diff --git a/common/source/java/ch/systemsx/cisd/common/annotation/CollectionMapping.java b/common/source/java/ch/systemsx/cisd/common/annotation/CollectionMapping.java
index 598b66c704ccacae549b1de43ebfc670b2cd0e3b..ca37b13986dfc8cad0eb5ce8d0cef8fbc376eaef 100644
--- a/common/source/java/ch/systemsx/cisd/common/annotation/CollectionMapping.java
+++ b/common/source/java/ch/systemsx/cisd/common/annotation/CollectionMapping.java
@@ -24,8 +24,8 @@ import java.lang.annotation.Target;
import java.util.Collection;
/**
- * An annotation that defines the type of collection and the type of elements to use when creating the collection in a
- * bean context.
+ * An annotation that defines the type of collection and the type of elements to use when creating
+ * the collection in a bean context.
*
* @author Bernd Rinn
*/
@@ -38,11 +38,13 @@ public @interface CollectionMapping
* The concrete class to use as a collection.
*/
@SuppressWarnings("unchecked")
- // No way to avoid the warning since the compiler doesn't accept something like ArrayList<String>.class
+ // No way to avoid the warning since the compiler doesn't accept something like
+ // ArrayList<String>.class
Class<? extends Collection> collectionClass();
/**
- * The class to use as the elements of the collection (since the generics type isn't known at run time).
+ * The class to use as the elements of the collection (since the generics type isn't known at
+ * run time).
*/
Class<?> elementClass();
}
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/AbstractCollectionDecorator.java b/common/source/java/ch/systemsx/cisd/common/collections/AbstractCollectionDecorator.java
index 24bf50f28c4b4532ec394dda9aee771dbd556880..8f179ed2e2c5eb385ba89f6aa3265b06c81ad36c 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/AbstractCollectionDecorator.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/AbstractCollectionDecorator.java
@@ -21,10 +21,11 @@ import java.util.Iterator;
/**
* Decorates another <code>Collection</code> to provide additional behaviour.
* <p>
- * Each method call made on this <code>Collection</code> is forwarded to the decorated <code>Collection</code>.
- * This class is used as a framework on which to build extensions. The main advantage of decoration is that one
- * decorator can wrap any implementation of <code>Collection</code>, whereas sub-classing requires a new class to be
- * written for each implementation.
+ * Each method call made on this <code>Collection</code> is forwarded to the decorated
+ * <code>Collection</code>. This class is used as a framework on which to build extensions. The
+ * main advantage of decoration is that one decorator can wrap any implementation of
+ * <code>Collection</code>, whereas sub-classing requires a new class to be written for each
+ * implementation.
* </p>
*
* @author Christian Ribeaud
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/CollectionIO.java b/common/source/java/ch/systemsx/cisd/common/collections/CollectionIO.java
index 222eeb502e9b74434c265ca2cd7944e1db01c373..52523267bad73e9d5138363e1b2e052f46701482 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/CollectionIO.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/CollectionIO.java
@@ -41,8 +41,8 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
- * I/O operations for collections. Allows to read and write collections of {@link String}s and other objects from and
- * to streams and files.
+ * I/O operations for collections. Allows to read and write collections of {@link String}s and
+ * other objects from and to streams and files.
*
* @author Bernd Rinn
*/
@@ -53,12 +53,14 @@ public class CollectionIO
LogFactory.getLogger(LogCategory.MACHINE, FileUtilities.class);
/**
- * Reads a collection of {@link String}s from a <var>resource</var>. One line in the resource corresponds to one
- * entry in the collection.
+ * Reads a collection of {@link String}s from a <var>resource</var>. One line in the resource
+ * corresponds to one entry in the collection.
*
* @param resource The resource to read the collection from.
- * @param collection The collection to add the entries from the file to. It will <i>not</i> be cleared initially.
- * @return <code>true</code> if the collection was read successfully, or <code>false</code> otherwise.
+ * @param collection The collection to add the entries from the file to. It will <i>not</i> be
+ * cleared initially.
+ * @return <code>true</code> if the collection was read successfully, or <code>false</code>
+ * otherwise.
*/
public static boolean readCollectionFromResource(String resource, Collection<String> collection)
{
@@ -67,13 +69,15 @@ public class CollectionIO
}
/**
- * Reads a collection from a <var>resource</var>. One line in the resource corresponds to one entry in the
- * collection.
+ * Reads a collection from a <var>resource</var>. One line in the resource corresponds to one
+ * entry in the collection.
*
* @param resource The resource to read the collection from.
- * @param collection The collection to add the entries from the file to. It will <i>not</i> be cleared initially.
+ * @param collection The collection to add the entries from the file to. It will <i>not</i> be
+ * cleared initially.
* @param converter The converter to use in order to convert each line in the file.
- * @return <code>true</code> if the collection was read successfully, or <code>false</code> otherwise.
+ * @return <code>true</code> if the collection was read successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean readCollectionFromResource(String resource, Collection<T> collection,
IFromStringConverter<T> converter)
@@ -89,12 +93,14 @@ public class CollectionIO
}
/**
- * Reads a collection of {@link String}s from a <var>file</var>. One line in the file corresponds to one entry in
- * the collection.
+ * Reads a collection of {@link String}s from a <var>file</var>. One line in the file
+ * corresponds to one entry in the collection.
*
* @param file The file to read the collection from.
- * @param collection The collection to add the entries from the file to. It will <i>not</i> be cleared initially.
- * @return <code>true</code> if the collection was read successfully, or <code>false</code> otherwise.
+ * @param collection The collection to add the entries from the file to. It will <i>not</i> be
+ * cleared initially.
+ * @return <code>true</code> if the collection was read successfully, or <code>false</code>
+ * otherwise.
*/
public static boolean readCollection(File file, Collection<String> collection)
{
@@ -102,12 +108,15 @@ public class CollectionIO
}
/**
- * Reads a collection from a <var>file</var>. One line in the file corresponds to one entry in the collection.
+ * Reads a collection from a <var>file</var>. One line in the file corresponds to one entry in
+ * the collection.
*
* @param file The file to read the collection from.
- * @param collection The collection to add the entries from the file to. It will <i>not</i> be cleared initially.
+ * @param collection The collection to add the entries from the file to. It will <i>not</i> be
+ * cleared initially.
* @param converter The converter to use in order to convert each line in the file.
- * @return <code>true</code> if the collection was read successfully, or <code>false</code> otherwise.
+ * @return <code>true</code> if the collection was read successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean readCollection(File file, Collection<T> collection,
IFromStringConverter<T> converter)
@@ -124,12 +133,14 @@ public class CollectionIO
}
/**
- * Reads a collection of {@link String}s from <var>istream</var>. One line as read from the stream corresponds to
- * one entry in the collection.
+ * Reads a collection of {@link String}s from <var>istream</var>. One line as read from the
+ * stream corresponds to one entry in the collection.
*
* @param istream The stream to read the collection from.
- * @param collection The collection to add the entries from the file to. It will <i>not</i> be cleared initially.
- * @return <code>true</code> if the collection was read successfully, or <code>false</code> otherwise.
+ * @param collection The collection to add the entries from the file to. It will <i>not</i> be
+ * cleared initially.
+ * @return <code>true</code> if the collection was read successfully, or <code>false</code>
+ * otherwise.
*/
public static boolean readCollection(InputStream istream, Collection<String> collection)
{
@@ -137,13 +148,15 @@ public class CollectionIO
}
/**
- * Reads a collection from a <var>istream</var>. One line read from the stream corresponds to one entry in the
- * collection.
+ * Reads a collection from a <var>istream</var>. One line read from the stream corresponds to
+ * one entry in the collection.
*
* @param istream The stream to read the collection from.
- * @param collection The collection to add the entries from the file to. It will <i>not</i> be cleared initially.
+ * @param collection The collection to add the entries from the file to. It will <i>not</i> be
+ * cleared initially.
* @param converter The converter to use in order to convert each line in the file.
- * @return <code>true</code> if the collection was read successfully, or <code>false</code> otherwise.
+ * @return <code>true</code> if the collection was read successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean readCollection(InputStream istream, Collection<T> collection,
IFromStringConverter<T> converter)
@@ -152,15 +165,17 @@ public class CollectionIO
}
/**
- * Reads a collection from a <var>istream</var>. One line read read from the stream corresponds to one entry in the
- * collection.
+ * Reads a collection from a <var>istream</var>. One line read read from the stream corresponds
+ * to one entry in the collection.
*
* @param istream The stream to read the collection from.
- * @param collection The collection to add the entries from the file to. It will <i>not</i> be cleared initially.
+ * @param collection The collection to add the entries from the file to. It will <i>not</i> be
+ * cleared initially.
* @param converter The converter to use in order to convert each line in the file.
- * @param id The identifier associated with the reader (for use in error messages) or <code>null</code>, if no
- * identifier is associated with the reader.
- * @return <code>true</code> if the collection was read successfully, or <code>false</code> otherwise.
+ * @param id The identifier associated with the reader (for use in error messages) or
+ * <code>null</code>, if no identifier is associated with the reader.
+ * @return <code>true</code> if the collection was read successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean readCollection(InputStream istream, Collection<T> collection,
IFromStringConverter<T> converter, String id)
@@ -211,12 +226,12 @@ public class CollectionIO
}
/**
- * Reads a list of {@link String}s from a <var>resource</var>. One line in the resource corresponds to one entry
- * in the list.
+ * Reads a list of {@link String}s from a <var>resource</var>. One line in the resource
+ * corresponds to one entry in the list.
*
* @param resource The resource to read the list from.
- * @return A new {@link ArrayList} containing the entries from the <var>file</var>, or <code>null</code> if there
- * is an error when reading the <var>file</var>.
+ * @return A new {@link ArrayList} containing the entries from the <var>file</var>, or
+ * <code>null</code> if there is an error when reading the <var>file</var>.
*/
public static List<String> readListFromResource(String resource)
{
@@ -224,12 +239,13 @@ public class CollectionIO
}
/**
- * Reads a list from a <var>file</var>. One line in the file corresponds to one entry in the list.
+ * Reads a list from a <var>file</var>. One line in the file corresponds to one entry in the
+ * list.
*
* @param resource The resource to read the list from.
* @param converter The converter to use in order to convert each line in the file.
- * @return A new {@link ArrayList} containing the entries from the <var>file</var>, or <code>null</code> if there
- * is an error when reading the <var>file</var>.
+ * @return A new {@link ArrayList} containing the entries from the <var>file</var>, or
+ * <code>null</code> if there is an error when reading the <var>file</var>.
*/
public static <T> List<T> readListFromResource(String resource,
IFromStringConverter<T> converter)
@@ -248,12 +264,12 @@ public class CollectionIO
}
/**
- * Reads a set of {@link String}s from a <var>r</var>. One line in the resource corresponds to one entry in the
- * set.
+ * Reads a set of {@link String}s from a <var>r</var>. One line in the resource corresponds to
+ * one entry in the set.
*
* @param resource The resource to read the set from.
- * @return A new {@link HashSet} containing the entries from the <var>file</var>, or <code>null</code> if there
- * is an error reading when the <var>file</var>.
+ * @return A new {@link HashSet} containing the entries from the <var>file</var>, or
+ * <code>null</code> if there is an error reading when the <var>file</var>.
*/
public static Set<String> readSetFromResource(String resource)
{
@@ -261,12 +277,13 @@ public class CollectionIO
}
/**
- * Reads a set from a <var>resource</var>. One line in the resource corresponds to one entry in the set.
+ * Reads a set from a <var>resource</var>. One line in the resource corresponds to one entry in
+ * the set.
*
* @param resource The resource to read the set from.
* @param converter The converter to use in order to convert each line in the file.
- * @return A new {@link HashSet} containing the entries from the <var>file</var>, or <code>null</code> if there
- * is an error reading when the <var>file</var>.
+ * @return A new {@link HashSet} containing the entries from the <var>file</var>, or
+ * <code>null</code> if there is an error reading when the <var>file</var>.
*/
public static <T> Set<T> readSetFromResource(String resource, IFromStringConverter<T> converter)
{
@@ -284,12 +301,12 @@ public class CollectionIO
}
/**
- * Reads a list of {@link String}s from a <var>file</var>. One line in the file corresponds to one entry in the
- * list.
+ * Reads a list of {@link String}s from a <var>file</var>. One line in the file corresponds to
+ * one entry in the list.
*
* @param file The file to read the list from.
- * @return A new {@link ArrayList} containing the entries from the <var>file</var>, or <code>null</code> if there
- * is an error when reading the <var>file</var>.
+ * @return A new {@link ArrayList} containing the entries from the <var>file</var>, or
+ * <code>null</code> if there is an error when reading the <var>file</var>.
*/
public static List<String> readList(File file)
{
@@ -297,12 +314,13 @@ public class CollectionIO
}
/**
- * Reads a list from a <var>file</var>. One line in the file corresponds to one entry in the list.
+ * Reads a list from a <var>file</var>. One line in the file corresponds to one entry in the
+ * list.
*
* @param file The file to read the list from.
* @param converter The converter to use in order to convert each line in the file.
- * @return A new {@link ArrayList} containing the entries from the <var>file</var>, or <code>null</code> if there
- * is an error when reading the <var>file</var>.
+ * @return A new {@link ArrayList} containing the entries from the <var>file</var>, or
+ * <code>null</code> if there is an error when reading the <var>file</var>.
*/
public static <T> List<T> readList(File file, IFromStringConverter<T> converter)
{
@@ -320,12 +338,12 @@ public class CollectionIO
}
/**
- * Reads a set of {@link String}s from a <var>file</var>. One line in the file corresponds to one entry in the
- * set.
+ * Reads a set of {@link String}s from a <var>file</var>. One line in the file corresponds to
+ * one entry in the set.
*
* @param file The file to read the set from.
- * @return A new {@link HashSet} containing the entries from the <var>file</var>, or <code>null</code> if there
- * is an error reading when the <var>file</var>.
+ * @return A new {@link HashSet} containing the entries from the <var>file</var>, or
+ * <code>null</code> if there is an error reading when the <var>file</var>.
*/
public static Set<String> readSet(File file)
{
@@ -333,12 +351,13 @@ public class CollectionIO
}
/**
- * Reads a set from a <var>file</var>. One line in the file corresponds to one entry in the set.
+ * Reads a set from a <var>file</var>. One line in the file corresponds to one entry in the
+ * set.
*
* @param file The file to read the set from.
* @param converter The converter to use in order to convert each line in the file.
- * @return A new {@link HashSet} containing the entries from the <var>file</var>, or <code>null</code> if there
- * is an error reading when the <var>file</var>.
+ * @return A new {@link HashSet} containing the entries from the <var>file</var>, or
+ * <code>null</code> if there is an error reading when the <var>file</var>.
*/
public static <T> Set<T> readSet(File file, IFromStringConverter<T> converter)
{
@@ -356,11 +375,14 @@ public class CollectionIO
}
/**
- * Writes a collection to a <var>file</var>. One entry in the collection corresponds to one line in the file.
+ * Writes a collection to a <var>file</var>. One entry in the collection corresponds to one
+ * line in the file.
*
- * @param file The file to write the collection to. The file <i>will</i> be truncated initially.
+ * @param file The file to write the collection to. The file <i>will</i> be truncated
+ * initially.
* @param iterable The iterable to write to the file.
- * @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
+ * @return <code>true</code> if the collection was written successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean writeIterable(File file, Iterable<T> iterable)
{
@@ -368,12 +390,16 @@ public class CollectionIO
}
/**
- * Writes a collection to a <var>file</var>. One entry in the collection corresponds to one line in the file.
+ * Writes a collection to a <var>file</var>. One entry in the collection corresponds to one
+ * line in the file.
*
- * @param file The file to write the collection to. The file <i>will</i> be truncated initially.
+ * @param file The file to write the collection to. The file <i>will</i> be truncated
+ * initially.
* @param iterable The iterable to write to the file.
- * @param converter The {@link IToStringConverter} to use to convert a <var>T</var> value into a {@link String}.
- * @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
+ * @param converter The {@link IToStringConverter} to use to convert a <var>T</var> value into
+ * a {@link String}.
+ * @return <code>true</code> if the collection was written successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean writeIterable(File file, Iterable<T> iterable,
IToStringConverter<? super T> converter)
@@ -404,12 +430,13 @@ public class CollectionIO
}
/**
- * Writes a collection to a {@link OutputStream}. One entry in the collection corresponds to one line written to
- * the stream.
+ * Writes a collection to a {@link OutputStream}. One entry in the collection corresponds to
+ * one line written to the stream.
*
* @param ostream The stream to write the collection to.
* @param iterable The iterable to write to the file.
- * @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
+ * @return <code>true</code> if the collection was written successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean writeIterable(OutputStream ostream, Iterable<T> iterable)
{
@@ -417,13 +444,15 @@ public class CollectionIO
}
/**
- * Writes a collection to a {@link OutputStream}. One entry in the collection corresponds to one line written to
- * the stream.
+ * Writes a collection to a {@link OutputStream}. One entry in the collection corresponds to
+ * one line written to the stream.
*
* @param ostream The stream to write the collection to.
* @param iterable The iterable to write to the file.
- * @param converter The {@link IToStringConverter} to use to convert a <var>T</var> value into a {@link String}.
- * @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
+ * @param converter The {@link IToStringConverter} to use to convert a <var>T</var> value into
+ * a {@link String}.
+ * @return <code>true</code> if the collection was written successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean writeIterable(OutputStream ostream, Iterable<T> iterable,
IToStringConverter<? super T> converter)
@@ -434,13 +463,15 @@ public class CollectionIO
}
/**
- * Writes a collection to a {@link PrintStream}. One entry in the collection corresponds to one line written to the
- * stream.
+ * Writes a collection to a {@link PrintStream}. One entry in the collection corresponds to one
+ * line written to the stream.
*
* @param printStream The stream to write the collection to.
* @param iterable The iterable to write to the file.
- * @param converter The {@link IToStringConverter} to use to convert a <var>T</var> value into a {@link String}.
- * @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
+ * @param converter The {@link IToStringConverter} to use to convert a <var>T</var> value into
+ * a {@link String}.
+ * @return <code>true</code> if the collection was written successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean writeIterable(PrintStream printStream, Iterable<T> iterable,
IToStringConverter<? super T> converter)
@@ -457,12 +488,13 @@ public class CollectionIO
}
/**
- * Writes a collection to a {@link PrintStream}. One entry in the collection corresponds to one line written to the
- * stream.
+ * Writes a collection to a {@link PrintStream}. One entry in the collection corresponds to one
+ * line written to the stream.
*
* @param printStream The stream to write the collection to.
* @param iterable The iterable to write to the file.
- * @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
+ * @return <code>true</code> if the collection was written successfully, or <code>false</code>
+ * otherwise.
*/
public static <T> boolean writeIterable(PrintStream printStream, Iterable<T> iterable)
{
@@ -470,12 +502,13 @@ public class CollectionIO
}
/**
- * Writes a collection to a {@link Writer}. One entry in the collection corresponds to one line written to the
- * stream.
+ * Writes a collection to a {@link Writer}. One entry in the collection corresponds to one line
+ * written to the stream.
*
* @param writer The writer to write the collection to.
* @param iterable The iterable to write to the writer.
- * @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
+ * @return <code>true</code> if the collection was written successfully, or <code>false</code>
+ * otherwise.
*/
public final static <T> boolean writeIterable(final Writer writer, final Iterable<T> iterable,
final IToStringConverter<? super T> converter)
@@ -485,12 +518,13 @@ public class CollectionIO
}
/**
- * Writes a collection to a {@link PrintWriter}. One entry in the collection corresponds to one line written to the
- * stream.
+ * Writes a collection to a {@link PrintWriter}. One entry in the collection corresponds to one
+ * line written to the stream.
*
* @param writer The writer to write the collection to.
* @param iterable The iterable to write to the writer.
- * @return <code>true</code> if the collection was written successfully, or <code>false</code> otherwise.
+ * @return <code>true</code> if the collection was written successfully, or <code>false</code>
+ * otherwise.
*/
public final static <T> boolean writeIterable(final PrintWriter writer,
final Iterable<T> iterable, final IToStringConverter<? super T> converterOrNull)
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/CollectionUtils.java b/common/source/java/ch/systemsx/cisd/common/collections/CollectionUtils.java
index f0f326bd62fdcc85c091a4957180397a7d74f5f0..fd9b3cfcd5116ac32f9d8ca7e44f873e9d67ed43 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/CollectionUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/CollectionUtils.java
@@ -35,12 +35,13 @@ public final class CollectionUtils
/**
* Abbreviates a given array of <code>Object</code>.
* <p>
- * By default it shows the number of items left, {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} and
- * {@link ToStringDefaultConverter} are used.
+ * By default it shows the number of items left,
+ * {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} and {@link ToStringDefaultConverter} are
+ * used.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final T[] objects, final int maxLength)
{
@@ -50,12 +51,13 @@ public final class CollectionUtils
/**
* Abbreviates a given <code>Collection</code>.
* <p>
- * By default it shows the number of items left, {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} and
- * {@link ToStringDefaultConverter} are used.
+ * By default it shows the number of items left,
+ * {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} and {@link ToStringDefaultConverter} are
+ * used.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength)
{
@@ -68,8 +70,8 @@ public final class CollectionUtils
* By default it shows the number of items left and {@link ToStringDefaultConverter} is used.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final T[] objects, final int maxLength,
final CollectionStyle style)
@@ -83,8 +85,8 @@ public final class CollectionUtils
* By default it shows the number of items left and {@link ToStringDefaultConverter} is used.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength,
final CollectionStyle style)
@@ -98,8 +100,8 @@ public final class CollectionUtils
* By default it shows the number of items left.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength,
final IToStringConverter<? super T> converter)
@@ -114,8 +116,8 @@ public final class CollectionUtils
* By default it shows the number of items left.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength,
final IToStringConverter<? super T> converter, final CollectionStyle style)
@@ -126,11 +128,12 @@ public final class CollectionUtils
/**
* Abbreviates a given array of <code>Object</code>.
* <p>
- * By default {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} and {@link ToStringDefaultConverter} are used.
+ * By default {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} and
+ * {@link ToStringDefaultConverter} are used.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final T[] objects, final int maxLength,
final boolean showLeft)
@@ -141,11 +144,12 @@ public final class CollectionUtils
/**
* Abbreviates a given <code>Collection</code>.
* <p>
- * By default {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} and {@link ToStringDefaultConverter} are used.
+ * By default {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} and
+ * {@link ToStringDefaultConverter} are used.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength,
final boolean showLeft)
@@ -159,8 +163,8 @@ public final class CollectionUtils
* By default {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} is used.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final T[] objects, final int maxLength,
final boolean showLeft, final IToStringConverter<? super T> converter)
@@ -187,8 +191,8 @@ public final class CollectionUtils
* By default {@link CollectionStyle#DEFAULT_COLLECTION_STYLE} is used.
* </p>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
*/
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength,
final boolean showLeft, final IToStringConverter<? super T> converter)
@@ -205,10 +209,10 @@ public final class CollectionUtils
* CollectionUtils.abbreviate(new String[] { "1", "2", "3", "4", "5" }, 3, true) = "[1, 2, 3, ... (2 left)]"
* </pre>
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
- * @param showLeft whether the number of items left should be displayed at the end of the output. This is only
- * relevant if you limit the number of items displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
+ * @param showLeft whether the number of items left should be displayed at the end of the
+ * output. This is only relevant if you limit the number of items displayed.
* @param style the style that should be applied to the output.
*/
public final static <T> String abbreviate(final T[] objects, final int maxLength,
@@ -222,10 +226,10 @@ public final class CollectionUtils
/**
* Abbreviates a given <code>Collection</code>.
*
- * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then all items will be
- * displayed.
- * @param showLeft whether the number of items left should be displayed at the end of the output. This is only
- * relevant if you limit the number of items displayed.
+ * @param maxLength the maximum number of items that should be shown. If <code>-1</code> then
+ * all items will be displayed.
+ * @param showLeft whether the number of items left should be displayed at the end of the
+ * output. This is only relevant if you limit the number of items displayed.
* @param style the style that should be applied to the output.
*/
public final static <T> String abbreviate(final Collection<T> collection, final int maxLength,
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/FilteredCollection.java b/common/source/java/ch/systemsx/cisd/common/collections/FilteredCollection.java
index b8a18e7c13e1e5f3dedf8c64f00bb64e825ed468..bbe6e12e8ae153c1a0b3a4b459049208b17ee634 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/FilteredCollection.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/FilteredCollection.java
@@ -20,7 +20,8 @@ import java.util.Collection;
import java.util.Iterator;
/**
- * Decorates another <code>Collection</code> to validate that additions match a specified <code>Validator</code>.
+ * Decorates another <code>Collection</code> to validate that additions match a specified
+ * <code>Validator</code>.
* <p>
* This collection exists to provide validation for the decorated collection.
* </p>
@@ -40,7 +41,8 @@ public class FilteredCollection<E> extends AbstractCollectionDecorator<E>
* </p>
*
* @param coll the collection to decorate. Must not be <code>null</code>.
- * @param validator the <code>Validator</code> to use for validation. Must not be <code>null</code>.
+ * @param validator the <code>Validator</code> to use for validation. Must not be
+ * <code>null</code>.
* @return a new filtered collection.
*/
public static <E> Collection<E> decorate(Collection<E> coll, Validator<E> validator)
@@ -52,7 +54,8 @@ public class FilteredCollection<E> extends AbstractCollectionDecorator<E>
* Constructor that filters given <code>Collection</code>.
*
* @param collection the collection to decorate. Must not be <code>null</code>.
- * @param validator the <code>Validator</code> to use for validation. Must not be <code>null</code>.
+ * @param validator the <code>Validator</code> to use for validation. Must not be
+ * <code>null</code>.
*/
protected FilteredCollection(Collection<E> collection, Validator<E> validator)
{
@@ -65,8 +68,8 @@ public class FilteredCollection<E> extends AbstractCollectionDecorator<E>
/**
* Filters given <var>collection</var> with given <var>validator</var>.
* <p>
- * Note that this operation changes passed <code>Collection</code> if some invalid elements are found. The
- * original collection does not get cloned before .
+ * Note that this operation changes passed <code>Collection</code> if some invalid elements
+ * are found. The original collection does not get cloned before .
* </p>
*/
@SuppressWarnings("unchecked")
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/FilteredList.java b/common/source/java/ch/systemsx/cisd/common/collections/FilteredList.java
index 843bc3a5edcb5a532c3343e7206ff7cb7f6cdf03..03be191e15fdbece50def0287ad76e88a86a31c6 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/FilteredList.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/FilteredList.java
@@ -21,9 +21,11 @@ import java.util.List;
import java.util.ListIterator;
/**
- * Decorates another <code>List</code> to validate that all additions match a specified <code>Validator</code>.
+ * Decorates another <code>List</code> to validate that all additions match a specified
+ * <code>Validator</code>.
* <p>
- * This list exists to provide validation for the decorated list. This class is not <code>Serializable</code>.
+ * This list exists to provide validation for the decorated list. This class is not
+ * <code>Serializable</code>.
* </p>
*
* @author Christian Ribeaud
@@ -35,7 +37,8 @@ public final class FilteredList<E> extends FilteredCollection<E> implements List
* Constructor that filters given <code>List</code>.
*
* @param list the list to decorate. Must not be <code>null</code>
- * @param validator the <code>Validator</code> to use for validation. Must not be <code>null</code>
+ * @param validator the <code>Validator</code> to use for validation. Must not be
+ * <code>null</code>
*/
protected FilteredList(List<E> list, Validator<E> validator)
{
@@ -49,7 +52,8 @@ public final class FilteredList<E> extends FilteredCollection<E> implements List
* </p>
*
* @param list the list to decorate. Must not be <code>null</code>
- * @param validator the <code>Validator</code> to use for validation. Must not be <code>null</code>
+ * @param validator the <code>Validator</code> to use for validation. Must not be
+ * <code>null</code>
*/
public static <E> List<E> decorate(List<E> list, Validator<E> validator)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/FromStringIdentityConverter.java b/common/source/java/ch/systemsx/cisd/common/collections/FromStringIdentityConverter.java
index 0292bbba2885bddd7f66cf9f20cdfcfb7dddf838..b34fb274d80ef0ef14a48be90568110a51963d4c 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/FromStringIdentityConverter.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/FromStringIdentityConverter.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.collections;
/**
- * The identity {@link IFromStringConverter} for {@link String}s, which returns the value itself as the converted
- * value. This class is a singleton.
+ * The identity {@link IFromStringConverter} for {@link String}s, which returns the value itself as
+ * the converted value. This class is a singleton.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/TableMap.java b/common/source/java/ch/systemsx/cisd/common/collections/TableMap.java
index 32303c63d3d0e1028376d6c403981a750f6d15f3..7e687f5fa81cc72de34cc79843008abf06ac0ad6 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/TableMap.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/TableMap.java
@@ -59,7 +59,8 @@ public class TableMap<K, E> implements Iterable<E>
* Creates a new instance for the specified rows and key extractor.
*
* @param rows Collection of rows of type <code>E</code>.
- * @param extractor Strategy to extract a key of type <code>E</code> for an object of type <code>E</code>.
+ * @param extractor Strategy to extract a key of type <code>E</code> for an object of type
+ * <code>E</code>.
* @throws UniqueKeyViolationException If the keys of <var>rows</var> are not unique and a
* <var>uniqueKeyViolationStrategy</var> of <code>ERROR</code> has been chosen.
*/
@@ -72,7 +73,8 @@ public class TableMap<K, E> implements Iterable<E>
* Creates a new instance for the specified rows and key extractor.
*
* @param rows Collection of rows of type <code>E</code>.
- * @param extractor Strategy to extract a key of type <code>E</code> for an object of type <code>E</code>.
+ * @param extractor Strategy to extract a key of type <code>E</code> for an object of type
+ * <code>E</code>.
* @param uniqueKeyViolationStrategy Strategy to react on unique key violations.
* @throws UniqueKeyViolationException If the keys of <var>rows</var> are not unique and a
* <var>uniqueKeyViolationStrategy</var> of <code>ERROR</code> has been chosen.
@@ -92,19 +94,22 @@ public class TableMap<K, E> implements Iterable<E>
}
/**
- * Adds the specified row to this table. What the method will do when a row is provided with a key that is already
- * in the map, depends on the unique key violation strategy as given to the constructor:
+ * Adds the specified row to this table. What the method will do when a row is provided with a
+ * key that is already in the map, depends on the unique key violation strategy as given to the
+ * constructor:
* <ul>
- * <li>For {@link UniqueKeyViolationStrategy#KEEP_FIRST} the first inserted row with this key will be kept and all
- * later ones will be ignored.</li>
- * <li>For {@link UniqueKeyViolationStrategy#KEEP_LAST} the last inserted row with a given key will replace all the
- * others.</li>
- * <li>For {@link UniqueKeyViolationStrategy#ERROR} a {@link UniqueKeyViolationException} will be thrown when
- * trying to insert a row with a key that is already in the map. <i>This is the default.</i>.</li>
+ * <li>For {@link UniqueKeyViolationStrategy#KEEP_FIRST} the first inserted row with this key
+ * will be kept and all later ones will be ignored.</li>
+ * <li>For {@link UniqueKeyViolationStrategy#KEEP_LAST} the last inserted row with a given key
+ * will replace all the others.</li>
+ * <li>For {@link UniqueKeyViolationStrategy#ERROR} a {@link UniqueKeyViolationException} will
+ * be thrown when trying to insert a row with a key that is already in the map. <i>This is the
+ * default.</i>.</li>
* </ul>
*
- * @throws UniqueKeyViolationException If the key of <var>row</var> is already in the map and a unique key
- * violation strategy of {@link UniqueKeyViolationStrategy#ERROR} has been chosen.
+ * @throws UniqueKeyViolationException If the key of <var>row</var> is already in the map and a
+ * unique key violation strategy of {@link UniqueKeyViolationStrategy#ERROR} has
+ * been chosen.
*/
public final void add(final E row) throws UniqueKeyViolationException
{
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKey.java b/common/source/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKey.java
index a82efcc2128845c93dbc360287b357341b70cce1..eb7e76fac64518890d0f88029a428ba63176a76b 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKey.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/TableMapNonUniqueKey.java
@@ -24,11 +24,11 @@ import java.util.NoSuchElementException;
import java.util.Set;
/**
- * A table of rows of type <code>E</code> with random access via a key of type <code>K</code> where the key does not
- * have to be unique.
+ * A table of rows of type <code>E</code> with random access via a key of type <code>K</code>
+ * where the key does not have to be unique.
* <p>
- * Note that the <i>values</i> still need to be unique (according to the {@link Object#equals(Object)} contract), only
- * duplicate <i>keys</i> are acceptable for this map.
+ * Note that the <i>values</i> still need to be unique (according to the
+ * {@link Object#equals(Object)} contract), only duplicate <i>keys</i> are acceptable for this map.
*
* @author Franz-Josef Elmer
* @author Bernd Rinn
@@ -64,7 +64,8 @@ public class TableMapNonUniqueKey<K, E> implements Iterable<E>
* Creates a new instance for the specified rows and key extractor.
*
* @param rows Collection of rows of type <code>E</code>.
- * @param extractor Strategy to extract a key of type <code>E</code> for an object of type <code>E</code>.
+ * @param extractor Strategy to extract a key of type <code>E</code> for an object of type
+ * <code>E</code>.
*/
public TableMapNonUniqueKey(final Iterable<E> rows, final IKeyExtractor<K, E> extractor)
{
@@ -75,7 +76,8 @@ public class TableMapNonUniqueKey<K, E> implements Iterable<E>
* Creates a new instance for the specified rows and key extractor.
*
* @param rows Collection of rows of type <code>E</code>.
- * @param extractor Strategy to extract a key of type <code>E</code> for an object of type <code>E</code>.
+ * @param extractor Strategy to extract a key of type <code>E</code> for an object of type
+ * <code>E</code>.
*/
public TableMapNonUniqueKey(final Iterable<E> rows, final IKeyExtractor<K, E> extractor,
UniqueValueViolationStrategy uniqueValueViolationStrategy)
@@ -92,19 +94,22 @@ public class TableMapNonUniqueKey<K, E> implements Iterable<E>
}
/**
- * Adds the specified row to this table. What the method will do when a row is provided that is equals to a row that
- * is already in the map (according to {@link Object#equals(Object)}, depends on the unique value violation
- * strategy as given to the constructor:
+ * Adds the specified row to this table. What the method will do when a row is provided that is
+ * equals to a row that is already in the map (according to {@link Object#equals(Object)},
+ * depends on the unique value violation strategy as given to the constructor:
* <ul>
- * <li>For {@link UniqueValueViolationStrategy#KEEP_FIRST} the first inserted row will be kept and all later ones
- * will be ignored.</li>
- * <li>For {@link UniqueValueViolationStrategy#KEEP_LAST} the last inserted row will replace all the others.</li>
- * <li>For {@link UniqueValueViolationStrategy#ERROR} a {@link UniqueValueViolationException} will be thrown when
- * trying to insert a row with a key that is already in the map. <i>This is the default.</i>.</li>
+ * <li>For {@link UniqueValueViolationStrategy#KEEP_FIRST} the first inserted row will be kept
+ * and all later ones will be ignored.</li>
+ * <li>For {@link UniqueValueViolationStrategy#KEEP_LAST} the last inserted row will replace
+ * all the others.</li>
+ * <li>For {@link UniqueValueViolationStrategy#ERROR} a {@link UniqueValueViolationException}
+ * will be thrown when trying to insert a row with a key that is already in the map. <i>This is
+ * the default.</i>.</li>
* </ul>
*
- * @throws UniqueValueViolationException If a row that equals the <var>row</var> is already in the map and a unique
- * value violation strategy of {@link UniqueValueViolationStrategy#ERROR} has been chosen.
+ * @throws UniqueValueViolationException If a row that equals the <var>row</var> is already in
+ * the map and a unique value violation strategy of
+ * {@link UniqueValueViolationStrategy#ERROR} has been chosen.
*/
public final void add(final E row) throws UniqueValueViolationException
{
@@ -133,7 +138,8 @@ public class TableMapNonUniqueKey<K, E> implements Iterable<E>
/**
* Gets the row set for the specified <var>key</var>.
*
- * @return The set, given in the order of addition, or <code>null</code> if the <var>key</var> is not found.
+ * @return The set, given in the order of addition, or <code>null</code> if the <var>key</var>
+ * is not found.
*/
public final Set<E> tryGet(final K key)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/Validator.java b/common/source/java/ch/systemsx/cisd/common/collections/Validator.java
index 431af03ba15a96ecdb57ff7d801b91f7d6855310..bc69211dbe505bc0f423be5a85da0e653e8c5315 100644
--- a/common/source/java/ch/systemsx/cisd/common/collections/Validator.java
+++ b/common/source/java/ch/systemsx/cisd/common/collections/Validator.java
@@ -19,8 +19,9 @@ package ch.systemsx.cisd.common.collections;
/**
* Defines a functor interface implemented by classes that perform a predicate test on an object.
* <p>
- * A <code>Validator</code> is the object equivalent of an <code>if</code> statement. It uses the input object to
- * return a <code>true</code> or <code>false</code> value, and is often used in validation or filtering.
+ * A <code>Validator</code> is the object equivalent of an <code>if</code> statement. It uses
+ * the input object to return a <code>true</code> or <code>false</code> value, and is often used
+ * in validation or filtering.
* </p>
*
* @author Christian Ribeaud
@@ -29,7 +30,8 @@ public interface Validator<E>
{
/**
- * Use the specified parameter to perform a test that returns <code>true</code> or <code>false</code>.
+ * Use the specified parameter to perform a test that returns <code>true</code> or
+ * <code>false</code>.
*
* @param object the typed object to evaluate
* @return <code>true</code> or <code>false</code>
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/file/FailureRecord.java b/common/source/java/ch/systemsx/cisd/common/compression/file/FailureRecord.java
index 36d5108825e6e5f15bd75d499e892e080bd231de..243df7ec8083188a92cc07ce623061908882fe75 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/file/FailureRecord.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/file/FailureRecord.java
@@ -59,8 +59,8 @@ public class FailureRecord
}
/**
- * Returns the {@link Status} of the failure. Can have a {@link StatusFlag} of {@link StatusFlag#RETRIABLE_ERROR} if
- * retrying the operation did not help.
+ * Returns the {@link Status} of the failure. Can have a {@link StatusFlag} of
+ * {@link StatusFlag#RETRIABLE_ERROR} if retrying the operation did not help.
*/
public final Status getFailureStatus()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/file/ICompressionMethod.java b/common/source/java/ch/systemsx/cisd/common/compression/file/ICompressionMethod.java
index 7bc8b3c36a099d0ed03bed98f4b7fde46957c2f0..2e3c310e325f9b7e844fdbd25de17a16c8dec830 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/file/ICompressionMethod.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/file/ICompressionMethod.java
@@ -22,8 +22,8 @@ import java.io.FileFilter;
import ch.systemsx.cisd.common.exceptions.Status;
/**
- * A role that compresses a file. A compression method may only be suitable for some files, thus it is also a
- * {@link FileFilter}.
+ * A role that compresses a file. A compression method may only be suitable for some files, thus it
+ * is also a {@link FileFilter}.
*
* @author Bernd Rinn
*/
@@ -33,7 +33,8 @@ public interface ICompressionMethod extends FileFilter
/**
* Compress the <var>fileToCompress</var>
*
- * @return {@link Status#OK} if the operation was successful, a status indicating the kind of problem otherwise.
+ * @return {@link Status#OK} if the operation was successful, a status indicating the kind of
+ * problem otherwise.
*/
public Status compress(File fileToCompress);
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/file/InPlaceCompressionMethod.java b/common/source/java/ch/systemsx/cisd/common/compression/file/InPlaceCompressionMethod.java
index b8da33aab31b21039a164af3e59436ef00f520ab..3d56e2260ca5ad89e27da815ca2013a88cac6605 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/file/InPlaceCompressionMethod.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/file/InPlaceCompressionMethod.java
@@ -31,8 +31,8 @@ import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
import ch.systemsx.cisd.common.utilities.ISelfTestable;
/**
- * An {@link ICompressionMethod} that performs in-place compression of a bulk of files by means of calling an external
- * compression program and running it per file in an external process.
+ * An {@link ICompressionMethod} that performs in-place compression of a bulk of files by means of
+ * calling an external compression program and running it per file in an external process.
*
* @author Bernd Rinn
*/
@@ -110,8 +110,8 @@ public abstract class InPlaceCompressionMethod implements ICompressionMethod, IS
protected abstract List<String> getAcceptedExtensions();
/**
- * Perform any check necessary to see whether the external program that has been found is suitable for the
- * compression task (e.g. program version).
+ * Perform any check necessary to see whether the external program that has been found is
+ * suitable for the compression task (e.g. program version).
*/
public abstract void check() throws EnvironmentFailureException, ConfigurationFailureException;
diff --git a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffZipCompressionMethod.java b/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffZipCompressionMethod.java
index 0f32b9d223834c1630cb1c71e7cfb0691cc4edb8..60a66735421ff33c54733335972806c6c77c1af9 100644
--- a/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffZipCompressionMethod.java
+++ b/common/source/java/ch/systemsx/cisd/common/compression/tiff/TiffZipCompressionMethod.java
@@ -29,8 +29,8 @@ import ch.systemsx.cisd.common.process.ProcessResult;
import ch.systemsx.cisd.common.utilities.OSUtilities;
/**
- * A compression method for TIFF files using the ImageMagick <code>convert</code> utility with compression
- * <code>Zip</code>.
+ * A compression method for TIFF files using the ImageMagick <code>convert</code> utility with
+ * compression <code>Zip</code>.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilities.java b/common/source/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilities.java
index 298d287b33883d8a0315b8b747473f1e947e4aa3..54720ea890c5e1bf0629c65efdec217bf817db78 100644
--- a/common/source/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/concurrent/ConcurrencyUtilities.java
@@ -41,8 +41,10 @@ public final class ConcurrencyUtilities
* Creates an {@link ExecutorService} where threads have a name starting with <var>name</var>.
*
* @param name The name prefix of new threads started by this pool.
- * @param corePoolSize The number of threads that should be kept running even if less theads are needed.
- * @param maximumPoolSize The number of threads that this executor service is maximally allowed to spawn.
+ * @param corePoolSize The number of threads that should be kept running even if less theads are
+ * needed.
+ * @param maximumPoolSize The number of threads that this executor service is maximally allowed
+ * to spawn.
*/
public static ExecutorService newNamedPool(final String name, int corePoolSize,
int maximumPoolSize)
@@ -60,13 +62,14 @@ public final class ConcurrencyUtilities
}
/**
- * Tries to get the result of a <var>future</var>, maximally waiting <var>timeoutMillis</var> for the result to
- * become available. Any {@link ExecutionException} that might occur in the future task is unwrapped and re-thrown.
+ * Tries to get the result of a <var>future</var>, maximally waiting <var>timeoutMillis</var>
+ * for the result to become available. Any {@link ExecutionException} that might occur in the
+ * future task is unwrapped and re-thrown.
*
- * @return The result of the future, or <code>null</code>, if the result does not become available within
- * <var>timeoutMillis</var> ms.
- * @throws CheckedExceptionTunnel of an {@link InterruptedException} if the current thread gets interrupted during
- * waiting for the result.
+ * @return The result of the future, or <code>null</code>, if the result does not become
+ * available within <var>timeoutMillis</var> ms.
+ * @throws CheckedExceptionTunnel of an {@link InterruptedException} if the current thread gets
+ * interrupted during waiting for the result.
*/
public static <T> T tryGetResult(Future<T> future, long timeoutMillis)
{
@@ -74,11 +77,13 @@ public final class ConcurrencyUtilities
}
/**
- * Tries to get the result of a <var>future</var>, maximally waiting <var>timeoutMillis</var> for the result to
- * become available. Any {@link ExecutionException} that might occur in the future task is unwrapped and re-thrown.
+ * Tries to get the result of a <var>future</var>, maximally waiting <var>timeoutMillis</var>
+ * for the result to become available. Any {@link ExecutionException} that might occur in the
+ * future task is unwrapped and re-thrown.
*
- * @return The result of the future, or <code>null</code>, if the result does not become available within
- * <var>timeoutMillis</var> ms or if the waiting thread gets interrupted.
+ * @return The result of the future, or <code>null</code>, if the result does not become
+ * available within <var>timeoutMillis</var> ms or if the waiting thread gets
+ * interrupted.
*/
public static <T> T tryGetResult(Future<T> future, long timeoutMillis,
ISimpleLogger loggerOrNull, String operationNameOrNull)
diff --git a/common/source/java/ch/systemsx/cisd/common/converter/Converter.java b/common/source/java/ch/systemsx/cisd/common/converter/Converter.java
index 58d1cbc873e44b2ab7c03a8e134cd643bd516a84..2eb72c5aae38eedb5c531dea7f6039b9dd51718c 100644
--- a/common/source/java/ch/systemsx/cisd/common/converter/Converter.java
+++ b/common/source/java/ch/systemsx/cisd/common/converter/Converter.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.converter;
/**
- * General purpose data type converter that can be registered and used in {@link ConverterPool} to manage the conversion
- * of objects from one type to another.
+ * General purpose data type converter that can be registered and used in {@link ConverterPool} to
+ * manage the conversion of objects from one type to another.
*
* @author Christian Ribeaud
*/
@@ -28,13 +28,15 @@ public interface Converter<T>
* Converts the <var>value</var> <code>String</code> into an object of type <code>T</code>.
*
* @param value The <code>String</code> to convert. <code>null</code> is acceptable here.
- * @return The converted value, or <code>null</code>, if the <var>value</var> was <code>null</code>.
+ * @return The converted value, or <code>null</code>, if the <var>value</var> was
+ * <code>null</code>.
*/
public T convert(String value);
/**
- * @return The default in case the value we try to convert is <code>null</code>. If the converter does not
- * support a default value, the return value of this method may be <code>null</code> as well.
+ * @return The default in case the value we try to convert is <code>null</code>. If the
+ * converter does not support a default value, the return value of this method may be
+ * <code>null</code> as well.
*/
public T getDefaultValue();
diff --git a/common/source/java/ch/systemsx/cisd/common/converter/ConverterPool.java b/common/source/java/ch/systemsx/cisd/common/converter/ConverterPool.java
index 89be0791e792281127885edce8119c3ae1eba918..16d249a2965b23a9c6c4def2ce34d90c7c5e64b0 100644
--- a/common/source/java/ch/systemsx/cisd/common/converter/ConverterPool.java
+++ b/common/source/java/ch/systemsx/cisd/common/converter/ConverterPool.java
@@ -22,7 +22,8 @@ import java.util.Map;
/**
* A pool of {@link Converter}s.
* <p>
- * You can have your own instance of this class or you can use the static accessor to get a 'public' instance.
+ * You can have your own instance of this class or you can use the static accessor to get a 'public'
+ * instance.
* </p>
*
* @author Christian Ribeaud
@@ -144,7 +145,8 @@ public final class ConverterPool
return returned;
}
- // The setter registerConverter() will ensure that no converter can be entered that is of the wrong type.
+ // The setter registerConverter() will ensure that no converter can be entered that is of the
+ // wrong type.
@SuppressWarnings("unchecked")
final <T> Converter<T> getConverter(Class<T> type)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/converter/DateConverter.java b/common/source/java/ch/systemsx/cisd/common/converter/DateConverter.java
index 23cbd5467ffd6512927825551abc04845b2cf948..ec738782c8c736725b9a1fe6225ec249f6308692 100644
--- a/common/source/java/ch/systemsx/cisd/common/converter/DateConverter.java
+++ b/common/source/java/ch/systemsx/cisd/common/converter/DateConverter.java
@@ -60,8 +60,8 @@ public final class DateConverter implements Converter<Date>
/**
* Converts given <code>value</code> to a <code>Date</code>.
* <p>
- * Return <code>null</code> if a <code>ParseException</code> occurs or if given <var>value</var> is
- * <code>null</code>.
+ * Return <code>null</code> if a <code>ParseException</code> occurs or if given <var>value</var>
+ * is <code>null</code>.
* </p>
*/
public final Date convert(String value)
diff --git a/common/source/java/ch/systemsx/cisd/common/db/DBRestrictionParser.java b/common/source/java/ch/systemsx/cisd/common/db/DBRestrictionParser.java
index 7bdfc67c389085297222b24a90d88374f4dd296a..0025254c7b83ac6aa13df21eb4e5e38c94a3242f 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/DBRestrictionParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/DBRestrictionParser.java
@@ -32,7 +32,8 @@ import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
/**
- * A parser for SQL92 data definition language scripts. The result are columns lengths and checked constraints.
+ * A parser for SQL92 data definition language scripts. The result are columns lengths and checked
+ * constraints.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutor.java b/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutor.java
index c697f5f905e9980b9fbdd6e23d262fb586112616..5f27849abee0353c3140019f37661275211d5287 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutor.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/ISqlScriptExecutor.java
@@ -29,10 +29,10 @@ public interface ISqlScriptExecutor
* Executes the specified SQL script.
*
* @param sqlScript The script to execute.
- * @param honorSingleStepMode If <code>false</code>, the single step mode will be ignored for this script, even
- * if configured in the properties.
- * @param loggerOrNull A logger to log the execution of the <var>sqlScript</var>, or <code>null</code>, if no
- * logging should be performed.
+ * @param honorSingleStepMode If <code>false</code>, the single step mode will be ignored for
+ * this script, even if configured in the properties.
+ * @param loggerOrNull A logger to log the execution of the <var>sqlScript</var>, or
+ * <code>null</code>, if no logging should be performed.
*/
public void execute(Script sqlScript, boolean honorSingleStepMode,
ISqlScriptExecutionLogger loggerOrNull);
diff --git a/common/source/java/ch/systemsx/cisd/common/db/SQLCommandTokenizer.java b/common/source/java/ch/systemsx/cisd/common/db/SQLCommandTokenizer.java
index c974ab12783a3d31c273ea97a1f88140ef7acf31..26038f5003de9f742f982f8c51cbc53dca1c1f52 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/SQLCommandTokenizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/SQLCommandTokenizer.java
@@ -48,7 +48,8 @@ public final class SQLCommandTokenizer
this.sqlScript = sqlScript;
}
- // TODO 2007-07-11, Franz-Josef Elmer: Can not handle end-of-line comments and multiline commands
+ // TODO 2007-07-11, Franz-Josef Elmer: Can not handle end-of-line comments and multiline
+ // commands
public final String getNextCommand()
{
final StringBuilder builder = new StringBuilder();
diff --git a/common/source/java/ch/systemsx/cisd/common/db/SQLStateUtils.java b/common/source/java/ch/systemsx/cisd/common/db/SQLStateUtils.java
index bba78cb41040165881b31cd2cbde0e88b43f4632..bde9bee43f165f71b32b09f4c7a805bedbb4711c 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/SQLStateUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/SQLStateUtils.java
@@ -21,9 +21,10 @@ import java.sql.SQLException;
/**
* Some utility methods regarding <i>SQL State</i>.
* <p>
- * Note: be careful not to duplicate functionality with the <i>Spring</i> framework. Have a look at at
- * <code>org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator</code> and
- * <code>org.springframework.util.StringUtils.SQLErrorCodes</code> before extending the functionality of this class.
+ * Note: be careful not to duplicate functionality with the <i>Spring</i> framework. Have a look at
+ * at <code>org.springframework.jdbc.support.SQLErrorCodeSQLExceptionTranslator</code> and
+ * <code>org.springframework.util.StringUtils.SQLErrorCodes</code> before extending the
+ * functionality of this class.
* </p>
*
* @author Christian Ribeaud
@@ -53,7 +54,8 @@ public final class SQLStateUtils
/**
* Tries to get the SQL state of given <code>Throwable</code>.
* <p>
- * This is only possible if {@link Throwable#getCause()} is an instance of <code>SQLException</code>.
+ * This is only possible if {@link Throwable#getCause()} is an instance of
+ * <code>SQLException</code>.
* </p>
*/
public final static String getSqlState(Throwable ex)
diff --git a/common/source/java/ch/systemsx/cisd/common/db/SqlUnitTestRunner.java b/common/source/java/ch/systemsx/cisd/common/db/SqlUnitTestRunner.java
index b6094ce5776d05f442fa9aaf6f9bdc51338cd520..711ecc01ac4888612c625f5ee8a047691d01f5be 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/SqlUnitTestRunner.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/SqlUnitTestRunner.java
@@ -32,8 +32,9 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
import ch.systemsx.cisd.common.utilities.OSUtilities;
/**
- * Runner of SQL Unit tests. Needs an implementation of {@link ISqlScriptExecutor} to do the actual tests. The runner
- * executes all test scripts found in the specified test scripts folder. The folder should have the following structure
+ * Runner of SQL Unit tests. Needs an implementation of {@link ISqlScriptExecutor} to do the actual
+ * tests. The runner executes all test scripts found in the specified test scripts folder. The
+ * folder should have the following structure
*
* <pre>
* <<i>test script folder</i>>
@@ -48,20 +49,22 @@ import ch.systemsx.cisd.common.utilities.OSUtilities;
* ...
* </pre>
*
- * Folder starting with '.' or <code>migration</code> are ignored. The test cases are executed in lexicographical
- * order of their name. For each test case <code>buildup.sql</code> will be executed first. The test scripts follow
- * the naming schema
+ * Folder starting with '.' or <code>migration</code> are ignored. The test cases are executed in
+ * lexicographical order of their name. For each test case <code>buildup.sql</code> will be
+ * executed first. The test scripts follow the naming schema
*
* <pre>
* <<i>decimal number</i>>=<<i>test name</i>>.sql
* </pre>
*
- * They are executed in ascending order of their numbers. Finally <code>teardown.sql</code> is executed. If execution
- * of <code>buildup.sql</code> failed all test scripts and the tear down script are skipped. Note that
- * <code>buildup.sql</code> and <code>teardown.sql</code> are optional.
+ * They are executed in ascending order of their numbers. Finally <code>teardown.sql</code> is
+ * executed. If execution of <code>buildup.sql</code> failed all test scripts and the tear down
+ * script are skipped. Note that <code>buildup.sql</code> and <code>teardown.sql</code> are
+ * optional.
* <p>
- * A script fails if its execution throws an exception. Its innermost cause (usually a {@link SQLException}) will be
- * recorded together with the name of the test case and the script. All failed scripts will be recorded.
+ * A script fails if its execution throws an exception. Its innermost cause (usually a
+ * {@link SQLException}) will be recorded together with the name of the test case and the script.
+ * All failed scripts will be recorded.
* <p>
* The runner throws an {@link AssertionError} if at least one script failed.
*
@@ -133,7 +136,8 @@ public class SqlUnitTestRunner
}
/**
- * Executes all scripts in the specified folder. Does nothing if it does not exists or if it is empty.
+ * Executes all scripts in the specified folder. Does nothing if it does not exists or if it is
+ * empty.
*
* @throws AssertionError if at least one script failed.
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/db/StandardSequenceNameMapper.java b/common/source/java/ch/systemsx/cisd/common/db/StandardSequenceNameMapper.java
index a2521bfd9f4dcebf866a6cc6cc313b5b8609d2ac..79c1d4ee9119b5cfe1538ee15e4a0d7d5cb50439 100644
--- a/common/source/java/ch/systemsx/cisd/common/db/StandardSequenceNameMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/db/StandardSequenceNameMapper.java
@@ -21,8 +21,9 @@ import java.util.Map;
import java.util.Set;
/**
- * Standard sequence name mapper which replaces the last character of the table name by <code>_id_seq</code>. This
- * generic rules applies only for sequence names not found in the map provided as constructor argument.
+ * Standard sequence name mapper which replaces the last character of the table name by
+ * <code>_id_seq</code>. This generic rules applies only for sequence names not found in the map
+ * provided as constructor argument.
*
* @author Franz-Josef Elmer
*/
@@ -41,7 +42,8 @@ public class StandardSequenceNameMapper implements ISequenceNameMapper
}
/**
- * Creates an instance for the specified map of sequence name which are not map by the above mentioned rule.
+ * Creates an instance for the specified map of sequence name which are not map by the above
+ * mentioned rule.
*/
public StandardSequenceNameMapper(final Map<String, String> nonstandardMapping,
final Set<String> tablesWithoutSequencers)
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/CheckedExceptionTunnel.java b/common/source/java/ch/systemsx/cisd/common/exceptions/CheckedExceptionTunnel.java
index 280ff42af4753251aa9c8539bac29c2dd29ac98a..ec843f27f5ea9c5e3f215c53efc7a56d8269f26f 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/CheckedExceptionTunnel.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/CheckedExceptionTunnel.java
@@ -39,9 +39,9 @@ public final class CheckedExceptionTunnel extends RuntimeException
}
/**
- * Returns a {@link RuntimeException} from an <var>exception</var>. If <var>exception</var> is already a
- * {@link RuntimeException}, itself is returned, otherwise a {@link CheckedExceptionTunnel} with <var>exception</var>
- * as checked exception argument.
+ * Returns a {@link RuntimeException} from an <var>exception</var>. If <var>exception</var> is
+ * already a {@link RuntimeException}, itself is returned, otherwise a
+ * {@link CheckedExceptionTunnel} with <var>exception</var> as checked exception argument.
*
* @param exception The exception to represent by the return value.
* @return A {@link RuntimeException} representing the <var>exception</var>.
@@ -58,8 +58,8 @@ public final class CheckedExceptionTunnel extends RuntimeException
}
/**
- * Returns the original exception before being wrapped, if the exception has been wrapped, or <var>exception</var>
- * otherwise.
+ * Returns the original exception before being wrapped, if the exception has been wrapped, or
+ * <var>exception</var> otherwise.
*/
public final static Exception unwrapIfNecessary(final Exception exception)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/ConfigurationFailureException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/ConfigurationFailureException.java
index 52ffd5e0c73a46a42f85788561175caaf727aa7b..4af3c1638643edffae7c4edaa6f7167fcb423e40 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/ConfigurationFailureException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/ConfigurationFailureException.java
@@ -17,8 +17,9 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * The <code>ConfigurationFailureException</code> is the super class of all exceptions that have their cause in an
- * inappropriate configuration of the system. This implies that an application administrator can fix the problem.
+ * The <code>ConfigurationFailureException</code> is the super class of all exceptions that have
+ * their cause in an inappropriate configuration of the system. This implies that an application
+ * administrator can fix the problem.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/EnvironmentFailureException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/EnvironmentFailureException.java
index 002a2c251a7f65261165f93f84e64583ac8992db..a8427790afd20fad3faee8a9481c647b2f5fd8b0 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/EnvironmentFailureException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/EnvironmentFailureException.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * The <code>EnvironmentFailureException</code> is the super class of all exceptions that have their cause in the
- * software or hardware environment of the system failing.
+ * The <code>EnvironmentFailureException</code> is the super class of all exceptions that have
+ * their cause in the software or hardware environment of the system failing.
* <p>
* Note that the user does not count as part of the environment in this respect.
*
@@ -56,8 +56,9 @@ public class EnvironmentFailureException extends HighLevelException
}
/**
- * Returns the assessment of the subsystem throwing the exception whether the failure could be temporarily and thus
- * retrying the operation (on a higher level) could possibly help to cure the problem.
+ * Returns the assessment of the subsystem throwing the exception whether the failure could be
+ * temporarily and thus retrying the operation (on a higher level) could possibly help to cure
+ * the problem.
* <p>
* This class will always return <code>false</code>, but sub classes can override the method.
*
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/HighLevelException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/HighLevelException.java
index a35cfd9d3570bb1b8561c5c60d12f495a5abee2f..2f275afa2a0de47a7aa3a429d94e4d9da6e884b8 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/HighLevelException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/HighLevelException.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * An exception that is "high-level" in the sense that we have a pretty good understanding what the failure means in the
- * context where the exception has been thrown.
+ * An exception that is "high-level" in the sense that we have a pretty good understanding what the
+ * failure means in the context where the exception has been thrown.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/InternalErr.java b/common/source/java/ch/systemsx/cisd/common/exceptions/InternalErr.java
index 00d7bf5ace8973e828dd2a6de68bf8c67cab8358..b209a0a83a08adb42b86ad9cd8ec3d09618175dc 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/InternalErr.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/InternalErr.java
@@ -17,14 +17,15 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * Exception representing internal error in the program caused by programmer error. It should never be caught. We throw
- * this exception to say the system (e.g. some data structure) is in the state, in which it never meant to be when a
- * particular piece of code was written. This is something different from the situation when a user has provided wrong
- * input data. <br>
- * This class becomes handy when we do comparition of some value with the enumerator. The following 'enum-match' pattern
- * should be applied: 1. all values of the enumerator should be checked 2. if no matching of the value and enumerator is
- * found, it is a programmer mistake and internal error occurs. It means that when one adds a new enumerator value, one
- * should check every comparition of other values and update them.
+ * Exception representing internal error in the program caused by programmer error. It should never
+ * be caught. We throw this exception to say the system (e.g. some data structure) is in the state,
+ * in which it never meant to be when a particular piece of code was written. This is something
+ * different from the situation when a user has provided wrong input data. <br>
+ * This class becomes handy when we do comparition of some value with the enumerator. The following
+ * 'enum-match' pattern should be applied: 1. all values of the enumerator should be checked 2. if
+ * no matching of the value and enumerator is found, it is a programmer mistake and internal error
+ * occurs. It means that when one adds a new enumerator value, one should check every comparition of
+ * other values and update them.
*
* <pre>
* Example:
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/MasqueradingException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/MasqueradingException.java
index f16be226c0402929f3a48aaa82e1447ab228897d..a442f2b820db44f25630d158b096a24216159989 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/MasqueradingException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/MasqueradingException.java
@@ -17,11 +17,11 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * A <code>RuntimeException</code> extension which almost clones given <var>rootException</var> without saving it as
- * cause.
+ * A <code>RuntimeException</code> extension which almost clones given <var>rootException</var>
+ * without saving it as cause.
* <p>
- * This means that it does not contain any third-party specific or proprietary <code>Exception</code> extension that
- * the client does not know about and does not understand.
+ * This means that it does not contain any third-party specific or proprietary
+ * <code>Exception</code> extension that the client does not know about and does not understand.
* </p>
*
* @author Christian Ribeaud
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/NotImplementedException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/NotImplementedException.java
index 2b79c591012fda00fb47c77a6faf9962bbe4e607..c48393843d2474682461a6b5da0d58e55e4ca076 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/NotImplementedException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/NotImplementedException.java
@@ -19,11 +19,11 @@ package ch.systemsx.cisd.common.exceptions;
import java.io.Serializable;
/**
- * This is an extension to the <code>RuntimeException</code> for unimplemented methods. The empty constructor tries to
- * get the method resp. the class name the exception has been thrown.
+ * This is an extension to the <code>RuntimeException</code> for unimplemented methods. The empty
+ * constructor tries to get the method resp. the class name the exception has been thrown.
* <p>
- * This class should be used everywhere where the <i>Apache</i> commons one can not (because the library is not
- * imported, for instance).
+ * This class should be used everywhere where the <i>Apache</i> commons one can not (because the
+ * library is not imported, for instance).
* </p>
*
* @author Chritian Ribeaud
@@ -71,8 +71,8 @@ public final class NotImplementedException extends RuntimeException
//
/**
- * Returns the error message for this exception. If the error message has not been defined in this class, returns
- * the error message defined in the super class.
+ * Returns the error message for this exception. If the error message has not been defined in
+ * this class, returns the error message defined in the super class.
*
* @see java.lang.Throwable#getMessage()
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/RetriableEnvironmentFailureException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/RetriableEnvironmentFailureException.java
index cbf0253ccf9c92761e619db98d7490d5bd8c0deb..6c5ef2d7e32d4472278305bb5b95738e7e56ad81 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/RetriableEnvironmentFailureException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/RetriableEnvironmentFailureException.java
@@ -17,9 +17,9 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * The <code>RetriableEnvironmentFailureException</code> is the super class of all exceptions that have their cause in
- * the software or hardware environment of the system failing and where, at least in principle, retrying the operation
- * could help.
+ * The <code>RetriableEnvironmentFailureException</code> is the super class of all exceptions that
+ * have their cause in the software or hardware environment of the system failing and where, at
+ * least in principle, retrying the operation could help.
* <p>
* If retrying doesn't help, use an {@link EnvironmentFailureException} instead.
* <p>
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/Status.java b/common/source/java/ch/systemsx/cisd/common/exceptions/Status.java
index e7a239e14cf4efe8d0c3db755302bd15b8ed9899..6e4e057ef40744f93fa68b4e489307874955cb29 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/Status.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/Status.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * A class that holds the information about the status of an operation. To be used whenever a failure of an operation is
- * signalled back via a return value rather than an exception.
+ * A class that holds the information about the status of an operation. To be used whenever a
+ * failure of an operation is signalled back via a return value rather than an exception.
*
* @author Bernd Rinn
*/
@@ -49,7 +49,8 @@ public final class Status
}
/**
- * @return The message of the operation if <code>getFlag() != OK</code>, or <code>null</code> otherwise.
+ * @return The message of the operation if <code>getFlag() != OK</code>, or <code>null</code>
+ * otherwise.
*/
public String getMessage()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/StatusFlag.java b/common/source/java/ch/systemsx/cisd/common/exceptions/StatusFlag.java
index 50555756b8b68b0c6376cb43db3386675422714c..c14250df91baa53af46b842246b3fbb7756f5edb 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/StatusFlag.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/StatusFlag.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * The status of an operation. To be used whenever a failure of an operation is signalled back via a return value rather
- * than an exception.
+ * The status of an operation. To be used whenever a failure of an operation is signalled back via a
+ * return value rather than an exception.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/exceptions/UserFailureException.java b/common/source/java/ch/systemsx/cisd/common/exceptions/UserFailureException.java
index c17919cf5c2cadb07ba80a2e1448dac1620a068c..3b101c956d68d94096b5ff8f0e36302135f1469b 100644
--- a/common/source/java/ch/systemsx/cisd/common/exceptions/UserFailureException.java
+++ b/common/source/java/ch/systemsx/cisd/common/exceptions/UserFailureException.java
@@ -17,9 +17,9 @@
package ch.systemsx.cisd.common.exceptions;
/**
- * The <code>UserFailureException</code> is the super class of all exceptions that have their cause in an
- * inappropriate usage of the system. This implies that the user himself (without help of an administrator) can fix the
- * problem.
+ * The <code>UserFailureException</code> is the super class of all exceptions that have their
+ * cause in an inappropriate usage of the system. This implies that the user himself (without help
+ * of an administrator) can fix the problem.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/BufferedAppender.java b/common/source/java/ch/systemsx/cisd/common/logging/BufferedAppender.java
index 96f2f0e73042e909148381f6d823aac683c2bc66..599b8807b6563421a93312c17f588acc574deb4d 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/BufferedAppender.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/BufferedAppender.java
@@ -25,12 +25,12 @@ import org.apache.log4j.PatternLayout;
import org.apache.log4j.WriterAppender;
/**
- * A <code>WriterAppender</code> extension that buffers its output in a <code>ByteArrayOutputStream</code> until you
- * ask for it by using {@link #getLogContent()}.
+ * A <code>WriterAppender</code> extension that buffers its output in a
+ * <code>ByteArrayOutputStream</code> until you ask for it by using {@link #getLogContent()}.
* <p>
- * It internally uses a <code>ByteArrayOutputStream</code> which collect the log output and can return it using
- * {@link #getLogContent()}. It is a good idea to reset the log recorder by calling {@link #resetLogContent()} before
- * calling a unit test method.
+ * It internally uses a <code>ByteArrayOutputStream</code> which collect the log output and can
+ * return it using {@link #getLogContent()}. It is a good idea to reset the log recorder by calling
+ * {@link #resetLogContent()} before calling a unit test method.
* </p>
*
* @author Christian Ribeaud
@@ -40,8 +40,8 @@ public final class BufferedAppender extends WriterAppender
private final ByteArrayOutputStream logRecorder;
/**
- * Constructor with default pattern layout (which is {@link PatternLayout#DEFAULT_CONVERSION_PATTERN}) and
- * {@link Level#DEBUG} as log level.
+ * Constructor with default pattern layout (which is
+ * {@link PatternLayout#DEFAULT_CONVERSION_PATTERN}) and {@link Level#DEBUG} as log level.
*/
public BufferedAppender()
{
@@ -49,7 +49,8 @@ public final class BufferedAppender extends WriterAppender
}
/**
- * Constructor with default pattern layout (which is {@link PatternLayout#DEFAULT_CONVERSION_PATTERN}).
+ * Constructor with default pattern layout (which is
+ * {@link PatternLayout#DEFAULT_CONVERSION_PATTERN}).
*
* @param logLevel
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/Log4jSimpleLogger.java b/common/source/java/ch/systemsx/cisd/common/logging/Log4jSimpleLogger.java
index 557cc23cb7b80de84de2155a7c5f1978ae3801e3..00112b59096923416d9ceebd2636ddca02317e2b 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/Log4jSimpleLogger.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/Log4jSimpleLogger.java
@@ -56,8 +56,9 @@ public class Log4jSimpleLogger implements ISimpleLogger
* Creates a logger that uses <var>log4jLogger<var> to do the real logging.
*
* @param log4jLogger The log4j logger to use.
- * @param log4jOverridePriorityOrNull If not <code>null</code>, use this log level instead of the one provided to
- * the {@link ISimpleLogger#log(ch.systemsx.cisd.common.logging.LogLevel, String)}.
+ * @param log4jOverridePriorityOrNull If not <code>null</code>, use this log level instead of
+ * the one provided to the
+ * {@link ISimpleLogger#log(ch.systemsx.cisd.common.logging.LogLevel, String)}.
*/
public Log4jSimpleLogger(Logger log4jLogger, Priority log4jOverridePriorityOrNull)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogCategory.java b/common/source/java/ch/systemsx/cisd/common/logging/LogCategory.java
index 23ef465420022f8784c114641b932a8c5185fc1c..331d84a9fa9c896ef776ff33509df9392d70f513 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogCategory.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/LogCategory.java
@@ -33,8 +33,9 @@ public enum LogCategory
/**
* Log category for events that require immediate notification of an administrator.
* <p>
- * This should be carefully used as each logging event sent to this category will be automatically emailed to a
- * specified recipient (assuming the event priority matches the configured one).
+ * This should be carefully used as each logging event sent to this category will be
+ * automatically emailed to a specified recipient (assuming the event priority matches the
+ * configured one).
* </p>
*/
NOTIFY,
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java b/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java
index ad2f343e46d334cc6d8d7dfd78804b6231fc9fdf..9821fd5aec53f38f408ab93e1664f5d7f6234b68 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java
@@ -32,8 +32,8 @@ public final class LogFactory
}
/**
- * @return The logger name for the given {@link LogCategory} and {@link Class}. It will contain the name of the
- * <var>category</var>, followed by the canonical name of <var>clazz</var>.
+ * @return The logger name for the given {@link LogCategory} and {@link Class}. It will contain
+ * the name of the <var>category</var>, followed by the canonical name of <var>clazz</var>.
*/
public static String getLoggerName(LogCategory category, Class<?> clazz)
{
@@ -41,9 +41,9 @@ public final class LogFactory
}
/**
- * @return The logger name for the given {@link LogCategory}. Needs to be used for admin logs (i.e.
- * {@link LogCategory#isAdminLog()} needs to return <code>true</code>). It will contain the name of the
- * <var>category</var>.
+ * @return The logger name for the given {@link LogCategory}. Needs to be used for admin logs
+ * (i.e. {@link LogCategory#isAdminLog()} needs to return <code>true</code>). It will
+ * contain the name of the <var>category</var>.
*/
public static String getLoggerName(LogCategory category)
{
@@ -56,8 +56,9 @@ public final class LogFactory
}
/**
- * @return The logger for the given {@link LogCategory} and {@link Class}. The name of the logger will contain the
- * name of the <var>category</var>, followed by the canonical name of <var>clazz</var>.
+ * @return The logger for the given {@link LogCategory} and {@link Class}. The name of the
+ * logger will contain the name of the <var>category</var>, followed by the canonical
+ * name of <var>clazz</var>.
*/
public static Logger getLogger(LogCategory category, Class<?> clazz)
{
@@ -66,8 +67,8 @@ public final class LogFactory
/**
* @return The logger for the given {@link LogCategory}. Needs to be an admin log (i.e.
- * {@link LogCategory#isAdminLog()} needs to return <code>true</code>). The name of the logger will
- * contain the name of the <var>category</var>.
+ * {@link LogCategory#isAdminLog()} needs to return <code>true</code>). The name of
+ * the logger will contain the name of the <var>category</var>.
*/
public static Logger getLogger(LogCategory category)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogInitializer.java b/common/source/java/ch/systemsx/cisd/common/logging/LogInitializer.java
index 6939d005ba3d538077e04391478b1370048e73aa..019419a0150500302970d175ae7ae2f617fbceff 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogInitializer.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/LogInitializer.java
@@ -25,7 +25,8 @@ import org.apache.log4j.helpers.LogLog;
import org.apache.log4j.xml.DOMConfigurator;
/**
- * Initializes the logging system. The {@link #init()} method needs to be called once at system startup.
+ * Initializes the logging system. The {@link #init()} method needs to be called once at system
+ * startup.
*
* @author Bernd Rinn
*/
@@ -57,7 +58,8 @@ public class LogInitializer
private final static void configureFromFile(final File logFile)
{
assert logFile != null && logFile.exists() : "Given log file must be not null and must exist.";
- // For non-XML files, you will use <code>PropertyConfigurator.configureAndWatch(String)</code>
+ // For non-XML files, you will use
+ // <code>PropertyConfigurator.configureAndWatch(String)</code>
DOMConfigurator.configureAndWatch(logFile.getPath());
LogLog.debug(String.format("Log configured from file '%s' (watching).", logFile
.getAbsolutePath()));
@@ -85,9 +87,11 @@ public class LogInitializer
/**
* Initializes logging system. Does nothing if already initialized.
* <p>
- * Logging configuration file is assumed to be in <code><working directory>/etc/log.xml</code>. If not
- * found we look for a classpath resource named <code>/etc/log.xml</code>.<br>
- * If nothing found in both locations <code>org.apache.log4j.BaseConfigurator.configure()</code> is used.
+ * Logging configuration file is assumed to be in
+ * <code><working directory>/etc/log.xml</code>. If not found we look for a classpath
+ * resource named <code>/etc/log.xml</code>.<br>
+ * If nothing found in both locations <code>org.apache.log4j.BaseConfigurator.configure()</code>
+ * is used.
* </p>
*/
public final static synchronized void init()
diff --git a/common/source/java/ch/systemsx/cisd/common/mail/MailClient.java b/common/source/java/ch/systemsx/cisd/common/mail/MailClient.java
index 28711540136db543b29893a61d9e76f6013a947f..fa5bfe3f0990554a29bcdb4f66411b9754a6ce2e 100644
--- a/common/source/java/ch/systemsx/cisd/common/mail/MailClient.java
+++ b/common/source/java/ch/systemsx/cisd/common/mail/MailClient.java
@@ -43,10 +43,11 @@ import ch.systemsx.cisd.common.utilities.FileUtilities;
/**
* A small mail client that simplifies the sending of emails using of <i>JavaMail API</i>.
* <p>
- * Just instantiate this class and use {@link #sendMessage(String, String, String[])} to send the email via SMTP.
+ * Just instantiate this class and use {@link #sendMessage(String, String, String[])} to send the
+ * email via SMTP.
* </p>
- * If the SMTP host starts with <code>file://</code> the mail is not send to a real SMTP server but it is stored in a
- * file in the directory specified by the relative path following this prefix.
+ * If the SMTP host starts with <code>file://</code> the mail is not send to a real SMTP server
+ * but it is stored in a file in the directory specified by the relative path following this prefix.
*
* @author Christian Ribeaud
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactory.java b/common/source/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactory.java
index c5c630ca9513858115c8940bb77ce29fe80495bd..1975a755690dcaa4247415b0cc340a81ccb64b54 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/AbstractParserObjectFactory.java
@@ -27,7 +27,8 @@ import ch.systemsx.cisd.common.converter.ConverterPool;
import ch.systemsx.cisd.common.utilities.ClassUtils;
/**
- * An abstract <code>IParserObjectFactory</code> which already implements and offers convenience methods.
+ * An abstract <code>IParserObjectFactory</code> which already implements and offers convenience
+ * methods.
*
* @author Christian Ribeaud
*/
@@ -98,9 +99,10 @@ public abstract class AbstractParserObjectFactory<E> implements IParserObjectFac
/**
* Checks given <code>IPropertyMapper</code>.
* <p>
- * This method tries to find properties declared in given <code>IPropertyMapper</code> that are not in labels in
- * annotated write methods (throws a <code>UnmatchedPropertiesException</code>) or mandatory fields that could
- * not be found in the same annotated write methods (throws a <code>MandatoryPropertyMissingException</code>).
+ * This method tries to find properties declared in given <code>IPropertyMapper</code> that
+ * are not in labels in annotated write methods (throws a
+ * <code>UnmatchedPropertiesException</code>) or mandatory fields that could not be found in
+ * the same annotated write methods (throws a <code>MandatoryPropertyMissingException</code>).
* </p>
*/
private final void checkPropertyMapper(final Class<E> clazz,
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/BeanAnalyzer.java b/common/source/java/ch/systemsx/cisd/common/parser/BeanAnalyzer.java
index 428e927173e2c1ec49cf20f6e606822721e8b789..3c3fafa51b2eff6633fc43bb6cf96d4d7ff851f7 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/BeanAnalyzer.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/BeanAnalyzer.java
@@ -32,7 +32,8 @@ import ch.systemsx.cisd.common.utilities.AnnotationUtils;
/**
* A <i>Bean</i> class analyzer.
* <p>
- * Its main role is to analyze a given <i>Bean</i> class and to list its mandatory resp. optional properties.
+ * Its main role is to analyze a given <i>Bean</i> class and to list its mandatory resp. optional
+ * properties.
* </p>
*
* @author Christian Ribeaud
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ColumnSizeMismatchException.java b/common/source/java/ch/systemsx/cisd/common/parser/ColumnSizeMismatchException.java
index 5f5c0dae934d37dd35bb8f7fac5225c1b90d8e1a..d94365fb8db92bb505f43b3e1c93c11583c51ea8 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ColumnSizeMismatchException.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ColumnSizeMismatchException.java
@@ -17,7 +17,8 @@
package ch.systemsx.cisd.common.parser;
/**
- * A <code>ParsingException</code> for column size mismatching between the header columns and line columns.
+ * A <code>ParsingException</code> for column size mismatching between the header columns and line
+ * columns.
*
* @author Christian Ribeaud
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultAliasPropertyMapper.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultAliasPropertyMapper.java
index 0b574df4742c537447073bce03d258f5a19b498f..714611aecf667f00016d48e794ccd7a91af01f7a 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultAliasPropertyMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultAliasPropertyMapper.java
@@ -26,7 +26,8 @@ import java.util.TreeSet;
*
* @author Christian Ribeaud
*/
-// TODO 2008-02-17, Tomasz Pylak: this class should be removed (we do not need or want field aliases)
+// TODO 2008-02-17, Tomasz Pylak: this class should be removed (we do not need or want field
+// aliases)
public class DefaultAliasPropertyMapper extends DefaultPropertyMapper implements
IAliasPropertyMapper
{
@@ -126,8 +127,8 @@ public class DefaultAliasPropertyMapper extends DefaultPropertyMapper implements
}
/**
- * Returns property names replaced with aliases that are really backed up by property names (alias can be specified
- * for a non-existing property name).
+ * Returns property names replaced with aliases that are really backed up by property names
+ * (alias can be specified for a non-existing property name).
*/
@Override
public final Set<String> getAllPropertyNames()
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java
index 9ec9d01d3a30ba5fea675dfa5082e31c7bd37378..db16bc4b767ae943de930085ea298a8c40f43267 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java
@@ -23,8 +23,8 @@ import org.apache.commons.lang.text.StrMatcher;
import org.apache.commons.lang.text.StrTokenizer;
/**
- * A default <code>ILineTokenizer</code> implementation that parses a line into an array of <code>String</code>
- * objects. This implementation uses {@link StrTokenizer} as internal worker.
+ * A default <code>ILineTokenizer</code> implementation that parses a line into an array of
+ * <code>String</code> objects. This implementation uses {@link StrTokenizer} as internal worker.
* <p>
* The default separator chars used here are <code>\t</code>. If you want to change that, use
* {@link #setProperty(PropertyKey, String)} with corresponding property key defined here.
@@ -82,8 +82,8 @@ public class DefaultLineTokenizer implements ILineTokenizer
/**
* Sets a property for this <code>TabReaderParser</code>.
* <p>
- * Does nothing if given <code>key</code> is <code>null</code> and resets <code>key</code> to default value if
- * given <code>value</code> is <code>null</code>.
+ * Does nothing if given <code>key</code> is <code>null</code> and resets <code>key</code>
+ * to default value if given <code>value</code> is <code>null</code>.
* </p>
*/
public final void setProperty(PropertyKey key, String value)
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
index 346e117cb2a1c7047ba02951880cbe1f91f1b142..c829d89ec96d07a5a85b087d5bc4206a6ee8ad4a 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
@@ -25,8 +25,8 @@ import ch.systemsx.cisd.common.parser.filter.ILineFilter;
/**
* A default {@link IParser} implementation.
* <p>
- * The object type returned by this implementation is generic. This implementation defines a <code>ILineFilter</code>
- * that filters out comment and empty lines.
+ * The object type returned by this implementation is generic. This implementation defines a
+ * <code>ILineFilter</code> that filters out comment and empty lines.
* </p>
*
* @author Christian Ribeaud
@@ -106,9 +106,12 @@ public class DefaultParser<E> implements IParser<E>
throw parsingException;
} catch (final RuntimeException runtimeException)
{
- // TODO 2008-02-18, Tomasz Pylak: we loose stack trace here. To be consulted with Christian.
- // I think that we should not catch RuntimeException at all - they are programming errors. We
- // could have catching such exceptions in one place at the very top level (like client
+ // TODO 2008-02-18, Tomasz Pylak: we loose stack trace here. To be consulted
+ // with Christian.
+ // I think that we should not catch RuntimeException at all - they are
+ // programming errors. We
+ // could have catching such exceptions in one place at the very top level
+ // (like client
// application).
throw new ParsingException(runtimeException, tokens, number);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
index a5fee8a621fefadd17b9c77c7fff967c0f1b674a..5701c069f1baa06444e006f5373b0b27f698cf4e 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
@@ -20,8 +20,8 @@ import ch.systemsx.cisd.common.parser.filter.ExcludeEmptyAndCommentLineFilter;
import ch.systemsx.cisd.common.parser.filter.ILineFilter;
/**
- * A <code>ILineFilter</code> implementation that extends {@link ExcludeEmptyAndCommentLineFilter} by excluding the
- * header line (if <code>> 1</code>) as well.
+ * A <code>ILineFilter</code> implementation that extends {@link ExcludeEmptyAndCommentLineFilter}
+ * by excluding the header line (if <code>> 1</code>) as well.
*
* @author Christian Ribeaud
*/
@@ -31,8 +31,8 @@ public final class HeaderLineFilter implements ILineFilter
/**
* The line number of the header line.
* <p>
- * If we set it bigger than <code>-1</code>, we assume that the header contains mapping information and should be
- * skipped by the parser.
+ * If we set it bigger than <code>-1</code>, we assume that the header contains mapping
+ * information and should be skipped by the parser.
* </p>
*/
private final int headerLineNumber;
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IAliasPropertyMapper.java b/common/source/java/ch/systemsx/cisd/common/parser/IAliasPropertyMapper.java
index 3604b5c8d2b74ef52b5f5a8d9ed55008e7969f36..da6437d86a39e7176c2d82db14355854019cf3a9 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IAliasPropertyMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IAliasPropertyMapper.java
@@ -19,20 +19,22 @@ package ch.systemsx.cisd.common.parser;
import java.util.Set;
/**
- * A <code>IPropertyMapper</code> extension that allows you to define an alias for a given property name.
+ * A <code>IPropertyMapper</code> extension that allows you to define an alias for a given
+ * property name.
*
* @author Christian Ribeaud
*/
-// TODO 2008-02-17, Tomasz Pylak: this class should be removed (we do not need or want field aliases)
+// TODO 2008-02-17, Tomasz Pylak: this class should be removed (we do not need or want field
+// aliases)
public interface IAliasPropertyMapper extends IPropertyMapper
{
/**
- * Sets an alias for given <var>propertyName</var>. Note that it does not check whether a property with the name
- * <var>propertyName</var> could be found because, for optional properties, this is not sure that we will find them
- * in the header.
+ * Sets an alias for given <var>propertyName</var>. Note that it does not check whether a
+ * property with the name <var>propertyName</var> could be found because, for optional
+ * properties, this is not sure that we will find them in the header.
* <p>
- * Only one alias for a given property name can be specified and it should not be possible to set the same alias for
- * two different properties.
+ * Only one alias for a given property name can be specified and it should not be possible to
+ * set the same alias for two different properties.
* </p>
* <p>
* Alias replaces the original property name in <code>Set</code> returned by
@@ -40,13 +42,15 @@ public interface IAliasPropertyMapper extends IPropertyMapper
* </p>
*
* @param aliasName can not be <code>null</code>. The is the property name found in the bean.
- * @param propertyName can not be <code>null</code>. This is the property name found in the parsed file.
+ * @param propertyName can not be <code>null</code>. This is the property name found in the
+ * parsed file.
*/
public void setAliasForPropertyName(final String aliasName, final String propertyName)
throws IllegalArgumentException;
/**
- * Returns the property name (in parsed file) that has been specified for given alias (<i>Bean</i> properties).
+ * Returns the property name (in parsed file) that has been specified for given alias (<i>Bean</i>
+ * properties).
*
* @throws IllegalArgumentException if given <var>alias</var> does not exist.
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java b/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java
index 71bc73639c7b73eb417ac48db458c0671a581bc9..de749399a5d78ebc82e73094b5be78cce48481b2 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.parser;
/**
- * A <code>ILineTokenizer</code> implementation is able to split a given <code>String</code> line in an array of
- * tokens.
+ * A <code>ILineTokenizer</code> implementation is able to split a given <code>String</code>
+ * line in an array of tokens.
*
* @author Christian Ribeaud
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java b/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
index 6c48a000a334b5cc20d34bf261a13268c0b68034..429b21fcef4ea52b694032aa4138698d028d52c6 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
@@ -22,8 +22,8 @@ import java.util.List;
import ch.systemsx.cisd.common.parser.filter.ILineFilter;
/**
- * <code>IReaderParser</code> is able to parse a given text lines and to return a list of objects of type
- * <code>E</code>.
+ * <code>IReaderParser</code> is able to parse a given text lines and to return a list of objects
+ * of type <code>E</code>.
*
* @author Christian Ribeaud
*/
@@ -31,7 +31,8 @@ public interface IParser<E>
{
/**
- * Parses the lines delivered by the specified iterator and creating elements of type <code>E</code>.
+ * Parses the lines delivered by the specified iterator and creating elements of type
+ * <code>E</code>.
*
* @param lineFilter A filter lines have to pass in order to be parsed.
* @param headerLength number of columns in the header
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactory.java b/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactory.java
index 83fdbaa52afe7e2b59df526d43c95ea7ca9376c4..93fb8bf241db2cf80246672cdb08ff294c897850 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactory.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IParserObjectFactory.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.common.parser;
/**
- * A <code>IParserObjectFactory</code> implementation knows how to deal with given line tokens and convert them into
- * an appropriate <code>Object</code>.
+ * A <code>IParserObjectFactory</code> implementation knows how to deal with given line tokens and
+ * convert them into an appropriate <code>Object</code>.
* <p>
* A <code>IParserObjectFactory</code> is typically registered in {@link IParser}.
* </p>
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapper.java b/common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapper.java
index a64cc458734bc1f9ffe4d5b0753c2f140839f582..aa17d274f36c98508b40fc409d474e76e3b74b91 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapper.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IPropertyMapper.java
@@ -19,7 +19,8 @@ package ch.systemsx.cisd.common.parser;
import java.util.Set;
/**
- * The job of <code>PropertyMapper</code> is to return mapping informations regarding a given property name.
+ * The job of <code>PropertyMapper</code> is to return mapping informations regarding a given
+ * property name.
*
* @author Christian Ribeaud
*/
@@ -37,7 +38,8 @@ public interface IPropertyMapper
/**
* Returns a set of all property names.
* <p>
- * Note that changes applied to returned <code>Set</code> are not reflected in the backed collection.
+ * Note that changes applied to returned <code>Set</code> are not reflected in the backed
+ * collection.
* </p>
*/
public Set<String> getAllPropertyNames();
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IPropertyModel.java b/common/source/java/ch/systemsx/cisd/common/parser/IPropertyModel.java
index ed72ed1859b316e9f9a1d52275f83ca633524018..7727a11ac58a6d232320e1999f547b09d995289a 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IPropertyModel.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IPropertyModel.java
@@ -17,7 +17,8 @@
package ch.systemsx.cisd.common.parser;
/**
- * This returns the mapping informations needed in {@link IParserObjectFactory} via the {@link IPropertyMapper}.
+ * This returns the mapping informations needed in {@link IParserObjectFactory} via the
+ * {@link IPropertyMapper}.
* <p>
* This model is specified by the parsed file.
* </p>
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IndexOutOfBoundsException.java b/common/source/java/ch/systemsx/cisd/common/parser/IndexOutOfBoundsException.java
index 74303463b3906992b470c9de12173336119b81d5..2655818cfb56fc9d8337ba5193ea575e8188e1ff 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IndexOutOfBoundsException.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IndexOutOfBoundsException.java
@@ -17,7 +17,8 @@
package ch.systemsx.cisd.common.parser;
/**
- * A <code>ParserException</code> extension which signalizes a lookup index outside of the currently available tokens.
+ * A <code>ParserException</code> extension which signalizes a lookup index outside of the
+ * currently available tokens.
*
* @author Christian Ribeaud
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java b/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
index c9c953c41678dc159fe91226a26163ff354beb9e..125e9b13f8453a211076ca2d61bfc292b439b63d 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
@@ -45,14 +45,16 @@ public final class ParserUtilities
}
/**
- * Returns the first <code>Line</code> that is not filtered out by given <code>ILineFilter</code>.
+ * Returns the first <code>Line</code> that is not filtered out by given
+ * <code>ILineFilter</code>.
* <p>
* You should not call this method if given <var>file</var> does not exist.
* </p>
*
- * @param lineFilter could be <code>null</code>. In this case, the {@link AlwaysAcceptLineFilter} implementation
- * will be used.
- * @param file the file that is going to be analyzed. Can not be <code>null</code> and must exists.
+ * @param lineFilter could be <code>null</code>. In this case, the
+ * {@link AlwaysAcceptLineFilter} implementation will be used.
+ * @param file the file that is going to be analyzed. Can not be <code>null</code> and must
+ * exists.
* @return <code>null</code> if all lines have been filtered out.
*/
public final static Line getFirstAcceptedLine(final File file, final ILineFilter lineFilter)
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
index a228461fe9ffd7dc05521b354f5a4680176a5c45..5f9d129b64ff82a3cb5f084b4c9a4a50790d83d8 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
@@ -37,8 +37,8 @@ import ch.systemsx.cisd.common.parser.filter.AlwaysAcceptLineFilter;
import ch.systemsx.cisd.common.parser.filter.ILineFilter;
/**
- * Convenient class to load a tab file and deliver a list of beans of type <code>T</code>. The following formats for
- * the column headers are recognized.
+ * Convenient class to load a tab file and deliver a list of beans of type <code>T</code>. The
+ * following formats for the column headers are recognized.
* <ol>
* <li>Column headers in first line:
*
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/UnmatchedPropertiesException.java b/common/source/java/ch/systemsx/cisd/common/parser/UnmatchedPropertiesException.java
index c0ff42beb03409ffc3b83085b20aae9b4ea22e63..61713b254a11320218d2c5382cade1a827ed95d4 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/UnmatchedPropertiesException.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/UnmatchedPropertiesException.java
@@ -44,8 +44,8 @@ public final class UnmatchedPropertiesException extends ParserException
private final Set<String> optionalNames;
/**
- * The property names of {@link #allPropertyNames} that can neither be found in {@link #mandatoryNames} nor in
- * {@link #optionalNames}.
+ * The property names of {@link #allPropertyNames} that can neither be found in
+ * {@link #mandatoryNames} nor in {@link #optionalNames}.
*/
private final Set<String> propertyNames;
diff --git a/common/source/java/ch/systemsx/cisd/common/process/CleanUpCallable.java b/common/source/java/ch/systemsx/cisd/common/process/CleanUpCallable.java
index 0879a73c306a19f0cf128b9a92f8c90cbf5dde48..e7165e06894d68c14030bef56fbda2f50926ae2a 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/CleanUpCallable.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/CleanUpCallable.java
@@ -17,9 +17,9 @@
package ch.systemsx.cisd.common.process;
/**
- * A class that implements the logic of cleaning up a resource even in case of an exception but re-throws an exception
- * of the clean up procedure only when the main procedure didn't throw one. <code>CleanUpRunner</code>s can be
- * stacked.
+ * A class that implements the logic of cleaning up a resource even in case of an exception but
+ * re-throws an exception of the clean up procedure only when the main procedure didn't throw one.
+ * <code>CleanUpRunner</code>s can be stacked.
*
* @author Bernd Rinn
*/
@@ -29,7 +29,8 @@ public final class CleanUpCallable
private final CleanUpRegistry registry = new CleanUpRegistry();
/**
- * Runs a {@link ICallableWithCleanUp} and ensures that all registered clean-ups are performed afterwards.
+ * Runs a {@link ICallableWithCleanUp} and ensures that all registered clean-ups are performed
+ * afterwards.
*/
public <T> T call(ICallableWithCleanUp<T> runnable)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/process/CleanUpRegistry.java b/common/source/java/ch/systemsx/cisd/common/process/CleanUpRegistry.java
index fb4b57e5ee2003bcf0657a42f4303ff976c2b90b..c83be2c54c919069457d0cb045d1cf9d8e635c1f 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/CleanUpRegistry.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/CleanUpRegistry.java
@@ -37,7 +37,8 @@ public final class CleanUpRegistry implements ICleanUpRegistry
/**
* Performs all clean-ups registered with {@link #registerCleanUp(Runnable)}.
*
- * @param suppressExceptions If <code>true</code>, all exceptions that happen during clean-up will be suppressed.
+ * @param suppressExceptions If <code>true</code>, all exceptions that happen during clean-up
+ * will be suppressed.
*/
public void cleanUp(boolean suppressExceptions)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/process/ICallableWithCleanUp.java b/common/source/java/ch/systemsx/cisd/common/process/ICallableWithCleanUp.java
index b60287510be528d395e4afce2afc927c017c84be..66ecca2929a490bbce3f0834491b31580165f285 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/ICallableWithCleanUp.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/ICallableWithCleanUp.java
@@ -17,8 +17,9 @@
package ch.systemsx.cisd.common.process;
/**
- * A role that calls a method which requires one or more clean-up steps that need to be run reliably at the end of the
- * method regardless of whether the method is finished normally or whether it exits with an exception.
+ * A role that calls a method which requires one or more clean-up steps that need to be run reliably
+ * at the end of the method regardless of whether the method is finished normally or whether it
+ * exits with an exception.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/process/ICleanUpRegistry.java b/common/source/java/ch/systemsx/cisd/common/process/ICleanUpRegistry.java
index d0a5b098c5626cecf37b5b58e914495b85f81a06..a8e55c708005e37a8d4aba7f85d55cafa35d6466 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/ICleanUpRegistry.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/ICleanUpRegistry.java
@@ -17,7 +17,8 @@
package ch.systemsx.cisd.common.process;
/**
- * A role that allows to register a clean-up method that is called regardless of whether an exception occurs or not.
+ * A role that allows to register a clean-up method that is called regardless of whether an
+ * exception occurs or not.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/process/IProcess.java b/common/source/java/ch/systemsx/cisd/common/process/IProcess.java
index 2e48694b0003ce7a8565bb646bcd4ba8f734e230..7d7bcb0cafcfbfc22c3d59b0a5736c17193cb30d 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/IProcess.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/IProcess.java
@@ -30,12 +30,14 @@ public interface IProcess extends Runnable
* Is typically called after {@link Runnable#run()} has performed.
* </p>
*
- * @return <code>true</code> if this <code>IProcess</code> succeeds, terminating so the whole running process.
+ * @return <code>true</code> if this <code>IProcess</code> succeeds, terminating so the
+ * whole running process.
*/
public boolean succeeded();
/**
- * The number of times we should try if this <code>IProcess</code> failed (including the first excecution).
+ * The number of times we should try if this <code>IProcess</code> failed (including the first
+ * excecution).
* <p>
* This is a static method: it only gets called once during the initialization process.
* </p>
diff --git a/common/source/java/ch/systemsx/cisd/common/process/ProcessExecutionHelper.java b/common/source/java/ch/systemsx/cisd/common/process/ProcessExecutionHelper.java
index 66366724fa2bec5e878719084e134357b5e27530..bf49ac7a7682489c5a12985c22af8b421eb3a1a8 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/ProcessExecutionHelper.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/ProcessExecutionHelper.java
@@ -49,14 +49,14 @@ public class ProcessExecutionHelper
public static final int EXIT_VALUE_OK = 0;
/**
- * The exit value returned by {@link Process#waitFor()} if the process was terminated by {@link Process#destroy()}
- * on a UNIX machine.
+ * The exit value returned by {@link Process#waitFor()} if the process was terminated by
+ * {@link Process#destroy()} on a UNIX machine.
*/
private static final int EXIT_VALUE_FOR_TERMINATION_UNIX = 143;
/**
- * The exit value returned by {@link Process#waitFor()} if the process was terminated by {@link Process#destroy()}
- * on a MS Windows machine.
+ * The exit value returned by {@link Process#waitFor()} if the process was terminated by
+ * {@link Process#destroy()} on a MS Windows machine.
*/
private static final int EXIT_VALUE_FOR_TERMINATION_WINDOWS = 1;
@@ -70,7 +70,8 @@ public class ProcessExecutionHelper
* @param commandLine The command line to run.
* @param operationLog The {@link Logger} to use for all message on the higher level.
* @param machineLog The {@link Logger} to use for all message on the lower (machine) level.
- * @return <code>true</code>, if the process did complete successfully, <code>false</code> otherwise.
+ * @return <code>true</code>, if the process did complete successfully, <code>false</code>
+ * otherwise.
*/
public static boolean runAndLog(List<String> commandLine, Logger operationLog, Logger machineLog)
{
@@ -94,11 +95,13 @@ public class ProcessExecutionHelper
* Runs an Operating System process, specified by <var>cmd</var>.
*
* @param cmd The command line to run.
- * @param millisToWaitForCompletion The time to wait for the process to complete in milli seconds. If the process is
- * not finished after that time, it will be terminated by a watch dog.
+ * @param millisToWaitForCompletion The time to wait for the process to complete in milli
+ * seconds. If the process is not finished after that time, it will be terminated by
+ * a watch dog.
* @param operationLog The {@link Logger} to use for all message on the higher level.
* @param machineLog The {@link Logger} to use for all message on the lower (machine) level.
- * @return <code>true</code>, if the process did complete successfully, <code>false</code> otherwise.
+ * @return <code>true</code>, if the process did complete successfully, <code>false</code>
+ * otherwise.
*/
public static boolean runAndLog(List<String> cmd, long millisToWaitForCompletion,
Logger operationLog, Logger machineLog)
@@ -111,8 +114,9 @@ public class ProcessExecutionHelper
* Runs an Operating System process, specified by <var>cmd</var>.
*
* @param cmd The command line to run.
- * @param millisToWaitForCompletion The time to wait for the process to complete in milli seconds. If the process is
- * not finished after that time, it will be terminated by a watch dog.
+ * @param millisToWaitForCompletion The time to wait for the process to complete in milli
+ * seconds. If the process is not finished after that time, it will be terminated by
+ * a watch dog.
* @param operationLog The {@link Logger} to use for all message on the higher level.
* @param machineLog The {@link Logger} to use for all message on the lower (machine) level.
* @return The process result.
@@ -125,8 +129,8 @@ public class ProcessExecutionHelper
}
/**
- * Returns <code>true</code> if the <var>exitValue</var> indicates that the process has been terminated on the
- * Operating System level.
+ * Returns <code>true</code> if the <var>exitValue</var> indicates that the process has been
+ * terminated on the Operating System level.
*/
public static boolean isProcessTerminated(final int exitValue)
{
@@ -140,8 +144,8 @@ public class ProcessExecutionHelper
}
/**
- * Returns the stdout (and stderr if {@link ProcessBuilder#redirectErrorStream(boolean)} has been called with
- * <code>true</code>).
+ * Returns the stdout (and stderr if {@link ProcessBuilder#redirectErrorStream(boolean)} has
+ * been called with <code>true</code>).
*/
public static List<String> readProcessOutputLines(Process processOrNull, Logger machineLog)
{
@@ -194,7 +198,8 @@ public class ProcessExecutionHelper
this.isInterruptedAfterTimeout = false;
}
- // this prevents interruption from watch-dog when we are outside of catch InterruptedException
+ // this prevents interruption from watch-dog when we are outside of catch
+ // InterruptedException
synchronized public void interruptionUnnecesary()
{
canInterrupt = false;
@@ -248,7 +253,8 @@ public class ProcessExecutionHelper
return createNotStartedResult(commandLine, ex);
}
process.waitFor();
- processStatus.interruptionUnnecesary(); // the process terminated and does not block anymore
+ processStatus.interruptionUnnecesary(); // the process terminated and does not block
+ // anymore
} catch (InterruptedException ex)
{
processStatus.interruptionUnnecesary();
@@ -272,7 +278,8 @@ public class ProcessExecutionHelper
{
operationLog.debug("Executing command: " + commandLine);
}
- // NOTE 2008-02-04, Tomasz Pylak: This operation can get blocked. I've observed it when ln was executed on NAS
+ // NOTE 2008-02-04, Tomasz Pylak: This operation can get blocked. I've observed it when ln
+ // was executed on NAS
// file system mounted locally.
final Process process = processBuilder.start();
return process;
@@ -306,7 +313,8 @@ public class ProcessExecutionHelper
private void logInterruption(final String commandLine, ProcessStatus terminationStatus,
InterruptedException ex)
{
- if (terminationStatus.isInterruptedAfterTimeout() == false) // have NOT been stopped by the watchDog
+ if (terminationStatus.isInterruptedAfterTimeout() == false) // have NOT been stopped by the
+ // watchDog
{
machineLog.error(String.format("Execution of %s interrupted", commandLine), ex);
} else
@@ -339,7 +347,8 @@ public class ProcessExecutionHelper
if (process != null)
{
process.destroy();
- sleep(millisToWaitForCompletion / 2); // allow the process to terminate normally
+ sleep(millisToWaitForCompletion / 2); // allow the process to
+ // terminate normally
}
synchronized (processStatus)
{
@@ -350,8 +359,10 @@ public class ProcessExecutionHelper
operationLog.info(String.format(
"Interrupting waiting for the process %s by the watchDog",
commandForLog));
- // stop waiting for the process. We want to prevent situations when the child process,
- // which is an external program, gets stuck during the start or cannot be destroyed. It
+ // stop waiting for the process. We want to prevent situations when
+ // the child process,
+ // which is an external program, gets stuck during the start or
+ // cannot be destroyed. It
// would cause the whole system to hang and we do not want that.
processThread.interrupt();
}
diff --git a/common/source/java/ch/systemsx/cisd/common/process/ProcessResult.java b/common/source/java/ch/systemsx/cisd/common/process/ProcessResult.java
index 8272c38bc209b3396339085c26a5b24540533fca..9e6f88ff41b7a42066eb3d4267b1c8807bd7702d 100644
--- a/common/source/java/ch/systemsx/cisd/common/process/ProcessResult.java
+++ b/common/source/java/ch/systemsx/cisd/common/process/ProcessResult.java
@@ -26,8 +26,8 @@ import org.apache.log4j.Logger;
/**
* Class that keeps around the result of running an Operating System process.
* <p>
- * Since the process output can only ever be read once from a process, it need to be kept around if it is needed more
- * than once. This is what this class is good for.
+ * Since the process output can only ever be read once from a process, it need to be kept around if
+ * it is needed more than once. This is what this class is good for.
*/
public final class ProcessResult
{
@@ -81,11 +81,12 @@ public final class ProcessResult
/**
* Calls the {@link Process#destroy()} method which explicitly closes some file handles.
* <p>
- * <i>Note that one must not call {#link {@link #getProcessOutput()} for the first time after this method has been
- * called.</i>
+ * <i>Note that one must not call {#link {@link #getProcessOutput()} for the first time after
+ * this method has been called.</i>
* <p>
- * Whether it is necessary to call this method depends on the JRE. For some JREs there occur {@link IOException}s
- * with code 24 ("Too many open files") when running processes with high frequency without calling this method.
+ * Whether it is necessary to call this method depends on the JRE. For some JREs there occur
+ * {@link IOException}s with code 24 ("Too many open files") when running processes with high
+ * frequency without calling this method.
*/
public void destroyProcess()
{
@@ -148,8 +149,8 @@ public final class ProcessResult
}
/**
- * Returns <code>true</code> if the process could not been terminated after the timeout and we stopped waiting for
- * it.
+ * Returns <code>true</code> if the process could not been terminated after the timeout and we
+ * stopped waiting for it.
*/
public boolean hasBlocked()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/test/InterfaceForRMIChecker.java b/common/source/java/ch/systemsx/cisd/common/test/InterfaceForRMIChecker.java
index 939a000fc2c290d38b41a968ce947550b6b27db7..b0c6445a063302937da718ae5419ccb029e92526 100644
--- a/common/source/java/ch/systemsx/cisd/common/test/InterfaceForRMIChecker.java
+++ b/common/source/java/ch/systemsx/cisd/common/test/InterfaceForRMIChecker.java
@@ -33,11 +33,11 @@ import java.util.Set;
public class InterfaceForRMIChecker
{
/**
- * Asserts that the specified interface is ready for RMI. That is, for all methods the parameter types and the
- * return type is {@link Serializable}.
+ * Asserts that the specified interface is ready for RMI. That is, for all methods the parameter
+ * types and the return type is {@link Serializable}.
*
- * @throws AssertionError if <code>interfaze</code> is not an interface or a parameter type or a return value is
- * not serializable.
+ * @throws AssertionError if <code>interfaze</code> is not an interface or a parameter type or
+ * a return value is not serializable.
*/
public static void assertInterfaceForRMI(Class<?> interfaze)
{
@@ -69,8 +69,8 @@ public class InterfaceForRMIChecker
/**
* Asserts that the specified class is serializable.
*
- * @throws AssertionError if <code>clazz</code> is not serializable or a non-transient non-static attribute isn't
- * serializable.
+ * @throws AssertionError if <code>clazz</code> is not serializable or a non-transient
+ * non-static attribute isn't serializable.
*/
public static void assertSerializable(Class<?> clazz)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/test/SerializabilityTest.java b/common/source/java/ch/systemsx/cisd/common/test/SerializabilityTest.java
index f0070e6db1fa18c5f334b49daff165161cd1c583..8a9eb8d30783d1324e03914ad6ece59e595665b9 100644
--- a/common/source/java/ch/systemsx/cisd/common/test/SerializabilityTest.java
+++ b/common/source/java/ch/systemsx/cisd/common/test/SerializabilityTest.java
@@ -23,9 +23,9 @@ import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
/**
- * Extend me in order to test the serializability of a class. Override my {@link #createInstance() createInstance}
- * methods to provide me with an object to test against. The object's class must implement
- * {@link java.io.Serializable Serializable}.
+ * Extend me in order to test the serializability of a class. Override my
+ * {@link #createInstance() createInstance} methods to provide me with an object to test against.
+ * The object's class must implement {@link java.io.Serializable Serializable}.
*
* @see java.io.Serializable
* @author Christian Ribeaud
@@ -56,7 +56,8 @@ public abstract class SerializabilityTest
}
/**
- * Verifies that an instance of the class under test can be serialized and deserialized without error.
+ * Verifies that an instance of the class under test can be serialized and deserialized without
+ * error.
*/
@Test
public final void testSerializability() throws Exception
@@ -67,9 +68,10 @@ public abstract class SerializabilityTest
}
/**
- * Template method--override this to perform checks on the deserialized form of the object serialized in
- * {@link #testSerializability}. If not overridden, this asserts that the pre-serialization and deserialized forms
- * of the object compare equal via {@link java.lang.Object#equals(Object) equals}.
+ * Template method--override this to perform checks on the deserialized form of the object
+ * serialized in {@link #testSerializability}. If not overridden, this asserts that the
+ * pre-serialization and deserialized forms of the object compare equal via
+ * {@link java.lang.Object#equals(Object) equals}.
*
* @param expected the pre-serialization form of the object
* @param actual the deserialized form of the object
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/AbstractHashable.java b/common/source/java/ch/systemsx/cisd/common/utilities/AbstractHashable.java
index 1170058be003411e258f362f16be1d1615311cb4..db358a922cfaeffb8ae30f36b0d5c844434853d3 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/AbstractHashable.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/AbstractHashable.java
@@ -24,11 +24,12 @@ import org.apache.commons.lang.builder.HashCodeBuilder;
import org.apache.commons.lang.builder.ToStringBuilder;
/**
- * If you want your class to behave correctly when used in {@link Map}s or {@link Set}s, you can do this by:
+ * If you want your class to behave correctly when used in {@link Map}s or {@link Set}s, you can
+ * do this by:
* <ol>
* <li>Extending this class</li>
- * <li>Ensuring that all used field types implement <code>equals()</code> and <code>hashCode()</code> (e.g. by
- * extending this class)</li>
+ * <li>Ensuring that all used field types implement <code>equals()</code> and
+ * <code>hashCode()</code> (e.g. by extending this class)</li>
* </ol>
*
* @author Tomasz Pylak on Oct 26, 2007
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/AnnotationUtils.java b/common/source/java/ch/systemsx/cisd/common/utilities/AnnotationUtils.java
index 43bb0c8766cf5e43fddf39299feb1d8c36ca11b0..4b4609402c4536ff102d9535ea6e0391d619b808 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/AnnotationUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/AnnotationUtils.java
@@ -36,7 +36,8 @@ public final class AnnotationUtils
}
/**
- * For given <code>Class</code> returns a list of methods that are annotated with given <var>annotationClass</var>.
+ * For given <code>Class</code> returns a list of methods that are annotated with given
+ * <var>annotationClass</var>.
*/
public final static List<Method> getAnnotatedMethodList(final Class<?> clazz,
final Class<? extends Annotation> annotationClass)
@@ -45,7 +46,8 @@ public final class AnnotationUtils
}
/**
- * For given <code>Class</code> returns a list of methods that are annotated with given <var>annotationClass</var>.
+ * For given <code>Class</code> returns a list of methods that are annotated with given
+ * <var>annotationClass</var>.
*
* @param methods if <code>null</code>, then a new <code>List</code> is created.
*/
@@ -75,7 +77,8 @@ public final class AnnotationUtils
}
/**
- * For given <code>Class</code> returns a list of fields that are annotated with given <var>annotationClass</var>.
+ * For given <code>Class</code> returns a list of fields that are annotated with given
+ * <var>annotationClass</var>.
*/
public final static List<Field> getAnnotatedFieldList(final Class<?> clazz,
final Class<? extends Annotation> annotationClass)
@@ -84,7 +87,8 @@ public final class AnnotationUtils
}
/**
- * For given <code>Class</code> returns a list of fields that are annotated with given <var>annotationClass</var>.
+ * For given <code>Class</code> returns a list of fields that are annotated with given
+ * <var>annotationClass</var>.
*
* @param fields if <code>null</code>, then a new <code>List</code> is created.
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/BeanUtils.java b/common/source/java/ch/systemsx/cisd/common/utilities/BeanUtils.java
index 27888099026406620ab12083cf0673fd705657ad..9b4a67513ee1443e4711f77089a77abeeb001b54 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/BeanUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/BeanUtils.java
@@ -126,17 +126,19 @@ public final class BeanUtils
}
/**
- * Marker interface for converter classes. The real method are determined via reflection. A converter needs to match
- * both the source and the destination bean. If the destination bean has a setter <code>setFoo(FooClass foo)</code>
- * and the converter has a method <code>FooClass convertToFoo(SourceBeanClass sourceBean)</code>, then this will
- * be called instead of any getter of the <var>sourceBean</var>.
+ * Marker interface for converter classes. The real method are determined via reflection. A
+ * converter needs to match both the source and the destination bean. If the destination bean
+ * has a setter <code>setFoo(FooClass foo)</code> and the converter has a method
+ * <code>FooClass convertToFoo(SourceBeanClass sourceBean)</code>, then this will be called
+ * instead of any getter of the <var>sourceBean</var>.
* <p>
* Note:
* <ul>
- * <li>The declared <code>SourceBeanClass</code> in the converter method can also be a superclass of
- * <code>sourceBean</code>or an interface implemented by <code>sourceBean</code>
- * <li>If there is a matching method <code>convertToFoo()</code>, it needs to have an appropriate return type or
- * else an {@link IllegalArgumentException} will be thrown.
+ * <li>The declared <code>SourceBeanClass</code> in the converter method can also be a
+ * superclass of <code>sourceBean</code>or an interface implemented by
+ * <code>sourceBean</code>
+ * <li>If there is a matching method <code>convertToFoo()</code>, it needs to have an
+ * appropriate return type or else an {@link IllegalArgumentException} will be thrown.
* </ul>
*/
public interface Converter
@@ -160,10 +162,10 @@ public final class BeanUtils
* Creates a new list of Beans of type <var>clazz</var>.
*
* @param clazz element type of the new list.
- * @param source The iterable to fill the new bean list from. Can be <code>null</code>, in which case the method
- * returns <code>null</code>.
- * @return The new list filled from <var>sourceList</var> or <code>null</code>, if <var>sourceList</var> is
- * <code>null</code>.
+ * @param source The iterable to fill the new bean list from. Can be <code>null</code>, in
+ * which case the method returns <code>null</code>.
+ * @return The new list filled from <var>sourceList</var> or <code>null</code>, if
+ * <var>sourceList</var> is <code>null</code>.
*/
public final static <T, S> List<T> createBeanList(final Class<T> clazz, final Iterable<S> source)
{
@@ -171,8 +173,8 @@ public final class BeanUtils
}
/**
- * Creates a new array of Beans of type <var>clazz</var>. See <code>createBeanList()</code> for parameter
- * specification.
+ * Creates a new array of Beans of type <var>clazz</var>. See <code>createBeanList()</code>
+ * for parameter specification.
*/
public final static <T, S> T[] createBeanArray(final Class<T> clazz, final Collection<S> source)
{
@@ -180,8 +182,8 @@ public final class BeanUtils
}
/**
- * Creates a new array of Beans of type <var>clazz</var>. See <code>createBeanList()</code> for parameter
- * specification.
+ * Creates a new array of Beans of type <var>clazz</var>. See <code>createBeanList()</code>
+ * for parameter specification.
*/
public final static <T, S> T[] createBeanArray(final Class<T> clazz,
final Collection<S> source, final Converter converter)
@@ -204,8 +206,8 @@ public final class BeanUtils
}
/**
- * Creates a new array of Beans of type <var>clazz</var>. See <code>createBeanList()</code> for parameter
- * specification.
+ * Creates a new array of Beans of type <var>clazz</var>. See <code>createBeanList()</code>
+ * for parameter specification.
*/
public static <T, S> T[] createBeanArray(final Class<T> clazz, final Iterable<S> source,
final Converter converter)
@@ -219,12 +221,13 @@ public final class BeanUtils
* Creates a new list of Beans of type <var>clazz</var>.
*
* @param clazz element type of the new list.
- * @param source The iterable to fill the new bean list from. Can be <code>null</code>, in which case the method
- * returns <code>null</code>.
- * @param converter The {@link Converter} to use to perform non-standard conversions when filling the bean. Can be
- * <code>null</code>, in which case only standard conversions are allowed.
- * @return The new list filled from <var>sourceList</var> or <code>null</code>, if <var>sourceList</var> is
- * <code>null</code>.
+ * @param source The iterable to fill the new bean list from. Can be <code>null</code>, in
+ * which case the method returns <code>null</code>.
+ * @param converter The {@link Converter} to use to perform non-standard conversions when
+ * filling the bean. Can be <code>null</code>, in which case only standard
+ * conversions are allowed.
+ * @return The new list filled from <var>sourceList</var> or <code>null</code>, if
+ * <var>sourceList</var> is <code>null</code>.
*/
public final static <T, S> List<T> createBeanList(final Class<T> clazz,
final Iterable<S> source, final Converter converter)
@@ -245,7 +248,8 @@ public final class BeanUtils
}
/**
- * Convenience method for {@link #createBean(Class, Object, ch.systemsx.cisd.common.utilities.BeanUtils.Converter)}
+ * Convenience method for
+ * {@link #createBean(Class, Object, ch.systemsx.cisd.common.utilities.BeanUtils.Converter)}
* where <var>converter</var> is <code>NULL_CONVERTER</code>.
*/
public static <T> T fillBean(final Class<T> beanClass, final T beanInstance,
@@ -255,7 +259,8 @@ public final class BeanUtils
}
/**
- * Convenience method for {@link #createBean(Class, Object, ch.systemsx.cisd.common.utilities.BeanUtils.Converter)}
+ * Convenience method for
+ * {@link #createBean(Class, Object, ch.systemsx.cisd.common.utilities.BeanUtils.Converter)}
* where <var>converter</var> is <code>NULL_CONVERTER</code>.
*/
public static <T> T createBean(final Class<T> beanClass, final Object sourceBean)
@@ -264,14 +269,17 @@ public final class BeanUtils
}
/**
- * Fills a new bean <var>beanInstance</var> of type <var>beanClass</var> with values from <var>sourceBean</var>.
+ * Fills a new bean <var>beanInstance</var> of type <var>beanClass</var> with values from
+ * <var>sourceBean</var>.
*
* @param beanClass The class to create a new instance from.
- * @param beanInstance Instance of the bean to be filled. If <code>null</code> a new instance will be created.
- * @param sourceBean The bean to get the values from. Can be <code>null</code>, in which case the method returns
- * <code>null</code>.
- * @param converter The {@link Converter} to use to perform non-standard conversions when filling the bean. Can be
- * <code>null</code>, in which case only standard conversions are allowed.
+ * @param beanInstance Instance of the bean to be filled. If <code>null</code> a new instance
+ * will be created.
+ * @param sourceBean The bean to get the values from. Can be <code>null</code>, in which case
+ * the method returns <code>null</code>.
+ * @param converter The {@link Converter} to use to perform non-standard conversions when
+ * filling the bean. Can be <code>null</code>, in which case only standard
+ * conversions are allowed.
* @return The new bean or <code>null</code> if <var>sourceBean</var> is <code>null</code>.
*/
public static <T> T fillBean(final Class<T> beanClass, final T beanInstance,
@@ -286,13 +294,15 @@ public final class BeanUtils
}
/**
- * Creates a new bean of type <var>beanClass</var> and fills it with values from <var>sourceBean</var>.
+ * Creates a new bean of type <var>beanClass</var> and fills it with values from
+ * <var>sourceBean</var>.
*
* @param beanClass The class to create a new instance from.
- * @param sourceBean The bean to get the values from. Can be <code>null</code>, in which case the method returns
- * <code>null</code>.
- * @param converter The {@link Converter} to use to perform non-standard conversions when filling the bean. Can be
- * <code>null</code>, in which case only standard conversions are allowed.
+ * @param sourceBean The bean to get the values from. Can be <code>null</code>, in which case
+ * the method returns <code>null</code>.
+ * @param converter The {@link Converter} to use to perform non-standard conversions when
+ * filling the bean. Can be <code>null</code>, in which case only standard
+ * conversions are allowed.
* @return The new bean or <code>null</code> if <var>sourceBean</var> is <code>null</code>.
*/
public static <T> T createBean(final Class<T> beanClass, final Object sourceBean,
@@ -310,13 +320,15 @@ public final class BeanUtils
* Fills the specified bean instance with values from <var>sourceBean</var>.
*
* @param beanClass The class to create a new instance from.
- * @param beanInstance Instance of the bean to be filled. If <code>null</code> a new instance will be created.
- * @param sourceBean The bean to get the values from. Can be <code>null</code>, in which case the method returns
- * <code>null</code>.
- * @param setterAnnotations The annotations attached to the setter that can be used to determine how the result
- * should be created.
- * @param converter The {@link Converter} to use to perform non-standard conversions when filling the bean. Can be
- * <code>null</code>, in which case only standard conversions are allowed.
+ * @param beanInstance Instance of the bean to be filled. If <code>null</code> a new instance
+ * will be created.
+ * @param sourceBean The bean to get the values from. Can be <code>null</code>, in which case
+ * the method returns <code>null</code>.
+ * @param setterAnnotations The annotations attached to the setter that can be used to determine
+ * how the result should be created.
+ * @param converter The {@link Converter} to use to perform non-standard conversions when
+ * filling the bean. Can be <code>null</code>, in which case only standard
+ * conversions are allowed.
* @return The new bean or <code>null</code> if <var>sourceBean</var> is <code>null</code>.
*/
@SuppressWarnings("unchecked")
@@ -457,7 +469,8 @@ public final class BeanUtils
}
@SuppressWarnings("unchecked")
- // No way to avoid the warning since the compiler doesn't accept something like ArrayList<String>.class
+ // No way to avoid the warning since the compiler doesn't accept something like
+ // ArrayList<String>.class
private final static <T> T createCollection(final int size,
final AnnotationMap setterAnnotations) throws InstantiationException,
IllegalAccessException, SecurityException, NoSuchMethodException,
@@ -482,8 +495,10 @@ public final class BeanUtils
throws InstantiationException, IllegalAccessException, IllegalArgumentException,
InvocationTargetException
{
- // This conversion _can_ go wrong if the concrete collection class doesn't implement the right sub-interface of
- // collection, e.g. when using a HashSet as concrete collection class where a List is required.
+ // This conversion _can_ go wrong if the concrete collection class doesn't implement the
+ // right sub-interface of
+ // collection, e.g. when using a HashSet as concrete collection class where a List is
+ // required.
return (T) constructorWithSize.newInstance(new Object[]
{ size });
}
@@ -492,8 +507,10 @@ public final class BeanUtils
private final static <T> T constructCollection(final Class<? extends Collection> collectionClazz)
throws InstantiationException, IllegalAccessException
{
- // This conversion _can_ go wrong if the concrete collection class doesn't implement the right sub-interface of
- // collection, e.g. when using a HashSet as concrete collection class where a List is required.
+ // This conversion _can_ go wrong if the concrete collection class doesn't implement the
+ // right sub-interface of
+ // collection, e.g. when using a HashSet as concrete collection class where a List is
+ // required.
return (T) collectionClazz.newInstance();
}
@@ -704,8 +721,10 @@ public final class BeanUtils
* <p>
* The logic of this method is the following:
* <ol>
- * <li>If a converter could be found for transferring the value from source bean to destination bean, then use it</li>
- * <li>If the value is of primitive type or one of the immutable types specified, then use it tel quel</li>
+ * <li>If a converter could be found for transferring the value from source bean to destination
+ * bean, then use it</li>
+ * <li>If the value is of primitive type or one of the immutable types specified, then use it
+ * tel quel</li>
* <li>If the value is a complexe type, then it should be filled using
* {@link #fillBean(Class, Object, Object, ch.systemsx.cisd.common.utilities.BeanUtils.AnnotationMap, ch.systemsx.cisd.common.utilities.BeanUtils.Converter)}
* before using it</li>
@@ -737,7 +756,8 @@ public final class BeanUtils
return (T) oldBean;
} else
{
- // If a non-null value could be found in the destination bean for <code>destinationOldBean</code>,
+ // If a non-null value could be found in the destination bean for
+ // <code>destinationOldBean</code>,
// then take it.
final T destinationOldBean = (T) getOldBean(setter, destinationGetters, destination);
return fillBean(parameterType, destinationOldBean, oldBean, annotationMap, converter);
@@ -745,8 +765,9 @@ public final class BeanUtils
}
/**
- * For given <var>setter</var> method, we try to get the corresponding <i>getter</i>. If this step succeeds, we
- * invoke the found <i>getter</i> on given <var>bean</var> and returns the value.
+ * For given <var>setter</var> method, we try to get the corresponding <i>getter</i>. If this
+ * step succeeds, we invoke the found <i>getter</i> on given <var>bean</var> and returns the
+ * value.
*/
private final static Object getOldBean(final Method setter, final Map<String, Method> getters,
final Object bean) throws IllegalArgumentException, IllegalAccessException,
@@ -862,10 +883,11 @@ public final class BeanUtils
}
/**
- * Returns a map of <code>PropertyDescriptor</code>s keyed by {@link PropertyDescriptor#getName()}.
+ * Returns a map of <code>PropertyDescriptor</code>s keyed by
+ * {@link PropertyDescriptor#getName()}.
* <p>
- * It introspects given class and remove each (bean) property that does not have a write method (like
- * <code>class</code>).
+ * It introspects given class and remove each (bean) property that does not have a write method
+ * (like <code>class</code>).
* </p>
*/
public final static Map<String, PropertyDescriptor> getPropertyDescriptors(final Class<?> clazz)
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/BuildAndEnvironmentInfo.java b/common/source/java/ch/systemsx/cisd/common/utilities/BuildAndEnvironmentInfo.java
index 5c41a1f25eb57778bb602b0f3331948364c3564e..7a72ac394d84fc7e2717c6cf39deb47c21fe5323 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/BuildAndEnvironmentInfo.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/BuildAndEnvironmentInfo.java
@@ -137,9 +137,10 @@ public final class BuildAndEnvironmentInfo
}
/**
- * @return <code>true</code> if the versioned entities of the working copy have been clean when this build has
- * been made, in other words, whether the revision given by {@link #getRevision()} does really identify the
- * source that is build has been produced from.
+ * @return <code>true</code> if the versioned entities of the working copy have been clean
+ * when this build has been made, in other words, whether the revision given by
+ * {@link #getRevision()} does really identify the source that is build has been
+ * produced from.
*/
public final boolean isCleanSources()
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ClassUtils.java b/common/source/java/ch/systemsx/cisd/common/utilities/ClassUtils.java
index a0d3b5c5c5d135c959f30203e2212ce52fda6aee..1f395a835aa8d7f52b76f654d74eed2fa6acd5c7 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ClassUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ClassUtils.java
@@ -85,14 +85,14 @@ public final class ClassUtils
/**
* Returns the <code>Method</code> on the stack of <var>level</var>.
* <p>
- * <code>level=0</code> is this method itself, <code>level=1</code> is the method that called it and so forth.
- * This method internally uses {@link Class#getMethods()} to retrieve the <code>Method</code> (meaning that
- * <code>private</code> methods will not be found).
+ * <code>level=0</code> is this method itself, <code>level=1</code> is the method that
+ * called it and so forth. This method internally uses {@link Class#getMethods()} to retrieve
+ * the <code>Method</code> (meaning that <code>private</code> methods will not be found).
* </p>
* <p>
- * IMPORTANT NOTE: You should carefully use this method in a class having more than one method with the same name.
- * The internal idea used here (<code>new Throwable().getStackTrace()</code>) only returns a method name and
- * does not make any other consideration.
+ * IMPORTANT NOTE: You should carefully use this method in a class having more than one method
+ * with the same name. The internal idea used here (<code>new Throwable().getStackTrace()</code>)
+ * only returns a method name and does not make any other consideration.
* </p>
*
* @see StackTraceElement#getMethodName()
@@ -130,9 +130,10 @@ public final class ClassUtils
*
* @param superClazz Super class <code>className</code> has to be implemented or extended.
* @param className Fully-qualified class name.
- * @param argumentsOrNull Optional constructor arguments. If <code>(Object[]) null</code> then the empty
- * constructor will be used. Note that <code>(Object) null</code> is not interpreted as
- * <code>null</code> arguments but rather as <code>new Object[]{null}</code>.
+ * @param argumentsOrNull Optional constructor arguments. If <code>(Object[]) null</code> then
+ * the empty constructor will be used. Note that <code>(Object) null</code> is not
+ * interpreted as <code>null</code> arguments but rather as
+ * <code>new Object[]{null}</code>.
* @return an instance of type <code>interface</code>.
*/
public static <T> T create(final Class<T> superClazz, final String className,
@@ -280,10 +281,12 @@ public final class ClassUtils
}
/**
- * Sets declared field named <var>fieldName</var> of given <var>object</var> to given new value <var>newValue</var>.
+ * Sets declared field named <var>fieldName</var> of given <var>object</var> to given new
+ * value <var>newValue</var>.
* <p>
- * This is useful when you want to set a <code>private</code> field on which you do not have access. Note that
- * this method should only be used in very special cases. You should consider it as a hack.
+ * This is useful when you want to set a <code>private</code> field on which you do not have
+ * access. Note that this method should only be used in very special cases. You should consider
+ * it as a hack.
* </p>
*
* @return a <code>true</code> if <code>fieldName</code> has been modified.
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java b/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java
index bf43a88d806a5e53e271db7d888c1a3f04377ef5..b23d48dc31d9c1907cad1b3b198dd9260c3ff382 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTask.java
@@ -31,12 +31,13 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.logging.LogLevel;
/**
- * A {@link TimerTask} that scans a source directory for entries that are accepted by some {@link FileFilter} and
- * handles the accepted entries by some {@link IPathHandler}. It maintains a list of faulty paths that failed to be
- * handled OK in the past. Clearing the list will make the class to retry handling the paths.
+ * A {@link TimerTask} that scans a source directory for entries that are accepted by some
+ * {@link FileFilter} and handles the accepted entries by some {@link IPathHandler}. It maintains a
+ * list of faulty paths that failed to be handled OK in the past. Clearing the list will make the
+ * class to retry handling the paths.
* <p>
- * The class should be constructed in the start-up phase and as part of the system's self-test in order to reveal
- * problems with incorrect paths timely.
+ * The class should be constructed in the start-up phase and as part of the system's self-test in
+ * order to reveal problems with incorrect paths timely.
*
* @author Bernd Rinn
*/
@@ -61,9 +62,9 @@ public final class DirectoryScanningTimerTask extends TimerTask
boolean exists(StoreItem item);
/**
- * returned description should give the user the idea about file location. You should not use the result for
- * something else than printing it for user. It should not be especially assumed that the result is the path
- * which could be used in java.io.File constructor.
+ * returned description should give the user the idea about file location. You should not
+ * use the result for something else than printing it for user. It should not be especially
+ * assumed that the result is the path which could be used in java.io.File constructor.
*/
String getLocationDescription(StoreItem item);
}
@@ -72,7 +73,10 @@ public final class DirectoryScanningTimerTask extends TimerTask
private final IScannedStore sourceDirectory;
- /** The number of consecutive errors of reading a directory that need to occur before the event is logged. */
+ /**
+ * The number of consecutive errors of reading a directory that need to occur before the event
+ * is logged.
+ */
private final int ignoredErrorCount;
private int errorCountReadingDirectory;
@@ -101,9 +105,9 @@ public final class DirectoryScanningTimerTask extends TimerTask
* @param sourceDirectory The directory to scan for entries.
* @param filter The file filter that picks the entries to handle.
* @param handler The handler that is used for treating the matching paths.
- * @param ignoredErrorCount The number of consecutive errors of reading the directory that need to occur before the
- * next error is logged (can be used to suppress error when the directory is on a remote share and the
- * server is flaky sometimes)
+ * @param ignoredErrorCount The number of consecutive errors of reading the directory that need
+ * to occur before the next error is logged (can be used to suppress error when the
+ * directory is on a remote share and the server is flaky sometimes)
*/
public DirectoryScanningTimerTask(File sourceDirectory, FileFilter filter,
IPathHandler handler, int ignoredErrorCount)
@@ -118,9 +122,9 @@ public final class DirectoryScanningTimerTask extends TimerTask
* @param scannedStore The store which is scan for entries.
* @param faultyPathDirectory The directory in which file with faulty paths is should be stored.
* @param handler The handler that is used for treating the matching paths.
- * @param ignoredErrorCount The number of consecutive errors of reading the directory that need to occur before the
- * next error is logged (can be used to suppress error when the directory is on a remote share and the
- * server is flaky sometimes)
+ * @param ignoredErrorCount The number of consecutive errors of reading the directory that need
+ * to occur before the next error is logged (can be used to suppress error when the
+ * directory is on a remote share and the server is flaky sometimes)
*/
public DirectoryScanningTimerTask(IScannedStore scannedStore, File faultyPathDirectory,
IStoreHandler handler, int ignoredErrorCount)
@@ -226,7 +230,8 @@ public final class DirectoryScanningTimerTask extends TimerTask
try
{
handle(path);
- } catch (Exception ex) // do not stop when processing of one file has failed, continue with other files
+ } catch (Exception ex) // do not stop when processing of one file has failed,
+ // continue with other files
{
printNotification(ex);
}
@@ -258,7 +263,8 @@ public final class DirectoryScanningTimerTask extends TimerTask
{
if (faultyPathsFile.exists())
{
- if (faultyPathsFile.lastModified() > faultyPathsLastChanged) // Handles manual manipulation.
+ if (faultyPathsFile.lastModified() > faultyPathsLastChanged) // Handles manual
+ // manipulation.
{
faultyPaths.clear();
CollectionIO.readCollection(faultyPathsFile, faultyPaths);
@@ -279,7 +285,9 @@ public final class DirectoryScanningTimerTask extends TimerTask
private StoreItem[] listFiles()
{
- final boolean logNotifyError = (errorCountReadingDirectory == ignoredErrorCount); // Avoid mailbox flooding.
+ final boolean logNotifyError = (errorCountReadingDirectory == ignoredErrorCount); // Avoid
+ // mailbox
+ // flooding.
final boolean logOperationError = (errorCountReadingDirectory < ignoredErrorCount);
final ISimpleLogger errorLogger =
logNotifyError ? createSimpleErrorLogger(LogCategory.NOTIFY)
@@ -333,7 +341,8 @@ public final class DirectoryScanningTimerTask extends TimerTask
handler.handle(item);
} finally
{
- // If the item still exists, we assume that it has not been handled. So it should be added to the faulty
+ // If the item still exists, we assume that it has not been handled. So it should be
+ // added to the faulty
// paths.
if (sourceDirectory.exists(item))
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ExceptionUtils.java b/common/source/java/ch/systemsx/cisd/common/utilities/ExceptionUtils.java
index f281a2eee110cefc5567661356b6962e23531914..41239df9755c54eed39a88b6152b5f31a68500c3 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ExceptionUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ExceptionUtils.java
@@ -38,8 +38,9 @@ public final class ExceptionUtils
}
/**
- * Creates a new {@link MasqueradingException} from given <var>exception</var> only if it is needed ({@link #isCandidateForMasquerading(Exception)}
- * returns <code>true</code>). Otherwise returns given <var>exception</var>.
+ * Creates a new {@link MasqueradingException} from given <var>exception</var> only if it is
+ * needed ({@link #isCandidateForMasquerading(Exception)} returns <code>true</code>).
+ * Otherwise returns given <var>exception</var>.
*/
private final static Exception createMasqueradingException(final Exception exception)
{
@@ -95,8 +96,8 @@ public final class ExceptionUtils
}
/**
- * Analyzes given <var>exception</var> and makes it independent to packages outside the
- * ones specified in an internal list, <code>ACCEPTED_PACKAGE_NAME_DEPENDENCIES</code>.
+ * Analyzes given <var>exception</var> and makes it independent to packages outside the ones
+ * specified in an internal list, <code>ACCEPTED_PACKAGE_NAME_DEPENDENCIES</code>.
*/
public final static Exception createMasqueradingExceptionIfNeeded(final Exception exception)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/FileComparator.java b/common/source/java/ch/systemsx/cisd/common/utilities/FileComparator.java
index fdf32d9078082ba8008951a0dba8c37fd5773ff7..a350454786f32e7e0896f16955b58120902570a2 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/FileComparator.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/FileComparator.java
@@ -52,8 +52,8 @@ public final class FileComparator
};
/**
- * A {@link File} <code>Comparator</code> implementation that considers value returned by {@link File#getName()}
- * to sort the files.
+ * A {@link File} <code>Comparator</code> implementation that considers value returned by
+ * {@link File#getName()} to sort the files.
*
* @author Christian Ribeaud
*/
@@ -71,8 +71,8 @@ public final class FileComparator
};
/**
- * A {@link File} <code>Comparator</code> implementation that sorts by type (file or directory): first the files
- * are listed then come the directories.
+ * A {@link File} <code>Comparator</code> implementation that sorts by type (file or
+ * directory): first the files are listed then come the directories.
*
* @author Christian Ribeaud
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcher.java b/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcher.java
index 2aa0ba20dfc3a75449dbabbcf458753515c44d03..4ce45d1e9a756665b4a7cb858721d1c82e14327c 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcher.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcher.java
@@ -136,8 +136,8 @@ public abstract class FileWatcher extends TimerTask
/**
* Whether the file state has changed.
* <p>
- * If the file state has changed, each implementation should save the new state before returning
- * <code>true</code>.
+ * If the file state has changed, each implementation should save the new state before
+ * returning <code>true</code>.
* </p>
*/
public boolean stateChanged(File fileToWatch);
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcherSynchronizer.java b/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcherSynchronizer.java
index 25b45c7c7bd809d2c0f99dbf59efc8d4e4c8574b..5c62545e536393f4e5dd239a2a4d589878c1c10c 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcherSynchronizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/FileWatcherSynchronizer.java
@@ -33,12 +33,13 @@ import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
/**
- * Kind of <code>FileWatcher</code> extension that allow registration of multiple <code>ChangeListener</code> for
- * one file watched.
+ * Kind of <code>FileWatcher</code> extension that allow registration of multiple
+ * <code>ChangeListener</code> for one file watched.
* <p>
- * You can use this class as <i>singleton</i> calling {@link #getInstance()} or you may instance it with a constructor.<br />
- * Note that access to this class is <i>synchronized</i> and that this class internally uses a {@link WeakHashMap} to
- * store the registered <code>ChangeListener</code>s.
+ * You can use this class as <i>singleton</i> calling {@link #getInstance()} or you may instance it
+ * with a constructor.<br />
+ * Note that access to this class is <i>synchronized</i> and that this class internally uses a
+ * {@link WeakHashMap} to store the registered <code>ChangeListener</code>s.
* </p>
*
* @author Christian Ribeaud
@@ -156,8 +157,8 @@ public class FileWatcherSynchronizer extends TimerTask
/**
* For given <var>file</var> returns the registered <code>ChangeListener</code>s.
*
- * @return <code>null</code> if given <var>file</var> is unknown or if no <code>ChangeListener</code> could be
- * found for given <var>file</var>.
+ * @return <code>null</code> if given <var>file</var> is unknown or if no
+ * <code>ChangeListener</code> could be found for given <var>file</var>.
*/
public final synchronized ChangeListener[] getChangeListeners(final File file)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/IPathHandler.java b/common/source/java/ch/systemsx/cisd/common/utilities/IPathHandler.java
index 8f4722ded0426ad3445c006dc51ae57de67795b9..8d6e777a0b455a17b6cb524ea535a983c648a9ad 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/IPathHandler.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/IPathHandler.java
@@ -19,15 +19,16 @@ package ch.systemsx.cisd.common.utilities;
import java.io.File;
/**
- * A role for handling paths. The paths are supposed to go away when they have been handled successfully.
+ * A role for handling paths. The paths are supposed to go away when they have been handled
+ * successfully.
*
* @author Bernd Rinn
*/
public interface IPathHandler
{
/**
- * Handles the <var>path</var>. Successful handling is indicated by <var>path</var> being gone when the method
- * returns.
+ * Handles the <var>path</var>. Successful handling is indicated by <var>path</var> being gone
+ * when the method returns.
*/
public void handle(File path);
}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/IPathImmutableCopier.java b/common/source/java/ch/systemsx/cisd/common/utilities/IPathImmutableCopier.java
index bae1498385e2350488e579e9ac41de9fe988ec96..d37c1c010c49f9a0f8e635ae218eea2d6586b6b3 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/IPathImmutableCopier.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/IPathImmutableCopier.java
@@ -26,15 +26,15 @@ import java.io.File;
public interface IPathImmutableCopier
{
/**
- * Creates a copy of <code>path</code> (which may be a file or a directory) in <code>destinationDirectory</code>,
- * which must not be modified later.
+ * Creates a copy of <code>path</code> (which may be a file or a directory) in
+ * <code>destinationDirectory</code>, which must not be modified later.
* <p>
* <i>Can use hard links if available.</i>
* </p>
*
* @param path the source path. Can be a file or a directory. Can not be <code>null</code>.
- * @param destinationDirectory the directory where given <var>path</var> should be copied. Can not be
- * <code>null</code> and must be an existing directory.
+ * @param destinationDirectory the directory where given <var>path</var> should be copied. Can
+ * not be <code>null</code> and must be an existing directory.
* @param nameOrNull the link name in the destination directory.
* @return the new path created, or <code>null</code> if the operation fails.
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ISelfTestable.java b/common/source/java/ch/systemsx/cisd/common/utilities/ISelfTestable.java
index bf1603897d73f2019b2190339604d603aefe5743..e465648afa7bad1d4bd89e053c45e94955fd306e 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ISelfTestable.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ISelfTestable.java
@@ -28,11 +28,12 @@ public interface ISelfTestable
{
/**
- * Checks this <code>ISelfTestable</code>. Implementations are not supposed to do any failure logging (debug
- * logging is OK), but the caller is in charge of this.
+ * Checks this <code>ISelfTestable</code>. Implementations are not supposed to do any failure
+ * logging (debug logging is OK), but the caller is in charge of this.
*
* @throws ConfigurationFailureException If the self-test fails due to a configuration problem.
- * @throws EnvironmentFailureException If the self-test fails due to a problem in the environment.
+ * @throws EnvironmentFailureException If the self-test fails due to a problem in the
+ * environment.
*/
public void check() throws EnvironmentFailureException, ConfigurationFailureException;
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ITerminable.java b/common/source/java/ch/systemsx/cisd/common/utilities/ITerminable.java
index e80ec5c500771a3bfe9ffb50fa7d5bd2f59164c1..8b8c1b9a8e0e0764170f0aa76b8880d4eec6bafd 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ITerminable.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ITerminable.java
@@ -37,7 +37,8 @@ public interface ITerminable
/**
* Terminates the {@link ITerminable}.
*
- * @return <code>true</code> if and only if the {@link ITerminable} has terminated successfully.
+ * @return <code>true</code> if and only if the {@link ITerminable} has terminated
+ * successfully.
*/
public boolean terminate();
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/MatrixComparator.java b/common/source/java/ch/systemsx/cisd/common/utilities/MatrixComparator.java
index 962f259f7fee05cbd27b4ac050d366400ab8ac94..9c6d343e33467c66cb6796f658d2fed36f33070d 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/MatrixComparator.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/MatrixComparator.java
@@ -20,11 +20,11 @@ import java.io.Serializable;
import java.util.Comparator;
/**
- * A <code>Comparator</code> implementation that is based on matrix labelling having the following form:
- * <code>[a-zA-Z]+[0-9]+</code>.
+ * A <code>Comparator</code> implementation that is based on matrix labelling having the following
+ * form: <code>[a-zA-Z]+[0-9]+</code>.
* <p>
- * A default natural sorting will place, for instance, <code>A3</code> before <code>A10</code>. This comparator can
- * also sort by letter first or by number first.
+ * A default natural sorting will place, for instance, <code>A3</code> before <code>A10</code>.
+ * This comparator can also sort by letter first or by number first.
* </p>
*
* @author Christian Ribeaud
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/ModifiedShortPrefixToStringStyle.java b/common/source/java/ch/systemsx/cisd/common/utilities/ModifiedShortPrefixToStringStyle.java
index b4806772d39fa69deadbcdc2ea13f5a0b7ff6f3e..f5513246b8b371e9c703e87b81b517de3ca75820 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/ModifiedShortPrefixToStringStyle.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/ModifiedShortPrefixToStringStyle.java
@@ -19,9 +19,10 @@ package ch.systemsx.cisd.common.utilities;
import org.apache.commons.lang.builder.ToStringStyle;
/**
- * A modified short prefix {@link ToStringStyle} which allows to work together with jmock and cruisecontrol. The problem
- * was that in jmock exception messages <code>]]></code> appeared which is the end of a <code><![CDATA[</code>
- * section in the XML test report. This yields a hiccup in cruisecontrol.
+ * A modified short prefix {@link ToStringStyle} which allows to work together with jmock and
+ * cruisecontrol. The problem was that in jmock exception messages <code>]]></code> appeared
+ * which is the end of a <code><![CDATA[</code> section in the XML test report. This yields a
+ * hiccup in cruisecontrol.
*
* @author Franz-Josef Elmer
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilter.java b/common/source/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilter.java
index 0d184a6ba91b935f046187f82ac6aa429a8f1d97..6df806d2476d879dfff21410ac7d7bc3234c91f8 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/NamePrefixFileFilter.java
@@ -20,8 +20,8 @@ import java.io.File;
import java.io.FileFilter;
/**
- * A {@link FileFilter} that checks whether the name part of the <var>pathname</var> starts (or does not start) with
- * the <var>prefix</var> specified.
+ * A {@link FileFilter} that checks whether the name part of the <var>pathname</var> starts (or
+ * does not start) with the <var>prefix</var> specified.
*
* @author Bernd Rinn
*/
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/OSUtilities.java b/common/source/java/ch/systemsx/cisd/common/utilities/OSUtilities.java
index fedbc80aedd76b38099e552245c37d540631ecae..5aabae64c70a10d21ac0c31093789c66f0ba09a3 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/OSUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/OSUtilities.java
@@ -25,9 +25,9 @@ import java.util.regex.Pattern;
/**
* Some useful methods related to the operating system.
* <p>
- * Does <em>not</em> depend on any library jar files. But before using or extending this class and if you do not mind
- * using <a href="http://jakarta.apache.org/commons/lang/">commons lang</a>, then have a look on
- * <code>SystemUtils</code>.
+ * Does <em>not</em> depend on any library jar files. But before using or extending this class and
+ * if you do not mind using <a href="http://jakarta.apache.org/commons/lang/">commons lang</a>,
+ * then have a look on <code>SystemUtils</code>.
* </p>
*
* @author Bernd Rinn
@@ -79,8 +79,8 @@ public class OSUtilities
}
/**
- * @return <code>true</code> if the user that runs this program is known to have root privileges (based on his
- * name).
+ * @return <code>true</code> if the user that runs this program is known to have root
+ * privileges (based on his name).
*/
public static boolean isRoot()
{
@@ -105,7 +105,8 @@ public class OSUtilities
/**
* @param root Whether the path should be prepared for root or not.
- * @return The path as provided by the operating system plus some path entries that should always be available.
+ * @return The path as provided by the operating system plus some path entries that should
+ * always be available.
* @see #getOSPath()
*/
public static Set<String> getSafeOSPath(boolean root)
@@ -139,7 +140,8 @@ public class OSUtilities
/**
* Convenience method for {@link #getSafeOSPath(boolean)} with <code>root=false</code>.
*
- * @return The path as provided by the operating system plus some path entries that should always be available.
+ * @return The path as provided by the operating system plus some path entries that should
+ * always be available.
* @see #getSafeOSPath(boolean)
*/
public static Set<String> getSafeOSPath()
@@ -148,12 +150,14 @@ public class OSUtilities
}
/**
- * Search for the binary program with name <code>binaryName</code> in the operating system path..
+ * Search for the binary program with name <code>binaryName</code> in the operating system
+ * path..
*
- * @param executableName The name of the executable to search for. Under Windows, a name with and without
- * <code>.exe</code> appended will work, but the executable found needs to have the .exe extension.
- * @return The binary file that has been found in the path, or <code>null</code>, if no binary file could be
- * found.
+ * @param executableName The name of the executable to search for. Under Windows, a name with
+ * and without <code>.exe</code> appended will work, but the executable found needs
+ * to have the .exe extension.
+ * @return The binary file that has been found in the path, or <code>null</code>, if no
+ * binary file could be found.
*/
public static File findExecutable(String executableName)
{
@@ -161,15 +165,17 @@ public class OSUtilities
}
/**
- * Search for the binary program with name <code>binaryName</code> in the set of paths denoted by
- * <code>pathSet</code>.
+ * Search for the binary program with name <code>binaryName</code> in the set of paths denoted
+ * by <code>pathSet</code>.
*
- * @param executableName The name of the executable to search for. Under Windows, a name with and without
- * <code>.exe</code> appended will work, but the executable found needs to have the .exe extension.
- * @param pathSet The set of paths to search for. It is recommended to use an ordered set like the
- * {@link LinkedHashSet} here in order to get results that are independent of the JRE implementation.
- * @return The binary file that has been found in the path, or <code>null</code>, if no binary file could be
- * found.
+ * @param executableName The name of the executable to search for. Under Windows, a name with
+ * and without <code>.exe</code> appended will work, but the executable found needs
+ * to have the .exe extension.
+ * @param pathSet The set of paths to search for. It is recommended to use an ordered set like
+ * the {@link LinkedHashSet} here in order to get results that are independent of the
+ * JRE implementation.
+ * @return The binary file that has been found in the path, or <code>null</code>, if no
+ * binary file could be found.
*/
public static File findExecutable(String executableName, Set<String> pathSet)
{
@@ -187,7 +193,8 @@ public class OSUtilities
}
/**
- * @return <code>true</code> if and only if an executable of name <var>executableName</var> exists.
+ * @return <code>true</code> if and only if an executable of name <var>executableName</var>
+ * exists.
*/
public static boolean executableExists(String executableName)
{
@@ -196,7 +203,8 @@ public class OSUtilities
}
/**
- * @return <code>true</code> if and only if an executable of name <var>executableName</var> exists.
+ * @return <code>true</code> if and only if an executable of name <var>executableName</var>
+ * exists.
*/
public static boolean executableExists(File executable)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/PathPrefixPrepender.java b/common/source/java/ch/systemsx/cisd/common/utilities/PathPrefixPrepender.java
index 6eb8cc20243e97d012c119a28c69074dab31209e..4425282f755b644781241afeb0b849c99e584e11 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/PathPrefixPrepender.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/PathPrefixPrepender.java
@@ -24,8 +24,8 @@ import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
/**
- * Class which adds a prefix to a path. Which prefix is added depends on whether the path starts with '/' (absolute
- * path) or not (relative path).
+ * Class which adds a prefix to a path. Which prefix is added depends on whether the path starts
+ * with '/' (absolute path) or not (relative path).
*
* @author Franz-Josef Elmer
*/
@@ -36,7 +36,8 @@ public final class PathPrefixPrepender
private final String prefixForRelativePaths;
/**
- * Creates an instances for the specified prefixes. <code>null</code> arguments are handled as empty strings.
+ * Creates an instances for the specified prefixes. <code>null</code> arguments are handled as
+ * empty strings.
*/
public PathPrefixPrepender(final String prefixForAbsolutePathsOrNull,
final String prefixForRelativePathsOrNull) throws ConfigurationFailureException
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMaker.java b/common/source/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMaker.java
index 81ac30951e6ab83efcc4ab452b6f969c7e269814..0be72e9250dabfa8211306891a4deb867fe59c1c 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMaker.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/RecursiveHardLinkMaker.java
@@ -29,8 +29,9 @@ import ch.systemsx.cisd.common.process.ProcessExecutionHelper;
import ch.systemsx.cisd.common.process.ProcessRunner;
/**
- * Utility to create a hard link of a file or copy recursively a directories structure, creating a hard link for each
- * file inside. Note that presence of <code>ln</code> executable is required, which is not available under Windows.
+ * Utility to create a hard link of a file or copy recursively a directories structure, creating a
+ * hard link for each file inside. Note that presence of <code>ln</code> executable is required,
+ * which is not available under Windows.
*
* @author Tomasz Pylak
*/
@@ -100,14 +101,14 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
}
/**
- * Creates copier which is able to retry the operation of creating each hard link of a file if it does not complete
- * after a specified timeout.
+ * Creates copier which is able to retry the operation of creating each hard link of a file if
+ * it does not complete after a specified timeout.
*
- * @param millisToWaitForCompletion The time to wait for the process to complete in milli seconds. If the process is
- * not finished after that time, it will be terminated.
+ * @param millisToWaitForCompletion The time to wait for the process to complete in milli
+ * seconds. If the process is not finished after that time, it will be terminated.
* @param maxRetryOnFailure The number of times we should try if copy operation fails.
- * @param millisToSleepOnFailure The number of milliseconds we should wait before re-executing the copy of a single
- * file. Specify 0 to wait till the first operation completes.
+ * @param millisToSleepOnFailure The number of milliseconds we should wait before re-executing
+ * the copy of a single file. Specify 0 to wait till the first operation completes.
*/
public static final IPathImmutableCopier tryCreateRetrying(
final long millisToWaitForCompletion, final int maxRetryOnFailure,
@@ -137,8 +138,8 @@ public final class RecursiveHardLinkMaker implements IPathImmutableCopier
}
/**
- * Copies <var>path</var> (file or directory) to <var>destinationDirectory</var> by duplicating directory
- * structure and creating hard link for each file.
+ * Copies <var>path</var> (file or directory) to <var>destinationDirectory</var> by
+ * duplicating directory structure and creating hard link for each file.
* <p>
* <i>Note that <var>nameOrNull</var> cannot already exist in given <var>destinationDirectory</var>.</i>
* </p>
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/RegexFileFilter.java b/common/source/java/ch/systemsx/cisd/common/utilities/RegexFileFilter.java
index 530ee22e72dccb0fb0c1d5936db58645fb9f8955..8bb6e94e78e479bfeaecfd4d9bee8b57e4ac9baf 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/RegexFileFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/RegexFileFilter.java
@@ -23,9 +23,10 @@ import java.util.Set;
import java.util.regex.Pattern;
/**
- * A {@link FileFilter} based on a set of path patterns. A path pattern consists of a {@link PathType} and a regular
- * expression matching (the entire region of) the name of the path entry as returned by {@link File#getName()}. If any
- * path pattern of the set matches a path entry, the filter will accept the path entry.
+ * A {@link FileFilter} based on a set of path patterns. A path pattern consists of a
+ * {@link PathType} and a regular expression matching (the entire region of) the name of the path
+ * entry as returned by {@link File#getName()}. If any path pattern of the set matches a path
+ * entry, the filter will accept the path entry.
*
* @author Bernd Rinn
*/
@@ -43,7 +44,10 @@ public class RegexFileFilter implements FileFilter
ALL
}
- /** A class specifying a pattern for files, combining a regular expression for the file name and a file type. */
+ /**
+ * A class specifying a pattern for files, combining a regular expression for the file name and
+ * a file type.
+ */
private static class PathPattern
{
private final PathType type;
@@ -125,10 +129,11 @@ public class RegexFileFilter implements FileFilter
}
/**
- * Adds a path pattern to this filter. Multiple path pattern can be added by calling this method several times. If
- * any path pattern matches a file, the file will be accepted by this filter.
+ * Adds a path pattern to this filter. Multiple path pattern can be added by calling this method
+ * several times. If any path pattern matches a file, the file will be accepted by this filter.
*
- * @param type The type of path that a path entry has to be of in order to be accepted by this filter.
+ * @param type The type of path that a path entry has to be of in order to be accepted by this
+ * filter.
* @param regexPattern The regular expression pattern that the name of the file (as returned by
* {@link File#getName()} has to match in order to be accepted by this filter.
*/
@@ -140,12 +145,13 @@ public class RegexFileFilter implements FileFilter
}
/**
- * Adds a path pattern to this filter. Multiple path pattern can be added by calling this method several times. If
- * any path pattern matches a file, the file will be accepted by this filter.
+ * Adds a path pattern to this filter. Multiple path pattern can be added by calling this method
+ * several times. If any path pattern matches a file, the file will be accepted by this filter.
*
- * @param type The type of path that a path entry has to be of in order to be accepted by this filter.
- * @param regex The regular expression that the name of the file (as returned by {@link File#getName()} has to match
- * in order to be accepted by this filter.
+ * @param type The type of path that a path entry has to be of in order to be accepted by this
+ * filter.
+ * @param regex The regular expression that the name of the file (as returned by
+ * {@link File#getName()} has to match in order to be accepted by this filter.
*/
public void add(PathType type, Pattern regex)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/StringUtilities.java b/common/source/java/ch/systemsx/cisd/common/utilities/StringUtilities.java
index 18e5451489cd6659345750048aff03bd171a0dd1..d24ce0c67e5870dfcddaba940af2201faaf64759 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/StringUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/StringUtilities.java
@@ -28,8 +28,8 @@ import ch.systemsx.cisd.common.exceptions.CheckedExceptionTunnel;
/**
* Some useful utlities methods for {@link String}s.
* <p>
- * If you are tempted to add new functionality to this class, ensure that the new functionality does not yet exist in
- * {@link StringUtils}, see <a
+ * If you are tempted to add new functionality to this class, ensure that the new functionality does
+ * not yet exist in {@link StringUtils}, see <a
* href="http://jakarta.apache.org/commons/lang/api-release/org/apache/commons/lang/StringUtils.html">javadoc</a>.
*
* @author Bernd Rinn
@@ -164,8 +164,8 @@ public final class StringUtilities
/**
* Splits a matrix coordinate and returns the result in a two-dimensional array.
* <p>
- * For instance the following matrix coordinate <code>H24</code> will returns the following array
- * <code>[H, 24]</code>.
+ * For instance the following matrix coordinate <code>H24</code> will returns the following
+ * array <code>[H, 24]</code>.
* </p>
*
* @return <code>null</code> if the operation fails.
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/Template.java b/common/source/java/ch/systemsx/cisd/common/utilities/Template.java
index 0e492528a3d2df8623db448b320e9b94d81759aa..022316d8f554f8a77aec6fc57a10405c676eec38 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/Template.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/Template.java
@@ -30,12 +30,13 @@ import java.util.Map;
* String text = template.createText();
* </pre>
*
- * The method {@link #bind(String, String)} throws an exception if the placeholder name is unknown. The method
- * {@link #attemptToBind(String, String)} returns <code>false</code> if the placeholder name is unknown. The method
- * {@link #createText()} throws an exception if not all placeholders have been bound.
+ * The method {@link #bind(String, String)} throws an exception if the placeholder name is unknown.
+ * The method {@link #attemptToBind(String, String)} returns <code>false</code> if the placeholder
+ * name is unknown. The method {@link #createText()} throws an exception if not all placeholders
+ * have been bound.
* <p>
- * Since placeholder bindings change the state of an instance of this class there is method {@link #createFreshCopy()}
- * which creates a copy without reparsing the template. Usage example:
+ * Since placeholder bindings change the state of an instance of this class there is method
+ * {@link #createFreshCopy()} which creates a copy without reparsing the template. Usage example:
*
* <pre>
* static final Template TEMPLATE = new Template("Hello ${name}!");
@@ -326,8 +327,8 @@ public class Template
/**
* Creates the text by using placeholder bindings.
*
- * @param complete If <code>true</code> an {@link IllegalStateException} will be thrown if not all bindings are
- * set.
+ * @param complete If <code>true</code> an {@link IllegalStateException} will be thrown if not
+ * all bindings are set.
*/
public String createText(boolean complete)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/TriggeringTimerTask.java b/common/source/java/ch/systemsx/cisd/common/utilities/TriggeringTimerTask.java
index 9e4a9644e3978ed895c750587b4775ac1b7af0c8..1c1cd516eb3b20ef4f4d23a6562dc33e658ab170 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/TriggeringTimerTask.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/TriggeringTimerTask.java
@@ -48,8 +48,8 @@ public class TriggeringTimerTask extends TimerTask
* Creates a <var>TriggeringTimerTask</var>.
*
* @param triggerFile The file that triggers.
- * @param triggerable The handler that can perform a recovery action, or <code>null</code> if there is no recovery
- * action available.
+ * @param triggerable The handler that can perform a recovery action, or <code>null</code> if
+ * there is no recovery action available.
*/
public TriggeringTimerTask(File triggerFile, ITriggerable triggerable)
{
@@ -60,8 +60,8 @@ public class TriggeringTimerTask extends TimerTask
* Creates a <var>TriggeringTimerTask</var>.
*
* @param triggerFile The file that triggers.
- * @param triggerable The handler that can perform a recovery action, or <code>null</code> if there is no recovery
- * action available.
+ * @param triggerable The handler that can perform a recovery action, or <code>null</code> if
+ * there is no recovery action available.
* @param monitor The monitor to synchronize on.
*/
public TriggeringTimerTask(File triggerFile, ITriggerable triggerable,
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/test/StoringUncaughtExceptionHandler.java b/common/sourceTest/java/ch/systemsx/cisd/common/test/StoringUncaughtExceptionHandler.java
index 2091bfac24f34c98682a27c10a9f94936bf055a1..12a25e4cbdb93ab21c12d49768a65eaafc4cbed0 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/test/StoringUncaughtExceptionHandler.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/test/StoringUncaughtExceptionHandler.java
@@ -18,7 +18,8 @@ package ch.systemsx.cisd.common.test;
import java.lang.Thread.UncaughtExceptionHandler;
/**
- * An exception handler that stores the first occurring exception for later investigation. Needs to be activated by
+ * An exception handler that stores the first occurring exception for later investigation. Needs to
+ * be activated by
*
* <pre>
* StoringUncaughtExceptionHandler exceptionHandler = new StoringUncaughtExceptionHandler();
@@ -51,7 +52,8 @@ public final class StoringUncaughtExceptionHandler implements UncaughtExceptionH
}
/**
- * @return <code>true</code> if an exception or error has occurred, <code>false</code> otherwise.
+ * @return <code>true</code> if an exception or error has occurred, <code>false</code>
+ * otherwise.
*/
public boolean hasExceptionOccurred()
{
@@ -67,8 +69,8 @@ public final class StoringUncaughtExceptionHandler implements UncaughtExceptionH
}
/**
- * @return The name of the thread where the exception or error has occurred, or <code>null</code>, if no
- * exception or error has occurred.
+ * @return The name of the thread where the exception or error has occurred, or
+ * <code>null</code>, if no exception or error has occurred.
*/
public String getThreadName()
{
@@ -76,8 +78,8 @@ public final class StoringUncaughtExceptionHandler implements UncaughtExceptionH
}
/**
- * Checks whether an exception or error has occurred and, if yes, throws a new {@link RuntimeException} with the
- * caught exception as cause in the current thread.
+ * Checks whether an exception or error has occurred and, if yes, throws a new
+ * {@link RuntimeException} with the caught exception as cause in the current thread.
*/
public void checkAndRethrowException()
{
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ClassUtilsTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ClassUtilsTest.java
index 4c92f4f0c119a4f096734bc84f016414cd8a10fd..bbe477f53b4ea208667cc66b8432c1e32687ef81 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ClassUtilsTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/ClassUtilsTest.java
@@ -120,8 +120,10 @@ public final class ClassUtilsTest
private final void privateMethodOnStack()
{
- // If <code>Class.getDeclaredMethods</code> were used instead of <code>Class.getDeclaredMethods</code>,
- // we will have 'ch.systemsx.cisd.common.utilities.ClassUtilsTest.privateMethodOnStack()' here.
+ // If <code>Class.getDeclaredMethods</code> were used instead of
+ // <code>Class.getDeclaredMethods</code>,
+ // we will have 'ch.systemsx.cisd.common.utilities.ClassUtilsTest.privateMethodOnStack()'
+ // here.
assertNull(ClassUtils.getMethodOnStack(1));
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTaskTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTaskTest.java
index 620fbfc9a85febb336668d237c2781472136d357..32b983603e22cb2a0467f6f57249cbcbe7c18516 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTaskTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/DirectoryScanningTimerTaskTest.java
@@ -249,7 +249,8 @@ public class DirectoryScanningTimerTaskTest
"Failed to get listing of directory");
try
{
- // The directory needs to exist when the scanner is created, otherwise the self-test will fail.
+ // The directory needs to exist when the scanner is created, otherwise the self-test
+ // will fail.
final DirectoryScanningTimerTask scanner =
new DirectoryScanningTimerTask(dir, ACCEPT_ALL_FILTER, mockPathHandler);
dir.delete();
@@ -272,7 +273,8 @@ public class DirectoryScanningTimerTaskTest
"Failed to get listing of directory");
try
{
- // The directory needs to exist when the scanner is created, otherwise the self-test will fail.
+ // The directory needs to exist when the scanner is created, otherwise the self-test
+ // will fail.
final DirectoryScanningTimerTask scanner =
new DirectoryScanningTimerTask(dir, ACCEPT_ALL_FILTER, mockPathHandler);
dir.delete();
@@ -305,7 +307,8 @@ public class DirectoryScanningTimerTaskTest
EXCEPTION_THROWING_FILE_FILTER_MESSAGE);
try
{
- // The directory needs to exist when the scanner is created, otherwise the self-test will fail.
+ // The directory needs to exist when the scanner is created, otherwise the self-test
+ // will fail.
final DirectoryScanningTimerTask scanner =
new DirectoryScanningTimerTask(dir, EXCEPTION_THROWING_FILE_FILTER,
mockPathHandler);
@@ -337,7 +340,8 @@ public class DirectoryScanningTimerTaskTest
try
{
final int numberOfErrorsToIgnore = 2;
- // The directory needs to exist when the scanner is created, otherwise the self-test will fail.
+ // The directory needs to exist when the scanner is created, otherwise the self-test
+ // will fail.
final DirectoryScanningTimerTask scanner =
new DirectoryScanningTimerTask(dir, ACCEPT_ALL_FILTER, mockPathHandler,
numberOfErrorsToIgnore);
@@ -381,7 +385,8 @@ public class DirectoryScanningTimerTaskTest
try
{
final int numberOfErrorsToIgnore = 2;
- // The directory needs to exist when the scanner is created, otherwise the self-test will fail.
+ // The directory needs to exist when the scanner is created, otherwise the self-test
+ // will fail.
final DirectoryScanningTimerTask scanner =
new DirectoryScanningTimerTask(dir, ACCEPT_ALL_FILTER, mockPathHandler,
numberOfErrorsToIgnore);
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesLastChangedTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesLastChangedTest.java
index 5cff1cfc264c8e79b638fcfb8eead3d7e8aa652c..0712747537b71de9ee3b9949fd656ad21f547c64 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesLastChangedTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesLastChangedTest.java
@@ -107,7 +107,8 @@ public class FileUtilitiesLastChangedTest
final long diff = Math.abs(lastChanged - now);
assert diff <= 2000 : "expected difference less than 2s, but was " + diff / 1000.0 + "s";
- // We need to wait for more than 1s because that's the granularity of the changed time attribute saved with
+ // We need to wait for more than 1s because that's the granularity of the changed time
+ // attribute saved with
// files.
restALittleBit();
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java
index 68bf4da94de7ef31d1c8b5dca69866801aea1b95..eaf087458ac4cbc8970b6052b5ead59f3b7113d3 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/utilities/FileUtilitiesTest.java
@@ -83,7 +83,8 @@ public final class FileUtilitiesTest extends AbstractFileSystemTestCase
String errorMsg = FileUtilities.checkDirectoryFullyAccessible(readOnlyDirectory, "test");
// --- clean before checking results
- // Unfortunately, with JDK 5 there is no portable way to set a file or directory read/write, once
+ // Unfortunately, with JDK 5 there is no portable way to set a file or directory read/write,
+ // once
// it has been set read-only, thus this test 'requires_unix' for the time being.
Runtime.getRuntime().exec(String.format("/bin/chmod u+w %s", readOnlyDirectory.getPath()))
.waitFor();