Author: ruschein
Date: 2010-05-27 14:42:28 -0700 (Thu, 27 May 2010)
New Revision: 20338
Added:
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Degrees.java
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Tan.java
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/Framework.java
Modified:
corelibs/trunk/equations/src/org/cytoscape/equations/Parser.java
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Cos.java
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Sin.java
Log:
New framework for the testing of built-in functions.
Modified: corelibs/trunk/equations/src/org/cytoscape/equations/Parser.java
===================================================================
--- corelibs/trunk/equations/src/org/cytoscape/equations/Parser.java
2010-05-27 20:49:12 UTC (rev 20337)
+++ corelibs/trunk/equations/src/org/cytoscape/equations/Parser.java
2010-05-27 21:42:28 UTC (rev 20338)
@@ -49,6 +49,7 @@
eqnParser.registerFunction(new Combin());
eqnParser.registerFunction(new Cos());
eqnParser.registerFunction(new Count());
+ eqnParser.registerFunction(new Degrees());
eqnParser.registerFunction(new Exp());
eqnParser.registerFunction(new First());
eqnParser.registerFunction(new GeoMean());
Modified: corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Cos.java
===================================================================
--- corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Cos.java
2010-05-27 20:49:12 UTC (rev 20337)
+++ corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Cos.java
2010-05-27 21:42:28 UTC (rev 20338)
@@ -47,7 +47,7 @@
* Used to provide help for users.
* @return a description of what this function does
*/
- public String getFunctionSummary() { return "Returns the cosine of a
number."; }
+ public String getFunctionSummary() { return "Returns the cosine of an
angle given in radians."; }
/**
* Used to provide help for users.
Copied:
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Degrees.java
(from rev 20337,
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Radians.java)
===================================================================
--- corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Degrees.java
(rev 0)
+++ corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Degrees.java
2010-05-27 21:42:28 UTC (rev 20338)
@@ -0,0 +1,99 @@
+/*
+ File: Degrees.java
+
+ Copyright (c) 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.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.List;
+import org.cytoscape.equations.Function;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Degrees implements Function {
+ /**
+ * Used to parse the function string. This name is treated in a
case-insensitive manner!
+ * @return the name by which you must call the function when used in
an attribute equation.
+ */
+ public String getName() { return "DEGREES"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the value in
degrees converted from radians."; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of how to use this function
+ */
+ public String getUsageDescription() { return "Call this with
\"DEGREES(radians)\""; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @return Double.class or null if there is not exactly 1 arg or the
arg is not of type Double, Long, String or Boolean
+ */
+ public Class validateArgTypes(final Class[] argTypes) {
+ if (argTypes.length != 1 ||
!FunctionUtil.isScalarArgType(argTypes[0]))
+ return null;
+
+ return Double.class;
+ }
+
+ /**
+ * @param args the function arguments which must be either one object
of type Double or Long
+ * @return the result of the function evaluation which is the natural
logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double angleInRadians =
FunctionUtil.getArgAsDouble(args[0]);
+ return angleInRadians * 180.0 / Math.PI;
+ }
+
+ /**
+ * Used with the equation builder.
+ *
+ * @param leadingArgs the types of the arguments that have already
been selected by the user.
+ * @return the set of arguments (must be a collection of String.class,
Long.class, Double.class,
+ * Boolean.class and List.class) that are candidates for the
next argument. An empty
+ * set indicates that no further arguments are valid.
+ */
+ public List<Class> getPossibleArgTypes(final Class[] leadingArgs) {
+ if (leadingArgs.length == 0) {
+ final List<Class> possibleNextArgs = new
ArrayList<Class>();
+ possibleNextArgs.add(Double.class);
+ possibleNextArgs.add(Long.class);
+ possibleNextArgs.add(String.class);
+ possibleNextArgs.add(Boolean.class);
+ return possibleNextArgs;
+ }
+
+ return null;
+ }
+}
Modified: corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Sin.java
===================================================================
--- corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Sin.java
2010-05-27 20:49:12 UTC (rev 20337)
+++ corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Sin.java
2010-05-27 21:42:28 UTC (rev 20338)
@@ -47,7 +47,7 @@
* Used to provide help for users.
* @return a description of what this function does
*/
- public String getFunctionSummary() { return "Returns the sine of a
number."; }
+ public String getFunctionSummary() { return "Returns the sine of an
angle given in radians."; }
/**
* Used to provide help for users.
Copied: corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Tan.java
(from rev 20337,
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Sin.java)
===================================================================
--- corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Tan.java
(rev 0)
+++ corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Tan.java
2010-05-27 21:42:28 UTC (rev 20338)
@@ -0,0 +1,104 @@
+/*
+ File: Tan.java
+
+ Copyright (c) 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.equations.builtins;
+
+
+import java.util.ArrayList;
+import java.util.List;
+import org.cytoscape.equations.Function;
+import org.cytoscape.equations.FunctionUtil;
+
+
+public class Tan implements Function {
+ /**
+ * Used to parse the function string. This name is treated in a
case-insensitive manner!
+ * @return the name by which you must call the function when used in
an attribute equation.
+ */
+ public String getName() { return "TAN"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Returns the tanget of an
angle given in radians."; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of how to use this function
+ */
+ public String getUsageDescription() { return "Call this with
\"TAN(radians)\""; }
+
+ public Class getReturnType() { return Double.class; }
+
+ /**
+ * @return Double.class or null if there is not exactly 1 arg or the
arg is not of type Double, Long, String or Boolean
+ */
+ public Class validateArgTypes(final Class[] argTypes) {
+ if (argTypes.length != 1 ||
!FunctionUtil.isScalarArgType(argTypes[0]))
+ return null;
+
+ return Double.class;
+ }
+
+ /**
+ * @param args the function arguments which must be either one object
of type Double or Long
+ * @return the result of the function evaluation which is the natural
logarithm of the first argument
+ */
+ public Object evaluateFunction(final Object[] args) {
+ final double angleInRadians =
FunctionUtil.getArgAsDouble(args[0]);
+
+ final double cos = Math.cos(angleInRadians);
+ if (cos == 0.0)
+ throw new IllegalArgumentException("division by zero in
call to TAN()!");
+
+ return Math.sin(angleInRadians) / cos;
+ }
+
+ /**
+ * Used with the equation builder.
+ *
+ * @param leadingArgs the types of the arguments that have already
been selected by the user.
+ * @return the set of arguments (must be a collection of String.class,
Long.class, Double.class,
+ * Boolean.class and List.class) that are candidates for the
next argument. An empty
+ * set indicates that no further arguments are valid.
+ */
+ public List<Class> getPossibleArgTypes(final Class[] leadingArgs) {
+ if (leadingArgs.length == 0) {
+ final List<Class> possibleNextArgs = new
ArrayList<Class>();
+ possibleNextArgs.add(Double.class);
+ possibleNextArgs.add(Long.class);
+ possibleNextArgs.add(String.class);
+ possibleNextArgs.add(Boolean.class);
+ return possibleNextArgs;
+ }
+
+ return null;
+ }
+}
Copied:
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/Framework.java
(from rev 20337,
corelibs/trunk/equations/tests/org/cytoscape/equations/interpreter/InterpreterTest.java)
===================================================================
---
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/Framework.java
(rev 0)
+++
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/Framework.java
2010-05-27 21:42:28 UTC (rev 20338)
@@ -0,0 +1,73 @@
+/*
+ File: Framework.java
+
+ Copyright (c) 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.equations.interpreter;
+
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Stack;
+import junit.framework.*;
+import org.cytoscape.equations.EqnCompiler;
+import org.cytoscape.equations.Function;
+import org.cytoscape.equations.Parser;
+import org.cytoscape.equations.builtins.*;
+
+
+class Framework {
+ static private class BadReturnFunction implements Function {
+ public String getName() { return "BAD"; }
+ public String getFunctionSummary() { return "Returns an invalid
type at runtime."; }
+ public String getUsageDescription() { return "Call this with
\"BAD()\"."; }
+ public Class getReturnType() { return Double.class; }
+ public Class validateArgTypes(final Class[] argTypes) { return
argTypes.length == 0 ? Double.class : null; }
+ public Object evaluateFunction(final Object[] args) { return
new Integer(1); }
+ public List<Class> getPossibleArgTypes(final Class[]
leadingArgs) { return null; }
+ }
+
+ private final EqnCompiler compiler = new EqnCompiler();
+
+ boolean executeTest(final String equation, final Map<String, Object>
variablesAndValues, final Object expectedResult)
+ {
+ final Map<String, Class> varNameToTypeMap = new HashMap<String,
Class>();
+ for (final String variableName : variablesAndValues.keySet())
+ varNameToTypeMap.put(variableName,
variablesAndValues.get(variableName).getClass());
+
+ if (!compiler.compile(equation, varNameToTypeMap))
+ return false;
+
+ final Map<String, IdentDescriptor> nameToDescriptorMap = new
HashMap<String, IdentDescriptor>();
+ for (final String variableName : variablesAndValues.keySet())
+ nameToDescriptorMap.put(variableName, new
IdentDescriptor(variablesAndValues.get(variableName)));
+
+ return true;
+ }
+}
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