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Merge branch 'cdk-1.2.x'

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commit 055f702c37989cfd0bb100bdbd3315eeb85e3a89 2 parents f0c7d0c + 1f8bb2d
@egonw egonw authored
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1  build.xml
@@ -886,7 +886,6 @@
<copy todir="${sourcedist.dir}/develjar">
<fileset dir="develjar">
<exclude name="pmd-1.8.jar"/>
- <exclude name="doccheck.jar"/>
<exclude name="dbdoclet*.*"/>
</fileset>
</copy>
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1  develjar/.gitignore
@@ -1 +0,0 @@
-doccheck.jar
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74 javadoc.xml
@@ -14,6 +14,9 @@
<property name="pathtojava3d" value="" />
<property name="build" value="build" />
+ <!-- Used in the html task to properly link to java library classes -->
+ <property name="javaURL" value="http://java.sun.com/j2se/1.5.0/docs/api/"/>
+
<path id="project.class.path">
<pathelement location="." />
<fileset dir="jar">
@@ -79,6 +82,7 @@
<packageset dir="${src}/main" defaultexcludes="yes">
<include name="org/openscience/cdk/**" />
</packageset>
+ <link href="${javaURL}"/>
</javadoc>
</target>
@@ -103,78 +107,8 @@
javacchome="jar"/>
</target>
- <!-- The doclet used in the following targets cannot be put in CVS because it is
- licensed otherwise, but it can be downloaded from:
-
- http://java.sun.com/j2se/javadoc/doccheck/
-
- -->
-
- <target name="doccheck" depends="check-doccheck" if="doccheck.present">
- <antcall target="doccheck-module"><param name="module" value="interfaces"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="core"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="data"/></antcall>
<antcall target="doccheck-module"><param name="module" value="log4j"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="datadebug"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="nonotify"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="standard"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="atomtype"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="io"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="ioformats"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="inchi"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="extra"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="fingerprint"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="formula"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="render"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="reaction"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="libiocml"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="libiomd"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="builder3d"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="smiles"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="smarts"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="sdg"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="forcefield"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="pdb"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="qsar"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="qsaratomic"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="qsarbond"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="qsarionpot"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="qsarmolecular"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="qsarprotein"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="pcore"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="structgen"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="valencycheck"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="charges"/></antcall>
- <antcall target="doccheck-module"><param name="module" value="diff"/></antcall>
<antcall target="doccheck-module"><param name="module" value="smsd"/></antcall>
- </target>
-
- <target name="check-doccheck">
- <available file="develjar/doccheck.jar" property="doccheck.present" />
- <fail unless="doccheck.present"
- message="This task requires DocCheck, which can be downloaded from http://java.sun.com/j2se/javadoc/doccheck/. Copy the doccheck.jar into develjar/."/>
- </target>
-
- <target name="doccheck-module">
- <mkdir dir="reports/javadoc/${module}/"/>
- <mkdir dir="${build}/src/${module}"/>
- <copy todir="${build}/src/${module}">
- <fileset dir="${src}/main">
- <includesfile name="${build}/${module}.javafiles"/>
- </fileset>
- </copy>
- <javadoc private="false" public="true"
- destdir="reports/javadoc/${module}/">
- <classpath refid="project.class.path" />
-
- <doclet name="com.sun.tools.doclets.doccheck.DocCheck"
- path="develjar/doccheck.jar" />
- <sourcepath>
- <pathelement path="${build}/src/${module}"/>
- </sourcepath>
- </javadoc>
- </target>
-
<target name="ojdcheck" depends="compileDocTests">
<antcall target="ojdcheck-module"><param name="module" value="interfaces"/></antcall>
<antcall target="ojdcheck-module"><param name="module" value="core"/></antcall>
View
1  pmd/custom-data.xml
@@ -23,5 +23,6 @@
<!-- Rules specific for CDK -->
<rule ref="pmd/customCDK-data.xml"/>
+ <rule ref="pmd/cdkinterfaces.xml"/>
</ruleset>
View
1  pmd/custom-qm.xml
@@ -27,5 +27,6 @@
<rule ref="pmd/customCDK.xml"/>
<rule ref="pmd/customOptimization.xml"/>
+ <rule ref="pmd/cdkinterfaces.xml"/>
</ruleset>
View
1  pmd/custom-test.xml
@@ -19,5 +19,6 @@
<!-- Rules specific for CDK -->
<rule ref="pmd/customJunit.xml"/>
+ <rule ref="pmd/cdkinterfaces.xml"/>
</ruleset>
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