Author: abeld
Date: 2009-03-15 06:19:49 -0700 (Sun, 15 Mar 2009)
New Revision: 16271
Modified:
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/ContinuousMapping.java
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/DiscreteMapping.java
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/PassthroughMappingCalculator.java
core3/vizmap-api/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/MappingCalculator.java
core3/vizmap-impl/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/internal/VisualStyleImpl.java
Log:
valuecalculator branch: implement 'valuecalculator' idea.
Note: although this code compiles, I haven't tested it. I have a hunch not
enough type-checking is done.
Modified:
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/ContinuousMapping.java
===================================================================
---
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/ContinuousMapping.java
2009-03-15 12:28:55 UTC (rev 16270)
+++
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/ContinuousMapping.java
2009-03-15 13:19:49 UTC (rev 16271)
@@ -151,50 +151,10 @@
this.attrName = attrName;
}
- public <T, V extends GraphObject> void apply(ViewColumn<T> column,
List<? extends View<V>> views){
- if (views.size() < 1)
- return; // empty list, nothing to do
- CyRow row = views.get(0).getSource().attrs(); // to check
types, have to peek at first view instance
- // check types:
- Class<?> attrType =
row.getDataTable().getColumnTypeMap().get(attrName);
- Class<?> vpType = vp.getType();
- if (vpType.isAssignableFrom(rangeClass) &&
Number.class.isAssignableFrom(attrType)){
- doMap(views, column, (Class<Number>)attrType); // due
to check in previous line, this is a safe cast
- } else {
- throw new IllegalArgumentException("Mapping
"+toString()+" can't map from attribute type "+attrType+" to VisualProperty
"+vp+" of type "+vp.getType());
- }
+ public <T, V> V valueFor(T attributeValue, Class<V> type){
+ return (V) getRangeValue((Number) attributeValue);
}
- /**
- * 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 <T> 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 <T,K extends Number, V extends GraphObject> void doMap(final
List<? extends View<V>> views, ViewColumn<T> column, Class<K> attrType){
- // aggregate changes to be made in these:
- Map<View<V>, T> valuesToSet = new HashMap<View<V>, T>();
- List<View<V>> valuesToClear = new ArrayList<View<V>>();
-
- for (View<V> v: views){
- CyRow row = v.getSource().attrs();
- if (row.contains(attrName, attrType) ){
- // skip Views where source attribute is not
defined;
- // ViewColumn will automatically substitute the
per-VS or global default, as appropriate
-
- final K attrValue = (K)
v.getSource().attrs().get(attrName, attrType);
- final T value = (T) getRangeValue(attrValue);
// FIXME: make getRangeValue type-parametric, so this shouldn't be needed (??)
- valuesToSet.put(v, value);
- } else { // remove value so that default value will be
used:
- valuesToClear.add(v);
- }
- }
- column.setValues(valuesToSet, valuesToClear);
- }
+
private Object getRangeValue(Number domainValue) {
ContinuousMappingPoint firstPoint = points.get(0);
Number minDomain = new Double(firstPoint.getValue());
Modified:
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/DiscreteMapping.java
===================================================================
---
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/DiscreteMapping.java
2009-03-15 12:28:55 UTC (rev 16270)
+++
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/DiscreteMapping.java
2009-03-15 13:19:49 UTC (rev 16271)
@@ -109,56 +109,13 @@
return vp;
}
- public <T, V extends GraphObject> void apply(ViewColumn<T> column,
List<? extends View<V>> views){
- if (views.size() < 1)
- return; // empty list, nothing to do
- CyRow row = views.get(0).getSource().attrs(); // to check
types, have to peek at first view instance
- // check types:
- Class<?> attrType =
row.getDataTable().getColumnTypeMap().get(attrName);
- Class<?> vpType = vp.getType();
- if (vpType.isAssignableFrom(rangeClass)){
- // FIXME: should check here? or does that not matter?
- // if (keyClass.isAssignableFrom(attrType))
- doMap(views, column, attrType);
+ public <T, V> V valueFor(T attributeValue, Class<V> type){
+ if (treeMap.containsKey(attributeValue)){
+ return (V) treeMap.get(attributeValue);
} else {
- throw new IllegalArgumentException("Mapping
"+toString()+" can't map from attribute type "+attrType+" to VisualProperty
"+vp+" of type "+vp.getType());
+ return null;
}
}
- /**
- * 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 <T> 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 <T,K, V extends GraphObject> void doMap(final List<? extends
View<V>> views, ViewColumn<T> column, Class<K> attrType){
- // aggregate changes to be made in these:
- Map<View<V>, T> valuesToSet = new HashMap<View<V>, T>();
- List<View<V>> valuesToClear = new ArrayList<View<V>>();
-
- for (View<V> v: views){
- CyRow row = v.getSource().attrs();
- if (row.contains(attrName, attrType) ){
- // skip Views where source attribute is not
defined;
- // ViewColumn will automatically substitute the
per-VS or global default, as appropriate
-
- final K key = (K)
v.getSource().attrs().get(attrName, attrType);
- if (treeMap.containsKey(key)){
- final T value = (T) treeMap.get(key);
- valuesToSet.put(v, value);
- } else { // remove value so that default value
will be used:
- valuesToClear.add(v);
- }
- } else { // remove value so that default value will be
used:
- valuesToClear.add(v);
- }
- }
- column.setValues(valuesToSet, valuesToClear);
- }
/**
* Gets Value for Specified Key.
Modified:
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/PassthroughMappingCalculator.java
===================================================================
---
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/PassthroughMappingCalculator.java
2009-03-15 12:28:55 UTC (rev 16270)
+++
core3/default-mappingcalculators/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/mappings/PassthroughMappingCalculator.java
2009-03-15 13:19:49 UTC (rev 16271)
@@ -99,57 +99,18 @@
return vp;
}
- /**
- * DOCUMENT ME!
- *
- * @param v DOCUMENT ME!
- */
- public <T, V extends GraphObject> void apply(ViewColumn<T> column,
List<? extends View<V>> views){
- if (views.size() < 1)
- return; // empty list, nothing to do
- CyRow row = views.get(0).getSource().attrs();
- Class<?> attrType =
row.getDataTable().getColumnTypeMap().get(attributeName);
- // since attributes can only store certain types of Objects, it
is enough to test for these:
- Class<?> vpType = vp.getType();
- // FIXME: also check that column's vp is internally-stored vp!
- if (vpType.isAssignableFrom(attrType)){ // can simply copy
object without any conversion
- // aggregate changes to be made in these:
- Map<View<V>, T> valuesToSet = new HashMap<View<V>, T>();
- List<View<V>> valuesToClear = new ArrayList<View<V>>();
- for (View<V> v: views){
- row = v.getSource().attrs();
- if (row.contains(attributeName, attrType) ){
- // skip Views where source attribute is
not defined; ViewColumn will automatically substitute the per-VS or global
default, as appropriate
- final T value = (T)
row.get(attributeName, attrType);
- valuesToSet.put(v, value);
- } else { // remove value so that default value
will be used:
- valuesToClear.add(v);
- }
- }
- column.setValues(valuesToSet, valuesToClear);
- } else if (String.class.isAssignableFrom(vpType)){
- // can convert any object to string, so no need to
check attribute type
- // also, since we have to convert the Object here,
can't use checkAndDoCopy()
- ViewColumn<String> c = (ViewColumn<String>) column; //
have to cast here, even though previous check ensures that T is
java.util.String
+ public <T, V> V valueFor(T attributeValue, Class<V> vpType){
+ if (String.class.isAssignableFrom(vpType)){
+ return (V) attributeValue.toString();
+ } else
+ return (V) attributeValue;
- // aggregate changes to be made in these:
- Map<View<V>, String> valuesToSet = new HashMap<View<V>,
String>();
- List<View<V>> valuesToClear = new ArrayList<View<V>>();
-
- for (View<V> v: views){
- row = v.getSource().attrs();
- if (row.contains(attributeName, attrType) ){
- // skip Views where source attribute is
not defined; ViewColumn will automatically substitute the per-VS or global
default, as appropriate
- final Object value = (Object)
row.get(attributeName, attrType);
- valuesToSet.put(v, value.toString());
- } else { // remove value so that default value
will be used:
- valuesToClear.add(v);
- }
- }
- c.setValues(valuesToSet, valuesToClear);
- } else {
- throw new IllegalArgumentException("Mapping
"+toString()+" can't map from attribute type "+attrType+" to VisualProperty
"+vp+" of type "+vp.getType());
+ /* This might be a more elegant way to do this: (but needs a
Class<T> type-token parameter)
+ if (vpType.isAssignableFrom(attrType){
+ return (V) attributeValue;
+ } else if (String.class.isAssignableFrom(vpType)){
+ return (V) attributeValue.toString();
}
- // FIXME: handle List & Map
+ */
}
}
Modified:
core3/vizmap-api/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/MappingCalculator.java
===================================================================
---
core3/vizmap-api/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/MappingCalculator.java
2009-03-15 12:28:55 UTC (rev 16270)
+++
core3/vizmap-api/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/MappingCalculator.java
2009-03-15 13:19:49 UTC (rev 16271)
@@ -82,14 +82,17 @@
VisualProperty<?> getVisualProperty();
/**
- * Since current MappingCalculators map from Attributes to
- * VisualProperties, have to restrict View<?> to those
- * generic types that have CyAttributes; currently this is
- * GraphObject.
- *
- * @param <V> DOCUMENT ME!
- * @param column DOCUMENT ME!
- * @param views DOCUMENT ME!
+ * Calculate the VisualProperty value for a given attribute value.
+ * Returns null if there is no calculated value, in this case the
default value will be used.
+ *
+ * Callers of this method are responsible for ensuring type-safety.
+ *
+ * For efficiency, implementations of this methods should make no
checks that T and V are
+ * correct for the given implementation: that will be checked and thus
correctness ensured by
+ * callers of this method.
+ *
+ * @param <T> the type-parameter of the attribute being mapped from
+ * @param V the type of the return value (a VisualProperty
type-parameter)
*/
- <T, V extends GraphObject> void apply(ViewColumn<T> column, List<?
extends View<V>> views);
+ <T, V> V valueFor(T attributeValue, Class<V> type);
}
Modified:
core3/vizmap-impl/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/internal/VisualStyleImpl.java
===================================================================
---
core3/vizmap-impl/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/internal/VisualStyleImpl.java
2009-03-15 12:28:55 UTC (rev 16270)
+++
core3/vizmap-impl/branches/valuecalculator/src/main/java/org/cytoscape/vizmap/internal/VisualStyleImpl.java
2009-03-15 13:19:49 UTC (rev 16271)
@@ -39,6 +39,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
import org.cytoscape.model.GraphObject;
import org.cytoscape.view.model.CyNetworkView;
@@ -50,6 +51,7 @@
import org.cytoscape.vizmap.MappingCalculator;
import org.cytoscape.vizmap.VisualStyle;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
@@ -131,11 +133,8 @@
perVSDefaults.put(vp, value);
}
- // ??
/**
- * DOCUMENT ME!
- *
- * @param view DOCUMENT ME!
+ * {...@inheritdoc}
*/
public void apply(final CyNetworkView view) {
final List<View<CyNode>> nodeviews = view.getCyNodeViews();
@@ -151,11 +150,7 @@
// 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 <T extends GraphObject> void applyImpl(final CyNetworkView view,
final List<View<T>> views,
final Collection<?
extends VisualProperty<?>> visualProperties) {
@@ -164,7 +159,7 @@
}
}
/**
- * DOCUMENT ME!
+ * I think this needs to be in a separate method to allow making it
generic -- abeld
*
* @param <T> DOCUMENT ME!
* @param views DOCUMENT ME!
@@ -178,12 +173,50 @@
column.setDefaultValue(perVSDefault);
}
if (c != null) {
- c.apply(column, views);
+ String attrName = c.getMappingAttributeName();
+ if (views.size() < 1)
+ return; // empty list, nothing to do
+ CyRow row = views.get(0).getSource().attrs(); // to
check types, have to peek at first view instance
+ // check types:
+ Class<?> attrType =
row.getDataTable().getColumnTypeMap().get(attrName);
+ Class<T> vpType = vp.getType();
+
+ if (true) {
+ doMap(views, c, attrName, attrType, column,
vpType);
+ } else {
+ throw new IllegalArgumentException("Mapping
"+toString()+" can't map from attribute type "+attrType+" to VisualProperty
"+vp+" of type "+vp.getType());
+ }
} else {
- // reset all rows to allow usage of default value:
- for (View<V>v: views){
- column.clearValue(v);
+ column.setValues(new HashMap<View<V>, T>(), views);
+ }
+ }
+ /**
+ * I think this needs to be in a separate method to allow making it
generic -- abeld
+ *
+ * @param T the VisualProperty type being mapped to
+ * @param A the attribute type being mapped from
+ * @param V the view type for which the mapping is made
+ */
+ private <T, A, V extends GraphObject> void doMap(final List<? extends
View<V>> views, MappingCalculator calc,
+ String attrName, Class<A> attrType, ViewColumn<T>
column, Class<T> visualType){
+ // aggregate changes to be made in these:
+ Map<View<V>, T> valuesToSet = new HashMap<View<V>, T>();
+ List<View<V>> valuesToClear = new ArrayList<View<V>>();
+
+ for (View<V> v: views){
+ CyRow row = v.getSource().attrs();
+ if (row.contains(attrName, attrType) ){ // skip Views
where source attribute is not defined;
+
// ViewColumn will automatically substitute the per-VS
or global default, as appropriate
+ T value = calc.valueFor((A)
v.getSource().attrs().get(attrName, attrType), visualType);
+ if (value != null){ // 'null' value mean
'revert to default'
+ valuesToSet.put(v, value);
+ } else { // remove value so that default value
will be used:
+ valuesToClear.add(v);
+ }
+ } else { // remove value so that default value will be
used:
+ valuesToClear.add(v);
}
}
+ column.setValues(valuesToSet, valuesToClear);
}
}
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