*/
package jalview.ext.jmol;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.gui.SequenceRenderer;
+import jalview.schemes.JalviewColourScheme;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import java.util.HashMap;
+
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
StructureMappingcommandSet[] commands = JmolCommands
.getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
}
+
+ @Test(groups = { "Functional" })
+ public void testGetColourBySequenceCommands_hiddenColumns()
+ {
+ /*
+ * load these sequences, coloured by Strand propensity,
+ * with columns 2-4 hidden
+ */
+ SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
+ SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
+ AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
+ AlignFrame af = new AlignFrame(al, 800, 500);
+ af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
+ ColumnSelection cs = new ColumnSelection();
+ cs.addElement(2);
+ cs.addElement(3);
+ cs.addElement(4);
+ af.getViewport().setColumnSelection(cs);
+ af.hideSelColumns_actionPerformed(null);
+ SequenceRenderer sr = new SequenceRenderer(af.getViewport());
+ SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
+ String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
+ StructureSelectionManager ssm = new StructureSelectionManager();
+
+ /*
+ * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
+ */
+ HashMap<Integer, int[]> map = new HashMap<Integer, int[]>();
+ for (int pos = 1; pos <= seq1.getLength(); pos++)
+ {
+ map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
+ }
+ StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
+ "A", map, null);
+ ssm.addStructureMapping(sm1);
+ StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
+ "B", map, null);
+ ssm.addStructureMapping(sm2);
+
+ StructureMappingcommandSet[] commands = JmolCommands
+ .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
+ assertEquals(commands.length, 2);
+ assertEquals(commands[0].commands.length, 1);
+
+ String chainACommand = commands[0].commands[0];
+ // M colour is #82827d == (130, 130, 125) (see strand.html help page)
+ assertTrue(chainACommand
+ .contains(";select 21:A/1.1;color[130,130,125]"));
+ // H colour is #60609f == (96, 96, 159)
+ assertTrue(chainACommand.contains(";select 22:A/1.1;color[96,96,159]"));
+ // hidden columns are Gray (128, 128, 128)
+ assertTrue(chainACommand
+ .contains(";select 23-25:A/1.1;color[128,128,128]"));
+ // S and G are both coloured #4949b6 == (73, 73, 182)
+ assertTrue(chainACommand
+ .contains(";select 26-30:A/1.1;color[73,73,182]"));
+
+ String chainBCommand = commands[1].commands[0];
+ // M colour is #82827d == (130, 130, 125)
+ assertTrue(chainBCommand
+ .contains(";select 21:B/2.1;color[130,130,125]"));
+ // V colour is #ffff00 == (255, 255, 0)
+ assertTrue(chainBCommand
+.contains(";select 22:B/2.1;color[255,255,0]"));
+ // hidden columns are Gray (128, 128, 128)
+ assertTrue(chainBCommand
+ .contains(";select 23-25:B/2.1;color[128,128,128]"));
+ // S and G are both coloured #4949b6 == (73, 73, 182)
+ assertTrue(chainBCommand
+ .contains(";select 26-30:B/2.1;color[73,73,182]"));
+ }
}
--- /dev/null
+/*
+ * Copyright 2004-2012 Sebastian Dietrich (Sebastian.Dietrich@e-movimento.com)
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package junit.extensions;
+
+import java.util.Collection;
+
+/**
+ * This class is used to access a method or field of an object no matter what the access modifier of the method or field. The syntax
+ * for accessing fields and methods is out of the ordinary because this class uses reflection to peel away protection.
+ * <p>
+ * a.k.a. The "ObjectMolester"
+ * <p>
+ * Here is an example of using this to access a private member: <br>
+ * Given the following class <code>MyClass</code>: <br>
+ *
+ * <pre>
+ * public class MyClass {
+ * private String name; // private attribute
+ *
+ * // private constructor
+ * private MyClass() {
+ * super();
+ * }
+ *
+ * // private method
+ * private void setName(String newName) {
+ * this.name = newName;
+ * }
+ * }
+ * </pre>
+ *
+ * We now want to access the class: <br>
+ *
+ * <pre>
+ * MyClass myObj = PA.instantiate(MyClass.class);
+ * PA.invokeMethod(myObj, "setName(java.lang.String)", "myNewName");
+ * String name = PA.getValue(myObj, "name");
+ * </pre>
+ *
+ * This class extends {@link PrivilegedAccessor} by re-throwing checked {@link Exception}s as {@link RuntimeException}s.
+ *
+ *
+ * @see PrivilegedAccessor
+ *
+ * @author Sebastian Dietrich (sebastian.dietrich@e-movimento.com)
+ * @author Lubos Bistak (lubos@bistak.sk)
+ */
+public class PA {
+ private final Object instanceOrClass;
+
+ /**
+ * Private constructor to make it impossible to instantiate this class from outside of PA.
+ *
+ * @param instanceOrClass
+ */
+ private PA(Object instanceOrClass) {
+ this.instanceOrClass = instanceOrClass;
+ }
+
+ /**
+ * Returns a string representation of the given object. The string has the following format: "<classname> {<attributes and values>}"
+ * whereas <attributes and values> is a comma separated list with <attributeName>=<attributeValue> <atributes and values> includes
+ * all attributes of the objects class followed by the attributes of its superclass (if any) and so on.
+ *
+ * @param instanceOrClass the object or class to get a string representation of
+ * @return a string representation of the given object
+ *
+ * @see PrivilegedAccessor#toString(Object)
+ */
+ public static String toString(final Object instanceOrClass) {
+ return PrivilegedAccessor.toString(instanceOrClass);
+ }
+
+ /**
+ * Gets the name of all fields (public, private, protected, default) of the given instance or class. This includes as well all
+ * fields (public, private, protected, default) of all its super classes.
+ *
+ * @param instanceOrClass the instance or class to get the fields of
+ * @return the collection of field names of the given instance or class
+ *
+ * @see PrivilegedAccessor#getFieldNames(Object)
+ */
+ public static Collection<String> getFieldNames(final Object instanceOrClass) {
+ return PrivilegedAccessor.getFieldNames(instanceOrClass);
+ }
+
+ /**
+ * Gets the signatures of all methods (public, private, protected, default) of the given instance or class. This includes as well
+ * all methods (public, private, protected, default) of all its super classes. This does not include constructors.
+ *
+ * @param instanceOrClass the instance or class to get the method signatures of
+ * @return the collection of method signatures of the given instance or class
+ *
+ * @see PrivilegedAccessor#getMethodSignatures(Object)
+ */
+ public static Collection<String> getMethodSignatures(final Object instanceOrClass) {
+ return PrivilegedAccessor.getMethodSignatures(instanceOrClass);
+ }
+
+ /**
+ * Gets the value of the named field and returns it as an object. If instanceOrClass is a class then a static field is returned.
+ *
+ * @param instanceOrClass the instance or class to get the field from
+ * @param fieldName the name of the field
+ * @return an object representing the value of the field
+ * @throws IllegalArgumentException if the field does not exist
+ *
+ * @see PrivilegedAccessor#getValue(Object,String)
+ */
+ public static Object getValue(final Object instanceOrClass, final String fieldName) {
+ try {
+ return PrivilegedAccessor.getValue(instanceOrClass, fieldName);
+ } catch (Exception e) {
+ throw new IllegalArgumentException("Can't get value of " + fieldName + " from " + instanceOrClass, e);
+ }
+ }
+
+ /**
+ * Gets the value of the named field and returns it as an object.
+ *
+ * @param fieldName the name of the field
+ * @return an object representing the value of the field
+ * @throws IllegalArgumentException if the field does not exist
+ *
+ * @see PA#getValue(Object,String)
+ */
+ public Object getValue(final String fieldName) {
+ return PA.getValue(instanceOrClass, fieldName);
+ }
+
+ /**
+ * Instantiates an object of the given class with the given arguments and the given argument types. If you want to instantiate a
+ * member class, you must provide the object it is a member of as first argument.
+ *
+ * @param fromClass the class to instantiate an object from
+ * @param arguments the arguments to pass to the constructor
+ * @param argumentTypes the fully qualified types of the arguments of the constructor
+ * @return an object of the given type
+ * @throws IllegalArgumentException if the class can't be instantiated. This could be the case if the number of actual and formal
+ * parameters differ; if an unwrapping conversion for primitive arguments fails; if, after possible unwrapping, a
+ * parameter value cannot be converted to the corresponding formal parameter type by a method invocation conversion; if
+ * this Constructor object enforces Java language access control and the underlying constructor is inaccessible; if the
+ * underlying constructor throws an exception; if the constructor could not be found; or if the class that declares the
+ * underlying constructor represents an abstract class.
+ *
+ * @see PrivilegedAccessor#instantiate(Class,Class[],Object[])
+ */
+ public static <T> T instantiate(final Class<? extends T> fromClass, final Class<?>[] argumentTypes, final Object... arguments) {
+ try {
+ return PrivilegedAccessor.instantiate(fromClass, argumentTypes, correctVarargs(arguments));
+ } catch (Exception e) {
+ throw new IllegalArgumentException("Can't instantiate class " + fromClass + " with arguments " + arguments, e);
+ }
+ }
+
+ /**
+ * Instantiates an object of the given class with the given arguments. If you want to instantiate a member class, you must provide
+ * the object it is a member of as first argument.
+ *
+ * @param fromClass the class to instantiate an object from
+ * @param arguments the arguments to pass to the constructor
+ * @return an object of the given type
+ * @throws IllegalArgumentException if the class can't be instantiated. This could be the case if the number of actual and formal
+ * parameters differ; if an unwrapping conversion for primitive arguments fails; or if, after possible unwrapping, a
+ * parameter value cannot be converted to the corresponding formal parameter type by a method invocation conversion; if
+ * this Constructor object enforces Java language access control and the underlying constructor is inaccessible; if the
+ * underlying constructor throws an exception; if the constructor could not be found; or if the class that declares the
+ * underlying constructor represents an abstract class.
+ *
+ * @see PrivilegedAccessor#instantiate(Class,Object[])
+ */
+ public static <T> T instantiate(final Class<? extends T> fromClass, final Object... arguments) {
+ try {
+ return PrivilegedAccessor.instantiate(fromClass, correctVarargs(arguments));
+ } catch (Exception e) {
+ throw new IllegalArgumentException("Can't instantiate class " + fromClass + " with arguments " + arguments, e);
+ }
+ }
+
+ /**
+ * Calls a method on the given object instance with the given arguments. Arguments can be object types or representations for
+ * primitives.
+ *
+ * @param instanceOrClass the instance or class to invoke the method on
+ * @param methodSignature the name of the method and the parameters <br>
+ * (e.g. "myMethod(java.lang.String, com.company.project.MyObject)")
+ * @param arguments an array of objects to pass as arguments
+ * @return the return value of this method or null if void
+ * @throws IllegalArgumentException if the method could not be invoked. This could be the case if the method is inaccessible; if the
+ * underlying method throws an exception; if no method with the given <code>methodSignature</code> could be found; or if
+ * an argument couldn't be converted to match the expected type
+ *
+ * @see PrivilegedAccessor#invokeMethod(Object,String,Object[])
+ */
+ public static Object invokeMethod(final Object instanceOrClass, final String methodSignature, final Object... arguments) {
+ try {
+ return PrivilegedAccessor.invokeMethod(instanceOrClass, methodSignature, correctVarargs(arguments));
+ } catch (Exception e) {
+ throw new IllegalArgumentException("Can't invoke method " + methodSignature + " on " + instanceOrClass + " with arguments "
+ + arguments, e);
+ }
+ }
+
+ /**
+ * Calls a method with the given arguments. Arguments can be object types or representations for primitives.
+ *
+ * @param methodSignature the name of the method and the parameters <br>
+ * (e.g. "myMethod(java.lang.String, com.company.project.MyObject)")
+ * @param arguments an array of objects to pass as arguments
+ * @return the return value of this method or null if void
+ * @throws IllegalArgumentException if the method could not be invoked. This could be the case if the method is inaccessible; if the
+ * underlying method throws an exception; if no method with the given <code>methodSignature</code> could be found; or if
+ * an argument couldn't be converted to match the expected type
+ * @see PA#invokeMethod(Object, String, Object...)
+ */
+ public Object invokeMethod(final String methodSignature, final Object... arguments) {
+ return PA.invokeMethod(instanceOrClass, methodSignature, arguments);
+ }
+
+ /**
+ * Corrects varargs to their initial form. If you call a method with an object-array as last argument the Java varargs mechanism
+ * converts this array in single arguments. This method returns an object array if the arguments are all of the same type.
+ *
+ * @param arguments the possibly converted arguments of a vararg method
+ * @return arguments possibly converted
+ */
+ private static Object[] correctVarargs(final Object... arguments) {
+ if ((arguments == null) || changedByVararg(arguments)) return new Object[] {arguments};
+ return arguments;
+ }
+
+ /**
+ * Tests if the arguments were changed by vararg. Arguments are changed by vararg if they are of a non primitive array type. E.g.
+ * arguments[] = Object[String[]] is converted to String[] while e.g. arguments[] = Object[int[]] is not converted and stays
+ * Object[int[]]
+ *
+ * Unfortunately we can't detect the difference for arg = Object[primitive] since arguments[] = Object[Object[primitive]] which is
+ * converted to Object[primitive] and arguments[] = Object[primitive] which stays Object[primitive]
+ *
+ * and we can't detect the difference for arg = Object[non primitive] since arguments[] = Object[Object[non primitive]] is converted
+ * to Object[non primitive] and arguments[] = Object[non primitive] stays Object[non primitive]
+ *
+ * @param parameters the parameters
+ * @return true if parameters were changes by varargs, false otherwise
+ */
+ private static boolean changedByVararg(final Object[] parameters) {
+ if ((parameters.length == 0) || (parameters[0] == null)) return false;
+
+ if (parameters.getClass() == Object[].class) return false;
+
+ return true;
+ }
+
+ /**
+ * Sets the value of the named field. If fieldName denotes a static field, provide a class, otherwise provide an instance. If the
+ * fieldName denotes a final field, this method could fail with an IllegalAccessException, since setting the value of final fields
+ * at other times than instantiation can have unpredictable effects.<br/>
+ * <br/>
+ * Example:<br/>
+ * <br/>
+ * <code>
+ * String myString = "Test"; <br/>
+ * <br/>
+ * //setting the private field value<br/>
+ * PrivilegedAccessor.setValue(myString, "value", new char[] {'T', 'e', 's', 't'});<br/>
+ * <br/>
+ * //setting the static final field serialVersionUID - MIGHT FAIL<br/>
+ * PrivilegedAccessor.setValue(myString.getClass(), "serialVersionUID", 1);<br/>
+ * <br/>
+ * </code>
+ *
+ * @param instanceOrClass the instance or class to set the field
+ * @param fieldName the name of the field
+ * @param value the new value of the field
+ * @throws IllegalArgumentException if the value could not be set. This could be the case if no field with the given
+ * <code>fieldName</code> can be found; or if the field was final
+ *
+ * @see PrivilegedAccessor.setValue(Object,String,Object)
+ */
+ public static PA setValue(final Object instanceOrClass, final String fieldName, final Object value) {
+ try {
+ PrivilegedAccessor.setValue(instanceOrClass, fieldName, value);
+ } catch (Exception e) {
+ throw new IllegalArgumentException("Can't set value " + value + " at " + fieldName + " in " + instanceOrClass, e);
+ }
+ return new PA(instanceOrClass);
+ }
+
+ /**
+ * Sets the value of the named field. If fieldName denotes a static field, provide a class, otherwise provide an instance. If the
+ * fieldName denotes a final field, this method could fail with an IllegalAccessException, since setting the value of final fields
+ * at other times than instantiation can have unpredictable effects.<br/>
+ * <br/>
+ * Example:<br/>
+ * <br/>
+ * <code>
+ * String myString = "Test"; <br/>
+ * <br/>
+ * //setting the private field value<br/>
+ * PrivilegedAccessor.setValue(myString, "value", new char[] {'T', 'e', 's', 't'});<br/>
+ * <br/>
+ * //setting the static final field serialVersionUID - MIGHT FAIL<br/>
+ * PrivilegedAccessor.setValue(myString.getClass(), "serialVersionUID", 1);<br/>
+ * <br/>
+ * </code>
+ *
+ * @param fieldName the name of the field
+ * @param value the new value of the field
+ * @throws IllegalArgumentException if the value could not be set. This could be the case if no field with the given
+ * <code>fieldName</code> can be found; or if the field was final
+ *
+ * @see PA.setValue(Object,String,Object)
+ */
+ public PA setValue(final String fieldName, final Object value) {
+ PA.setValue(instanceOrClass, fieldName, value);
+ return this;
+ }
+}
--- /dev/null
+/*
+ * Copyright 2004-2012 Sebastian Dietrich (Sebastian.Dietrich@e-movimento.com)
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package junit.extensions;
+
+import java.lang.reflect.Array;
+import java.lang.reflect.Constructor;
+import java.lang.reflect.Field;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.lang.reflect.Modifier;
+import java.security.InvalidParameterException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.StringTokenizer;
+
+/**
+ * This class is used to access a method or field of an object no matter what the access modifier of the method or field. The syntax
+ * for accessing fields and methods is out of the ordinary because this class uses reflection to peel away protection.
+ * <p>
+ * a.k.a. The "ObjectMolester"
+ * <p>
+ * Here is an example of using this to access a private member: <br>
+ * <code>myObject</code> is an object of type <code>MyClass</code>. <code>setName(String)</code> is a private method of
+ * <code>MyClass</code>.
+ *
+ * <pre>
+ * PrivilegedAccessor.invokeMethod(myObject, "setName(java.lang.String)", "newName");
+ * </pre>
+ *
+ * @author Charlie Hubbard (chubbard@iss.net)
+ * @author Prashant Dhokte (pdhokte@iss.net)
+ * @author Sebastian Dietrich (sebastian.dietrich@e-movimento.com)
+ *
+ * @deprecated use PA instead. PA improves the functionality of PrivilegedAccessor by introducing support for varargs and removal of
+ * the necessity to catch exceptions.
+ */
+@Deprecated
+final class PrivilegedAccessor
+{
+ /**
+ * Private constructor to make it impossible to instantiate this class.
+ */
+ private PrivilegedAccessor() {
+ assert false : "You mustn't instantiate PrivilegedAccessor, use its methods statically";
+ }
+
+ /**
+ * Returns a string representation of the given object. The string has the following format: "<classname> {<attributes and values>}"
+ * whereas <attributes and values> is a comma separated list with <attributeName>=<attributeValue> <atributes and values> includes
+ * all attributes of the objects class followed by the attributes of its superclass (if any) and so on.
+ *
+ * @param instanceOrClass the object or class to get a string representation of
+ * @return a string representation of the given object
+ */
+ public static String toString(final Object instanceOrClass) {
+ Collection<String> fields = getFieldNames(instanceOrClass);
+
+ if (fields.isEmpty())
+ {
+ return getClass(instanceOrClass).getName();
+ }
+
+ StringBuffer stringBuffer = new StringBuffer();
+
+ stringBuffer.append(getClass(instanceOrClass).getName() + " {");
+
+ for (String fieldName : fields) {
+ try {
+ stringBuffer.append(fieldName + "=" + getValue(instanceOrClass, fieldName) + ", ");
+ } catch (NoSuchFieldException e) {
+ assert false : "It should always be possible to get a field that was just here";
+ }
+ }
+
+ stringBuffer.replace(stringBuffer.lastIndexOf(", "), stringBuffer.length(), "}");
+ return stringBuffer.toString();
+ }
+
+ /**
+ * Gets the name of all fields (public, private, protected, default) of the given instance or class. This includes as well all
+ * fields (public, private, protected, default) of all its super classes.
+ *
+ * @param instanceOrClass the instance or class to get the fields of
+ * @return the collection of field names of the given instance or class
+ */
+ public static Collection<String> getFieldNames(final Object instanceOrClass) {
+ if (instanceOrClass == null)
+ {
+ return Collections.EMPTY_LIST;
+ }
+
+ Class<?> clazz = getClass(instanceOrClass);
+ Field[] fields = clazz.getDeclaredFields();
+ Collection<String> fieldNames = new ArrayList<String>(fields.length);
+
+ for (Field field : fields) {
+ fieldNames.add(field.getName());
+ }
+ fieldNames.addAll(getFieldNames(clazz.getSuperclass()));
+
+ return fieldNames;
+ }
+
+ /**
+ * Gets the signatures of all methods (public, private, protected, default) of the given instance or class. This includes as well
+ * all methods (public, private, protected, default) of all its super classes. This does not include constructors.
+ *
+ * @param instanceOrClass the instance or class to get the method signatures of
+ * @return the collection of method signatures of the given instance or class
+ */
+ public static Collection<String> getMethodSignatures(final Object instanceOrClass) {
+ if (instanceOrClass == null)
+ {
+ return Collections.EMPTY_LIST;
+ }
+
+ Class<?> clazz = getClass(instanceOrClass);
+ Method[] methods = clazz.getDeclaredMethods();
+ Collection<String> methodSignatures = new ArrayList<String>(methods.length + Object.class.getDeclaredMethods().length);
+
+ for (Method method : methods) {
+ methodSignatures.add(method.getName() + "(" + getParameterTypesAsString(method.getParameterTypes()) + ")");
+ }
+ methodSignatures.addAll(getMethodSignatures(clazz.getSuperclass()));
+
+ return methodSignatures;
+ }
+
+ /**
+ * Gets the value of the named field and returns it as an object. If instanceOrClass is a class then a static field is returned.
+ *
+ * @param instanceOrClass the instance or class to get the field from
+ * @param fieldName the name of the field
+ * @return an object representing the value of the field
+ * @throws NoSuchFieldException if the field does not exist
+ */
+ public static Object getValue(final Object instanceOrClass, final String fieldName) throws NoSuchFieldException {
+ Field field = getField(instanceOrClass, fieldName);
+ try {
+ return field.get(instanceOrClass);
+ } catch (IllegalAccessException e) {
+ assert false : "getField() should have setAccessible(true), so an IllegalAccessException should not occur in this place";
+ return null;
+ }
+ }
+
+ /**
+ * Instantiates an object of the given class with the given arguments. If you want to instantiate a member class, you must provide
+ * the object it is a member of as first argument.
+ *
+ * @param fromClass the class to instantiate an object from
+ * @param args the arguments to pass to the constructor
+ * @return an object of the given type
+ * @throws IllegalArgumentException if the number of actual and formal parameters differ; if an unwrapping conversion for primitive
+ * arguments fails; or if, after possible unwrapping, a parameter value cannot be converted to the corresponding formal
+ * parameter type by a method invocation conversion.
+ * @throws IllegalAccessException if this Constructor object enforces Java language access control and the underlying constructor is
+ * inaccessible.
+ * @throws InvocationTargetException if the underlying constructor throws an exception.
+ * @throws NoSuchMethodException if the constructor could not be found
+ * @throws InstantiationException if the class that declares the underlying constructor represents an abstract class.
+ *
+ * @see PrivilegedAccessor#instantiate(Class,Class[],Object[])
+ */
+ public static <T> T instantiate(final Class<? extends T> fromClass, final Object[] args) throws IllegalArgumentException,
+ InstantiationException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
+ return instantiate(fromClass, getParameterTypes(args), args);
+ }
+
+ /**
+ * Instantiates an object of the given class with the given arguments and the given argument types. If you want to instantiate a
+ * member class, you must provide the object it is a member of as first argument.
+ *
+ *
+ * @param fromClass the class to instantiate an object from
+ * @param args the arguments to pass to the constructor
+ * @param argumentTypes the fully qualified types of the arguments of the constructor
+ * @return an object of the given type
+ * @throws IllegalArgumentException if the number of actual and formal parameters differ; if an unwrapping conversion for primitive
+ * arguments fails; or if, after possible unwrapping, a parameter value cannot be converted to the corresponding formal
+ * parameter type by a method invocation conversion.
+ * @throws IllegalAccessException if this Constructor object enforces Java language access control and the underlying constructor is
+ * inaccessible.
+ * @throws InvocationTargetException if the underlying constructor throws an exception.
+ * @throws NoSuchMethodException if the constructor could not be found
+ * @throws InstantiationException if the class that declares the underlying constructor represents an abstract class.
+ *
+ * @see PrivilegedAccessor#instantiate(Class,Object[])
+ */
+ public static <T> T instantiate(final Class<? extends T> fromClass, final Class<?>[] argumentTypes, final Object[] args)
+ throws IllegalArgumentException, InstantiationException, IllegalAccessException, InvocationTargetException,
+ NoSuchMethodException {
+ return getConstructor(fromClass, argumentTypes).newInstance(args);
+ }
+
+ /**
+ * Calls a method on the given object instance with the given arguments. Arguments can be object types or representations for
+ * primitives.
+ *
+ * @param instanceOrClass the instance or class to invoke the method on
+ * @param methodSignature the name of the method and the parameters <br>
+ * (e.g. "myMethod(java.lang.String, com.company.project.MyObject)")
+ * @param arguments an array of objects to pass as arguments
+ * @return the return value of this method or null if void
+ * @throws IllegalAccessException if the method is inaccessible
+ * @throws InvocationTargetException if the underlying method throws an exception.
+ * @throws NoSuchMethodException if no method with the given <code>methodSignature</code> could be found
+ * @throws IllegalArgumentException if an argument couldn't be converted to match the expected type
+ */
+ public static Object invokeMethod(final Object instanceOrClass, final String methodSignature, final Object[] arguments)
+ throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
+ if ((methodSignature.indexOf('(') == -1) || (methodSignature.indexOf('(') >= methodSignature.indexOf(')')))
+ {
+ throw new NoSuchMethodException(methodSignature);
+ }
+ Class<?>[] parameterTypes = getParameterTypes(methodSignature);
+ return getMethod(instanceOrClass, getMethodName(methodSignature), parameterTypes).invoke(instanceOrClass,
+ getCorrectedArguments(parameterTypes, arguments));
+ }
+
+ /**
+ * Gets the given arguments corrected to match the given methodSignature. Correction is necessary for array arguments not to be
+ * mistaken by varargs.
+ *
+ * @param parameterTypes the method signatue the given arguments should match
+ * @param arguments the arguments that should be corrected
+ * @return the corrected arguments
+ */
+ private static Object[] getCorrectedArguments(Class<?>[] parameterTypes, Object[] arguments) {
+ if (arguments == null)
+ {
+ return arguments;
+ }
+ if (parameterTypes.length > arguments.length)
+ {
+ return arguments;
+ }
+ if (parameterTypes.length < arguments.length)
+ {
+ return getCorrectedArguments(parameterTypes, new Object[] {arguments});
+ }
+
+ Object[] correctedArguments = new Object[arguments.length];
+ int currentArgument = 0;
+ for (Class<?> parameterType : parameterTypes) {
+ correctedArguments[currentArgument] = getCorrectedArgument(parameterType, arguments[currentArgument]);
+ currentArgument++;
+ }
+ return correctedArguments;
+ }
+
+ /**
+ * Gets the given argument corrected to match the given parameterType. Correction is necessary for array arguments not to be
+ * mistaken by varargs.
+ *
+ * @param parameterType the type to match the given argument upon
+ * @param argument the argument to match the given parameterType
+ * @return the corrected argument
+ */
+ private static Object getCorrectedArgument(Class<?> parameterType, Object argument) {
+ if (!parameterType.isArray() || (argument == null)) {
+ return argument; // normal argument for normal parameterType
+ }
+
+ if (!argument.getClass().isArray()) {
+ return new Object[] {argument};
+ }
+
+ if (parameterType.equals(argument.getClass()))
+ {
+ return argument; // no need to cast
+ }
+
+ // (typed) array argument for (object) array parameterType, elements need to be casted
+ Object correctedArrayArgument = Array.newInstance(parameterType.getComponentType(), Array.getLength(argument));
+ for (int index = 0; index < Array.getLength(argument); index++) {
+ if (parameterType.getComponentType().isPrimitive()) { // rely on autoboxing
+ Array.set(correctedArrayArgument, index, Array.get(argument, index));
+ } else { // cast to expected type
+ try {
+ Array.set(correctedArrayArgument, index, parameterType.getComponentType().cast(Array.get(argument, index)));
+ } catch (ClassCastException e) {
+ throw new IllegalArgumentException("Argument " + argument + " of type " + argument.getClass()
+ + " does not match expected argument type " + parameterType + ".");
+ }
+ }
+ }
+ return correctedArrayArgument;
+ }
+
+ /**
+ * Sets the value of the named field. If fieldName denotes a static field, provide a class, otherwise provide an instance. If the
+ * fieldName denotes a final field, this method could fail with an IllegalAccessException, since setting the value of final fields
+ * at other times than instantiation can have unpredictable effects.<br/>
+ * <br/>
+ * Example:<br/>
+ * <br/>
+ * <code>
+ * String myString = "Test"; <br/>
+ * <br/>
+ * //setting the private field value<br/>
+ * PrivilegedAccessor.setValue(myString, "value", new char[] {'T', 'e', 's', 't'});<br/>
+ * <br/>
+ * //setting the static final field serialVersionUID - MIGHT FAIL<br/>
+ * PrivilegedAccessor.setValue(myString.getClass(), "serialVersionUID", 1);<br/>
+ * <br/>
+ * </code>
+ *
+ * @param instanceOrClass the instance or class to set the field
+ * @param fieldName the name of the field
+ * @param value the new value of the field
+ * @throws NoSuchFieldException if no field with the given <code>fieldName</code> can be found
+ * @throws IllegalAccessException possibly if the field was final
+ */
+ public static void setValue(final Object instanceOrClass, final String fieldName, final Object value) throws NoSuchFieldException,
+ IllegalAccessException {
+ Field field = getField(instanceOrClass, fieldName);
+ if (Modifier.isFinal(field.getModifiers())) {
+ PrivilegedAccessor.setValue(field, "modifiers", field.getModifiers() ^ Modifier.FINAL);
+ }
+ field.set(instanceOrClass, value);
+ }
+
+ /**
+ * Gets the class with the given className.
+ *
+ * @param className the name of the class to get
+ * @return the class for the given className
+ * @throws ClassNotFoundException if the class could not be found
+ */
+ private static Class<?> getClassForName(final String className) throws ClassNotFoundException {
+ if (className.indexOf('[') > -1) {
+ Class<?> clazz = getClassForName(className.substring(0, className.indexOf('[')));
+ return Array.newInstance(clazz, 0).getClass();
+ }
+
+ if (className.indexOf("...") > -1) {
+ Class<?> clazz = getClassForName(className.substring(0, className.indexOf("...")));
+ return Array.newInstance(clazz, 0).getClass();
+ }
+
+ try {
+ return Class.forName(className, false, Thread.currentThread().getContextClassLoader());
+ } catch (ClassNotFoundException e) {
+ return getSpecialClassForName(className);
+ }
+ }
+
+ /**
+ * Maps string representation of primitives to their corresponding classes.
+ */
+ private static final Map<String, Class<?>> PRIMITIVE_MAPPER = new HashMap<String, Class<?>>(8);
+
+ /**
+ * Fills the map with all java primitives and their corresponding classes.
+ */
+ static {
+ PRIMITIVE_MAPPER.put("int", Integer.TYPE);
+ PRIMITIVE_MAPPER.put("float", Float.TYPE);
+ PRIMITIVE_MAPPER.put("double", Double.TYPE);
+ PRIMITIVE_MAPPER.put("short", Short.TYPE);
+ PRIMITIVE_MAPPER.put("long", Long.TYPE);
+ PRIMITIVE_MAPPER.put("byte", Byte.TYPE);
+ PRIMITIVE_MAPPER.put("char", Character.TYPE);
+ PRIMITIVE_MAPPER.put("boolean", Boolean.TYPE);
+ }
+
+ /**
+ * Gets special classes for the given className. Special classes are primitives and "standard" Java types (like String)
+ *
+ * @param className the name of the class to get
+ * @return the class for the given className
+ * @throws ClassNotFoundException if the class could not be found
+ */
+ private static Class<?> getSpecialClassForName(final String className) throws ClassNotFoundException {
+ if (PRIMITIVE_MAPPER.containsKey(className))
+ {
+ return PRIMITIVE_MAPPER.get(className);
+ }
+
+ if (missesPackageName(className))
+ {
+ return getStandardClassForName(className);
+ }
+
+ throw new ClassNotFoundException(className);
+ }
+
+ /**
+ * Gets a 'standard' java class for the given className.
+ *
+ * @param className the className
+ * @return the class for the given className (if any)
+ * @throws ClassNotFoundException of no 'standard' java class was found for the given className
+ */
+ private static Class<?> getStandardClassForName(String className) throws ClassNotFoundException {
+ try {
+ return Class.forName("java.lang." + className, false, Thread.currentThread().getContextClassLoader());
+ } catch (ClassNotFoundException e) {
+ try {
+ return Class.forName("java.util." + className, false, Thread.currentThread().getContextClassLoader());
+ } catch (ClassNotFoundException e1) {
+ throw new ClassNotFoundException(className);
+ }
+ }
+ }
+
+ /**
+ * Tests if the given className possibly misses its package name.
+ *
+ * @param className the className
+ * @return true if the className might miss its package name, otherwise false
+ */
+ private static boolean missesPackageName(String className) {
+ if (className.contains("."))
+ {
+ return false;
+ }
+ if (className.startsWith(className.substring(0, 1).toUpperCase()))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Gets the constructor for a given class with the given parameters.
+ *
+ * @param type the class to instantiate
+ * @param parameterTypes the types of the parameters
+ * @return the constructor
+ * @throws NoSuchMethodException if the method could not be found
+ */
+ private static <T> Constructor<T> getConstructor(final Class<T> type, final Class<?>[] parameterTypes) throws NoSuchMethodException {
+ Constructor<T> constructor = type.getDeclaredConstructor(parameterTypes);
+ constructor.setAccessible(true);
+ return constructor;
+ }
+
+ /**
+ * Return the named field from the given instance or class. Returns a static field if instanceOrClass is a class.
+ *
+ * @param instanceOrClass the instance or class to get the field from
+ * @param fieldName the name of the field to get
+ * @return the field
+ * @throws NoSuchFieldException if no such field can be found
+ * @throws InvalidParameterException if instanceOrClass was null
+ */
+ private static Field getField(final Object instanceOrClass, final String fieldName) throws NoSuchFieldException,
+ InvalidParameterException {
+ if (instanceOrClass == null)
+ {
+ throw new InvalidParameterException("Can't get field on null object/class");
+ }
+
+ Class<?> type = getClass(instanceOrClass);
+
+ try {
+ Field field = type.getDeclaredField(fieldName);
+ field.setAccessible(true);
+ return field;
+ } catch (NoSuchFieldException e) {
+ if (type.getSuperclass() == null)
+ {
+ throw e;
+ }
+ return getField(type.getSuperclass(), fieldName);
+ }
+ }
+
+ /**
+ * Gets the class of the given parameter. If the parameter is a class, it is returned, if it is an object, its class is returned
+ *
+ * @param instanceOrClass the instance or class to get the class of
+ * @return the class of the given parameter
+ */
+ private static Class<?> getClass(final Object instanceOrClass) {
+ if (instanceOrClass instanceof Class)
+ {
+ return (Class<?>) instanceOrClass;
+ }
+
+ return instanceOrClass.getClass();
+ }
+
+ /**
+ * Return the named method with a method signature matching classTypes from the given class.
+ *
+ * @param type the class to get the method from
+ * @param methodName the name of the method to get
+ * @param parameterTypes the parameter-types of the method to get
+ * @return the method
+ * @throws NoSuchMethodException if the method could not be found
+ */
+ private static Method getMethod(final Class<?> type, final String methodName, final Class<?>[] parameterTypes)
+ throws NoSuchMethodException {
+ try {
+ return type.getDeclaredMethod(methodName, parameterTypes);
+ } catch (NoSuchMethodException e) {
+ if (type.getSuperclass() == null)
+ {
+ throw e;
+ }
+ return getMethod(type.getSuperclass(), methodName, parameterTypes);
+ }
+ }
+
+ /**
+ * Gets the method with the given name and parameters from the given instance or class. If instanceOrClass is a class, then we get a
+ * static method.
+ *
+ * @param instanceOrClass the instance or class to get the method of
+ * @param methodName the name of the method
+ * @param parameterTypes the parameter-types of the method to get
+ * @return the method
+ * @throws NoSuchMethodException if the method could not be found
+ */
+ private static Method getMethod(final Object instanceOrClass, final String methodName, final Class<?>[] parameterTypes)
+ throws NoSuchMethodException {
+ Class<?> type;
+
+ type = getClass(instanceOrClass);
+
+ Method accessMethod = getMethod(type, methodName, parameterTypes);
+ accessMethod.setAccessible(true);
+ return accessMethod;
+ }
+
+ /**
+ * Gets the name of a method.
+ *
+ * @param methodSignature the signature of the method
+ * @return the name of the method
+ */
+ private static String getMethodName(final String methodSignature) {
+ try {
+ return methodSignature.substring(0, methodSignature.indexOf('(')).trim();
+ } catch (StringIndexOutOfBoundsException e) {
+ assert false : "Signature must have been checked before this method was called";
+ return null;
+ }
+ }
+
+ /**
+ * Gets the types of the parameters.
+ *
+ * @param parameters the parameters
+ * @return the class-types of the arguments
+ */
+ private static Class<?>[] getParameterTypes(final Object[] parameters) {
+ if (parameters == null)
+ {
+ return new Class[0];
+ }
+
+ Class<?>[] typesOfParameters = new Class[parameters.length];
+
+ for (int i = 0; i < parameters.length; i++) {
+ typesOfParameters[i] = parameters[i].getClass();
+ }
+ return typesOfParameters;
+ }
+
+ /**
+ * Gets the types of the given parameters. If the parameters don't match the given methodSignature an IllegalArgumentException is
+ * thrown.
+ *
+ * @param methodSignature the signature of the method
+ * @return the parameter types as class[]
+ * @throws NoSuchMethodException if the method could not be found
+ * @throws IllegalArgumentException if one of the given parameters doesn't math the given methodSignature
+ */
+ private static Class<?>[] getParameterTypes(final String methodSignature) throws NoSuchMethodException, IllegalArgumentException {
+ String signature = getSignatureWithoutBraces(methodSignature);
+
+ StringTokenizer tokenizer = new StringTokenizer(signature, ", *");
+ Class<?>[] typesInSignature = new Class[tokenizer.countTokens()];
+
+ for (int x = 0; tokenizer.hasMoreTokens(); x++) {
+ String className = tokenizer.nextToken();
+ try {
+ typesInSignature[x] = getClassForName(className);
+ } catch (ClassNotFoundException e) {
+ NoSuchMethodException noSuchMethodException = new NoSuchMethodException(methodSignature);
+ noSuchMethodException.initCause(e);
+ throw noSuchMethodException;
+ }
+ }
+ return typesInSignature;
+ }
+
+ /**
+ * Gets the parameter types as a string.
+ *
+ * @param classTypes the types to get as names.
+ * @return the parameter types as a string
+ *
+ * @see java.lang.Class#argumentTypesToString(Class[])
+ */
+ private static String getParameterTypesAsString(final Class<?>[] classTypes) {
+ assert classTypes != null : "getParameterTypes() should have been called before this method and should have provided not-null classTypes";
+ if (classTypes.length == 0)
+ {
+ return "";
+ }
+
+ StringBuilder parameterTypes = new StringBuilder();
+ for (Class<?> clazz : classTypes) {
+ assert clazz != null : "getParameterTypes() should have been called before this method and should have provided not-null classTypes";
+ parameterTypes.append(clazz.getName()).append(", ");
+ }
+
+ return parameterTypes.substring(0, parameterTypes.length() - 2);
+ }
+
+ /**
+ * Removes the braces around the methods signature.
+ *
+ * @param methodSignature the signature with braces
+ * @return the signature without braces
+ */
+ private static String getSignatureWithoutBraces(final String methodSignature) {
+ try {
+ return methodSignature.substring(methodSignature.indexOf('(') + 1, methodSignature.indexOf(')'));
+ } catch (IndexOutOfBoundsException e) {
+ assert false : "signature must have been checked before this method";
+ return null;
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff