Author: ruschein
Date: 2010-05-27 16:07:06 -0700 (Thu, 27 May 2010)
New Revision: 20339
Added:
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/ListToString.java
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/ListToStringTest.java
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/TanTest.java
Modified:
corelibs/trunk/equations/src/org/cytoscape/equations/FunctionUtil.java
corelibs/trunk/equations/src/org/cytoscape/equations/Parser.java
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/Framework.java
Log:
Added new built-in LISTTOSTRING().
Modified: corelibs/trunk/equations/src/org/cytoscape/equations/FunctionUtil.java
===================================================================
--- corelibs/trunk/equations/src/org/cytoscape/equations/FunctionUtil.java
2010-05-27 21:42:28 UTC (rev 20338)
+++ corelibs/trunk/equations/src/org/cytoscape/equations/FunctionUtil.java
2010-05-27 23:07:06 UTC (rev 20339)
@@ -32,8 +32,16 @@
import java.util.Arrays;
import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.Stack;
+import java.util.Vector;
+import java.util.concurrent.CopyOnWriteArrayList;
+import javax.management.AttributeList;
+import javax.management.relation.RoleList;
+import javax.management.relation.RoleUnresolvedList;
+
/**
* A collection of static methods that may be useful for the implementation
of built-in functions.
*/
@@ -209,4 +217,28 @@
static public boolean isScalarArgType(final Class type) {
return type == Double.class || type == Long.class || type ==
String.class || type == Boolean.class;
}
+
+ /**
+ * @return true if "listClassCandidate" is an implementer of interface
List, else false
+ */
+ static public boolean someKindOfList(final Class listClassCandidate) {
+ if (listClassCandidate == ArrayList.class)
+ return true;
+ if (listClassCandidate == Vector.class)
+ return true;
+ if (listClassCandidate == Stack.class)
+ return true;
+ if (listClassCandidate == AttributeList.class)
+ return true;
+ if (listClassCandidate == CopyOnWriteArrayList.class)
+ return true;
+ if (listClassCandidate == LinkedList.class)
+ return true;
+ if (listClassCandidate == RoleList.class)
+ return true;
+ if (listClassCandidate == RoleUnresolvedList.class)
+ return true;
+
+ return false;
+ }
}
Modified: corelibs/trunk/equations/src/org/cytoscape/equations/Parser.java
===================================================================
--- corelibs/trunk/equations/src/org/cytoscape/equations/Parser.java
2010-05-27 21:42:28 UTC (rev 20338)
+++ corelibs/trunk/equations/src/org/cytoscape/equations/Parser.java
2010-05-27 23:07:06 UTC (rev 20339)
@@ -60,6 +60,7 @@
eqnParser.registerFunction(new Last());
eqnParser.registerFunction(new Left());
eqnParser.registerFunction(new Len());
+ eqnParser.registerFunction(new ListToString());
eqnParser.registerFunction(new Ln());
eqnParser.registerFunction(new Log());
eqnParser.registerFunction(new Max());
@@ -82,6 +83,7 @@
eqnParser.registerFunction(new StDev());
eqnParser.registerFunction(new Sqrt());
eqnParser.registerFunction(new Substitute());
+ eqnParser.registerFunction(new Tan());
eqnParser.registerFunction(new Trunc());
eqnParser.registerFunction(new UCase());
eqnParser.registerFunction(new Value());
Copied:
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/ListToString.java
(from rev 20310,
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/Abs.java)
===================================================================
---
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/ListToString.java
(rev 0)
+++
corelibs/trunk/equations/src/org/cytoscape/equations/builtins/ListToString.java
2010-05-27 23:07:06 UTC (rev 20339)
@@ -0,0 +1,110 @@
+/*
+ File: ListToString.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 ListToString 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 "LISTTOSTRING"; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of what this function does
+ */
+ public String getFunctionSummary() { return "Converts a list to a
string, given a separator."; }
+
+ /**
+ * Used to provide help for users.
+ * @return a description of how to use this function
+ */
+ public String getUsageDescription() { return "Call this with
\"LISTTOSTRING(list,separator)\""; }
+
+ public Class getReturnType() { return String.class; }
+
+ /**
+ * @return Double.class or null if there is not exactly 1 arg or the
arg is not of type Double or Long
+ */
+ public Class validateArgTypes(final Class[] argTypes) {
+ if (argTypes.length != 2 ||
!FunctionUtil.someKindOfList(argTypes[0]) || argTypes[1] != String.class)
+ return null;
+
+ return String.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 List list = (List)args[0];
+ final String separator = (String)args[1];
+
+ final StringBuilder result = new StringBuilder();
+ int count = 0;
+ for (final Object listEntry : list) {
+ result.append(listEntry.toString());
+ if (++count < list.size())
+ result.append(separator);
+ }
+
+ return result.toString();
+ }
+
+ /**
+ * 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) {
+ final List<Class> possibleNextArgs = new ArrayList<Class>();
+ if (leadingArgs.length == 0) {
+ possibleNextArgs.add(List.class);
+ return possibleNextArgs;
+ }
+ else if (leadingArgs.length == 1) {
+ possibleNextArgs.add(String.class);
+ return possibleNextArgs;
+ }
+
+ return null;
+ }
+}
Modified:
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/Framework.java
===================================================================
---
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/Framework.java
2010-05-27 21:42:28 UTC (rev 20338)
+++
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/Framework.java
2010-05-27 23:07:06 UTC (rev 20339)
@@ -27,19 +27,18 @@
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;
+package org.cytoscape.equations.builtins;
-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.*;
+import org.cytoscape.equations.interpreter.IdentDescriptor;
+import org.cytoscape.equations.interpreter.Interpreter;
class Framework {
@@ -53,21 +52,51 @@
public List<Class> getPossibleArgTypes(final Class[]
leadingArgs) { return null; }
}
- private final EqnCompiler compiler = new EqnCompiler();
+ private static final EqnCompiler compiler = new EqnCompiler();
- boolean executeTest(final String equation, final Map<String, Object>
variablesAndValues, final Object expectedResult)
- {
+ static {
+ Parser.getParser().registerFunction(new BadReturnFunction());
+ }
+
+ static 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))
+
+ try {
+ if (!compiler.compile(equation, varNameToTypeMap)) {
+ System.err.println("Error while compiling \"" +
equation + "\": " + compiler.getLastErrorMsg());
+ return false;
+ }
+ } catch (final Exception e) {
+ System.err.println("Error while compiling \"" +
equation + "\": " + e.getMessage());
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)));
+ try {
+ for (final String variableName :
variablesAndValues.keySet())
+ nameToDescriptorMap.put(variableName, new
IdentDescriptor(variablesAndValues.get(variableName)));
+ } catch (final Exception e) {
+ System.err.println("Error while processing variables
for \"" + equation + "\": " + e.getMessage());
+ return false;
+ }
- return true;
+ final Interpreter interpreter = new
Interpreter(compiler.getEquation(), nameToDescriptorMap);
+ try {
+ final Object actualResult = interpreter.run();
+ if (!actualResult.equals(expectedResult)) {
+ System.err.println("[" + equation + "]
expected: " + expectedResult + ", found: " + actualResult);
+ return false;
+ } else
+ return true;
+ } catch (final Exception e) {
+ return false;
+ }
}
+
+ static boolean executeTest(final String equation, final Object
expectedResult) {
+ final Map<String, Object> variablesAndValues = new
HashMap<String, Object>();
+ return executeTest(equation, variablesAndValues,
expectedResult);
+ }
}
Copied:
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/ListToStringTest.java
(from rev 20337,
corelibs/trunk/equations/tests/org/cytoscape/equations/interpreter/InterpreterTest.java)
===================================================================
---
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/ListToStringTest.java
(rev 0)
+++
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/ListToStringTest.java
2010-05-27 23:07:06 UTC (rev 20339)
@@ -0,0 +1,53 @@
+/*
+ File: ListToStringTest.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.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import junit.framework.*;
+
+
+public class ListToStringTest extends TestCase {
+ public void testAll() throws Exception {
+ final List<Object> list = new ArrayList<Object>();
+ list.add("Fred");
+ list.add(Long.valueOf(3L));
+ list.add(Double.valueOf(1.3));
+
+ final Map<String, Object> variablesAndValues = new
HashMap<String, Object>();
+ variablesAndValues.put("LIST", list);
+
+ assertTrue(Framework.executeTest("=LISTTOSTRING($LIST,\",\")",
variablesAndValues, new String("Fred,3,1.3")));
+ }
+}
Copied:
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/TanTest.java
(from rev 20337,
corelibs/trunk/equations/tests/org/cytoscape/equations/interpreter/InterpreterTest.java)
===================================================================
---
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/TanTest.java
(rev 0)
+++
corelibs/trunk/equations/tests/org/cytoscape/equations/builtins/TanTest.java
2010-05-27 23:07:06 UTC (rev 20339)
@@ -0,0 +1,40 @@
+/*
+ File: TanTest.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 junit.framework.*;
+
+
+public class TanTest extends TestCase {
+ public void testAll() throws Exception {
+ assertTrue(Framework.executeTest("=TAN(1.047197551)", new
Double(1.7320508067824862)));
+ }
+}
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