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[Cdk-commits] SF.net SVN: cdk: [11175] cdk/branches/miguelrojasch-ReactionOntology
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From: <mig...@us...> - 2008-05-26 17:37:32
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Revision: 11175
http://cdk.svn.sourceforge.net/cdk/?rev=11175&view=rev
Author: miguelrojasch
Date: 2008-05-26 10:37:27 -0700 (Mon, 26 May 2008)
Log Message:
-----------
Synchronized with trunk the branches.miguelrojasch-ReactionOntology, Rev=11158:11174
Modified Paths:
--------------
cdk/branches/miguelrojasch-ReactionOntology/META-INF/MANIFEST.MF
cdk/branches/miguelrojasch-ReactionOntology/src/main/net/sf/cdk/tools/MakeJavafilesFiles.java
cdk/branches/miguelrojasch-ReactionOntology/src/main/org/openscience/cdk/io/random/RandomAccessReader.java
cdk/branches/miguelrojasch-ReactionOntology/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
cdk/branches/miguelrojasch-ReactionOntology/src/test/org/openscience/cdk/io/random/RandomAccessTest.java
Modified: cdk/branches/miguelrojasch-ReactionOntology/META-INF/MANIFEST.MF
===================================================================
--- cdk/branches/miguelrojasch-ReactionOntology/META-INF/MANIFEST.MF 2008-05-26 17:29:51 UTC (rev 11174)
+++ cdk/branches/miguelrojasch-ReactionOntology/META-INF/MANIFEST.MF 2008-05-26 17:37:27 UTC (rev 11175)
@@ -106,5 +106,13 @@
jar/vecmath1.2-1.14.jar,
jar/xom-1.1.jar,
jar/jama-1.0.2.jar,
+ jar/commons-cli-1.0.jar,
+ jar/xml-apis.jar,
+ jar/xpp3-1.1.4c.jar,
+ jar/log4j.jar,
+ develjar/junit-4.4.jar,
+ develjar/com-sun-javadoc.jar,
+ develjar/com-sun-tools-doclets-Taglet.jar,
+ develjar/junit-4.3.1.jar,
cdk.jar
Bundle-RequiredExecutionEnvironment: J2SE-1.5
Modified: cdk/branches/miguelrojasch-ReactionOntology/src/main/net/sf/cdk/tools/MakeJavafilesFiles.java
===================================================================
--- cdk/branches/miguelrojasch-ReactionOntology/src/main/net/sf/cdk/tools/MakeJavafilesFiles.java 2008-05-26 17:29:51 UTC (rev 11174)
+++ cdk/branches/miguelrojasch-ReactionOntology/src/main/net/sf/cdk/tools/MakeJavafilesFiles.java 2008-05-26 17:37:27 UTC (rev 11175)
@@ -46,6 +46,8 @@
private Map<String,List<String>> cdkPackages;
private Map<String,List<String>> cdkSets;
+ private String default_module;
+
/** Java files that should not be processed because they are
* listed in a *.autogenerated file.
*/
@@ -62,6 +64,11 @@
this.outputDir = outputDir;
this.metainfDir = metainfDir;
readBlackList();
+ if (sourceDir.contains("test")) {
+ default_module = "test-extra";
+ } else {
+ default_module = "extra";
+ }
}
private void readBlackList() {
@@ -166,7 +173,7 @@
public String[] getModuleAndSet(File file) {
try {
String[] results = new String[2];
- results[0] = "extra";
+ results[0] = default_module;
results[1] = null;
BufferedReader reader = new BufferedReader(
new FileReader(file)
Modified: cdk/branches/miguelrojasch-ReactionOntology/src/main/org/openscience/cdk/io/random/RandomAccessReader.java
===================================================================
--- cdk/branches/miguelrojasch-ReactionOntology/src/main/org/openscience/cdk/io/random/RandomAccessReader.java 2008-05-26 17:29:51 UTC (rev 11174)
+++ cdk/branches/miguelrojasch-ReactionOntology/src/main/org/openscience/cdk/io/random/RandomAccessReader.java 2008-05-26 17:37:27 UTC (rev 11175)
@@ -32,7 +32,6 @@
import java.io.IOException;
import java.io.RandomAccessFile;
import java.io.StringReader;
-import java.security.AccessController;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IChemObject;
@@ -46,8 +45,6 @@
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.tools.LoggingTool;
-import sun.security.action.GetPropertyAction;
-
/**
* Random access to text files of compounds.
* Reads the file as a text and builds an index file, if the index file doesn't already exist.
@@ -324,8 +321,7 @@
* @throws Exception
*/
public static File getIndexFile(String filename) throws Exception {
- GetPropertyAction a = new GetPropertyAction("java.io.tmpdir");
- String tmpDir = ((String) AccessController.doPrivileged(a));
+ String tmpDir = System.getProperty("java.io.tmpdir");
File f = new File(filename);
File indexFile = new File(tmpDir,f.getName()+"_cdk.index");
f = null;
Modified: cdk/branches/miguelrojasch-ReactionOntology/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
===================================================================
--- cdk/branches/miguelrojasch-ReactionOntology/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java 2008-05-26 17:29:51 UTC (rev 11174)
+++ cdk/branches/miguelrojasch-ReactionOntology/src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java 2008-05-26 17:37:27 UTC (rev 11175)
@@ -337,9 +337,6 @@
// TODO Auto-generated catch block
e.printStackTrace();
}
- if (clonedAtom != null) {
- clonedAtom.setHydrogenCount(0);
- }
mol.addAtom(clonedAtom);
map.put(atom, clonedAtom);
}
@@ -392,7 +389,10 @@
// Process neighbours.
for (IAtom iAtom : atomContainer.getConnectedAtomsList(aRemove)) {
final IAtom neighb = map.get(iAtom);
- neighb.setHydrogenCount(neighb.getHydrogenCount() + 1);
+ neighb.setHydrogenCount(
+ (neighb.getHydrogenCount() == null ? 0 : neighb.getHydrogenCount())
+ + 1
+ );
}
}
mol.setProperties(atomContainer.getProperties());
Modified: cdk/branches/miguelrojasch-ReactionOntology/src/test/org/openscience/cdk/io/random/RandomAccessTest.java
===================================================================
--- cdk/branches/miguelrojasch-ReactionOntology/src/test/org/openscience/cdk/io/random/RandomAccessTest.java 2008-05-26 17:29:51 UTC (rev 11174)
+++ cdk/branches/miguelrojasch-ReactionOntology/src/test/org/openscience/cdk/io/random/RandomAccessTest.java 2008-05-26 17:37:27 UTC (rev 11175)
@@ -1,12 +1,9 @@
-/* RandomAccessTest.java
- * Author: Nina Jeliazkova
- * Date: Jul 12, 2006
- * Revision: 0.1
+/* $Revision$ $Author$ $Date$
*
- * Copyright (C) 2005-2006 Nina Jeliazkova
+ * Copyright (C) 2005-2008 Nina Jeliazkova <ni...@ac...>
+ *
+ * Contact: cdk...@li...
*
- * Contact: ni...@ac...
- *
* 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
@@ -24,9 +21,7 @@
* 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
- *
*/
-
package org.openscience.cdk.io.random;
import java.io.File;
@@ -39,8 +34,9 @@
/**
* Test for {@link RandomAccessSDFReader}.
- * @author Nina Jeliazkova ni...@ac...
- * <b>Modified</b> May 25, 2008
+ *
+ * @author Nina Jeliazkova <ni...@ac...>
+ * @cdk.module test-extra
*/
public class RandomAccessTest extends CDKTestCase {
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