Separated cdk-pdbcml from cdk-libiocml and created module suite for c…

…dk-test-pdbcml. Conflicts: src/main/org/openscience/cdk/libio/cml/PDBAtomCustomizer.java Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · Jul 31, 2013 · caac9da · caac9da
1 parent a0b8dcf
commit caac9da
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Showing 7 changed files with 63 additions and 34 deletions.
diff --git a/build.xml b/build.xml
@@ -594,7 +594,7 @@
         <foreach target="compile-module" param="module" trim="true"
             parallel="${parallel}" maxthreads="${threadCount}"
             list="test-formula,test-qsaratomic,test-qsarbond,
-                  test-pdb,test-smiles,test-extra,test-fragment,test-atomtype,
+                  test-pdb,test-pdbcml,test-smiles,test-extra,test-fragment,test-atomtype,
                   test-structgen,test-iordf,test-silent"/>
         <foreach target="compile-module" param="module" trim="true"
             parallel="${parallel}" maxthreads="${threadCount}"
@@ -1147,7 +1147,7 @@
                       io,builder3d,forcefield,valencycheck,charges,reaction,
                       smarts,fingerprint,smiles,qsar,qsaratomic,qsarbond,
                       qsarmolecular,qsarionpot,qsarprotein,pdb,pcore,inchi,
-                      structgen,libiomd,libiocml,formula,render,extra,fragment,sdg,
+                      structgen,libiomd,libiocml,pdbcml,formula,render,extra,fragment,sdg,
                       ioformats,log4j,smsd,signature,iordf,cip,tautomer,
                       isomorphism,renderbasic,renderawt,renderextra,silent,group,
                       hash,pdbcml"/>

diff --git a/src/META-INF/test-libiocml.cdkdepends b/src/META-INF/test-libiocml.cdkdepends
@@ -16,7 +16,6 @@ cdk-qsarcml.jar
 cdk-atomtype.jar
 cdk-silent.jar
 cdk-pdb.jar
-cdk-pdbcml.jar
 cdk-formula.jar
 cdk-testdata.jar
 cdk-diff.jar
diff --git a/src/main/org/openscience/cdk/libio/cml/ICMLCustomizer.java b/src/main/org/openscience/cdk/libio/cml/ICMLCustomizer.java
@@ -40,7 +40,7 @@
  *
  * @author        egonw
  * @cdk.created   2005-05-04
- * @cdk.module    standard
+ * @cdk.module    interfaces
  * @cdk.githash
  */
 public interface ICMLCustomizer {

diff --git a/src/main/org/openscience/cdk/libio/cml/PDBAtomCustomizer.java b/src/main/org/openscience/cdk/libio/cml/PDBAtomCustomizer.java
@@ -28,6 +28,8 @@
 import nu.xom.Element;
 
 import org.openscience.cdk.interfaces.IPDBAtom;
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.annotations.TestMethod;
 import org.xmlcml.cml.element.CMLScalar;
 
 import org.openscience.cdk.exception.CDKException;
@@ -46,8 +48,11 @@
  * @cdk.set       libio-cml-customizers
  * @cdk.require   java1.5+
  */
+@TestClass("org.openscience.cdk.io.cml.PDBAtomCustomizerTest")
 public class PDBAtomCustomizer implements ICMLCustomizer {
 
+
+    @TestMethod("testPDBAtomCustomization")
     public void customize(IAtom atom, Object nodeToAdd) throws Exception {
     	if (!(nodeToAdd instanceof Element))
     		throw new CDKException("NodeToAdd must be of type nu.xom.Element!");

diff --git a/src/test/org/openscience/cdk/io/cml/CML2WriterTest.java b/src/test/org/openscience/cdk/io/cml/CML2WriterTest.java
@@ -49,12 +49,9 @@
 import org.openscience.cdk.interfaces.ICrystal;
 import org.openscience.cdk.interfaces.IIsotope;
 import org.openscience.cdk.interfaces.IMolecularFormula;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IPDBAtom;
 import org.openscience.cdk.interfaces.IReaction;
 import org.openscience.cdk.interfaces.IReactionScheme;
 import org.openscience.cdk.io.CMLWriter;
-import org.openscience.cdk.libio.cml.PDBAtomCustomizer;
 import org.openscience.cdk.libio.cml.QSARCustomizer;
 import org.openscience.cdk.qsar.DescriptorValue;
 import org.openscience.cdk.qsar.IMolecularDescriptor;
@@ -63,7 +60,6 @@
 import org.openscience.cdk.silent.AtomContainerSet;
 import org.openscience.cdk.silent.ChemModel;
 import org.openscience.cdk.silent.Crystal;
-import org.openscience.cdk.silent.PDBAtom;
 import org.openscience.cdk.silent.Reaction;
 import org.openscience.cdk.templates.MoleculeFactory;
 import org.openscience.cdk.tools.ILoggingTool;
@@ -235,25 +231,7 @@ public class CML2WriterTest extends CDKTestCase {
         Assert.assertTrue(cmlContent.indexOf("<molecule id=\"product") != -1);
         Assert.assertTrue(cmlContent.indexOf("<molecule id=\"agent") != -1);
     }
-
-    @Test public void testPDBAtomCustomization() throws Exception {
-        StringWriter writer = new StringWriter();
-        IAtomContainer molecule = new AtomContainer();
-        IPDBAtom atom = new PDBAtom("C");
-        atom.setName("CA");
-        atom.setResName("PHE");
-        molecule.addAtom(atom);
-
-        CMLWriter cmlWriter = new CMLWriter(writer);
-        cmlWriter.registerCustomizer(new PDBAtomCustomizer());
-        cmlWriter.write(molecule);
-        String cmlContent = writer.toString();
-        logger.debug("****************************** testPDBAtomCustomization()");
-        logger.debug(cmlContent);
-        logger.debug("******************************");
-        Assert.assertTrue(cmlContent.indexOf("<scalar dictRef=\"pdb:resName") != -1);
-    }
-
+
     @Test public void testReactionScheme1() throws Exception {
     	StringWriter writer = new StringWriter();
     	IReactionScheme scheme1 = DefaultChemObjectBuilder.getInstance().newInstance(IReactionScheme.class);

diff --git a/src/test/org/openscience/cdk/libio/cml/PDBAtomCustomizerTest.java b/src/test/org/openscience/cdk/libio/cml/PDBAtomCustomizerTest.java
@@ -0,0 +1,40 @@
+package org.openscience.cdk.libio.cml;
+
+import org.junit.Assert;
+import org.junit.Test;
+import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IPDBAtom;
+import org.openscience.cdk.io.CMLWriter;
+import org.openscience.cdk.protein.data.PDBAtom;
+import org.openscience.cdk.tools.ILoggingTool;
+import org.openscience.cdk.tools.LoggingToolFactory;
+
+import java.io.StringWriter;
+
+/**
+ * @author John May
+ * @cdk.module test-pdbcml
+ */
+public class PDBAtomCustomizerTest {
+
+    private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(PDBAtomCustomizerTest.class);
+
+    @Test public void testPDBAtomCustomization() throws Exception {
+        StringWriter writer = new StringWriter();
+        IAtomContainer molecule = new AtomContainer();
+        IPDBAtom atom = new PDBAtom("C");
+        atom.setName("CA");
+        atom.setResName("PHE");
+        molecule.addAtom(atom);
+
+        CMLWriter cmlWriter = new CMLWriter(writer);
+        cmlWriter.registerCustomizer(new PDBAtomCustomizer());
+        cmlWriter.write(molecule);
+        String cmlContent = writer.toString();
+        logger.debug("****************************** testPDBAtomCustomization()");
+        logger.debug(cmlContent);
+        logger.debug("******************************");
+        Assert.assertTrue(cmlContent.indexOf("<scalar dictRef=\"pdb:resName") != -1);
+    }
+}
diff --git a/src/test/org/openscience/cdk/modulesuites/MpdbcmlTests.java b/src/test/org/openscience/cdk/modulesuites/MpdbcmlTests.java
@@ -1,11 +1,16 @@
-/* Copyright (C) 2013  Egon Willighagen <egonw@users.sf.net>
+/*
+ * Copyright (c) 2013. John May <jwmay@users.sf.net>
  *
  * Contact: cdk-devel@lists.sourceforge.net
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
  * as published by the Free Software Foundation; either version 2.1
  * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
  *
  * This program is distributed in the hope that it will be useful,
  * but WITHOUT ANY WARRANTY; without even the implied warranty of
@@ -14,22 +19,24 @@
  *
  * You should have received a copy of the GNU Lesser General Public License
  * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
  * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
  */
 package org.openscience.cdk.modulesuites;
 
 import org.junit.runner.RunWith;
 import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
-import org.openscience.cdk.io.cml.PDBAtomCustomizerTest;
+import org.openscience.cdk.libio.cml.PDBAtomCustomizerTest;
 
 /**
- * TestSuite that runs all the unit tests for the CDK module pdbcml.
+ * TestSuite that runs all the sample tests for the CDK module pdbcml.
  *
  * @cdk.module test-pdbcml
  */
-@RunWith(value=Suite.class)
-@SuiteClasses(value={
-    PDBAtomCustomizerTest.class
+@RunWith(value = Suite.class)
+@SuiteClasses(value = {
+        PDBAtomCustomizerTest.class
 })
-public class MpdbcmlTests {}
+public class MpdbcmlTests {
+}