Author: mes
Date: 2010-10-25 10:37:04 -0700 (Mon, 25 Oct 2010)
New Revision: 22359
Modified:
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/ContinuousMapping.java
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/DiscreteMapping.java
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/PassthroughMapping.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttribute.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
Log:
updated method names in CyRow to be a bit more sensible
Modified:
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/ContinuousMapping.java
===================================================================
---
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/ContinuousMapping.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/ContinuousMapping.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -182,7 +182,7 @@
CyRow row = view.getModel().attrs();
- if (row.contains(attrName, attrType)) {
+ if (row.isSet(attrName, attrType)) {
// skip Views where source attribute is not defined;
// ViewColumn will automatically substitute the per-VS
or global
// default, as appropriate
Modified:
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/DiscreteMapping.java
===================================================================
---
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/DiscreteMapping.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/DiscreteMapping.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -109,7 +109,7 @@
final CyRow row = view.getModel().attrs();
- if (row.contains(attrName, attrType)) {
+ if (row.isSet(attrName, attrType)) {
// skip Views where source attribute is not defined;
// ViewColumn will automatically substitute the per-VS
or global
// default, as appropriate
Modified:
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/PassthroughMapping.java
===================================================================
---
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/PassthroughMapping.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/default-mappingcalculators/trunk/src/main/java/org/cytoscape/view/vizmap/mappings/PassthroughMapping.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -77,7 +77,7 @@
- if (row.contains(attrName, attrType)) {
+ if (row.isSet(attrName, attrType)) {
// skip Views where source attribute is not defined;
// ViewColumn will automatically substitute the per-VS
or
// global default, as appropriate
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -303,17 +303,17 @@
// must make sure to clear out any existing values before we
parse.
case LIST:
manager.currentAttributeID = name;
- if (List.class == cyAtts.contains(name))
+ if (List.class == cyAtts.getType(name))
cyAtts.set(name, null);
return ParseState.LISTATT;
case MAP:
manager.currentAttributeID = name;
- if (Map.class == cyAtts.contains(name))
+ if (Map.class == cyAtts.getType(name))
cyAtts.set(name, null);
return ParseState.MAPATT;
case COMPLEX:
manager.currentAttributeID = name;
- if (Map.class == cyAtts.contains(name)) // assuming
complex will
+ if (Map.class == cyAtts.getType(name)) // assuming
complex will
// become Map
cyAtts.set(name, null);
// If this is a complex attribute, we know that the
value attribute
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttribute.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttribute.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/HandleComplexAttribute.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -58,7 +58,7 @@
manager.valueType =
attributeValueUtil.getMultHashMapType(type);
// See if we've defined the attribute already
if (Map.class == manager.currentAttributes
- .contains(manager.currentAttributeID)) {
+ .getType(manager.currentAttributeID)) {
manager.currentAttributes.getDataTable().createColumn(
manager.currentAttributeID,
Map.class, false);
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -691,7 +691,7 @@
private void writeAttribute(final CyRow attributes, final String
attributeName)
throws IOException {
// create an attribute and its type
- final Class attType = attributes.contains(attributeName);
+ final Class attType = attributes.getType(attributeName);
if ( attType == null )
return;
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -112,10 +112,10 @@
// System.out.println("Setting weight for "+layoutEdge+" using
"+weightAttribute);
if (weightAttribute != null) {
- if (row.contains(weightAttribute, Integer.class)) {
+ if (row.isSet(weightAttribute, Integer.class)) {
Integer val = row.get(weightAttribute,
Integer.class);
eValue = (double) val.intValue();
- } else if (row.contains(weightAttribute, Double.class))
{
+ } else if (row.isSet(weightAttribute, Double.class)) {
Double val = row.get(weightAttribute,
Double.class);
eValue = val.doubleValue();
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -58,7 +58,7 @@
r *= spacing;
if (this.attribute != null && count > 0) {
- Class<?> klass =
nodes.get(0).getNode().getCyRow(namespace).contains(attribute);
+ Class<?> klass =
nodes.get(0).getNode().getCyRow(namespace).getType(attribute);
if (klass != null &&
Comparable.class.isAssignableFrom(klass)){
// FIXME: I assume this would be better, but
get type errors if I try:
//Class<Comparable<?>> kasted =
(Class<Comparable<?>>) klass;
Modified: core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
2010-10-25 17:34:18 UTC (rev 22358)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -66,7 +66,7 @@
* return null if the column has not been defined. Will always return
* a base type.
*/
- Class<?> contains(String columnName);
+ Class<?> getType(String columnName);
/**
* Indicates whether the column of the specified type contains
@@ -76,7 +76,7 @@
* @return true if the value specified in this row at this column
* of the specified type is not null.
*/
- <T> boolean contains(String columnName, Class<?extends T> type);
+ <T> boolean isSet(String columnName, Class<?extends T> type);
/**
* Returns a map of column names to Objects that contain the values
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -153,8 +153,8 @@
CyNode n2 = net.addNode();
CyEdge e1 = net.addEdge(n1,n2,true);
- assertEquals( String.class, e1.attrs().contains("name"));
- assertEquals( Boolean.class, e1.attrs().contains("selected"));
- assertEquals( String.class, e1.attrs().contains("interaction"));
+ assertEquals( String.class, e1.attrs().getType("name"));
+ assertEquals( Boolean.class, e1.attrs().getType("selected"));
+ assertEquals( String.class, e1.attrs().getType("interaction"));
}
}
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -961,6 +961,6 @@
* Make sure the proper default attributes are created
*/
public void testDefaultAttributes() {
- assertEquals(String.class,net.attrs().contains("name"));
+ assertEquals(String.class,net.attrs().getType("name"));
}
}
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -71,8 +71,8 @@
public void testDefaultAttributes() {
CyNode n1 = net.addNode();
- assertEquals( String.class, n1.attrs().contains("name"));
- assertEquals( Boolean.class, n1.attrs().contains("selected"));
+ assertEquals( String.class, n1.attrs().getType("name"));
+ assertEquals( Boolean.class, n1.attrs().getType("selected"));
}
// by default a node should have a null nested network
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyTableTest.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -76,9 +76,9 @@
attrs.set("someString", "apple");
attrs.set("someStringElse", "orange");
- assertTrue(attrs.contains("someString", String.class));
- assertTrue(attrs.contains("someStringElse", String.class));
- assertFalse(attrs.contains("yetAnotherString", String.class));
+ assertTrue(attrs.isSet("someString", String.class));
+ assertTrue(attrs.isSet("someStringElse", String.class));
+ assertFalse(attrs.isSet("yetAnotherString", String.class));
assertEquals("apple", attrs.get("someString", String.class));
assertEquals("orange", attrs.get("someStringElse",
String.class));
@@ -94,9 +94,9 @@
attrs.set("someInt", 50);
attrs.set("someOtherInt", 100);
- assertTrue(attrs.contains("someInt", Integer.class));
- assertTrue(attrs.contains("someOtherInt", Integer.class));
- assertFalse(attrs.contains("yetAnotherInteger", Integer.class));
+ assertTrue(attrs.isSet("someInt", Integer.class));
+ assertTrue(attrs.isSet("someOtherInt", Integer.class));
+ assertFalse(attrs.isSet("yetAnotherInteger", Integer.class));
assertEquals(50, attrs.get("someInt",
Integer.class).intValue());
assertEquals(100, attrs.get("someOtherInt",
Integer.class).intValue());
@@ -112,9 +112,9 @@
attrs.set("someDouble", 3.14);
attrs.set("someOtherDouble", 2.76);
- assertTrue(attrs.contains("someDouble", Double.class));
- assertTrue(attrs.contains("someOtherDouble", Double.class));
- assertFalse(attrs.contains("yetAnotherDouble", Double.class));
+ assertTrue(attrs.isSet("someDouble", Double.class));
+ assertTrue(attrs.isSet("someOtherDouble", Double.class));
+ assertFalse(attrs.isSet("yetAnotherDouble", Double.class));
assertEquals(3.14, attrs.get("someDouble",
Double.class).doubleValue());
assertEquals(2.76, attrs.get("someOtherDouble",
Double.class).doubleValue());
@@ -130,9 +130,9 @@
attrs.set("someBoolean", true);
attrs.set("someOtherBoolean", false);
- assertTrue(attrs.contains("someBoolean", Boolean.class));
- assertTrue(attrs.contains("someOtherBoolean", Boolean.class));
- assertFalse(attrs.contains("yetAnotherBoolean", Boolean.class));
+ assertTrue(attrs.isSet("someBoolean", Boolean.class));
+ assertTrue(attrs.isSet("someOtherBoolean", Boolean.class));
+ assertFalse(attrs.isSet("yetAnotherBoolean", Boolean.class));
assertTrue(attrs.get("someBoolean", Boolean.class));
assertFalse(attrs.get("someOtherBoolean", Boolean.class));
@@ -150,7 +150,7 @@
attrs.set("someList", l);
- assertTrue(attrs.contains("someList", List.class));
+ assertTrue(attrs.isSet("someList", List.class));
assertEquals(2, attrs.get("someList", List.class).size());
}
@@ -167,7 +167,7 @@
attrs.set("someMap", m);
- assertTrue(attrs.contains("someMap", Map.class));
+ assertTrue(attrs.isSet("someMap", Map.class));
assertEquals(2, attrs.get("someMap", Map.class).size());
}
Modified:
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
===================================================================
---
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2010-10-25 17:34:18 UTC (rev 22358)
+++
core3/model-impl/trunk/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2010-10-25 17:37:04 UTC (rev 22359)
@@ -448,11 +448,11 @@
return getRawX(suid, attributeName);
}
- public <T> boolean contains(String attributeName, Class<?
extends T> c) {
+ public <T> boolean isSet(String attributeName, Class<? extends
T> c) {
return containsX(suid, attributeName, c);
}
- public Class<?> contains(String attributeName) {
+ public Class<?> getType(String attributeName) {
return containsX(suid, attributeName);
}
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