Author: ruschein
Date: 2011-09-14 16:15:09 -0700 (Wed, 14 Sep 2011)
New Revision: 26803
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/data/CyAttributesImpl.java
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnCompiler.java
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParser.java
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParserImpl.java
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/Equation.java
Log:
Made default cell references work.
Modified:
cytoscape/trunk/application/src/main/java/cytoscape/data/CyAttributesImpl.java
===================================================================
---
cytoscape/trunk/application/src/main/java/cytoscape/data/CyAttributesImpl.java
2011-09-14 22:37:59 UTC (rev 26802)
+++
cytoscape/trunk/application/src/main/java/cytoscape/data/CyAttributesImpl.java
2011-09-14 23:15:09 UTC (rev 26803)
@@ -1138,6 +1138,7 @@
currentlyActiveAttributes.add(attribName);
final Collection<String> attribReferences =
equation.getAttribReferences();
+ final Map<String, Object> defaultValues =
equation.getDefaultValues();
final Map<String, IdentDescriptor> nameToDescriptorMap = new
TreeMap<String, IdentDescriptor>();
for (final String attribRef : attribReferences) {
@@ -1146,14 +1147,19 @@
continue;
}
- final Object attribValue = getAttribute(id, attribRef);
+ Object attribValue = getAttribute(id, attribRef);
if (attribValue == null) {
- currentlyActiveAttributes.clear();
- errorMessage.append("Missing value for
referenced attribute \"" + attribRef + "\"!");
- logger.warn("Missing value for \"" + attribRef
- + "\" while evaluating an equation
(ID:" + id
- + ", attribute name:" + attribName
+ ")");
- return null;
+ final Object defaultValue =
defaultValues.get(attribRef);
+ if (defaultValue != null)
+ attribValue = defaultValue;
+ else {
+ currentlyActiveAttributes.clear();
+ errorMessage.append("Missing value for
referenced attribute \"" + attribRef + "\"!");
+ logger.warn("Missing value for \"" +
attribRef
+ + "\" while evaluating an
equation (ID:" + id
+ + ", attribute name:" +
attribName + ")");
+ return null;
+ }
}
try {
Modified:
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnCompiler.java
===================================================================
---
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnCompiler.java
2011-09-14 22:37:59 UTC (rev 26802)
+++
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnCompiler.java
2011-09-14 23:15:09 UTC (rev 26803)
@@ -71,7 +71,9 @@
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.getDefaultValues(), code,
sourceLocations,
+ parser.getType());
errorMsg = null;
return true;
Modified:
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParser.java
===================================================================
---
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParser.java
2011-09-14 22:37:59 UTC (rev 26802)
+++
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParser.java
2011-09-14 23:15:09 UTC (rev 26803)
@@ -77,6 +77,11 @@
public Set<String> getVariableReferences();
/**
+ * @return a map from variable names to their default values, if any
+ */
+ public Map<String, Object> getDefaultValues();
+
+ /**
* @return the parse tree. Must only be called if parse() returns
true!
*/
public Node getParseTree();
Modified:
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParserImpl.java
===================================================================
---
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParserImpl.java
2011-09-14 22:37:59 UTC (rev 26802)
+++
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/EqnParserImpl.java
2011-09-14 23:15:09 UTC (rev 26803)
@@ -1,7 +1,7 @@
/*
File: EqnParserImpl.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.parse_tree.*;
@@ -47,6 +48,7 @@
private Node parseTree;
private Map<String, Class> variableNameToTypeMap;
private Set<String> variableReferences;
+ private Map<String, Object> defaultValues;
private Set<Function> registeredFunctions;
public EqnParserImpl() {
@@ -92,6 +94,7 @@
this.formula = formula;
this.variableNameToTypeMap = variableNameToTypeMap;
this.variableReferences = new TreeSet<String>();
+ this.defaultValues = new TreeMap<String, Object>();
this.tokeniser = new Tokeniser(formula.substring(1));
this.lastErrorMessage = null;
@@ -131,6 +134,8 @@
public Set<String> getVariableReferences() { return variableReferences;
}
+ public Map<String, Object> getDefaultValues() { return defaultValues; }
+
/**
* @return the parse tree. Must only be called if parse() returns
true!
*/
@@ -232,11 +237,12 @@
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) {
@@ -265,6 +271,8 @@
if (token != Token.CLOSE_BRACE)
throw new
IllegalStateException(sourceLocation + ": closing brace expected!");
+
+ defaultValues.put(ident, defaultValue);
}
return new IdentNode(varRefStartPos,
tokeniser.getIdent(), defaultValue, varRefType);
Modified:
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/Equation.java
===================================================================
---
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/Equation.java
2011-09-14 22:37:59 UTC (rev 26802)
+++
cytoscape/trunk/corelibs/equations/src/main/java/org/cytoscape/equations/Equation.java
2011-09-14 23:15:09 UTC (rev 26803)
@@ -38,6 +38,7 @@
public class Equation {
private final String equation;
private final Set<String> attribReferences;
+ private final Map<String, Object> defaultValues;
private final Object[] code;
private final int[] sourceLocations;
private final Class type;
@@ -45,14 +46,17 @@
/**
* @param equation the string representing this equation
* @param attribReferences other attributes that are referenced by
this equation
+ * @param defaultValues default values for attribute references,
if any
* @param code the instruction sequence representing the
compiled equation
* @param type the type of the equation, String.class,
Boolean.class or Double.class
*/
- Equation(final String equation, final Set<String> attribReferences,
final Object[] code,
+ Equation(final String equation, final Set<String> attribReferences,
+ final Map<String, Object> defaultValues, final Object[] code,
final int[] sourceLocations, final Class type)
{
this.equation = equation;
this.attribReferences = attribReferences;
+ this.defaultValues = defaultValues;
this.code = code;
this.sourceLocations = sourceLocations;
this.type = type;
@@ -69,6 +73,7 @@
}
public Set<String> getAttribReferences() { return attribReferences; }
+ public Map<String, Object> getDefaultValues() { return defaultValues; }
public Object[] getCode() { return code; }
public int[] getSourceLocations() { return sourceLocations; }
public Class getType() { return type; }
@@ -88,7 +93,8 @@
final Equation errorEquation = compiler.getEquation();
- return new Equation(equation, errorEquation.attribReferences,
errorEquation.code,
+ return new Equation(equation, errorEquation.attribReferences,
+ errorEquation.defaultValues,
errorEquation.code,
errorEquation.sourceLocations, type);
}
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