Author: ruschein
Date: 2011-09-15 08:59:03 -0700 (Thu, 15 Sep 2011)
New Revision: 26807
Modified:
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/Equation.java
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/EquationParser.java
core3/api/trunk/equations-api/src/test/java/org/cytoscape/equations/EquationTest.java
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationCompilerImpl.java
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java
Log:
Fixed a problem with default values for variable references in equations.
Modified:
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/Equation.java
===================================================================
---
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/Equation.java
2011-09-15 15:10:45 UTC (rev 26806)
+++
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/Equation.java
2011-09-15 15:59:03 UTC (rev 26807)
@@ -1,7 +1,7 @@
/*
File: Equation.java
- Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2010-2011, 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
@@ -38,27 +38,31 @@
public final class Equation {
private final String equation;
private final Set<String> variableReferences;
+ private final Map<String, Object> defaultVariableValues;
private final Object[] code;
private final int[] sourceLocations;
private final Class type;
/**
* Constructs an <code>Equation</code>.
- * @param equation the string representing this equation
- * @param variableReferences other variables that are referenced by
this equation
- * @param code the instruction sequence representing
the compiled equation
- * @param sourceLocations the starting points in the original
equation for each node in the parse tree that resulted from
- * the original equation
- * @param type the type of the equation, String.class,
Boolean.class or Double.class
+ * @param equation the string representing this equation
+ * @param variableReferences other variables that are referenced by
this equation
+ * @param defaultVariableValues
+ * @param code the instruction sequence representing
the compiled equation
+ * @param sourceLocations the starting points in the original
equation for each node
+ * in the parse tree that resulted from
the original equation
+ * @param type the type of the equation,
String.class, Boolean.class or Double.class
*/
- public Equation(final String equation, final Set<String>
variableReferences, final Object[] code,
- final int[] sourceLocations, final Class type)
+ public Equation(final String equation, final Set<String>
variableReferences,
+ final Map<String, Object> defaultVariableValues, final
Object[] code,
+ final int[] sourceLocations, final Class type)
{
- this.equation = equation;
- this.variableReferences = variableReferences;
- this.code = code;
- this.sourceLocations = sourceLocations;
- this.type = type;
+ this.equation = equation;
+ this.variableReferences = variableReferences;
+ this.defaultVariableValues = defaultVariableValues;
+ this.code = code;
+ this.sourceLocations = sourceLocations;
+ this.type = type;
}
/** Returns a textual representation of an <code>Equation</code>.
@@ -86,6 +90,11 @@
*/
public Set<String> getVariableReferences() { return variableReferences;
}
+ /** Returns default values for variable references, if any.
+ * @return a map of variable names to their default values, if any
+ */
+ public Map<String, Object> getDefaultVariableValues() { return
defaultVariableValues; }
+
/** Returns the compiled code (not Java byte code!) for the VM
representing this <code>Equation</code>.
* @return the code representing this <code>Equation</code>
*/
Modified:
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/EquationParser.java
===================================================================
---
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/EquationParser.java
2011-09-15 15:10:45 UTC (rev 26806)
+++
core3/api/trunk/equations-api/src/main/java/org/cytoscape/equations/EquationParser.java
2011-09-15 15:59:03 UTC (rev 26807)
@@ -40,43 +40,48 @@
* @param func the function that will be registered
* @throws IllegalArgumentException will be thrown if "func" is null
or the function has previously been registered
*/
- public void registerFunction(final Function func) throws
IllegalArgumentException;
+ void registerFunction(final Function func) throws
IllegalArgumentException;
/**
* @return the function associated with the name "functionName" or
null if no such function exists
*/
- public Function getFunction(final String functionName);
+ Function getFunction(final String functionName);
/**
* @return the set of currently registered functions
*/
- public Set<Function> getRegisteredFunctions();
+ Set<Function> getRegisteredFunctions();
/**
* @param eqn a valid attribute equation which must
start with an equal sign
* @param attribNameToTypeMap a list of existing attribute names and
their types
* @return true if the parse succeeded otherwise false
*/
- public boolean parse(final String eqn, final Map<String, Class<?>>
attribNameToTypeMap);
+ boolean parse(final String eqn, final Map<String, Class<?>>
attribNameToTypeMap);
/**
* @return the result type of the parsed equation if the parse
succeeded, otherwise null
*/
- public Class<?> getType();
+ Class<?> getType();
/**
* If parse() failed, this will return the last error messages.
* @return the last error message of null
*/
- public String getErrorMsg();
+ String getErrorMsg();
/**
* @return all the variable names that have been detected in the most
recently parsed equation
*/
- public Set<String> getVariableReferences();
+ Set<String> getVariableReferences();
/**
+ * @return a map of variable names to their default values, if any
+ */
+ Map<String, Object> getDefaultVariableValues();
+
+ /**
* @return the parse tree. Must only be called if parse() returns
true!
*/
- public Node getParseTree();
+ Node getParseTree();
}
Modified:
core3/api/trunk/equations-api/src/test/java/org/cytoscape/equations/EquationTest.java
===================================================================
---
core3/api/trunk/equations-api/src/test/java/org/cytoscape/equations/EquationTest.java
2011-09-15 15:10:45 UTC (rev 26806)
+++
core3/api/trunk/equations-api/src/test/java/org/cytoscape/equations/EquationTest.java
2011-09-15 15:59:03 UTC (rev 26807)
@@ -3,6 +3,7 @@
import java.util.HashSet;
import java.util.Set;
+import java.util.TreeMap;
import static org.junit.Assert.*;
import org.junit.Before;
@@ -22,7 +23,8 @@
variableReferences.add("B");
code = new Object[2];
sourceLocations = new int[] { 12, 117 };
- eqn = new Equation("=$A+$B", variableReferences, code,
sourceLocations, Long.class);
+ eqn = new Equation("=$A+$B", variableReferences, new
TreeMap<String, Object>(), code,
+ sourceLocations, Long.class);
}
@Test
@@ -52,7 +54,9 @@
@Test
public void testEqualsWithExpectedSuccess() {
- final Equation other = new Equation("=$A+$B",
variableReferences, code, sourceLocations, Long.class);
+ final Equation other =
+ new Equation("=$A+$B", variableReferences, new
TreeMap<String, Object>(),
+ code, sourceLocations, Long.class);
assertTrue("equals() failed!", eqn.equals(other));
}
Modified:
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationCompilerImpl.java
===================================================================
---
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationCompilerImpl.java
2011-09-15 15:10:45 UTC (rev 26806)
+++
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationCompilerImpl.java
2011-09-15 15:59:03 UTC (rev 26807)
@@ -76,7 +76,9 @@
code[i] = codeAndSourceLocation.getCode();
sourceLocations[i] =
codeAndSourceLocation.getSourceLocation();
}
- this.equation = new Equation(equation,
parser.getVariableReferences(), code, sourceLocations, parser.getType());
+ this.equation = new Equation(equation,
parser.getVariableReferences(),
+ parser.getDefaultVariableValues(),
code, sourceLocations,
+ parser.getType());
errorMsg = null;
return true;
@@ -101,7 +103,8 @@
throw new IllegalStateException("internal error in
Equation.getErrorEquation(). This should *never* happen!");
final Equation errorEquation = getEquation();
- return new Equation(equation,
errorEquation.getVariableReferences(), errorEquation.getCode(),
+ return new Equation(equation,
errorEquation.getVariableReferences(),
+ errorEquation.getDefaultVariableValues(),
errorEquation.getCode(),
errorEquation.getSourceLocations(), type);
}
Modified:
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
===================================================================
---
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
2011-09-15 15:10:45 UTC (rev 26806)
+++
core3/impl/trunk/equations-impl/src/main/java/org/cytoscape/equations/internal/EquationParserImpl.java
2011-09-15 15:59:03 UTC (rev 26807)
@@ -1,7 +1,7 @@
/*
File: EquationParserImpl.java
- Copyright (c) 2010, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2010-2011, 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
@@ -35,6 +35,7 @@
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
+import java.util.TreeMap;
import java.util.TreeSet;
import org.cytoscape.equations.EquationParser;
@@ -53,6 +54,7 @@
private Node parseTree;
private Map<String, Class<?>> variableNameToTypeMap;
private Set<String> variableReferences;
+ private Map<String, Object> defaultVariableValues;
private Set<Function> registeredFunctions;
public EquationParserImpl() {
@@ -100,6 +102,7 @@
this.formula = formula;
this.variableNameToTypeMap = variableNameToTypeMap;
this.variableReferences = new TreeSet<String>();
+ this.defaultVariableValues = new TreeMap<String, Object>();
this.tokeniser = new Tokeniser(formula.substring(1));
this.lastErrorMessage = null;
@@ -139,6 +142,8 @@
public Set<String> getVariableReferences() { return variableReferences;
}
+ public Map<String, Object> getDefaultVariableValues() { return
defaultVariableValues; }
+
/**
* @return the parse tree. Must only be called if parse() returns
true!
*/
@@ -240,11 +245,12 @@
if (token != Token.IDENTIFIER)
throw new IllegalStateException(sourceLocation
+ ": identifier expected!");
- final Class<?> varRefType =
variableNameToTypeMap.get(tokeniser.getIdent());
+ final String ident = tokeniser.getIdent();
+ final Class<?> varRefType =
variableNameToTypeMap.get(ident);
if (varRefType == null)
throw new IllegalStateException(sourceLocation
+ ": unknown variable reference name: \""
- +
tokeniser.getIdent() + "\"!");
- variableReferences.add(tokeniser.getIdent());
+ + ident +
"\"!");
+ variableReferences.add(ident);
Object defaultValue = null;
if (usingOptionalBraces) {
@@ -273,6 +279,8 @@
if (token != Token.CLOSE_BRACE)
throw new
IllegalStateException(sourceLocation + ": closing brace expected!");
+
+ defaultVariableValues.put(ident, defaultValue);
}
return new IdentNode(varRefStartPos,
tokeniser.getIdent(), defaultValue, varRefType);
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java
2011-09-15 15:10:45 UTC (rev 26806)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EqnSupport.java
2011-09-15 15:59:03 UTC (rev 26807)
@@ -136,6 +136,7 @@
currentlyActiveAttributes.add(columnName);
final Collection<String> attribReferences =
equation.getVariableReferences();
+ final Map<String, Object> defaultValues =
equation.getDefaultVariableValues();
final Map<String, IdentDescriptor> nameToDescriptorMap = new
TreeMap<String, IdentDescriptor>();
for (final String attribRef : attribReferences) {
@@ -144,20 +145,25 @@
continue;
}
- final Object attribValue = tableImpl.getValue(key,
attribRef);
+ Object attribValue = tableImpl.getValue(key, attribRef);
if (attribValue == null) {
- currentlyActiveAttributes.clear();
- try {
- lastInternalError.append(
- "Missing value for referenced
attribute \""
- + attribRef + "\"!");
- } catch (Exception e) {
- // Intentionally empty!
+ final Object defaultValue =
defaultValues.get(attribRef);
+ if (defaultValue != null)
+ attribValue = defaultValue;
+ else {
+ currentlyActiveAttributes.clear();
+ try {
+ lastInternalError.append(
+ "Missing value for
referenced attribute \""
+ + attribRef + "\"!");
+ } catch (Exception e) {
+ // Intentionally empty!
+ }
+ logger.warn("Missing value for \"" +
attribRef
+ + "\" while evaluating an
equation (ID:" + key
+ + ", attribute name:" +
columnName + ")");
+ return null;
}
- logger.warn("Missing value for \"" + attribRef
- + "\" while evaluating an equation
(ID:" + key
- + ", attribute name:" + columnName
+ ")");
- return null;
}
try {
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