// RJavaTools.java: rJava - low level R to java interface

//

// :tabSize=2:indentSize=2:noTabs=false:folding=explicit:collapseFolds=1:

//

// Copyright (C) 2009 - 2010 Simon Urbanek and Romain Francois

//

// This file is part of rJava.

//

// rJava is free software: you can redistribute it and/or modify it

// under the terms of the GNU General Public License as published by

// the Free Software Foundation, either version 2 of the License, or

// (at your option) any later version.

//

// rJava 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. See the

// GNU General Public License for more details.

//

// You should have received a copy of the GNU General Public License

// along with rJava. If not, see <http://www.gnu.org/licenses/>.

import java.lang.reflect.Array ;

import java.util.Map;

import java.util.HashMap;

import java.util.Vector ;

import java.util.Arrays ;

import java.util.Iterator;

import java.lang.reflect.Method ;

import java.lang.reflect.InvocationTargetException ;

public class RJavaArrayTools {

// TODO: maybe factor this out of this class

private static Map primitiveClasses = initPrimitiveClasses() ;

private static Map initPrimitiveClasses(){

Map primitives = new HashMap();

primitives.put( "I", Integer.TYPE );

primitives.put( "Z", Boolean.TYPE );

primitives.put( "B", Byte.TYPE );

primitives.put( "J", Long.TYPE );

primitives.put( "S", Short.TYPE );

primitives.put( "D", Double.TYPE );

primitives.put( "C", Character.TYPE );

primitives.put( "F", Float.TYPE );

return primitives;

}

// {{{ getObjectTypeName

/**

* Get the object type name of an multi dimensional array.

*

* @param o object

* @throws NotAnArrayException if the object is not an array

*/

public static String getObjectTypeName(Object o) throws NotAnArrayException {

Class o_clazz = o.getClass();

if( !o_clazz.isArray() ) throw new NotAnArrayException( o_clazz );

String cl = o_clazz.getName();

return cl.replaceFirst("\\[+L?", "").replace(";", "") ;

}

public static int getObjectTypeName(int x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : int ") ; }

public static int getObjectTypeName(boolean x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : boolean ") ; }

public static int getObjectTypeName(byte x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : byte ") ; }

public static int getObjectTypeName(long x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : long ") ; }

public static int getObjectTypeName(short x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : short ") ; }

public static int getObjectTypeName(double x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : double ") ; }

public static int getObjectTypeName(char x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : char ") ; }

public static int getObjectTypeName(float x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : float ") ; }

// }}}

// {{{ makeArraySignature

// TODO: test

public static String makeArraySignature( String typeName, int depth ){

StringBuffer buffer = new StringBuffer() ;

for( int i=0; i<depth; i++){

buffer.append( '[' ) ;

}

buffer.append( typeName );

if( ! isPrimitiveTypeName( typeName ) ){

buffer.append( ';') ;

}

return buffer.toString();

}

// }}}

// {{{ getClassForSignature

public static Class getClassForSignature(String signature, ClassLoader loader) throws ClassNotFoundException {

if( primitiveClasses.containsKey(signature) ){

return (Class)primitiveClasses.get( signature ) ;

}

return Class.forName(signature, true, loader) ;

}

// }}}

// {{{ isSingleDimensionArray

public static boolean isSingleDimensionArray( Object o) throws NotAnArrayException{

if( !isArray(o) ) throw new NotAnArrayException( o.getClass() ) ;

String cn = o.getClass().getName() ;

if( cn.lastIndexOf('[') != 0 ) return false;

return true ;

}

// }}}

// {{{ isPrimitiveTypeName

public static boolean isPrimitiveTypeName(String name){

if( name.length() > 1 ) return false;

if( name.equals("I") ) return true ;

if( name.equals("Z") ) return true ;

if( name.equals("B") ) return true ;

if( name.equals("J") ) return true ;

if( name.equals("S") ) return true ;

if( name.equals("D") ) return true ;

if( name.equals("C") ) return true ;

if( name.equals("F") ) return true ;

return false;

}

// }}}

// {{{ isRectangularArray

/**

* Indicates if o is a rectangular array

*

* @param o an array

* @deprecated use new ArrayWrapper(o).isRectangular() instead

*/

public static boolean isRectangularArray(Object o) {

if( !isArray(o) ) return false;

boolean res = false;

try{

if( getDimensionLength( o ) == 1 ) return true ;

res = ( new ArrayWrapper(o) ).isRectangular() ;

} catch( NotAnArrayException e){

res = false;

}

return res ;

}

// thoose below make java < 1.5 happy and me unhappy ;-)

public static boolean isRectangularArray(int x) { return false ; }

public static boolean isRectangularArray(boolean x) { return false ; }

public static boolean isRectangularArray(byte x) { return false ; }

public static boolean isRectangularArray(long x) { return false ; }

public static boolean isRectangularArray(short x) { return false ; }

public static boolean isRectangularArray(double x) { return false ; }

public static boolean isRectangularArray(char x) { return false ; }

public static boolean isRectangularArray(float x) { return false ; }

// }}}

// {{{ getDimensionLength

/**

* Returns the number of dimensions of an array

*

* @param o an array

* @throws NotAnArrayException if this is not an array

*/

public static int getDimensionLength( Object o) throws NotAnArrayException, NullPointerException {

if( o == null ) throw new NullPointerException( "array is null" ) ;

Class clazz = o.getClass();

if( !clazz.isArray() ) throw new NotAnArrayException(clazz) ;

int n = 0;

while( clazz.isArray() ){

n++ ;

clazz = clazz.getComponentType() ;

}

return n ;

}

// thoose below make java < 1.5 happy and me unhappy ;-)

public static int getDimensionLength(int x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : int ") ; }

public static int getDimensionLength(boolean x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : boolean ") ; }

public static int getDimensionLength(byte x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : byte ") ; }

public static int getDimensionLength(long x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : long ") ; }

public static int getDimensionLength(short x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : short ") ; }

public static int getDimensionLength(double x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : double ") ; }

public static int getDimensionLength(char x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : char ") ; }

public static int getDimensionLength(float x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : float ") ; }

// }}}

// {{{ getDimensions

/**

* Returns the dimensions of an array

*

* @param o an array

* @throws NotAnArrayException if this is not an array

* @return the dimensions of the array or null if the object is null

*/

public static int[] getDimensions( Object o) throws NotAnArrayException, NullPointerException {

if( o == null ) throw new NullPointerException( "array is null" ) ;

Class clazz = o.getClass();

if( !clazz.isArray() ) throw new NotAnArrayException(clazz) ;

Object a = o ;

int n = getDimensionLength( o ) ;

int[] dims = new int[n] ;

int i=0;

int current ;

while( clazz.isArray() ){

current = Array.getLength( a ) ;

dims[i] = current ;

i++;

if( current == 0 ){

break ; // the while loop

} else {

a = Array.get( a, 0 ) ;

clazz = clazz.getComponentType() ;

}

}

/* in case of premature stop, we fill the rest of the array with 0 */

// this might not be true:

// Object[][] = new Object[0][10] will return c(0,0)

while( i < dims.length){

dims[i] = 0 ;

i++ ;

}

return dims ;

}

// thoose below make java < 1.5 happy and me unhappy ;-)

public static int[] getDimensions(int x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : int ") ; }

public static int[] getDimensions(boolean x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : boolean ") ; }

public static int[] getDimensions(byte x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : byte ") ; }

public static int[] getDimensions(long x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : long ") ; }

public static int[] getDimensions(short x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : short ") ; }

public static int[] getDimensions(double x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : double ") ; }

public static int[] getDimensions(char x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : char ") ; }

public static int[] getDimensions(float x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : float ") ; }

// }}}

// {{{ getTrueLength

/**

* Returns the true length of an array (the product of its dimensions)

*

* @param o an array

* @throws NotAnArrayException if this is not an array

* @return the number of objects in the array (the product of its dimensions).

*/

public static int getTrueLength( Object o) throws NotAnArrayException, NullPointerException {

if( o == null ) throw new NullPointerException( "array is null" ) ;

Class clazz = o.getClass();

if( !clazz.isArray() ) throw new NotAnArrayException(clazz) ;

Object a = o ;

int len = 1 ;

int i = 0;

while( clazz.isArray() ){

len = len * Array.getLength( a ) ;

if( len == 0 ) return 0 ; /* no need to go further */

i++;

a = Array.get( a, 0 ) ;

clazz = clazz.getComponentType() ;

}

return len ;

}

// thoose below make java < 1.5 happy and me unhappy ;-)

public static int getTrueLength(int x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : int ") ; }

public static int getTrueLength(boolean x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : boolean ") ; }

public static int getTrueLength(byte x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : byte ") ; }

public static int getTrueLength(long x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : long ") ; }

public static int getTrueLength(short x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : short ") ; }

public static int getTrueLength(double x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : double ") ; }

public static int getTrueLength(char x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : char ") ; }

public static int getTrueLength(float x) throws NotAnArrayException { throw new NotAnArrayException("primitive type : float ") ; }

// }}}

// {{{ isArray

/**

* Indicates if a java object is an array

*

* @param o object

* @return true if the object is an array

* @deprecated use RJavaArrayTools#isArray

*/

public static boolean isArray(Object o){

if( o == null) return false ;

return o.getClass().isArray() ;

}

// thoose below make java < 1.5 happy and me unhappy ;-)

public static boolean isArray(int x){ return false ; }

public static boolean isArray(boolean x){ return false ; }

public static boolean isArray(byte x){ return false ; }

public static boolean isArray(long x){ return false ; }

public static boolean isArray(short x){ return false ; }

public static boolean isArray(double x){ return false ; }

public static boolean isArray(char x){ return false ; }

public static boolean isArray(float x){ return false ; }

// }}}

// {{{ ArrayDimensionMismatchException

public static class ArrayDimensionMismatchException extends Exception {

public ArrayDimensionMismatchException( int index_dim, int actual_dim ){

super( "dimension of indexer (" + index_dim + ") too large for array (depth ="+ actual_dim+ ")") ;

}

}

// }}}

// {{{ get

/**

* Gets a single object from a multi dimensional array

*

* @param array java array

* @param position

*/

public static Object get( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return Array.get( getArray( array, position ), position[ position.length -1] );

}

public static int getInt( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return Array.getInt( getArray( array, position ), position[ position.length -1] );

}

public static boolean getBoolean( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return Array.getBoolean( getArray( array, position ), position[ position.length -1] );

}

public static byte getByte( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return Array.getByte( getArray( array, position ), position[ position.length -1] );

}

public static long getLong( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return Array.getLong( getArray( array, position ), position[ position.length -1] );

}

public static short getShort( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return Array.getShort( getArray( array, position ), position[ position.length -1] );

}

public static double getDouble( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return Array.getDouble( getArray( array, position ), position[ position.length -1] );

}

public static char getChar( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return Array.getChar( getArray( array, position ), position[ position.length -1] );

}

public static float getFloat( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return Array.getFloat( getArray( array, position ), position[ position.length -1] );

}

public static Object get( Object array, int position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return get( array, new int[]{position} ) ;

}

public static int getInt( Object array, int position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return getInt( array, new int[]{position} ) ;

}

public static boolean getBoolean( Object array, int position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return getBoolean( array, new int[]{position} ) ;

}

public static byte getByte( Object array, int position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return getByte( array, new int[]{position} ) ;

}

public static long getLong( Object array, int position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return getLong( array, new int[]{position} ) ;

}

public static short getShort( Object array, int position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return getShort( array, new int[]{position} ) ;

}

public static double getDouble( Object array, int position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return getDouble( array, new int[]{position} ) ;

}

public static char getChar( Object array, int position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return getChar( array, new int[]{position} ) ;

}

public static float getFloat( Object array, int position ) throws NotAnArrayException, ArrayDimensionMismatchException {

return getFloat( array, new int[]{position} ) ;

}

private static void checkDimensions(Object array, int[] position) throws NotAnArrayException, ArrayDimensionMismatchException {

int poslength = position.length ;

int actuallength = getDimensionLength(array);

if( poslength > actuallength ){

throw new ArrayDimensionMismatchException( poslength, actuallength ) ;

}

}

// }}}

// {{{ set

/**

* Replaces a single value of the array

*

* @param array array

* @param position index

* @param value the new value

*

* @throws NotAnArrayException if array is not an array

* @throws ArrayDimensionMismatchException if the length of position is too big

*/

public static void set( Object array, int[] position, Object value ) throws NotAnArrayException, ArrayDimensionMismatchException{

Array.set( getArray( array, position ), position[ position.length - 1], value ) ;

}

/* primitive versions */

public static void set( Object array, int[] position, int value ) throws NotAnArrayException, ArrayDimensionMismatchException{

Array.setInt( getArray( array, position ), position[ position.length - 1], value ) ;

}

public static void set( Object array, int[] position, boolean value ) throws NotAnArrayException, ArrayDimensionMismatchException{

Array.setBoolean( getArray( array, position ), position[ position.length - 1], value ) ;

}

public static void set( Object array, int[] position, byte value ) throws NotAnArrayException, ArrayDimensionMismatchException{

Array.setByte( getArray( array, position ), position[ position.length - 1], value ) ;

}

public static void set( Object array, int[] position, long value ) throws NotAnArrayException, ArrayDimensionMismatchException{

Array.setLong( getArray( array, position ), position[ position.length - 1], value ) ;

}

public static void set( Object array, int[] position, short value ) throws NotAnArrayException, ArrayDimensionMismatchException{

Array.setShort( getArray( array, position ), position[ position.length - 1], value ) ;

}

public static void set( Object array, int[] position, double value ) throws NotAnArrayException, ArrayDimensionMismatchException{

Array.setDouble( getArray( array, position ), position[ position.length - 1], value ) ;

}

public static void set( Object array, int[] position, char value ) throws NotAnArrayException, ArrayDimensionMismatchException{

Array.setChar( getArray( array, position ), position[ position.length - 1], value ) ;

}

public static void set( Object array, int[] position, float value ) throws NotAnArrayException, ArrayDimensionMismatchException{

Array.setFloat( getArray( array, position ), position[ position.length - 1], value ) ;

}

public static void set( Object array, int position, Object value ) throws NotAnArrayException, ArrayDimensionMismatchException{

set( array, new int[]{ position }, value );

}

public static void set( Object array, int position, int value ) throws NotAnArrayException, ArrayDimensionMismatchException{

set( array, new int[]{ position }, value );

}

public static void set( Object array, int position, boolean value ) throws NotAnArrayException, ArrayDimensionMismatchException{

set( array, new int[]{ position }, value );

}

public static void set( Object array, int position, byte value ) throws NotAnArrayException, ArrayDimensionMismatchException{

set( array, new int[]{ position }, value );

}

public static void set( Object array, int position, long value ) throws NotAnArrayException, ArrayDimensionMismatchException{

set( array, new int[]{ position }, value );

}

public static void set( Object array, int position, short value ) throws NotAnArrayException, ArrayDimensionMismatchException{

set( array, new int[]{ position }, value );

}

public static void set( Object array, int position, double value ) throws NotAnArrayException, ArrayDimensionMismatchException{

set( array, new int[]{ position }, value );

}

public static void set( Object array, int position, char value ) throws NotAnArrayException, ArrayDimensionMismatchException{

set( array, new int[]{ position }, value );

}

public static void set( Object array, int position, float value ) throws NotAnArrayException, ArrayDimensionMismatchException{

set( array, new int[]{ position }, value );

}

private static Object getArray( Object array, int[] position ) throws NotAnArrayException, ArrayDimensionMismatchException{

checkDimensions( array, position ) ;

int poslength = position.length ;

Object o = array ;

int i=0 ;

if( poslength > 1 ){

while( i< (poslength-1) ){

o = Array.get( o, position[i] ) ;

i++ ;

}

}

return o ;

}

// TODO: also have primitive types in value

// }}}

// {{{ unique

// TODO: cannot use LinkedHashSet because it first was introduced in 1.4

// and code in this area needs to work on 1.2 jvm

public static Object[] unique( Object[] array ){

int n = array.length ;

boolean[] unique = new boolean[ array.length ];

for( int i=0; i<array.length; i++){

unique[i] = true ;

}

Vector res = new Vector();

boolean added ;

for( int i=0; i<n; i++){

if( !unique[i] ) continue ;

Object current = array[i];

added = false;

for( int j=i+1; j<n; j++){

Object o_j = array[j] ;

if( unique[j] && current.equals( o_j ) ){

if( !added ){

unique[i] = false;

res.add( current );

added = true ;

}

unique[j] = false;

}

}

}

// build the array using newInstance so that it has the same

// component type as the original array and not just Object

Object[] res_array = (Object[])Array.newInstance( array.getClass().getComponentType(), res.size() ) ;

res.toArray( res_array );

return res_array ;

}

// }}}

// {{{ duplicated

public static boolean[] duplicated( Object[] array ){

int n = array.length ;

boolean[] duplicated = new boolean[ array.length ];

for( int i=0; i<array.length; i++){

duplicated[i] = false ;

}

for( int i=0; i<n; i++){

if( duplicated[i] ) continue ;

Object current = array[i];

for( int j=i+1; j<n; j++){

Object o_j = array[j] ;

if( !duplicated[j] && current.equals( o_j ) ){

duplicated[j] = true;

}

}

}

return duplicated ;

}

// }}}

// {{{ anyDuplicated

public static int anyDuplicated( Object[] array ){

int n = array.length ;

for( int i=0; i<n; i++){

Object current = array[i];

for( int j=i+1; j<n; j++){

Object o_j = array[j] ;

if( current.equals( o_j ) ){

return j ;

}

}

}

return -1 ;

}

// }}}

// {{{ sort

/**

* Returns a copy of the array where elements are sorted

*

* @param array array of Objects.

* @param decreasing if true the sort is in decreasing order

*

* @throws NotComparableException if the component type of the array does not

* implement the Comparable interface

*/

public static Object[] sort( Object[] array, boolean decreasing ) throws NotComparableException {

Class ct = array.getClass().getComponentType() ;

if( Comparable.class.isAssignableFrom( ct ) ){

throw new NotComparableException( ct ) ;

}

int n = array.length ;

Object[] res = copy( array ) ;

Arrays.sort( res ) ;

if( !decreasing ){

return res ;

} else{

Object current ;

int top = (res.length) / 2 ;

for( int i=0; i<top ; i++ ){

current = res[i] ;

res[ i ] = res[ n-i-1 ] ;

res[ n-i-1 ] = current ;

}

}

return res ;

}

// }}}

// {{{ rev

/**

* Returns a copy of the input array with elements in

* reverse order

*

* @param original input array

*/

public static Object[] rev( Object[] original ){

int n = original.length ;

Object[] copy = (Object[])Array.newInstance( original.getClass().getComponentType() , n );

for( int i=0; i<n ; i++ ){

copy[n-i-1] = original[i] ;

}

return copy ;

}

// }}}

// {{{ copy

public static Object[] copy( Object[] original ){

int n = original.length ;

Object[] copy = (Object[])Array.newInstance( original.getClass().getComponentType() , n );

for( int i=0; i<n ; i++ ){

copy[i] = original[i] ;

}

return copy ;

}

// }}}

// {{{ getIterableContent

public static Object[] getIterableContent( Iterable o){

Vector v = new Vector();

Iterator iterator = o.iterator();

while( iterator.hasNext() ){

v.add( iterator.next() );

}

return v.toArray();

}

// }}}

// {{{ rep

/**

* Creates a java array by cloning o several times

*

* @param o object to clone

* @param size number of times to replicate the object

*/

public static Object[] rep( Object o, int size ) throws Throwable {

Object[] res = (Object[])Array.newInstance( o.getClass(), size ) ;

if( ! ( o instanceof Cloneable )){

return res ;

}

Method m = getCloneMethod( o.getClass() ) ;

boolean access = m.isAccessible() ;

m.setAccessible( true ) ;

try{

for( int i=0; i<size; i++){

Object cloned = o.getClass().cast( m.invoke( o, (Object[])null ) );

res[i] = cloned ;

}

} catch( IllegalAccessException e) {

m.setAccessible( access );

/* should not happen */

} catch( InvocationTargetException e){

m.setAccessible( access );

throw e.getCause() ;

}

return res ;

}

private static Method getCloneMethod(Class cl){

Method[] methodz ;

Method m = null ;

while( cl != null ){

methodz = cl.getDeclaredMethods( ) ;

for( int i=0; i<methodz.length; i++){

m = methodz[i];

if( "clone".equals( m.getName() ) && m.getParameterTypes().length == 0 ){

return m ;

}

}

cl = cl.getSuperclass();

}

return null ; /* never happens */

}

// }}}

// {{{ cloneObject

public static Object cloneObject( Object o) throws Throwable {

Method m = getCloneMethod( o.getClass() ) ;

boolean access = m.isAccessible() ;

m.setAccessible( true ) ;

Object copy = null ;

try{

copy = o.getClass().cast( m.invoke( o, (Object[])null ) );

} catch( IllegalAccessException e) {

m.setAccessible( access );

/* should not happen */

} catch( InvocationTargetException e){

m.setAccessible( access );

throw e.getCause() ;

}

return copy ;

}

// }}}

/// boxing and unboxing for Double[] and Integer[]

public static final int NA_INTEGER = -2147483648;

public static final double NA_REAL = Double.longBitsToDouble(0x7ff00000000007a2L);

static final long NA_bits = Double.doubleToRawLongBits(Double.longBitsToDouble(0x7ff00000000007a2L));

public static double[] unboxDoubles(Double[] o) {

if (o == null) return null;

int i = 0, n = o.length;

double d[] = new double[n];

for (i = 0; i < n; i++) d[i] = (o[i] == null) ? NA_REAL : o[i].doubleValue();

return d;

}

public static int[] unboxIntegers(Integer[] o) {

if (o == null) return null;

int i = 0, n = o.length;

int d[] = new int[n];

for (i = 0; i < n; i++) d[i] = (o[i] == null) ? NA_INTEGER : o[i].intValue();

return d;

}

public static int[] unboxBooleans(Boolean[] o) {

if (o == null) return null;

int i = 0, n = o.length;

int d[] = new int[n];

for (i = 0; i < n; i++) d[i] = (o[i] == null) ? NA_INTEGER : (o[i].booleanValue() ? 1 : 0);

return d;

}

public static boolean isNA(double value) {

/* on OS X i386 the MSB of the fraction is set even though R doesn't set it.

Although this is technically a good idea (to make it a QNaN) it's not what R does and thus makes the comparison tricky */

return (Double.doubleToRawLongBits(value) & 0xfff7ffffffffffffL) == (NA_bits & 0xfff7ffffffffffffL);

}

public static Double[] boxDoubles(double[] d) {

if (d == null) return null;

int i = 0, n = d.length;

Double o[] = new Double[i];

for (i = 0; i < n; i++) if (!isNA(d[i])) o[i] = new Double(d[i]);

return o;

}

public static Integer[] boxIntegers(int[] d) {

if (d == null) return null;

int i = 0, n = d.length;

Integer o[] = new Integer[i];

for (i = 0; i < n; i++) if (d[i] != NA_INTEGER) o[i] = new Integer(d[i]);

return o;

}

public static Boolean[] boxBooleans(int[] d) {

if (d == null) return null;

int i = 0, n = d.length;

Boolean o[] = new Boolean[i];

for (i = 0; i < n; i++) if (d[i] != NA_INTEGER) o[i] = new Boolean((d[i] == 0) ? false : true);

return o;

}

}