Author: kono
Date: 2010-09-15 16:28:35 -0700 (Wed, 15 Sep 2010)
New Revision: 21884
Added:
core3/vizmap-impl/branches/vp-tree/
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
Removed:
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
Modified:
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
Log:
Visual Property Tree version of view model.
Copied: core3/vizmap-impl/branches/vp-tree (from rev 21529,
core3/vizmap-impl/trunk)
Property changes on: core3/vizmap-impl/branches/vp-tree
___________________________________________________________________
Name: svn:ignore
+ .settings
target
.classpath
.project
.springBeans
Name: svn:mergeinfo
+
Modified:
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
===================================================================
---
core3/vizmap-impl/trunk/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
2010-08-23 17:19:54 UTC (rev 21529)
+++
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
2010-09-15 23:28:35 UTC (rev 21884)
@@ -42,7 +42,7 @@
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.RootVisualLexicon;
+import org.cytoscape.view.model.VisualLexiconManager;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.vizmap.VisualMappingFunction;
import org.cytoscape.view.vizmap.VisualMappingManager;
@@ -58,7 +58,7 @@
private final Map<CyNetworkView, VisualStyle> vsForNetwork;
private final Set<VisualStyle> visualStyles;
private CyEventHelper cyEventHelper;
- private RootVisualLexicon rootLexicon;
+ private VisualLexiconManager rootLexicon;
/**
*
@@ -66,7 +66,7 @@
* DOCUMENT ME!
*/
public VisualMappingManagerImpl(final CyEventHelper eventHelper,
- final RootVisualLexicon rootLexicon) {
+ final VisualLexiconManager rootLexicon)
{
if (eventHelper == null)
throw new IllegalArgumentException("CyEventHelper
cannot be null");
@@ -167,10 +167,6 @@
return visualStyles;
}
- public RootVisualLexicon getRootVisualLexicon() {
- // TODO Auto-generated method stub
- return null;
- }
public <K, V> VisualMappingFunction<K, V> createMapping(String
mappingType,
String attrName, Class<K> attrType, VisualProperty<V>
vp) {
Deleted:
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
===================================================================
---
core3/vizmap-impl/trunk/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
2010-08-23 17:19:54 UTC (rev 21529)
+++
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
2010-09-15 23:28:35 UTC (rev 21884)
@@ -1,264 +0,0 @@
-/*
- Copyright (c) 2008, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
- This library is free software; you can redistribute it and/or modify it
- under the terms of the GNU Lesser General Public License as published
- by the Free Software Foundation; either version 2.1 of the License, or
- any later version.
-
- This library is distributed in the hope that it will be useful, but
- WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- documentation provided hereunder is on an "as is" basis, and the
- Institute for Systems Biology and the Whitehead Institute
- have no obligations to provide maintenance, support,
- updates, enhancements or modifications. In no event shall the
- Institute for Systems Biology and the Whitehead Institute
- be liable to any party for direct, indirect, special,
- incidental or consequential damages, including lost profits, arising
- out of the use of this software and its documentation, even if the
- Institute for Systems Biology and the Whitehead Institute
- have been advised of the possibility of such damage. See
- the GNU Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public License
- along with this library; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
-*/
-package org.cytoscape.view.vizmap.internal;
-
-import static org.cytoscape.model.GraphObject.EDGE;
-import static org.cytoscape.model.GraphObject.NETWORK;
-import static org.cytoscape.model.GraphObject.NODE;
-
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.GraphObject;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.RootVisualLexicon;
-import org.cytoscape.view.model.View;
-import org.cytoscape.view.model.VisualLexicon;
-import org.cytoscape.view.model.VisualProperty;
-import org.cytoscape.view.vizmap.VisualMappingFunction;
-import org.cytoscape.view.vizmap.VisualStyle;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-
-/**
- */
-public class VisualStyleImpl implements VisualStyle {
-
- private static final Logger logger =
LoggerFactory.getLogger(VisualStyleImpl.class);
-
- private Map<VisualProperty<?>, VisualMappingFunction<?, ?>> mappings;
- private Map<VisualProperty<?>, Object> perVSDefaults;
- private RootVisualLexicon rootLexicon;
- private static final String DEFAULT_TITLE = "?";
- private String title;
-
- /**
- * Creates a new VisualStyleImpl object.
- *
- * @param rootLexicon DOCUMENT ME!
- */
- public VisualStyleImpl(final RootVisualLexicon rootLexicon) {
- this(rootLexicon, null);
- }
-
- /**
- * Creates a new VisualStyleImpl object.
- *
- * @param eventHelper DOCUMENT ME!
- * @param rootLexicon DOCUMENT ME!
- */
- public VisualStyleImpl(final RootVisualLexicon rootLexicon, final
String title) {
- if (rootLexicon == null)
- throw new NullPointerException("rootLexicon is null");
-
- if (title == null)
- this.title = DEFAULT_TITLE;
- else
- this.title = title;
-
- this.rootLexicon = rootLexicon;
- mappings = new HashMap<VisualProperty<?>,
VisualMappingFunction<?, ?>>();
- perVSDefaults = new HashMap<VisualProperty<?>, Object>();
- // Copy immutable defaults from each VP
- for(VisualProperty<?> vp:
this.rootLexicon.getAllVisualProperties())
- perVSDefaults.put(vp, vp.getDefault());
-
- logger.info("New Visual Style Constructed: " + this.title);
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- */
- public void addVisualMappingFunction(final VisualMappingFunction<?, ?>
mapping) {
- mappings.put(mapping.getVisualProperty(), mapping);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param <V> DOCUMENT ME!
- * @param t DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @SuppressWarnings("unchecked")
- public <V> VisualMappingFunction<?, V>
getVisualMappingFunction(VisualProperty<V> t) {
- return (VisualMappingFunction<?, V>) mappings.get(t);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param <V> DOCUMENT ME!
- * @param t DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @SuppressWarnings("unchecked")
- public <V> VisualMappingFunction<?, V>
removeVisualMappingFunction(VisualProperty<V> t) {
- return (VisualMappingFunction<?, V>) mappings.remove(t);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param <T> DOCUMENT ME!
- * @param vp DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @SuppressWarnings("unchecked")
- public <V> V getDefaultValue(final VisualProperty<? extends V> vp) {
- // Since setter checks type, this cast is always legal.
- return (V) perVSDefaults.get(vp);
- }
-
- /**
- * Set the default value for a Visual Property
- *
- * @param <T> Default value data type.
- * @param vp DOCUMENT ME!
- * @param value DOCUMENT ME!
- */
- public <T> void setDefaultValue(final VisualProperty<? extends T> vp,
final T value) {
- perVSDefaults.put(vp, value);
- }
-
- // ??
- /**
- * DOCUMENT ME!
- *
- * @param view DOCUMENT ME!
- */
- public void apply(final CyNetworkView view) {
- final Collection<View<CyNode>> nodeviews = view.getNodeViews();
- final Collection<View<CyEdge>> edgeviews = view.getEdgeViews();
-
- applyImpl(view, nodeviews,
- rootLexicon.getVisualProperties(nodeviews, NODE));
- applyImpl(view, edgeviews,
- rootLexicon.getVisualProperties(edgeviews, EDGE));
- applyImpl(view, Arrays.asList((View<CyNetwork>) view),
- rootLexicon.getVisualProperties(NETWORK));
- }
-
- // note: can't use applyImpl(List<View<?>>views ... ) because that does
not compile
- /**
- * DOCUMENT ME!
- *
- * @param <T> DOCUMENT ME!
- * @param views DOCUMENT ME!
- * @param visualProperties DOCUMENT ME!
- */
- public <G extends GraphObject> void applyImpl(final CyNetworkView view,
- final Collection<View<G>>
views,
- final Collection<?extends
VisualProperty<?>> visualProperties) {
-
- for (VisualProperty<?> vp : visualProperties)
- applyImpl(view, views, vp);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param <T> DOCUMENT ME!
- * @param views DOCUMENT ME!
- * @param visualProperties DOCUMENT ME!
- */
- public <V, G extends GraphObject> void applyImpl(final CyNetworkView
view,
- final
Collection<View<G>> views,
- final
VisualProperty<V> vp) {
-
- final VisualMappingFunction<?, V> mapping =
getVisualMappingFunction(vp);
- final V defaultValue = getDefaultValue(vp);
-
-
- // If mapping is available for this VP, apply the mapping.
- if (mapping != null) {
- mapping.apply(views);
- } else {
- // reset all rows to allow usage of default value:
- for(View<G> v: views)
- v.setVisualProperty(vp, defaultValue);
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param title DOCUMENT ME!
- */
- public void setTitle(String title) {
- this.title = title;
- }
-
- /**
- * toString method returns title of this Visual Style.
- *
- * @return DOCUMENT ME!
- */
- @Override
- public String toString() {
- return this.title;
- }
-
- public Collection<VisualMappingFunction<?,?>>
getAllVisualMappingFunctions() {
- return mappings.values();
- }
-
- //TODO Is this the right set of lexicon?
- public VisualLexicon getVisualLexicon() {
- return rootLexicon;
- }
-
-}
Copied:
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
(from rev 21781,
core3/vizmap-impl/trunk/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java)
===================================================================
---
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
(rev 0)
+++
core3/vizmap-impl/branches/vp-tree/src/main/java/org/cytoscape/view/vizmap/internal/VisualStyleImpl.java
2010-09-15 23:28:35 UTC (rev 21884)
@@ -0,0 +1,328 @@
+/*
+ Copyright (c) 2008, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package org.cytoscape.view.vizmap.internal;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.VisualLexicon;
+import org.cytoscape.view.model.VisualLexiconManager;
+import org.cytoscape.view.model.VisualProperty;
+import org.cytoscape.view.vizmap.VisualMappingFunction;
+import org.cytoscape.view.vizmap.VisualStyle;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ */
+public class VisualStyleImpl implements VisualStyle {
+
+ private static final Logger logger = LoggerFactory
+ .getLogger(VisualStyleImpl.class);
+
+ private static final String DEFAULT_TITLE = "?";
+
+ private final Map<VisualProperty<?>, VisualMappingFunction<?, ?>>
mappings;
+ private final Map<VisualProperty<?>, Object> perVSDefaults;
+ private final VisualLexiconManager lexiconManager;
+
+ private String title;
+
+ /**
+ * Creates a new VisualStyleImpl object.
+ *
+ * @param rootLexicon
+ * DOCUMENT ME!
+ */
+ public VisualStyleImpl(final VisualLexiconManager lexiconManager) {
+ this(lexiconManager, null);
+ }
+
+ /**
+ * Creates a new VisualStyleImpl object.
+ *
+ * @param eventHelper
+ * DOCUMENT ME!
+ * @param rootLexicon
+ * DOCUMENT ME!
+ */
+ public VisualStyleImpl(final VisualLexiconManager lexiconManager,
+ final String title) {
+ if (lexiconManager == null)
+ throw new NullPointerException("rootLexicon is null");
+
+ if (title == null)
+ this.title = DEFAULT_TITLE;
+ else
+ this.title = title;
+
+ this.lexiconManager = lexiconManager;
+ mappings = new HashMap<VisualProperty<?>,
VisualMappingFunction<?, ?>>();
+ perVSDefaults = new HashMap<VisualProperty<?>, Object>();
+
+ // Copy immutable defaults from each VP
+ final VisualLexicon root = lexiconManager.getLexicon();
+
+ for (VisualProperty<?> vp : root.getAllVisualProperties())
+ perVSDefaults.put(vp, vp.getDefault());
+
+ logger.info("New Visual Style Created: Style Name = " +
this.title);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ */
+ public void addVisualMappingFunction(
+ final VisualMappingFunction<?, ?> mapping) {
+ mappings.put(mapping.getVisualProperty(), mapping);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param <V>
+ * DOCUMENT ME!
+ * @param t
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @SuppressWarnings("unchecked")
+ public <V> VisualMappingFunction<?, V> getVisualMappingFunction(
+ VisualProperty<V> t) {
+ return (VisualMappingFunction<?, V>) mappings.get(t);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param <V>
+ * DOCUMENT ME!
+ * @param t
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @SuppressWarnings("unchecked")
+ public <V> VisualMappingFunction<?, V> removeVisualMappingFunction(
+ VisualProperty<V> t) {
+ return (VisualMappingFunction<?, V>) mappings.remove(t);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param <T>
+ * DOCUMENT ME!
+ * @param vp
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @SuppressWarnings("unchecked")
+ public <V> V getDefaultValue(final VisualProperty<? extends V> vp) {
+ // Since setter checks type, this cast is always legal.
+ return (V) perVSDefaults.get(vp);
+ }
+
+ /**
+ * Set the default value for a Visual Property
+ *
+ * @param <T>
+ * Default value data type.
+ * @param vp
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ */
+ public <T> void setDefaultValue(final VisualProperty<? extends T> vp,
+ final T value) {
+ perVSDefaults.put(vp, value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param networkView
+ * DOCUMENT ME!
+ */
+ @Override
+ public void apply(final CyNetworkView networkView) {
+
+ logger.debug("Visual Style Apply method called: " + this.title);
+
+ final Collection<View<CyNode>> nodeviews =
networkView.getNodeViews();
+ final Collection<View<CyEdge>> edgeviews =
networkView.getEdgeViews();
+ // final Collection<View<CyNetwork>> networkviews = new
+ // HashSet<View<CyNetwork>>();
+ // networkviews.add(networkView);
+
+ // Current visual prop tree.
+ final VisualLexicon lexicon = lexiconManager.getLexicon();
+ Collection<View<? extends CyTableEntry>> allViews = networkView
+ .getAllViews();
+ applyImpl(allViews, lexicon.getAllVisualProperties());
+ // applyImpl(networkView, nodeviews,
+ // lexicon.getVisualProperties(nodeviews));
+ // applyImpl(networkView, edgeviews,
+ // lexicon.getVisualProperties(edgeviews));
+ // applyImpl(networkView, networkviews,
+ // lexicon.getVisualProperties(NETWORK));
+
+ logger.debug("Visual Style applied: " + this.title + "\n");
+ }
+
+ private void traverse() {
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param <T>
+ * DOCUMENT ME!
+ * @param views
+ * DOCUMENT ME!
+ * @param visualProperties
+ * DOCUMENT ME!
+ */
+ private void applyImpl(
+ final Collection<View<? extends CyTableEntry>> views,
+ final Collection<? extends VisualProperty<?>>
visualProperties) {
+
+ for (VisualProperty<?> vp : visualProperties)
+ applyImpl(views, vp);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param <T>
+ * DOCUMENT ME!
+ * @param views
+ * DOCUMENT ME!
+ * @param visualProperties
+ * DOCUMENT ME!
+ */
+ private void applyImpl(
+ final Collection<View<? extends CyTableEntry>> views,
+ final VisualProperty<?> vp) {
+
+ final VisualMappingFunction<?, ?> mapping =
getVisualMappingFunction(vp);
+
+
+ // If mapping is available for this VP, apply the mapping.
+ if (mapping != null) {
+ mapping.apply(views);
+ } else if (!vp.isIgnoreDefault()) { // Check ignore flag first.
+ applyStyleDefaults(views, vp);
+ } else
+ logger.debug(vp.getDisplayName()
+ + " is set to ignore defaults.
Skipping...");
+ }
+
+
+ private void applyStyleDefaults(Collection<View<? extends
CyTableEntry>> views, final VisualProperty<?> vp) {
+
+ final Object defaultValue = getDefaultValue(vp);
+
+ // reset all rows to allow usage of default value:
+ for (final View<? extends CyTableEntry> viewModel : views) {
+
+ // If equals, it is not necessary to set new value.
+ if
(viewModel.getVisualProperty(vp).equals(defaultValue))
+ continue;
+
+ // Not a leaf VP. We can ignore those.
+ if(vp.getChildren().size() != 0)
+ continue;
+
+ // This is a leaf
+ viewModel.setVisualProperty(vp, defaultValue);
+ // logger.debug(vp.getDisplayName() + " updated: " +
+ // defaultValue);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param title
+ * DOCUMENT ME!
+ */
+ public void setTitle(String title) {
+ this.title = title;
+ }
+
+ /**
+ * toString method returns title of this Visual Style.
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public String toString() {
+ return this.title;
+ }
+
+ public Collection<VisualMappingFunction<?, ?>>
getAllVisualMappingFunctions() {
+ return mappings.values();
+ }
+
+ // TODO Is this the right set of lexicon?
+ public VisualLexicon getVisualLexicon() {
+ return lexiconManager.getLexicon();
+ }
+
+}
--
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