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[Cdk-commits] SF.net SVN: cdk:[14368] cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk /io
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From: <eg...@us...> - 2009-03-06 19:48:13
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Revision: 14368
http://cdk.svn.sourceforge.net/cdk/?rev=14368&view=rev
Author: egonw
Date: 2009-03-06 19:47:55 +0000 (Fri, 06 Mar 2009)
Log Message:
-----------
Fixed the use of the iterating readers for Jython, by reverting an patch r10907. Problem was reported on http://chem-bla-ics.blogspot.com/2009/02/cdk-12-release-candidate.html
Modified Paths:
--------------
cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/iterator/IIteratingChemObjectReader.java
cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java
cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/IRandomAccessChemObjectReader.java
cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/RandomAccessReader.java
cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/RandomAccessSDFReader.java
Added Paths:
-----------
cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/DefaultRandomAccessChemObjectReader.java
Modified: cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/iterator/IIteratingChemObjectReader.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/iterator/IIteratingChemObjectReader.java 2009-03-06 16:27:45 UTC (rev 14367)
+++ cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/iterator/IIteratingChemObjectReader.java 2009-03-06 19:47:55 UTC (rev 14368)
@@ -27,8 +27,8 @@
*/
package org.openscience.cdk.io.iterator;
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.IChemObject;
+import java.util.Iterator;
+
import org.openscience.cdk.io.IChemObjectReader;
/**
@@ -44,11 +44,8 @@
* @author Egon Willighagen <eg...@sc...>
* @cdk.created 2003-10-19
*/
-public interface IIteratingChemObjectReader extends IChemObjectReader {
+public interface IIteratingChemObjectReader
+ extends IChemObjectReader, Iterator {
- public boolean hasNext() throws CDKException;
-
- public IChemObject next() throws CDKException;
-
}
Modified: cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java 2009-03-06 16:27:45 UTC (rev 14367)
+++ cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java 2009-03-06 19:47:55 UTC (rev 14368)
@@ -107,7 +107,7 @@
return PubChemSubstancesXMLFormat.getInstance();
}
- public boolean hasNext() throws CDKException {
+ public boolean hasNext() {
if (!nextAvailableIsKnown) {
hasNext = false;
@@ -128,7 +128,7 @@
} catch (Exception e) {
if (mode == Mode.STRICT) {
- throw new CDKException("Error while parsing the XML: " + e.getMessage(), e);
+ throw new RuntimeException("Error while parsing the XML: " + e.getMessage(), e);
}
hasNext = false;
}
@@ -139,7 +139,7 @@
return hasNext;
}
- public IChemObject next() throws CDKException {
+ public IChemObject next() {
if (!nextAvailableIsKnown) {
hasNext();
}
Added: cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/DefaultRandomAccessChemObjectReader.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/DefaultRandomAccessChemObjectReader.java (rev 0)
+++ cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/DefaultRandomAccessChemObjectReader.java 2009-03-06 19:47:55 UTC (rev 14368)
@@ -0,0 +1,75 @@
+/* $Revision$ $Author$ $Date$
+ *
+ * Copyright (C) 2003-2007 The Jmol Development Team
+ * 2009 Egon Willighagen <eg...@us...>
+ *
+ * Contact: cdk...@li...
+ *
+ * This library 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.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.io.random;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.openscience.cdk.interfaces.IChemObject;
+import org.openscience.cdk.io.IChemObjectReader;
+import org.openscience.cdk.io.ISimpleChemObjectReader;
+import org.openscience.cdk.io.listener.IChemObjectIOListener;
+import org.openscience.cdk.io.setting.IOSetting;
+
+/**
+ * Abstract class that {@link IRandomAccessChemObjectReader}'s can implement to
+ * have it take care of basic stuff, like managing the ReaderListeners.
+ *
+ * @cdk.module io
+ * @cdk.svnrev $Revision$
+ */
+public abstract class DefaultRandomAccessChemObjectReader
+ implements IRandomAccessChemObjectReader<IChemObject> {
+
+ protected IChemObjectReader.Mode mode = IChemObjectReader.Mode.RELAXED;
+
+ /**
+ * Holder of reader event listeners.
+ */
+ private List<IChemObjectIOListener> listenerList = new ArrayList<IChemObjectIOListener>();
+
+ public void addChemObjectIOListener(IChemObjectIOListener listener) {
+ listenerList.add(listener);
+ }
+
+ public void removeChemObjectIOListener(IChemObjectIOListener listener) {
+ listenerList.remove(listener);
+ }
+
+ /* Extra convenience methods */
+
+ protected void fireIOSettingQuestion(IOSetting setting) {
+ for (int i = 0; i < listenerList.size(); ++i) {
+ IChemObjectIOListener listener = listenerList.get(i);
+ listener.processIOSettingQuestion(setting);
+ }
+ }
+
+ public IOSetting[] getIOSettings() {
+ return new IOSetting[0];
+ }
+
+ public void setReaderMode(ISimpleChemObjectReader.Mode mode) {
+ this.mode = mode;
+ }
+
+}
Modified: cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/IRandomAccessChemObjectReader.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/IRandomAccessChemObjectReader.java 2009-03-06 16:27:45 UTC (rev 14367)
+++ cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/IRandomAccessChemObjectReader.java 2009-03-06 19:47:55 UTC (rev 14368)
@@ -22,16 +22,15 @@
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*
*/
-
-
package org.openscience.cdk.io.random;
import java.util.ListIterator;
/**
- * Extension of {@link java.util.ListIterator}
- * @author Nina Jeliazkova ni...@ac...
- * <b>Modified</b> May 25, 2008
+ * Extension of {@link java.util.ListIterator}.
+ *
+ * @author Nina Jeliazkova <ni...@ac...>
+ * @cdk.module io
*/
public interface IRandomAccessChemObjectReader<T> extends ListIterator<T> {
Modified: cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/RandomAccessReader.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/RandomAccessReader.java 2009-03-06 16:27:45 UTC (rev 14367)
+++ cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/RandomAccessReader.java 2009-03-06 19:47:55 UTC (rev 14368)
@@ -1,6 +1,7 @@
/* $Revision:$
*
* Copyright (C) 2005-2008 Nina Jeliazkova <ni...@ac...>
+ * 2009 Egon Willighagen <eg...@us...>
*
* Contact: cdk...@li...
*
@@ -39,7 +40,6 @@
import org.openscience.cdk.io.IChemObjectReader;
import org.openscience.cdk.io.ISimpleChemObjectReader;
import org.openscience.cdk.io.ReaderEvent;
-import org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader;
import org.openscience.cdk.io.listener.IChemObjectIOListener;
import org.openscience.cdk.io.listener.IReaderListener;
import org.openscience.cdk.io.setting.IOSetting;
@@ -52,9 +52,13 @@
* Subsequent access for a record N uses this index to seek the record and return the molecule.
* Useful for very big files.
*
- * @author Nina Jeliazkova ni...@ac...
+ * @author Nina Jeliazkova <ni...@ac...>
+ * @cdk.module io
*/
-public abstract class RandomAccessReader extends DefaultIteratingChemObjectReader implements IRandomAccessChemObjectReader<IChemObject> {
+public abstract class RandomAccessReader
+ extends DefaultRandomAccessChemObjectReader
+ implements IRandomAccessChemObjectReader<IChemObject> {
+
protected static LoggingTool logger = new LoggingTool(RandomAccessReader.class);
protected RandomAccessFile raFile;
protected IOSetting[] headerOptions = null;
Modified: cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/RandomAccessSDFReader.java
===================================================================
--- cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/RandomAccessSDFReader.java 2009-03-06 16:27:45 UTC (rev 14367)
+++ cdk/branches/cdk-1.2.x/src/main/org/openscience/cdk/io/random/RandomAccessSDFReader.java 2009-03-06 19:47:55 UTC (rev 14368)
@@ -44,9 +44,11 @@
import org.openscience.cdk.io.listener.IReaderListener;
/**
- * Random access of SDF file. Doesn't load molecules in memory, uses prebuilt index and seeks to find the correct record offset.
+ * Random access of SDF file. Doesn't load molecules in memory, uses prebuilt
+ * index and seeks to find the correct record offset.
*
- * @author Nina Jeliazkova ni...@ac...
+ * @author Nina Jeliazkova <ni...@ac...>
+ * @cdk.module io
*/
public class RandomAccessSDFReader extends RandomAccessReader {
@@ -120,4 +122,9 @@
return chemObjectReader.accepts(classObject);
}
+ public void remove() {
+ throw new UnsupportedOperationException("Cannot remove entries with " +
+ "the RandomAccessSDFReader");
+ }
+
}
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