Author: mes
Date: 2011-07-05 17:49:28 -0700 (Tue, 05 Jul 2011)
New Revision: 26054
Added:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingFactory.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingImpl.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingFactory.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingImpl.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingFactory.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingImpl.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/
core3/vizmap-impl/trunk/impl/src/test/java/org/cytoscape/view/vizmap/mappings/
core3/vizmap-impl/trunk/impl/src/test/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingTest.java
Removed:
core3/vizmap-impl/trunk/impl/src/test/java/org/cytoscape/view/vizmap/internal/
core3/vizmap-impl/trunk/impl/src/test/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingTest.java
Modified:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/FlatInterpolator.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/Interpolator.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/LinearNumberInterpolator.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/LinearNumberToColorInterpolator.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/LinearNumberToNumberInterpolator.java
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/NumberInterpolator.java
Log:
moved from API
Copied:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingFactory.java
(from rev 26051,
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/ContinuousMappingFactory.java)
===================================================================
---
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingFactory.java
(rev 0)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingFactory.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -0,0 +1,36 @@
+package org.cytoscape.view.vizmap.internal.mappings;
+
+import org.cytoscape.view.model.VisualProperty;
+import org.cytoscape.view.vizmap.VisualMappingFunction;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
+import org.cytoscape.view.vizmap.mappings.ContinuousMapping;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class ContinuousMappingFactory implements VisualMappingFunctionFactory {
+
+ private static final Logger logger =
LoggerFactory.getLogger(ContinuousMappingFactory.class);
+
+ @Override
+ public <K, V> VisualMappingFunction<K, V>
createVisualMappingFunction(final String attributeName,
+ Class<K> attrValueType, VisualProperty<V> vp) {
+
+ logger.debug("Trying to create Continuous mapping. Data Type
is " + attrValueType);
+
+ // Validate attribute type: Continuous Mapping is compatible
with Numbers only.
+ if(Number.class.isAssignableFrom(attrValueType) == false)
+ throw new IllegalArgumentException("ContinuousMapping
can be used for numerical attributes only.");
+
+ return new ContinuousMappingImpl<K, V>(attributeName,
attrValueType, vp);
+ }
+
+ @Override public String toString() {
+ return ContinuousMapping.CONTINUOUS;
+ }
+
+ @Override
+ public Class<?> getMappingFunctionType() {
+ return ContinuousMapping.class;
+ }
+
+}
Copied:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingImpl.java
(from rev 26051,
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/ContinuousMappingImpl.java)
===================================================================
---
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingImpl.java
(rev 0)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/ContinuousMappingImpl.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -0,0 +1,291 @@
+/*
+ File: ContinuousMappingImpl.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ 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.mappings;
+
+
+import java.awt.Color;
+import java.awt.Paint;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.VisualProperty;
+import
org.cytoscape.view.vizmap.internal.mappings.interpolators.FlatInterpolator;
+import org.cytoscape.view.vizmap.internal.mappings.interpolators.Interpolator;
+import
org.cytoscape.view.vizmap.internal.mappings.interpolators.LinearNumberToColorInterpolator;
+import
org.cytoscape.view.vizmap.internal.mappings.interpolators.LinearNumberToNumberInterpolator;
+import org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction;
+import org.cytoscape.view.vizmap.mappings.BoundaryRangeValues;
+import org.cytoscape.view.vizmap.mappings.ContinuousMapping;
+import org.cytoscape.view.vizmap.mappings.ContinuousMappingPoint;
+
+
+/**
+ * Implements an interpolation table mapping data to values of a particular
+ * class. The data value is extracted from a bundle of attributes by using a
+ * specified data attribute name.
+ *
+ * @param <V>
+ * Type of object Visual Property holds
+ *
+ * For refactoring changes in this class, please refer to:
+ * cytoscape.visual.mappings.continuous.README.txt.
+ *
+ */
+public class ContinuousMappingImpl<K, V> extends
AbstractVisualMappingFunction<K, V> implements ContinuousMapping<K, V> {
+
+ // used to interpolate between boundaries
+ private Interpolator<K, V> interpolator;
+
+ // Contains List of Data Points
+ private List<ContinuousMappingPoint<K, V>> points;
+
+ ContinuousMappingImpl(final String attrName, final Class<K> attrType,
final VisualProperty<V> vp) {
+ super(attrName, attrType, vp);
+
+ // Validate type. K is always a number.
+ if(Number.class.isAssignableFrom(attrType) == false)
+ throw new IllegalArgumentException("Attribute type
should be Number.");
+
+ this.points = new ArrayList<ContinuousMappingPoint<K, V>>();
+
+ // TODO FIXME use factory here.
+ // Create Interpolator
+ if (vp.getRange().getType() == Color.class ||
vp.getRange().getType() == Paint.class)
+ interpolator = (Interpolator<K, V>) new
LinearNumberToColorInterpolator();
+ else if (Number.class.isAssignableFrom(vp.getRange().getType()))
+ interpolator = (Interpolator<K, V>) new
LinearNumberToNumberInterpolator();
+ else
+ interpolator = (Interpolator<K, V>) new
FlatInterpolator();
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.cytoscape.view.vizmap.mappings.ContinuousMapping#toString()
+ */
+ @Override
+ public String toString() {
+ return ContinuousMapping.CONTINUOUS;
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.ContinuousMapping#getAllPoints()
+ */
+ @Override
+ public List<ContinuousMappingPoint<K, V>> getAllPoints() {
+ return points;
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.ContinuousMapping#addPoint(K,
org.cytoscape.view.vizmap.mappings.BoundaryRangeValues)
+ */
+ @Override
+ public void addPoint(K value, BoundaryRangeValues<V> brv) {
+ points.add(new ContinuousMappingPoint<K, V>(value, brv));
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.ContinuousMapping#removePoint(int)
+ */
+ @Override
+ public void removePoint(int index) {
+ points.remove(index);
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.ContinuousMapping#getPointCount()
+ */
+ @Override
+ public int getPointCount() {
+ return points.size();
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.ContinuousMapping#getPoint(int)
+ */
+ @Override
+ public ContinuousMappingPoint<K, V> getPoint(int index) {
+ return points.get(index);
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.ContinuousMapping#apply(org.cytoscape.view.model.View)
+ */
+ @Override
+ public void apply(final View<? extends CyTableEntry> view) {
+ if (view == null)
+ return;
+
+ if(this.points.size() == 0)
+ return;
+
+ doMap(view);
+ }
+
+ /**
+ * Read attribute from row, map it and apply it.
+ *
+ * types are guaranteed to be correct (? FIXME: check this)
+ *
+ * Putting this in a separate method makes it possible to make it
+ * type-parametric.
+ *
+ * @param <V>
+ * the type-parameter of the ViewColumn column
+ * @param <K>
+ * the type-parameter of the domain of the mapping (the
object
+ * read as an attribute value has to be is-a K)
+ * @param <V>
+ * the type-parameter of the View
+ */
+ private void doMap(final View<? extends CyTableEntry> view) {
+
+ final CyRow row = view.getModel().getCyRow();
+
+ if (row.isSet(attrName)) {
+ // skip Views where source attribute is not defined;
+ // ViewColumn will automatically substitute the per-VS
or global
+ // default, as appropriate
+
+ // In all cases, attribute value should be a number for
continuous
+ // mapping.
+ final K attrValue = view.getModel().getCyRow()
+ .get(attrName, attrType);
+ final V value = getRangeValue(attrValue);
+ view.setVisualProperty(vp, value);
+ } else { // remove value so that default value will be used:
+ view.setVisualProperty(vp, null);
+ }
+
+ }
+
+ private V getRangeValue(K domainValue) {
+ ContinuousMappingPoint<K, V> firstPoint = points.get(0);
+ K minDomain = firstPoint.getValue();
+
+ // if given domain value is smaller than any in our list,
+ // return the range value for the smallest domain value we have.
+ int firstCmp = compareValues(domainValue, minDomain);
+
+ if (firstCmp <= 0) {
+ BoundaryRangeValues<V> bv = firstPoint.getRange();
+
+ if (firstCmp < 0)
+ return bv.lesserValue;
+ else
+
+ return bv.equalValue;
+ }
+
+ // if given domain value is larger than any in our Vector,
+ // return the range value for the largest domain value we have.
+ ContinuousMappingPoint<K, V> lastPoint =
points.get(points.size() - 1);
+ K maxDomain = lastPoint.getValue();
+
+ if (compareValues(domainValue, maxDomain) > 0) {
+ BoundaryRangeValues<V> bv = lastPoint.getRange();
+
+ return bv.greaterValue;
+ }
+
+ // OK, it's somewhere in the middle, so find the boundaries and
+ // pass to our interpolator function. First check for a null
+ // interpolator function
+ if (this.interpolator == null)
+ return null;
+
+ // Note that the list of Points is sorted.
+ // Also, the case of the inValue equalling the smallest key was
+ // checked above.
+ ContinuousMappingPoint<K, V> currentPoint;
+ int index = 0;
+
+ for (index = 0; index < points.size(); index++) {
+ currentPoint = points.get(index);
+
+ K currentValue = currentPoint.getValue();
+ int cmpValue = compareValues(domainValue, currentValue);
+
+ if (cmpValue == 0) {
+ BoundaryRangeValues<V> bv =
currentPoint.getRange();
+
+ return bv.equalValue;
+ } else if (cmpValue < 0)
+ break;
+ }
+
+ return getRangeValue(index, domainValue);
+ }
+
+ /**
+ * This is tricky. The desired domain value is greater than lowerDomain
and
+ * less than upperDomain. Therefore, we want the "greater" field of the
+ * lower boundary value (because the desired domain value is greater)
and
+ * the "lesser" field of the upper boundary value (semantic
difficulties).
+ */
+ private V getRangeValue(int index, K domainValue) {
+ // Get Lower Domain and Range
+ ContinuousMappingPoint<K, V> lowerBound = points.get(index - 1);
+ K lowerDomain = lowerBound.getValue();
+ BoundaryRangeValues<V> lv = lowerBound.getRange();
+ V lowerRange = lv.greaterValue;
+
+ // Get Upper Domain and Range
+ ContinuousMappingPoint<K, V> upperBound = points.get(index);
+ K upperDomain = upperBound.getValue();
+ BoundaryRangeValues<V> gv = upperBound.getRange();
+ V upperRange = gv.lesserValue;
+
+ V value = interpolator.getRangeValue(lowerDomain, lowerRange,
upperDomain, upperRange, domainValue);
+
+ return value;
+ }
+
+ /**
+ * Helper function to compare Number objects. This is needed because
Java
+ * doesn't allow comparing, for example, Integer objects to Double
objects.
+ */
+ private int compareValues(K probe, K target) {
+
+ final Number n1 = (Number) probe;
+ final Number n2 = (Number) target;
+ double d1 = n1.doubleValue();
+ double d2 = n2.doubleValue();
+
+ if (d1 < d2)
+ return -1;
+ else if (d1 > d2)
+ return 1;
+ else
+ return 0;
+ }
+}
Copied:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingFactory.java
(from rev 26051,
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingFactory.java)
===================================================================
---
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingFactory.java
(rev 0)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingFactory.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -0,0 +1,27 @@
+package org.cytoscape.view.vizmap.internal.mappings;
+
+import org.cytoscape.view.model.VisualProperty;
+import org.cytoscape.view.vizmap.VisualMappingFunction;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
+import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
+
+public class DiscreteMappingFactory implements
+ VisualMappingFunctionFactory {
+
+ @Override
+ public <K, V> VisualMappingFunction<K, V>
createVisualMappingFunction(final String attributeName,
+ Class<K> attrValueType, final VisualProperty<V> vp) {
+
+ return new DiscreteMappingImpl<K, V>(attributeName,
attrValueType, vp);
+ }
+
+ @Override public String toString() {
+ return DiscreteMapping.DISCRETE;
+ }
+
+ @Override
+ public Class<?> getMappingFunctionType() {
+ return DiscreteMapping.class;
+ }
+
+}
Copied:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingImpl.java
(from rev 26051,
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingImpl.java)
===================================================================
---
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingImpl.java
(rev 0)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/DiscreteMappingImpl.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -0,0 +1,170 @@
+/*
+ File: DiscreteMappingImpl.java
+
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ 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.mappings;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.VisualProperty;
+import org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction;
+import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Implements a lookup table mapping data to values of a particular class. The
+ * data value is extracted from a bundle of attributes by using a specified
data
+ * attribute name.
+ */
+public class DiscreteMappingImpl<K, V> extends
AbstractVisualMappingFunction<K, V> implements DiscreteMapping<K, V> {
+
+ private static final Logger logger =
LoggerFactory.getLogger(DiscreteMapping.class);
+
+ // contains the actual map elements (sorted)
+ private final Map<K, V> attribute2visualMap;
+
+ /**
+ * Constructor.
+ *
+ * @param defObj
+ * Default Object.
+ */
+ public DiscreteMappingImpl(final String attrName, final Class<K>
attrType, final VisualProperty<V> vp) {
+ super(attrName, attrType, vp);
+ attribute2visualMap = new HashMap<K, V>();
+ }
+
+ /* (non-Javadoc)
+ * @see org.cytoscape.view.vizmap.mappings.DiscreteMapping#toString()
+ */
+ @Override
+ public String toString() {
+ return DiscreteMapping.DISCRETE;
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.DiscreteMapping#apply(org.cytoscape.view.model.View)
+ */
+ @Override
+ public void apply(View<? extends CyTableEntry> view) {
+ if (view == null)
+ return; // empty view, nothing to do
+
+ applyDiscreteMapping(view);
+ }
+
+ /**
+ * Read attribute from row, map it and apply it.
+ *
+ * types are guaranteed to be correct (? FIXME: check this)
+ *
+ * Putting this in a separate method makes it possible to make it
+ * type-parametric.
+ *
+ * @param <V>
+ * the type-parameter of the ViewColumn column
+ * @param <K>
+ * the type-parameter of the key stored in the mapping (the
+ * object read as an attribute value has to be is-a K)
+ * @param <V>
+ * the type-parameter of the View
+ */
+ private void applyDiscreteMapping(final View<? extends CyTableEntry>
view) {
+ final CyRow row = view.getModel().getCyRow();
+ V value = null;
+
+ if (row.isSet(attrName)) {
+ // skip Views where source attribute is not defined;
+ // ViewColumn will automatically substitute the per-VS
or global
+ // default, as appropriate
+ final CyColumn column =
row.getTable().getColumn(attrName);
+ final Class<?> attrClass = column.getType();
+
+ if (attrClass.isAssignableFrom(List.class)) {
+ List<?> list = row.getList(attrName,
column.getListElementType());
+
+ if (list != null) {
+ for (Object item : list) {
+ // TODO: should we convert
other types to String?
+ String key = item.toString();
+ value =
attribute2visualMap.get(key);
+ if (value != null)
+ break;
+ }
+ }
+ } else {
+ Object key = row.get(attrName, attrType);
+
+ if (key != null)
+ value = attribute2visualMap.get(key);
+ }
+ }
+
+ // set a new value or null to use the default one:
+ view.setVisualProperty(vp, value);
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.DiscreteMapping#getMapValue(K)
+ */
+ @Override
+ public V getMapValue(K key) {
+ return attribute2visualMap.get(key);
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.DiscreteMapping#putMapValue(K, T)
+ */
+ @Override
+ public <T extends V> void putMapValue(final K key, final T value) {
+ attribute2visualMap.put(key, value);
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.DiscreteMapping#putAll(java.util.Map)
+ */
+ @Override
+ public <T extends V> void putAll(Map<K, T> map) {
+ attribute2visualMap.putAll(map);
+ }
+
+ /* (non-Javadoc)
+ * @see org.cytoscape.view.vizmap.mappings.DiscreteMapping#getAll()
+ */
+ @Override
+ public Map<K, V> getAll() {
+ return attribute2visualMap;
+ }
+}
Copied:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingFactory.java
(from rev 26051,
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/PassthroughMappingFactory.java)
===================================================================
---
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingFactory.java
(rev 0)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingFactory.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -0,0 +1,25 @@
+package org.cytoscape.view.vizmap.internal.mappings;
+
+import org.cytoscape.view.model.VisualProperty;
+import org.cytoscape.view.vizmap.VisualMappingFunction;
+import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
+import org.cytoscape.view.vizmap.mappings.PassthroughMapping;
+
+public class PassthroughMappingFactory implements VisualMappingFunctionFactory{
+
+ @Override
+ public <K, V> VisualMappingFunction<K, V>
createVisualMappingFunction(final String attributeName,
+ Class<K> attrValueType, VisualProperty<V> vp) {
+ return new PassthroughMappingImpl<K, V>(attributeName,
attrValueType, vp);
+ }
+
+ @Override public String toString() {
+ return PassthroughMapping.PASSTHROUGH;
+ }
+
+ @Override
+ public Class<?> getMappingFunctionType() {
+ return PassthroughMapping.class;
+ }
+
+}
Copied:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingImpl.java
(from rev 26051,
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/PassthroughMappingImpl.java)
===================================================================
---
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingImpl.java
(rev 0)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/PassthroughMappingImpl.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -0,0 +1,118 @@
+/*
+ Copyright (c) 2006, 2007, 2010, The Cytoscape Consortium (www.cytoscape.org)
+
+ 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.mappings;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.model.VisualProperty;
+import org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction;
+import org.cytoscape.view.vizmap.mappings.PassthroughMapping;
+
+/**
+ */
+public class PassthroughMappingImpl<K, V> extends
+ AbstractVisualMappingFunction<K, V> implements
PassthroughMapping<K, V> {
+
+ /**
+ * dataType is the type of the _attribute_ !! currently we force that
to be
+ * the same as the VisualProperty; FIXME: allow different once? but how
to
+ * coerce?
+ */
+ public PassthroughMappingImpl(final String attrName, final Class<K>
attrType,
+ final VisualProperty<V> vp) {
+ super(attrName, attrType, vp);
+ }
+
+ /* (non-Javadoc)
+ * @see org.cytoscape.view.vizmap.mappings.PassthroughMapping#toString()
+ */
+ @Override
+ public String toString() {
+ return PassthroughMapping.PASSTHROUGH;
+ }
+
+ /* (non-Javadoc)
+ * @see
org.cytoscape.view.vizmap.mappings.PassthroughMapping#apply(org.cytoscape.view.model.View)
+ */
+ @Override
+ public void apply(final View<? extends CyTableEntry> view) {
+ if (view == null)
+ return; // empty list, nothing to do
+
+ final CyRow row = view.getModel().getCyRow();
+
+ if (row.isSet(attrName)) {
+ // skip Views where source attribute is not defined;
+ // ViewColumn will automatically substitute the per-VS
or
+ // global default, as appropriate
+ final CyColumn column =
row.getTable().getColumn(attrName);
+ final Class<?> attrClass = column.getType();
+ K value = null;
+
+ if (attrClass.isAssignableFrom(List.class)) {
+ List<?> list = row.getList(attrName,
column.getListElementType());
+ StringBuffer sb = new StringBuffer();
+
+ if (list != null && !list.isEmpty()) {
+ for (Object item : list)
+ sb.append(item.toString() +
"\n");
+
+ sb.deleteCharAt(sb.length() - 1);
+ }
+
+ value = (K) sb.toString();
+ } else {
+ value = row.get(attrName, attrType);
+ }
+
+ final V converted = convertToValue(value);
+
+ view.setVisualProperty(vp, converted);
+ } else {
+ // remove value, so that default value will be used:
+ view.setVisualProperty(vp, null);
+ }
+ }
+
+ // TODO: make this converter pluggable
+ private V convertToValue(final K key) {
+ try {
+ return (V) key;
+ } catch (Exception e) {
+ return null;
+ }
+
+ }
+}
Modified:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/FlatInterpolator.java
===================================================================
---
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/FlatInterpolator.java
2011-07-05 23:08:15 UTC (rev 26049)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/FlatInterpolator.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -41,9 +41,11 @@
// $Date: 2007-04-17 19:50:13 -0700 (Tue, 17 Apr 2007) $
// $Author: kono $
//----------------------------------------------------------------------------
-package org.cytoscape.view.vizmap.mappings.interpolators;
+package org.cytoscape.view.vizmap.internal.mappings.interpolators;
+import org.cytoscape.view.vizmap.mappings.interpolators.Interpolator;
+
//----------------------------------------------------------------------------
/**
* This simple Interpolator returns the value at either the lower or upper
Modified:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/Interpolator.java
===================================================================
---
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/Interpolator.java
2011-07-05 23:08:15 UTC (rev 26049)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/Interpolator.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -42,7 +42,7 @@
// $Date: 2007-03-19 17:25:45 -0700 (Mon, 19 Mar 2007) $
// $Author: mes $
//----------------------------------------------------------------------------
-package org.cytoscape.view.vizmap.mappings.interpolators;
+package org.cytoscape.view.vizmap.internal.mappings.interpolators;
//----------------------------------------------------------------------------
Modified:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/LinearNumberInterpolator.java
===================================================================
---
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/LinearNumberInterpolator.java
2011-07-05 23:08:15 UTC (rev 26049)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/LinearNumberInterpolator.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -41,8 +41,10 @@
// $Date: 2007-04-17 19:50:13 -0700 (Tue, 17 Apr 2007) $
// $Author: kono $
//----------------------------------------------------------------------------
-package org.cytoscape.view.vizmap.mappings.interpolators;
+package org.cytoscape.view.vizmap.internal.mappings.interpolators;
+import org.cytoscape.view.vizmap.mappings.interpolators.NumberInterpolator;
+
//----------------------------------------------------------------------------
/**
* This subclass of NumberInterpolator further assumes a linear interpolation,
Modified:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/LinearNumberToColorInterpolator.java
===================================================================
---
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/LinearNumberToColorInterpolator.java
2011-07-05 23:08:15 UTC (rev 26049)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/LinearNumberToColorInterpolator.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -36,11 +36,13 @@
*/
//LinearNumberToColorInterpolator.java
-package org.cytoscape.view.vizmap.mappings.interpolators;
+package org.cytoscape.view.vizmap.internal.mappings.interpolators;
import java.awt.*;
+import
org.cytoscape.view.vizmap.mappings.interpolators.LinearNumberInterpolator;
+
/**
* The class provides a linear interpolation between color values. The
* (red,green,blue,alpha) values of the returned color are linearly
Modified:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/LinearNumberToNumberInterpolator.java
===================================================================
---
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/LinearNumberToNumberInterpolator.java
2011-07-05 23:08:15 UTC (rev 26049)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/LinearNumberToNumberInterpolator.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -41,8 +41,10 @@
// $Date: 2007-04-17 19:50:13 -0700 (Tue, 17 Apr 2007) $
// $Author: kono $
//----------------------------------------------------------------------------
-package org.cytoscape.view.vizmap.mappings.interpolators;
+package org.cytoscape.view.vizmap.internal.mappings.interpolators;
+import
org.cytoscape.view.vizmap.mappings.interpolators.LinearNumberInterpolator;
+
//----------------------------------------------------------------------------
/**
* The class assumes that the supplied range objects are Numbers, and returns a
Modified:
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/NumberInterpolator.java
===================================================================
---
core3/vizmap-api/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/interpolators/NumberInterpolator.java
2011-07-05 23:08:15 UTC (rev 26049)
+++
core3/vizmap-impl/trunk/impl/src/main/java/org/cytoscape/view/vizmap/internal/mappings/interpolators/NumberInterpolator.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -41,8 +41,10 @@
// $Date: 2007-03-19 17:25:45 -0700 (Mon, 19 Mar 2007) $
// $Author: mes $
//----------------------------------------------------------------------------
-package org.cytoscape.view.vizmap.mappings.interpolators;
+package org.cytoscape.view.vizmap.internal.mappings.interpolators;
+import org.cytoscape.view.vizmap.mappings.interpolators.Interpolator;
+
//----------------------------------------------------------------------------
/**
* This partial implementation of Interpolator assumes that the domain values
Deleted:
core3/vizmap-impl/trunk/impl/src/test/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingTest.java
===================================================================
---
core3/vizmap-api/trunk/src/test/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingTest.java
2011-07-05 23:08:15 UTC (rev 26049)
+++
core3/vizmap-impl/trunk/impl/src/test/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingTest.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -1,60 +0,0 @@
-package org.cytoscape.view.vizmap.mappings;
-
-import static org.junit.Assert.*;
-import static org.junit.Assert.assertEquals;
-
-import java.awt.Color;
-import java.awt.Paint;
-
-import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
-import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-public class DiscreteMappingTest {
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testDiscreteMapping() {
- final String attrName = "sample attr 1";
- final DiscreteMapping<String, Paint> mapping =
createDiscreteMapping(attrName);
-
- assertEquals(attrName, mapping.getMappingAttributeName());
- assertEquals(String.class, mapping.getMappingAttributeType());
- assertEquals(MinimalVisualLexicon.NODE_FILL_COLOR,
mapping.getVisualProperty());
-
- mapping.putMapValue("r", Color.RED);
- mapping.putMapValue("g", Color.GREEN);
- mapping.putMapValue("b", Color.BLUE);
-
- assertEquals(Color.RED, mapping.getMapValue("r"));
- assertEquals(Color.GREEN, mapping.getMapValue("g"));
- assertEquals(Color.BLUE, mapping.getMapValue("b"));
- assertEquals(null, mapping.getMapValue("p"));
-
- mapping.putMapValue("g", Color.GRAY);
- assertEquals(Color.GRAY, mapping.getMapValue("g"));
- mapping.putMapValue("g", null);
- assertNull(mapping.getMapValue("g"));
- }
-
-
- private DiscreteMapping<String, Paint> createDiscreteMapping(final
String attrName) {
-
- final Class<String> type = String.class;
-
- final DiscreteMapping<String, Paint> mapping = new
DiscreteMapping<String, Paint>(attrName, type,
- MinimalVisualLexicon.NODE_FILL_COLOR);
-
- return mapping;
- }
-
-}
Copied:
core3/vizmap-impl/trunk/impl/src/test/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingTest.java
(from rev 26051,
core3/vizmap-api/trunk/src/test/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingTest.java)
===================================================================
---
core3/vizmap-impl/trunk/impl/src/test/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingTest.java
(rev 0)
+++
core3/vizmap-impl/trunk/impl/src/test/java/org/cytoscape/view/vizmap/mappings/DiscreteMappingTest.java
2011-07-06 00:49:28 UTC (rev 26054)
@@ -0,0 +1,61 @@
+package org.cytoscape.view.vizmap.mappings;
+
+import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+
+import java.awt.Color;
+import java.awt.Paint;
+
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
+import org.cytoscape.view.vizmap.internal.mappings.DiscreteMappingImpl;
+import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class DiscreteMappingTest {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testDiscreteMapping() {
+ final String attrName = "sample attr 1";
+ final DiscreteMapping<String, Paint> mapping =
createDiscreteMapping(attrName);
+
+ assertEquals(attrName, mapping.getMappingAttributeName());
+ assertEquals(String.class, mapping.getMappingAttributeType());
+ assertEquals(MinimalVisualLexicon.NODE_FILL_COLOR,
mapping.getVisualProperty());
+
+ mapping.putMapValue("r", Color.RED);
+ mapping.putMapValue("g", Color.GREEN);
+ mapping.putMapValue("b", Color.BLUE);
+
+ assertEquals(Color.RED, mapping.getMapValue("r"));
+ assertEquals(Color.GREEN, mapping.getMapValue("g"));
+ assertEquals(Color.BLUE, mapping.getMapValue("b"));
+ assertEquals(null, mapping.getMapValue("p"));
+
+ mapping.putMapValue("g", Color.GRAY);
+ assertEquals(Color.GRAY, mapping.getMapValue("g"));
+ mapping.putMapValue("g", null);
+ assertNull(mapping.getMapValue("g"));
+ }
+
+
+ private DiscreteMapping<String, Paint> createDiscreteMapping(final
String attrName) {
+
+ final Class<String> type = String.class;
+
+ final DiscreteMapping<String, Paint> mapping = new
DiscreteMappingImpl<String, Paint>(attrName, type,
+ MinimalVisualLexicon.NODE_FILL_COLOR);
+
+ return mapping;
+ }
+
+}
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