mkdir dir="${build}" />
468
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
469 <javac srcdir="${src}"
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
470 destdir="${build}" optimize="${optimization}"
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
471 debug="${debug}" deprecation="${deprecation}"
26336c0 Fixed build.xml for proper reference to java3d.javafiles (thanks to Gemm...
egonw authored
472 includesfile="${src}/java3d.javafiles">
aa6535c Don't compile java source files in ${sourcedist} with java3D too.
egonw authored
473
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
474 <classpath refid="project.class.path" />
475 </javac>
476 </target>
477
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
478 <target id="dist.init" name="dist.init">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
479 <mkdir dir="${dist}/jar" />
480
f3efa88 Add string resources for IUPAC name generator to jar
egonw authored
481 <!-- copy data files -->
482
51eff2f Updated for new config data dir
egonw authored
483 <mkdir dir="${build}/org/openscience/cdk/config/data" />
f3efa88 Add string resources for IUPAC name generator to jar
egonw authored
484 <mkdir dir="${build}/org/openscience/cdk/io/cml/data" />
0ac9cc0 Include dictionaries in jar
egonw authored
485 <mkdir dir="${build}/org/openscience/cdk/dict/data" />
f3efa88 Add string resources for IUPAC name generator to jar
egonw authored
486 <mkdir dir="${build}/org/openscience/cdk/iupac/generator/data" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
487
488 <copy
360783a AtomTypeFactory and IsotopeFactory moved from cdk.tools to cdk.config an...
egonw authored
489 file="${src}/org/openscience/cdk/config/data/isotopes.xml"
490 tofile="${build}/org/openscience/cdk/config/data/isotopes.xml" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
491 <copy
360783a AtomTypeFactory and IsotopeFactory moved from cdk.tools to cdk.config an...
egonw authored
492 file="${src}/org/openscience/cdk/config/data/structgen_atomtypes.xml"
493 tofile="${build}/org/openscience/cdk/config/data/structgen_atomtypes.xml" />
c3ba50b Added Log4J configuration file.
egonw authored
494 <copy
360783a AtomTypeFactory and IsotopeFactory moved from cdk.tools to cdk.config an...
egonw authored
495 file="${src}/org/openscience/cdk/config/data/valency_atomtypes.xml"
496 tofile="${build}/org/openscience/cdk/config/data/valency_atomtypes.xml" />
ff82543 Added ValencyCheckerInterface which enables HydrogenAdder to make use of...
egonw authored
497 <copy
51eff2f Updated for new config data dir
egonw authored
498 file="${src}/org/openscience/cdk/config/data/mol2_atomtypes.xml"
499 tofile="${build}/org/openscience/cdk/config/data/mol2_atomtypes.xml" />
500 <copy
360783a AtomTypeFactory and IsotopeFactory moved from cdk.tools to cdk.config an...
egonw authored
501 file="${src}/org/openscience/cdk/config/data/jmol_atomtypes.txt"
502 tofile="${build}/org/openscience/cdk/config/data/jmol_atomtypes.txt" />
d525829 Also copy jmol_atomtypes.txt into jars.
egonw authored
503 <copy
360783a AtomTypeFactory and IsotopeFactory moved from cdk.tools to cdk.config an...
egonw authored
504 file="${src}/org/openscience/cdk/config/data/log4j.properties"
505 tofile="${build}/org/openscience/cdk/config/data/log4j.properties" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
506
507 <copy
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
508 file="${src}/org/openscience/cdk/io/cml/data/cml1_0.dtd"
f8fea66 Put new CML DTDs in the distribution.
egonw authored
509 tofile="${build}/org/openscience/cdk/io/cml/data/cml1_0.dtd" />
510 <copy
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
511 file="${src}/org/openscience/cdk/io/cml/data/cml1_0_1.dtd"
f8fea66 Put new CML DTDs in the distribution.
egonw authored
512 tofile="${build}/org/openscience/cdk/io/cml/data/cml1_0_1.dtd" />
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
513
0ac9cc0 Include dictionaries in jar
egonw authored
514 <copy
f3efa88 Add string resources for IUPAC name generator to jar
egonw authored
515 file="${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties"
516 tofile="${build}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties" />
517
0ac9cc0 Include dictionaries in jar
egonw authored
518 <copy
519 file="${src}/org/openscience/cdk/dict/data/chemical.xml"
520 tofile="${build}/org/openscience/cdk/dict/data/chemical.xml" />
521 <copy
522 file="${src}/org/openscience/cdk/dict/data/elements.xml"
523 tofile="${build}/org/openscience/cdk/dict/data/elements.xml" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
524 </target>
d313d03 Also include cml.dtd in normal jar.
egonw authored
525
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
526 <target id="dist-core" name="dist-core" depends="compile-core, dist.init">
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
527 <jar jarfile="${dist}/jar/cdk-core.jar">
528 <fileset dir="${build}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
529 <includesfile name="${src}/core.classes" />
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
530 </fileset>
531 </jar>
532 </target>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
533
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
534 <target id="dist-extra" name="dist-extra" depends="dist-core, compile-extra">
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
535 <jar jarfile="${dist}/jar/cdk-extra.jar">
536 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
537 <includesfile name="${src}/extra.classes" />
538 </fileset>
026da28 Removed last trace of patch system: compile errors in IDE tools work aga...
egonw authored
539 <fileset dir="${build}">
2679b69 Added missing dictionaries to cdk-extra.jar
egonw authored
540 <include name="org/openscience/cdk/dict/data/*.xml" />
541 </fileset>
0ef4af6 Added cdk-experimental package
egonw authored
542 </jar>
543 </target>
544
545 <target id="dist-experimental" name="dist-experimental" depends="compile-experimental, dist.init">
546 <jar jarfile="${dist}/jar/cdk-experimental.jar">
547 <fileset dir="${build}">
548 <includesfile name="${src}/experimental.classes" />
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
549 </fileset>
43d9399 Splitted cdk.jar into cdk-core.jar and cdk-extra.jar.
egonw authored
550 </jar>
551 </target>
552
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
553 <target id="dist-apps" name="dist-apps" depends="compile-apps">
4ae9e15 Compile PublicJmol when doing compile-libio.
egonw authored
554 <jar jarfile="${dist}/jar/cdk-apps.jar" manifest="${src}/cdk-apps.manifest">
38401bd Put applications in separate jar.
egonw authored
555 <fileset dir="${build}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
556 <includesfile name="${src}/applications.classes" />
38401bd Put applications in separate jar.
egonw authored
557 </fileset>
558 </jar>
559 </target>
560
df42e11 Fixed a few dependencies for the test target
egonw authored
561 <target id="dist-test" name="dist-test" depends="compile-test">
2c7c43d Fixed loading of files in JUnit IO tests: now using get resource.
egonw authored
562 <jar jarfile="${dist}/jar/cdk-test.jar">
563 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
564 <includesfile name="${src}/test.classes" />
2c7c43d Fixed loading of files in JUnit IO tests: now using get resource.
egonw authored
565 </fileset>
566 <fileset dir=".">
567 <include name="data/**" />
568 </fileset>
569 </jar>
570 </target>
571
0386767 More @cdkPackage completed for test classes
egonw authored
572 <target id="dist-libio" name="dist-libio" depends="compile-libio" unless="libio.present">
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
573 <jar jarfile="${dist}/jar/cdk-libio.jar">
574 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
575 <includesfile name="${src}/libio.classes" />
4ae9e15 Compile PublicJmol when doing compile-libio.
egonw authored
576 </fileset>
577 <fileset dir="${build}">
578 <include name="org/openscience/jmol/**" />
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
579 </fileset>
580 </jar>
581 </target>
582
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
583 <target id="dist-io" name="dist-io" depends="compile-io">
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
584 <jar jarfile="${dist}/jar/cdk-io.jar">
585 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
586 <includesfile name="${src}/io.classes" />
2b0ab15 Make sure the CML DTDs are in the cdk-io.jar again
egonw authored
587 <include name="org/openscience/cdk/io/cml/data/**" />
4784091 New module: cdk-io. It only depends on cdk-core.
egonw authored
588 </fileset>
589 </jar>
590 </target>
591
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
592 <target id="dist-render" name="dist-render" depends="compile-render">
8095921 Added rendering of wedged bonds.
egonw authored
593 <jar jarfile="${dist}/jar/cdk-render.jar">
594 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
595 <includesfile name="${src}/render.classes" />
8095921 Added rendering of wedged bonds.
egonw authored
596 </fileset>
597 </jar>
598 </target>
599
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
600 <target id="dist-render-with-java3d" name="dist-render-with-java3d" depends="compile-render-with-java3d"
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
601 if="java3D.present">
602 <jar jarfile="${dist}/jar/cdk-render.jar">
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
603 <fileset dir="${build}">
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
604 <includesfile name="${src}/render.classes" />
26336c0 Fixed build.xml for proper reference to java3d.javafiles (thanks to Gemm...
egonw authored
605 <includesfile name="${src}/java3d.classes" />
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
606 </fileset>
607 </jar>
608 </target>
609
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
610 <target id="dist-standard" name="dist-standard" depends="compile-standard, dist.init">
36b733d Adding cdk-standard module.
egonw authored
611 <jar jarfile="${dist}/jar/cdk-standard.jar">
612 <fileset dir="${build}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
613 <includesfile name="${src}/standard.classes" />
95c12c2 Added config files to cdk-standard module.
egonw authored
614 <include name="org/openscience/cdk/config/**" />
36b733d Adding cdk-standard module.
egonw authored
615 </fileset>
616 </jar>
617 </target>
618
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
619 <target id="dist-large" name="dist-large" depends="compile-all, dist.init, libjars"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
620 description="Builds on big jar file for the CDK, including experimental classes.">
e3792d4 Added description for sourcedist target, and target for putting all cdk ...
egonw authored
621 <jar jarfile="${dist}/jar/cdk-all.jar">
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
622 <manifest>
623 <attribute name="Main-Class" value="org.openscience.cdk.applications.DistLargeInfo"/>
624 <section name="org.openscience.cdk">
625 <attribute name="Specification-Title" value="The Chemistry Development Kit"/>
626 <attribute name="Specification-Version" value="1.0"/>
627 <attribute name="Specification-Vendor" value="The CDK Project"/>
628 <attribute name="Implementation-Title" value="org.openscience.cdk"/>
629 <attribute name="Implementation-Version" value="${version}"/>
630 <attribute name="Implementation-Vendor" value="The CDK Project"/>
631 </section>
632 </manifest>
555ce1a Fixed build.xml to properly generate a self-containing cdk-all.jar ready...
egonw authored
633 <fileset dir="${build}">
e3792d4 Added description for sourcedist target, and target for putting all cdk ...
egonw authored
634 <include name="org/openscience/cdk/**" />
635 </fileset>
555ce1a Fixed build.xml to properly generate a self-containing cdk-all.jar ready...
egonw authored
636 <fileset dir=".">
637 <include name="CHANGELOG" />
638 <include name="README" />
639 <include name="BUGS" />
640 </fileset>
641 <fileset dir="${doc}">
642 <include name="lgpl.license" />
643 </fileset>
644 <fileset dir="packages/tar/cdk">
645 <include name="AUTHORS" />
646 </fileset>
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
647 <fileset dir="${appjars.dir}" includes="**/*.class"/>
e3792d4 Added description for sourcedist target, and target for putting all cdk ...
egonw authored
648 </jar>
649 </target>
650
af5b768 cdk-all is now a self containing one-jar big CDK library (try java -jar ...
egonw authored
651 <target name="check.libjars" id="check.libjars">
652 <uptodate property="libjars.uptodate" targetfile="${appjars.dir}">
653 <srcfiles dir="${lib}" includes="base.jar"/>
654 <srcfiles dir="${lib}" includes="batik-dom.jar"/>
655 <srcfiles dir="${lib}" includes="batik-awt-util.jar"/>
656 <srcfiles dir="${lib}" includes="batik-svggen.jar"/>
657 <srcfiles dir="${lib}" includes="batik-util.jar"/>
658 <srcfiles dir="${lib}" includes="batik-xml.jar"/>
659 <srcfiles dir="${lib}" includes="castor-0.9.5-xml.jar"/>
660 <srcfiles dir="${lib}" includes="cmlAll.jar"/>
661 <srcfiles dir="${lib}" includes="commons-cli-1.0.jar"/>
662 <srcfiles dir="${lib}" includes="dadml.jar"/>
663 <srcfiles dir="${lib}" includes="gnujaxp.jar"/>
664 <srcfiles dir="${lib}" includes="jmolApis.jar"/>
665 <srcfiles dir="${lib}" includes="jmolIO.jar"/>
666 <srcfiles dir="${lib}" includes="junit.jar"/>
667 <srcfiles dir="${lib}" includes="log4j-core.jar"/>
668 <srcfiles dir="${lib}" includes="log4j.jar"/>
669 <srcfiles dir="${lib}" includes="mysql-2.0.4.jar"/>
670 <srcfiles dir="${lib}" includes="pmrlib.jar"/>
671 <srcfiles dir="${lib}" includes="postgresql7.0-1.2.jar"/>
672 <srcfiles dir="${lib}" includes="printf.jar"/>
673 <srcfiles dir="${lib}" includes="stmml.jar"/>
674 <srcfiles dir="${lib}" includes="vecmath1.2-1.14.jar"/>
675 <srcfiles dir="${lib}" includes="xerces-2.6.2.jar"/>
676 <srcfiles dir="${lib}" includes="xindice.jar"/>
677 <srcfiles dir="${lib}" includes="xmlApis-2.6.2.jar"/>
678 <srcfiles dir="${lib}" includes="xmldb.jar"/>
679 </uptodate>
680 </target>
681
682 <target name="libjars" id="libjars" depends="check.libjars" unless="libjars.uptodate">
683 <mkdir dir="${appjars.dir}"/>
684 <unjar dest="${appjars.dir}" src="${lib}/base.jar"/>
685 <unjar dest="${appjars.dir}" src="${lib}/batik-dom.jar"/>
686 <unjar dest="${appjars.dir}" src="${lib}/batik-awt-util.jar"/>
687 <unjar dest="${appjars.dir}" src="${lib}/batik-svggen.jar"/>
688 <unjar dest="${appjars.dir}" src="${lib}/batik-util.jar"/>
689 <unjar dest="${appjars.dir}" src="${lib}/batik-xml.jar"/>
690 <unjar dest="${appjars.dir}" src="${lib}/castor-0.9.5-xml.jar"/>
691 <unjar dest="${appjars.dir}" src="${lib}/cmlAll.jar"/>
692 <unjar dest="${appjars.dir}" src="${lib}/commons-cli-1.0.jar"/>
693 <unjar dest="${appjars.dir}" src="${lib}/dadml.jar"/>
694 <unjar dest="${appjars.dir}" src="${lib}/gnujaxp.jar"/>
695 <unjar dest="${appjars.dir}" src="${lib}/jmolApis.jar"/>
696 <unjar dest="${appjars.dir}" src="${lib}/jmolIO.jar"/>
697 <unjar dest="${appjars.dir}" src="${lib}/junit.jar"/>
698 <unjar dest="${appjars.dir}" src="${lib}/log4j-core.jar"/>
699 <unjar dest="${appjars.dir}" src="${lib}/log4j.jar"/>
700 <unjar dest="${appjars.dir}" src="${lib}/mysql-2.0.4.jar"/>
701 <unjar dest="${appjars.dir}" src="${lib}/pmrlib.jar"/>
702 <unjar dest="${appjars.dir}" src="${lib}/postgresql7.0-1.2.jar"/>
703 <unjar dest="${appjars.dir}" src="${lib}/printf.jar"/>
704 <unjar dest="${appjars.dir}" src="${lib}/stmml.jar"/>
705 <unjar dest="${appjars.dir}" src="${lib}/vecmath1.2-1.14.jar"/>
706 <unjar dest="${appjars.dir}" src="${lib}/xerces-2.6.2.jar"/>
707 <unjar dest="${appjars.dir}" src="${lib}/xindice.jar"/>
708 <unjar dest="${appjars.dir}" src="${lib}/xmlApis-2.6.2.jar"/>
709 <unjar dest="${appjars.dir}" src="${lib}/xmldb.jar"/>
710 </target>
711
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
712 <target id="dist-all" name="dist-all" depends="dist, dist-experimental, dist-apps"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
713 description="Builds the jar files for the CDK, including experimental classes."/>
53aff7c dist-all should also build cdk-experimental.jar, dist should not
egonw authored
714
715 <target id="dist" name="dist" depends="dist-core, dist-standard,
90025c1 Added missing editor classes to cdk-render.jar when compiling with-java3...
egonw authored
716 dist-io, dist-render,
88b3428 Don't build accelerated 3D viewer class if Java3D is not present
egonw authored
717 dist-extra, dist-libio,
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
718 dist-render-with-java3d"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
719 description="Builds the jar files for the CDK."/>
ce6c169 Include config and data files in dist-with-java3d too.
egonw authored
720
e3792d4 Added description for sourcedist target, and target for putting all cdk ...
egonw authored
721 <target id="sourcedist" name="sourcedist" depends="init"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
722 description="Builds the source packages.">
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
723 <property name="package" value="cdk-source-${DSTAMP}"/>
724 <property name="sourcedist.dir" value="${sourcedist}/${package}"/>
725 <copy todir="${sourcedist.dir}/${src}">
36bec3a Make use of new class-is-in-module lists in src/
egonw authored
726 <fileset dir="${src}" includes="*.javafiles" />
ad5a692 Included *.jj files in sourcedist (closes #888710)
egonw authored
727 <fileset dir="${src}" includes="**/*.java" />
728 <fileset dir="${src}" includes="**/*.jj" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
729 <fileset dir="${src}" includes="org/openscience/cdk/io/cml/data/**" />
730 </copy>
731 <copy todir="${sourcedist.dir}">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
732 <fileset dir="." includes="build.xml" />
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
733 <fileset dir="." includes="javadoc.xml" />
734 <fileset dir="." includes="README" />
735 <fileset dir="." includes="CHANGELOG" />
736 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
737 <copy todir="${sourcedist.dir}/jar">
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
738 <fileset dir="jar" />
739 </copy>
740 <copy todir="${sourcedist.dir}/data">
741 <fileset dir="data" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
742 </copy>
ad5a692 Included *.jj files in sourcedist (closes #888710)
egonw authored
743 <copy tofile="${sourcedist.dir}/doc/javadoc/source//MakeJavaFilesFilesDoclet.java"
744 file="doc/javadoc/source/MakeJavaFilesFilesDoclet.java"/>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
745 <copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/">
5d39146 Fixed bug in build.xml.
egonw authored
746 <fileset dir="${src}/org/openscience/cdk/config/"
e1f7ebb Do not try to build classes that depend on classes that depend on Java3D
egonw authored
747 includes="*" />
748 </copy>
a289167 Minor tweak to get distribs working
egonw authored
749 <copy
750 file="${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties"
751 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/iupac/generator/data/IUPACNames.properties" />
752 <copy
753 file="${src}/org/openscience/cdk/dict/data/chemical.xml"
754 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/chemical.xml" />
755 <copy
756 file="${src}/org/openscience/cdk/dict/data/elements.xml"
757 tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/elements.xml" />
9496005 Added missing manifest
egonw authored
758 <copy todir="${sourcedist.dir}/${src}/">
759 <fileset dir="${src}/" includes="*.manifest" />
760 </copy>
d6cda7b Distribute LGPL license with sourcecode
egonw authored
761 <mkdir dir="${sourcedist.dir}/doc/" />
762 <copy todir="${sourcedist.dir}/doc/">
763 <fileset dir="doc/" includes="lgpl.license" />
764 </copy>
24c8548 Fixed building of sourcedist. Now can be compiled.
egonw authored
765 <tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
766 <gzip zipfile="${package}.tar.gz" src="cdk-source-${DSTAMP}.tar" />
767 <delete file="${package}.tar" />
768 <zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
769 </target>
770
cd012c0 Added posibility to just check the experimental classes
egonw authored
771 <target id="test-all" name="test-all" depends="test, test-experimental"/>
772
773 <target id="test-experimental" name="test-experimental" depends="noJunit"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
774 description="Performs a full JUnit test for the CDK, including experimental classes.">
7f7ea85 Have the experimental JME reader actually compile
egonw authored
775 <mkdir dir="${reports.tests}"/>
60b89d5 Added test suite for cdk-experimental, and moved Association to experime...
egonw authored
776 <junit printsummary="yes" haltonfailure="yes" fork="yes">
777 <classpath>
778 <pathelement location="${dist}/jar/cdk-core.jar" />
779 <pathelement location="${dist}/jar/cdk-standard.jar" />
780 <pathelement location="${dist}/jar/cdk-io.jar" />
781 <pathelement location="${dist}/jar/cdk-render.jar" />
782 <pathelement location="${dist}/jar/cdk-extra.jar" />
783 <pathelement location="${dist}/jar/cdk-apps.jar" />
784 <pathelement location="${dist}/jar/cdk-test.jar" />
785 <pathelement location="${dist}/jar/cdk-libio.jar" />
786 <pathelement location="${dist}/jar/cdk-experimental.jar" />
787 <fileset dir="${lib}">
788 <include name="*.jar" />
789 </fileset>
790 <fileset dir="${lib}/libio">
791 <include name="*.jar" />
792 </fileset>
793 </classpath>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
794 <test name="org.openscience.cdk.test.ExperimentalClassesTests"
60b89d5 Added test suite for cdk-experimental, and moved Association to experime...
egonw authored
795 haltonfailure="no"
796 todir="${reports.tests}"
0c93d33 Put results of tests for experimental classes in result.experimental.txt...
egonw authored
797 outfile="result.experimental">
60b89d5 Added test suite for cdk-experimental, and moved Association to experime...
egonw authored
798 <formatter type="brief" />
799 </test>
800 </junit>
801 </target>
802
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_HOM...
egonw authored
803 <target id="noJunit" name="noJunit" depends="check" unless="junit.present">
804 <fail message="JUnit is not installed in Ant. Please copy cdk/jar/junit.jar to ${ant.home}/lib/."/>
805 </target>
806
807 <target id="test" name="test" depends="dist-test, noJunit"
808 description="Performs a full JUnit test for the CDK." if="junit.present">
7f7ea85 Have the experimental JME reader actually compile
egonw authored
809 <mkdir dir="${reports.tests}"/>
9344d76 Fork testing, and removed reference to classpaths "." and "${java.class....
egonw authored
810 <junit printsummary="yes" haltonfailure="yes" fork="yes">
811 <classpath>
812 <pathelement location="${dist}/jar/cdk-core.jar" />
813 <pathelement location="${dist}/jar/cdk-standard.jar" />
814 <pathelement location="${dist}/jar/cdk-io.jar" />
815 <pathelement location="${dist}/jar/cdk-render.jar" />
816 <pathelement location="${dist}/jar/cdk-extra.jar" />
817 <pathelement location="${dist}/jar/cdk-apps.jar" />
818 <pathelement location="${dist}/jar/cdk-test.jar" />
819 <pathelement location="${dist}/jar/cdk-libio.jar" />
4c961ee Added missing jar file
egonw authored
820 <pathelement location="${dist}/jar/cdk-experimental.jar" />
9344d76 Fork testing, and removed reference to classpaths "." and "${java.class....
egonw authored
821 <fileset dir="${lib}">
822 <include name="*.jar" />
823 </fileset>
824 <fileset dir="${lib}/libio">
825 <include name="*.jar" />
826 </fileset>
827 </classpath>
1f14ffa More @cdkPackage completed: dist-test now also works with kaffe
egonw authored
828 <test name="org.openscience.cdk.test.CDKTests"
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
829 haltonfailure="no"
830 todir="${reports.tests}"
831 outfile="result">
81258bd Added Ant task for doing Junit tests on the cdk-core and cdk-standard mo...
egonw authored
832 <formatter type="brief" />
3790797 Splitted tests which are supposed to fail from those which are supposed ...
egonw authored
833 </test>
834 </junit>
835 </target>
836
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_HOM...
egonw authored
837 <target id="limitations" name="limitations" depends="dist-test, noJunit"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
838 description="Performs a JUnit tests that indicate limitations of certain CDK algorithms/classes.">
3790797 Splitted tests which are supposed to fail from those which are supposed ...
egonw authored
839 <junit printsummary="yes" haltonfailure="yes" fork="yes">
840 <classpath>
841 <pathelement location="${dist}/jar/cdk-core.jar" />
842 <pathelement location="${dist}/jar/cdk-standard.jar" />
843 <pathelement location="${dist}/jar/cdk-io.jar" />
844 <pathelement location="${dist}/jar/cdk-render.jar" />
845 <pathelement location="${dist}/jar/cdk-extra.jar" />
846 <pathelement location="${dist}/jar/cdk-apps.jar" />
847 <pathelement location="${dist}/jar/cdk-test.jar" />
848 <pathelement location="${dist}/jar/cdk-libio.jar" />
849 <fileset dir="${lib}">
850 <include name="*.jar" />
851 </fileset>
852 <fileset dir="${lib}/libio">
853 <include name="*.jar" />
854 </fileset>
855 </classpath>
856 <test name="org.openscience.cdk.test.limitations.AlgorithmLimitations"
857 haltonfailure="no"
858 todir="${reports.tests}"
859 outfile="limitations">
860 <formatter type="brief" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
861 </test>
862 </junit>
863 </target>
864
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
865 <target name="test-libio" depends="dist-libio">
866 <java classname="org.openscience.cdk.test.libio.joelib.JOELibIOTest" fork="yes">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
867 <classpath>
7b0e32f Updated run-with-java3d task for some recent changes.
egonw authored
868 <pathelement location="${dist}/jar/cdk-core.jar" />
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
869 <pathelement location="${dist}/jar/cdk-extra.jar" />
870 <pathelement location="${dist}/jar/cdk-libio.jar" />
7b0e32f Updated run-with-java3d task for some recent changes.
egonw authored
871 <pathelement path="${java.class.path}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
872 <pathelement location="." />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
873 <fileset dir="${lib}">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
874 <include name="*.jar" />
875 </fileset>
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
876 <fileset dir="${lib}/libio">
7b0e32f Updated run-with-java3d task for some recent changes.
egonw authored
877 <include name="*.jar" />
878 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
879 </classpath>
880 </java>
881 </target>
882
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
883 <target name="run-with-java3d"
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
884 depends="dist-extra, dist-io, dist-extra, dist-render-with-java3d">
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
885 <java
886 classname="org.openscience.cdk.test.OrbitalsRenderer3DTest"
887 fork="yes">
888 <arg value="data/reserpine.mol" />
889
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
890 <classpath>
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
891 <pathelement location="${dist}/jar/cdk-core.jar" />
e8dadc5 Finished rewriting Ant tasks into cdk modules.
egonw authored
892 <pathelement location="${dist}/jar/cdk-standard.jar" />
893 <pathelement location="${dist}/jar/cdk-extra.jar" />
894 <pathelement location="${dist}/jar/cdk-io.jar" />
895 <pathelement location="${dist}/jar/cdk-render.jar" />
896 <pathelement location="${dist}/jar/cdk-render-with-java3d.jar" />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
897 <pathelement path="${java.class.path}" />
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
898 <pathelement location="." />
6bcf896 Edited build file in order to reflect the move of the src folder
steinbeck authored
899 <fileset dir="${lib}">
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
900 <include name="*.jar" />
901 </fileset>
bd0b7db Added JUnit test for libio/joelib/Convertor.java. Adapted build.xml
egonw authored
902 <fileset dir="${pathto3djava}">
903 <include name="*.jar" />
904 </fileset>
5e15181 The class org.openscience.cdk.structgen.SingleStructureRandomGenerator
steinbeck authored
905 </classpath>
906 </java>
907 </target>
908
58425b9 Added use of properties to run target
steinbeck authored
909 <target id="run-test" name="run-test" depends="dist-core, dist-extra, dist-test, dist-standard"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
910 description="Runs one specific JUnit test suite (org.openscience.cdk.test.&lt;class>) as a standalone application with -Dtestclass=&lt;class>.">
f1c49ce Added some feedback on what is tested
egonw authored
911 <echo message="Running test class: testclass=${testclass}"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
912 <java classname="org.openscience.cdk.test.${testclass}" fork="yes">
3d88ed4 Turn on CDK debugging while running JUnit test
egonw authored
913 <jvmarg value="-Dcdk.debugging=true"/>
756bd80 When running a specific test (e.g. 'ant -Dtestclass=ringsearch.RingSearc...
egonw authored
914 <classpath>
915 <pathelement location="${dist}/jar/cdk-core.jar" />
916 <pathelement location="${dist}/jar/cdk-standard.jar" />
917 <pathelement location="${dist}/jar/cdk-io.jar" />
918 <pathelement location="${dist}/jar/cdk-render.jar" />
919 <pathelement location="${dist}/jar/cdk-extra.jar" />
920 <pathelement location="${dist}/jar/cdk-apps.jar" />
921 <pathelement location="${dist}/jar/cdk-test.jar" />
922 <pathelement location="${dist}/jar/cdk-libio.jar" />
923 <fileset dir="${lib}">
924 <include name="*.jar" />
925 </fileset>
926 <fileset dir="${lib}/libio">
927 <include name="*.jar" />
928 </fileset>
929 </classpath>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
930 </java>
931 </target>
932
6fa4411 Fail build process for test (etc) when JUnit is not installed in ANT_HOM...
egonw authored
933 <target id="junit-test" name="junit-test" depends="dist-core, dist-extra, dist-test, dist-standard, noJunit"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
934 description="Runs one specific JUnit test suite (org.openscience.cdk.test.&lt;class>) with -Dtestclass=&lt;class>.">
f1c49ce Added some feedback on what is tested
egonw authored
935 <echo message="JUnit tests class: testclass=${testclass}"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
936 <junit printsummary="yes" haltonfailure="no" fork="yes">
79f7451 Switch debugging on in run-test target
steinbeck authored
937 <jvmarg value="-Dcdk.debugging=true"/>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
938 <jvmarg value="-Dcdk.debug.stdout=true"/>
939 <classpath>
58425b9 Added use of properties to run target
steinbeck authored
940 <pathelement location="${dist}/jar/cdk-core.jar" />
941 <pathelement location="${dist}/jar/cdk-standard.jar" />
942 <pathelement location="${dist}/jar/cdk-io.jar" />
943 <pathelement location="${dist}/jar/cdk-render.jar" />
944 <pathelement location="${dist}/jar/cdk-extra.jar" />
945 <pathelement location="${dist}/jar/cdk-apps.jar" />
946 <pathelement location="${dist}/jar/cdk-test.jar" />
947 <pathelement location="${dist}/jar/cdk-libio.jar" />
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
948 <pathelement location="${dist}/jar/cdk-experimental.jar" />
58425b9 Added use of properties to run target
steinbeck authored
949 <pathelement path="${java.class.path}" />
950 <pathelement location="." />
951 <fileset dir="${lib}">
952 <include name="*.jar" />
953 </fileset>
954 <fileset dir="${lib}/libio">
955 <include name="*.jar" />
956 </fileset>
957 </classpath>
3af98a0 Added target for running one JUnit test *with* debug info
egonw authored
958 <test name="org.openscience.cdk.test.${testclass}"
959 haltonfailure="no"
960 todir="${reports.tests}"
961 outfile="result.${testclass}">
962 <formatter type="brief" />
963 </test>
964 </junit>
58425b9 Added use of properties to run target
steinbeck authored
965 </target>
966
967
86b1231 Added id's to target for easy browsing with jEdit's StructureBrowser
egonw authored
968 <target id="run" name="run" depends="dist-core, dist-extra, dist-test, dist-standard"
7d866cb Updated and synched descriptions: try ant -projecthelp
egonw authored
969 description="Runs an application (org.openscience.cdk.&lt;class>) with -Drunclass=&lt;class>.">
58425b9 Added use of properties to run target
steinbeck authored
970 <java classname="org.openscience.cdk.${runclass}" fork="yes" >
971 <arg value="${arg1}" />
972 <arg value="${arg2}" />
973 <arg value="${arg3}" />
974 <arg value="${arg4}" />
ac448e9 Nothing happend here.
steinbeck authored
975 <classpath>
8095921 Added rendering of wedged bonds.
egonw authored
976 <pathelement location="${dist}/jar/cdk-core.jar" />
977 <pathelement location="${dist}/jar/cdk-standard.jar" />
978 <pathelement location="${dist}/jar/cdk-io.jar" />
979 <pathelement location="${dist}/jar/cdk-render.jar" />
980 <pathelement location="${dist}/jar/cdk-extra.jar" />
981 <pathelement location="${dist}/jar/cdk-apps.jar" />
982 <pathelement location="${dist}/jar/cdk-test.jar" />
983 <pathelement location="${dist}/jar/cdk-libio.jar" />
984 <pathelement path="${java.class.path}" />
985 <pathelement location="." />
986 <fileset dir="${lib}">
987 <include name="*.jar" />
988 </fileset>
989 <fileset dir="${lib}/libio">
990 <include name="*.jar" />
991 </fileset>
992 </classpath>
8713d91 Finished work on basic JOELib <-> CDK convertor.
egonw authored
993 </java>
994 </target>
995
c5eb7ec Added Ant build file.
egonw authored
996 </project>
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