Author: jm
Date: 2010-11-09 14:54:03 -0800 (Tue, 09 Nov 2010)
New Revision: 22790
Added:
core3/filter-api/trunk/
core3/filter-api/trunk/osgi.bnd
core3/filter-api/trunk/pom.xml
core3/filter-api/trunk/src/
core3/filter-api/trunk/src/main/
core3/filter-api/trunk/src/main/java/
core3/filter-api/trunk/src/main/java/org/
core3/filter-api/trunk/src/main/java/org/cytoscape/
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilter.java
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterFactory.java
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterManager.java
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterResult.java
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterResultFactory.java
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/MergeType.java
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/TunableCyFilter.java
core3/filter-api/trunk/src/main/resources/
core3/filter-api/trunk/src/test/
core3/filter-api/trunk/src/test/java/
core3/filter-api/trunk/src/test/resources/
Log:
Initial import
Property changes on: core3/filter-api/trunk
___________________________________________________________________
Name: svn:ignore
+ .settings
.classpath
.project
target
Added: core3/filter-api/trunk/osgi.bnd
===================================================================
--- core3/filter-api/trunk/osgi.bnd (rev 0)
+++ core3/filter-api/trunk/osgi.bnd 2010-11-09 22:54:03 UTC (rev 22790)
@@ -0,0 +1,7 @@
+#-----------------------------------------------------------------
+# Use this file to add customized Bnd instructions for the bundle
+#-----------------------------------------------------------------
+
+Spring-Context: META-INF/spring/*.xml
+Private-Package: ${bundle.namespace}.internal.*
+Export-Package:
!${bundle.namespace}.internal.*,${bundle.namespace}.*;version="${pom.version}"
Added: core3/filter-api/trunk/pom.xml
===================================================================
--- core3/filter-api/trunk/pom.xml (rev 0)
+++ core3/filter-api/trunk/pom.xml 2010-11-09 22:54:03 UTC (rev 22790)
@@ -0,0 +1,98 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";
+ xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";>
+ <parent>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>parent</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </parent>
+ <properties>
+
<bundle.symbolicName>org.cytoscape.filter-api</bundle.symbolicName>
+ <bundle.namespace>org.cytoscape.filter</bundle.namespace>
+ </properties>
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>filter-api</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ <name>${bundle.symbolicName}
+ [${bundle.namespace}]</name>
+ <packaging>bundle</packaging>
+ <dependencies>
+ <dependency>
+ <groupId>cytoscape</groupId>
+ <artifactId>application</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>osgi_R4_core</artifactId>
+ <version>1.0</version>
+ <scope>provided</scope>
+ <optional>true</optional>
+ </dependency>
+ <dependency>
+ <groupId>org.osgi</groupId>
+ <artifactId>osgi_R4_compendium</artifactId>
+ <version>1.0</version>
+ <scope>provided</scope>
+ <optional>true</optional>
+ </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>test-support</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-all</artifactId>
+ <version>1.8.1</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+ <repositories>
+ <repository>
+ <id>cytoscape_thirdparty</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ <enabled>true</enabled>
+ </releases>
+ <name>Wrapped Third Party Libraries</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/thirdparty/</url>
+ </repository>
+ </repositories>
+
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.ops4j</groupId>
+ <artifactId>maven-pax-plugin</artifactId>
+ <version>1.4</version>
+ <extensions>true</extensions>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <version>1.4.3</version>
+ <configuration>
+ <instructions>
+
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+
<Bundle-Version>${pom.version}</Bundle-Version>
+ <_include>-osgi.bnd</_include>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+</project>
\ No newline at end of file
Added: core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilter.java
===================================================================
--- core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilter.java
(rev 0)
+++ core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilter.java
2010-11-09 22:54:03 UTC (rev 22790)
@@ -0,0 +1,65 @@
+package org.cytoscape.filter;
+
+import java.util.Map;
+
+import javax.swing.JComponent;
+
+/**
+ * Selects nodes and edges from a <code>CyNetwork</code> through some
+ * implementation-defined heuristic.
+ */
+public interface CyFilter {
+ /**
+ * Returns the name of this filter.
+ * @return
+ */
+ String getName();
+
+ /**
+ * Sets the name of this filter to <code>name</code>.
+ * @param name
+ */
+ void setName(String name);
+
+ /**
+ * Returns the value associated with the property named <code>name</code>,
+ * or <code>null</code> if no value was previously associated.
+ * @param <T> the type of the property value to fetch.
+ * @param name the name of the property
+ * @param type
+ * @return
+ */
+ <T> T getProperty(String name, Class<T> type);
+
+ /**
+ * Associates the given value with the property named <code>name</code>.
+ * Setting the value to <code>null</code> effectively removes the
+ * association.
+ * @param <T> the type of the property value to set.
+ * @param name
+ * @param value
+ */
+ <T> void setProperty(String name, T value);
+
+ /**
+ * Returns a <code>Map</code> where the keys are property names and the
+ * values are their respective values. Each supported property name is
+ * present as a key in this map. The values of unset properties is
+ * <code>null</code>.
+ * @return
+ */
+ Map<String, Object> getAllProperties();
+
+ /**
+ * Adds the nodes and edges selected by the filter to <code>result</code>.
+ * @param result
+ */
+ void apply(CyFilterResult result);
+
+ /**
+ * Returns a Swing component that contains a GUI for configuring the
+ * properties of this <code>CyFilter</code>.
+ * @return
+ */
+ JComponent getSettingsUI();
+}
Added:
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterFactory.java
===================================================================
---
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterFactory.java
(rev 0)
+++
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterFactory.java
2010-11-09 22:54:03 UTC (rev 22790)
@@ -0,0 +1,29 @@
+package org.cytoscape.filter;
+
+import java.io.Reader;
+
+/**
+ * A factory for creating a specific type of <code>CyFilter</code>.
+ */
+public interface CyFilterFactory {
+ /**
+ * Returns the unique identifier of the type of filter created by this
+ * factory.
+ * @return
+ */
+ String getIdentifier();
+
+ /**
+ * Returns a new <code>CyFilter</code> instance.
+ * @return
+ */
+ CyFilter getFilter();
+
+ /**
+ * Returns a new <code>CyFilter</code> instance from its serialized
+ * representation.
+ * @param reader
+ * @return
+ */
+ CyFilter getFilter(Reader reader);
+}
Added:
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterManager.java
===================================================================
---
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterManager.java
(rev 0)
+++
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterManager.java
2010-11-09 22:54:03 UTC (rev 22790)
@@ -0,0 +1,24 @@
+package org.cytoscape.filter;
+
+import java.util.Collection;
+
+/**
+ * The central registry for all <code>CyFilter</code>s and their
+ * corresponding factories.
+ */
+public interface CyFilterManager {
+ /**
+ * Returns the <code>CyFilterFactory</code> with the given identifier,
or
+ * null, if no such factory was previously registered.
+ * @param identifier
+ * @return
+ */
+ CyFilterFactory getFilterFactory(String identifier);
+
+ /**
+ * Returns all of the <code>CyFilterFactory</code>s registered with this
+ * object.
+ * @return
+ */
+ Collection<CyFilterFactory> getAllFilterFactories();
+}
Added:
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterResult.java
===================================================================
---
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterResult.java
(rev 0)
+++
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterResult.java
2010-11-09 22:54:03 UTC (rev 22790)
@@ -0,0 +1,87 @@
+package org.cytoscape.filter;
+
+import org.cytoscape.model.CyNetwork;
+
+/**
+ * Tracks the nodes and edges that have been filtered from a
+ * <code>CyNetwork</code>.
+ */
+public interface CyFilterResult {
+ /**
+ * Returns the <code>CyNetwork</code> this result set applies to.
+ * @return
+ */
+ CyNetwork getNetwork();
+
+ /**
+ * Adds the edge with the given index to this result set. If the edge
+ * was previously added, this method does nothing.
+ * @param index
+ */
+ void addEdge(int index);
+
+ /**
+ * Removes the edge with the given index from this result set. If the
+ * edge was not previously added, this method does nothing.
+ * @param index
+ */
+ void removeEdge(int index);
+
+ /**
+ * Returns <code>true</code> if the edge with the given index is part of
+ * this result set, and <code>false</code> otherwise.
+ * @param index
+ * @return
+ */
+ boolean hasEdge(int index);
+
+ /**
+ * Returns an <code>Iterable</code> over all the edges in this result set.
+ * @return
+ */
+ Iterable<Integer> edges();
+
+ /**
+ * Adds the node with the given index to this result set. If the node
+ * was previously added, this method does nothing.
+ * @param index
+ */
+ void addNode(int index);
+
+ /**
+ * Removes the node with the given index from this result set. If the
+ * node was not previously added, this method does nothing.
+ * @param index
+ */
+ void removeNode(int index);
+
+ /**
+ * Returns <code>true</code> if the node with the given index is part of
+ * this result set, and <code>false</code> otherwise.
+ * @param index
+ * @return
+ */
+ boolean hasNode(int index);
+
+ /**
+ * Returns an <code>Iterable</code> over all the nodes in this result set.
+ * @return
+ */
+ Iterable<Integer> nodes();
+
+ /**
+ * Merges this object with <code>result</code> using the combination
+ * method specified by <code>type</code>.
+ * @param result
+ * @param type
+ */
+ void merge(CyFilterResult result, MergeType type);
+
+ /**
+ * Updates this object so that it contains the set complement of its
+ * edges and its nodes, with respect to the network it belongs to.
+ */
+ void invert();
+
+ void clear();
+}
Added:
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterResultFactory.java
===================================================================
---
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterResultFactory.java
(rev 0)
+++
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/CyFilterResultFactory.java
2010-11-09 22:54:03 UTC (rev 22790)
@@ -0,0 +1,17 @@
+package org.cytoscape.filter;
+
+import org.cytoscape.model.CyNetwork;
+
+/**
+ * A factory for creating <code>CyFilterResult</code>s for specific
+ * <code>CyNetwork</code>s.
+ */
+public interface CyFilterResultFactory {
+ /**
+ * Creates a <code>CyFilterResult</code> for tracking filtered nodes and
+ * edges from the given network.
+ * @param network
+ * @return
+ */
+ CyFilterResult getResult(CyNetwork network);
+}
Added: core3/filter-api/trunk/src/main/java/org/cytoscape/filter/MergeType.java
===================================================================
--- core3/filter-api/trunk/src/main/java/org/cytoscape/filter/MergeType.java
(rev 0)
+++ core3/filter-api/trunk/src/main/java/org/cytoscape/filter/MergeType.java
2010-11-09 22:54:03 UTC (rev 22790)
@@ -0,0 +1,22 @@
+package org.cytoscape.filter;
+
+/**
+ * Different methods for combining two <code>CyFilterResult</code>s together.
+ */
+public enum MergeType {
+ /**
+ * Computes the set-union of the nodes and edges in both
+ * <code>CyFilterResult</code>s. In other words, the resulting
+ * <code>CyFilterResult</code> will contain nodes and edges that
+ * occur in either of the input <code>CyFilterResult</code>s.
+ */
+ UNION,
+
+ /**
+ * Computes the set-intersection of the nodes and edges in both
+ * <code>CyFilterResult</code>s. In other words, the resulting
+ * <code>CyFilterResult</code> will only contain the nodes and
+ * edges that occur in both input <code>CyFilterResult</code>s.
+ */
+ INTERSECTION,
+}
Added:
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/TunableCyFilter.java
===================================================================
---
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/TunableCyFilter.java
(rev 0)
+++
core3/filter-api/trunk/src/main/java/org/cytoscape/filter/TunableCyFilter.java
2010-11-09 22:54:03 UTC (rev 22790)
@@ -0,0 +1,181 @@
+package org.cytoscape.filter;
+
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+import javax.swing.JComponent;
+
+import org.cytoscape.work.Tunable;
+
+/**
+ * A base class for <code>CyFilter</code>s that declare their properties
+ * through <code>Tunable</code>s.
+ */
+public abstract class TunableCyFilter implements CyFilter {
+ private static final Collection<String> GETTER_NAME_PREFIXES =
Collections.unmodifiableCollection(Arrays.asList(new String[] { "get", "is",
"has" })); //$NON-NLS-1$ //$NON-NLS-2$ //$NON-NLS-3$
+
+ private String name;
+
+ @Override
+ public String getName() {
+ return name;
+ }
+
+ @Override
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public <T> T getProperty(String name, Class<T> type) {
+ Class<?> currentClass = getClass();
+ while (currentClass != null) {
+ for (String prefix : GETTER_NAME_PREFIXES) {
+ String suffix = name.substring(0,
1).toLowerCase() + name.substring(1);
+ try {
+ Method method =
currentClass.getDeclaredMethod(String.format("%s%s", prefix, suffix));
//$NON-NLS-1$
+ if
(!method.isAnnotationPresent(Tunable.class)) {
+ continue;
+ }
+ if
(!type.isAssignableFrom(method.getReturnType())) {
+ throw new ClassCastException();
+ }
+ return (T) method.invoke(this);
+ } catch (SecurityException e) {
+ } catch (IllegalArgumentException e) {
+ } catch (IllegalAccessException e) {
+ } catch (NoSuchMethodException e) {
+ } catch (InvocationTargetException e) {
+ }
+ }
+
+ try {
+ Field field =
currentClass.getDeclaredField(name);
+ if (!field.isAnnotationPresent(Tunable.class)) {
+ continue;
+ }
+ return (T) field.get(this);
+ } catch (SecurityException e) {
+ } catch (NoSuchFieldException e) {
+ } catch (IllegalArgumentException e) {
+ } catch (IllegalAccessException e) {
+ }
+ currentClass = currentClass.getSuperclass();
+ }
+ return null;
+ }
+
+ @Override
+ public <T> void setProperty(String name, T value) {
+ String suffix = Character.toUpperCase(name.charAt(0)) +
name.substring(1);
+ String setterName = String.format("set%s", suffix);
//$NON-NLS-1$
+ Class<?> currentClass = getClass();
+
+ while (currentClass != null) {
+ try {
+ for (String prefix : GETTER_NAME_PREFIXES) {
+ String getterName =
String.format("%s%s", prefix, suffix); //$NON-NLS-1$
+ Method getter =
currentClass.getDeclaredMethod(getterName);
+ if
(!getter.isAnnotationPresent(Tunable.class)) {
+ continue;
+ }
+ Method setter =
currentClass.getDeclaredMethod(setterName, value.getClass());
+ setter.invoke(this, value);
+ return;
+ }
+ } catch (SecurityException e) {
+ } catch (NoSuchMethodException e) {
+ } catch (IllegalArgumentException e) {
+ } catch (IllegalAccessException e) {
+ } catch (InvocationTargetException e) {
+ }
+
+ try {
+ Field field =
currentClass.getDeclaredField(name);
+ if (!field.isAnnotationPresent(Tunable.class)) {
+ continue;
+ }
+ field.set(this, value);
+ return;
+ } catch (SecurityException e) {
+ } catch (NoSuchFieldException e) {
+ } catch (IllegalArgumentException e) {
+ } catch (IllegalAccessException e) {
+ }
+ currentClass = currentClass.getSuperclass();
+ }
+ };
+
+ @Override
+ public Map<String, Object> getAllProperties() {
+ Map<String, Object> properties = new HashMap<String, Object>();
+ Class<?> currentClass = getClass();
+
+ while (currentClass != null) {
+ for (Method method : currentClass.getDeclaredMethods())
{
+ if (method.getParameterTypes().length > 0) {
+ continue;
+ }
+ String name =
extractPropertyName(method.getName());
+ if (name == null) {
+ continue;
+ }
+ try {
+ if
(!method.isAnnotationPresent(Tunable.class)) {
+ continue;
+ }
+ Object value = method.invoke(this);
+ properties.put(name, value);
+ } catch (SecurityException e) {
+ } catch (IllegalArgumentException e) {
+ } catch (IllegalAccessException e) {
+ } catch (InvocationTargetException e) {
+ }
+ }
+ for (Field field : currentClass.getDeclaredFields()) {
+ if (!field.isAnnotationPresent(Tunable.class)) {
+ continue;
+ }
+ try {
+ Object value = field.get(this);
+ properties.put(field.getName(), value);
+ } catch (IllegalArgumentException e) {
+ } catch (IllegalAccessException e) {
+ }
+ }
+ currentClass = currentClass.getSuperclass();
+ }
+ return properties;
+ }
+
+ private String extractPropertyName(String fullName) {
+ for (String prefix : GETTER_NAME_PREFIXES) {
+ if (!fullName.startsWith(prefix)) {
+ return null;
+ }
+
+ String suffix = fullName.substring(prefix.length());
+ char firstLetter = suffix.charAt(0);
+ if (!Character.isUpperCase(firstLetter)) {
+ return null;
+ }
+
+ return Character.toLowerCase(firstLetter) +
suffix.substring(1);
+ }
+ return null;
+ }
+
+ @Override
+ public JComponent getSettingsUI() {
+ // TODO Should we reuse Tunable UI bits in work-swing-impl or
create
+ // a different UI widget library for filters?
+ return null;
+ }
+}
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