package org.rosuda.JRI;
import java.util.Vector;
/**
* This class encapsulates and caches R objects as returned from R. Currently it
* only converts certain SEXPs references from R into Java obejcts, but
* eventually bi-directional support should be added. The currently supported
* objects are string, integer and numeric vectors. All other types can be
* accessed only using {@link #xp} reference and RNI methods.
*/
public class REXP {
/** xpression type: NULL */
public static final int XT_NULL = 0;
/** xpression type: integer */
public static final int XT_INT = 1;
/** xpression type: double */
public static final int XT_DOUBLE = 2;
/** xpression type: String */
public static final int XT_STR = 3;
/** xpression type: language construct (currently content is same as list) */
public static final int XT_LANG = 4;
/** xpression type: symbol (content is symbol name: String) */
public static final int XT_SYM = 5;
/** xpression type: RBool */
public static final int XT_BOOL = 6;
/** xpression type: Vector */
public static final int XT_VECTOR = 16;
/** xpression type: RList */
public static final int XT_LIST = 17;
/**
* xpression type: closure (there is no java class for that type (yet?).
* currently the body of the closure is stored in the content part of the
* REXP. Please note that this may change in the future!)
*/
public static final int XT_CLOS = 18;
/** xpression type: int[] */
public static final int XT_ARRAY_INT = 32;
/** xpression type: double[] */
public static final int XT_ARRAY_DOUBLE = 33;
/** xpression type: String[] (currently not used, Vector is used instead) */
public static final int XT_ARRAY_STR = 34;
/** internal use only! this constant should never appear in a REXP */
public static final int XT_ARRAY_BOOL_UA = 35;
/** xpression type: RBool[] */
public static final int XT_ARRAY_BOOL = 36;
/** xpression type: int[] to be interpreted as boolean */
public static final int XT_ARRAY_BOOL_INT = 37;
/** xpression type: unknown; no assumptions can be made about the content */
public static final int XT_UNKNOWN = 48;
/** xpression type: pure reference, no internal type conversion performed */
public static final int XT_NONE = -1;
/**
* xpression type: RFactor; this XT is internally generated (ergo is does
* not come from Rsrv.h) to support RFactor class which is built from
* XT_ARRAY_INT
*/
public static final int XT_FACTOR = 127;
/* internal SEXP types in R - taken directly from Rinternals.h */
public static final int NILSXP = 0; /* nil = NULL */
public static final int SYMSXP = 1; /* symbols */
public static final int LISTSXP = 2; /* lists of dotted pairs */
public static final int CLOSXP = 3; /* closures */
public static final int ENVSXP = 4; /* environments */
public static final int PROMSXP = 5; /*
* promises: [un]evaluated closure
* arguments
*/
public static final int LANGSXP = 6; /*
* language constructs (special
* lists)
*/
public static final int SPECIALSXP = 7; /* special forms */
public static final int BUILTINSXP = 8; /* builtin non-special forms */
public static final int CHARSXP = 9; /*
* "scalar" string type (internal
* only)
*/
public static final int LGLSXP = 10; /* logical vectors */
public static final int INTSXP = 13; /* integer vectors */
public static final int REALSXP = 14; /* real variables */
public static final int CPLXSXP = 15; /* complex variables */
public static final int STRSXP = 16; /* string vectors */
public static final int DOTSXP = 17; /* dot-dot-dot object */
public static final int ANYSXP = 18; /* make "any" args work */
public static final int VECSXP = 19; /* generic vectors */
public static final int EXPRSXP = 20; /* expressions vectors */
public static final int BCODESXP = 21; /* byte code */
public static final int EXTPTRSXP = 22; /* external pointer */
public static final int WEAKREFSXP = 23; /* weak reference */
public static final int RAWSXP = 24; /* raw bytes */
public static final int S4SXP = 25; /* S4 object */
public static final int FUNSXP = 99; /* Closure or Builtin */
/**
* Engine which this EXP was obtained from. EXPs are valid only for the
* engine they were obtained from - it's illegal to mix EXP between engines.
* There is a speacial case when the engine may be null - if a REXP creating
* was requested but deferred until an engine is available.
*/
Rengine eng;
/**
* native reference to the SEXP represented in R. It's usually a pointer,
* but can be any handle obtained from the engine. This reference can be
* used when calling RNI commands directly.
*/
public long xp;
/**
* native type of the represented expression (see ...SXP constants in R).
* Please note that this type is cached and may have changed in the
* meantime. If the possibility of changing type exists (mainly list/lang)
* then use rniExpType to make sure
*/
public int rtype;
/**
* create a REXP directly from a R SEXP reference. SEXP types STRSXP, INTSXP
* and REALSXP are automatically converted. All others are represented as
* SEXP references only.
*/
public REXP(Rengine re, long exp) {
this(re, exp, true);
}
protected void finalize() throws Throwable {
try {
if (Xt == XT_NONE && xp != 0 && eng != null) // release underlying R obejct if it was preserved
eng.rniRelease(xp);
} finally {
super.finalize();
}
}
public REXP(Rengine re, long exp, boolean convert) {
eng = re;
xp = exp;
rtype = re.rniExpType(xp);
//System.out.println("["+rtype+"@"+exp+","+convert+"]");
if (!convert) {
Xt = XT_NONE;
if (re != null && xp != 0)
re.rniPreserve(xp); // preserve the object so it doesn't get garbage-collected while we are referencing it
return;
}
if (rtype == STRSXP) {
String[] s = re.rniGetStringArray(xp);
if (s != null && s.length == 1) {
cont = s[0];
Xt = XT_STR;
} else {
cont = s;
Xt = XT_ARRAY_STR;
}
} else if (rtype == INTSXP) {
cont = null;
if (re.rniInherits(xp, "factor")) {
long levx = re.rniGetAttr(xp, "levels");
if (levx != 0) {
String[] levels = null;
// we're using low-lever calls here (FIXME?)
int rlt = re.rniExpType(levx);
if (rlt == STRSXP) {
levels = re.rniGetStringArray(levx);
int[] ids = re.rniGetIntArray(xp);
cont = new RFactor(ids, levels, 1);
Xt = XT_FACTOR;
}
}
}
// if it's not a factor, then we use int[] instead
if (cont == null ) {
cont = re.rniGetIntArray(xp);
Xt = XT_ARRAY_INT;
}
} else if (rtype == REALSXP) {
cont = re.rniGetDoubleArray(xp);
Xt = XT_ARRAY_DOUBLE;
} else if (rtype == LGLSXP) {
cont = re.rniGetBoolArrayI(xp);
Xt = XT_ARRAY_BOOL_INT;
} else if (rtype == VECSXP) {
long[] l = re.rniGetVector(xp);
cont = new RVector();
int i = 0;
//System.out.println("VECSXP, length="+l.length);
Xt = XT_VECTOR;
while (i < l.length)
((RVector)cont).addElement(new REXP(re, l[i++]));
long na = re.rniGetAttr(xp, "names");
if (na!=0 && re.rniExpType(na)==STRSXP)
((RVector)cont).setNames(re.rniGetStringArray(na));
} else if (rtype == LISTSXP) {
long car = re.rniCAR(xp);
long cdr = re.rniCDR(xp);
long tag = re.rniTAG(xp);
REXP cdrx = (cdr==0 || re.rniExpType(cdr)!=LISTSXP)?null:new REXP(re,re.rniCDR(xp));
cont = new RList(new REXP(re,car), (tag==0)?null:new REXP(re,tag), cdrx);
Xt = XT_LIST;
} else if (rtype == SYMSXP) {
cont = re.rniGetSymbolName(xp);
Xt = XT_SYM;
} else
Xt = XT_NULL;
//System.out.println("new REXP: "+toString());
}
/** xpression type */
int Xt;
/** attribute xpression or null if none */
REXP attr;
/** content of the xpression - its object type is dependent of {@link #Xt} */
Object cont;
/** cached binary length; valid only if positive */
long cachedBinaryLength = -1;
/** construct a new, empty (NULL) expression w/o attribute */
public REXP() {
Xt = XT_NULL;
attr = null;
cont = null;
}
/**
* construct a new xpression of type t and content o, but no attribute
*
* @param t
* xpression type (XT_...)
* @param o
* content
*/
public REXP(int t, Object o) {
Xt = t;
cont = o;
attr = null;
}
/**
* construct a new xpression of type t, content o and attribute at
*
* @param t
* xpression type
* @param o
* content
* @param at
* attribute
*/
public REXP(int t, Object o, REXP at) {
Xt = t;
cont = o;
attr = at;
}
/**
* construct a new xpression of type XT_ARRAY_DOUBLE and content val
*
* @param val
* array of doubles to store in the REXP
*/
public REXP(double[] val) {
this(XT_ARRAY_DOUBLE, val);
}
/**
* construct a new xpression of type XT_ARRAY_INT and content val
*
* @param val
* array of integers to store in the REXP
*/
public REXP(int[] val) {
this(XT_ARRAY_INT, val);
}
/**
* construct a new xpression of type XT_ARRAY_INT and content val
*
* @param val
* array of integers to store in the REXP
*/
public REXP(String[] val) {
this(XT_ARRAY_STR, val);
}
/** construct new expression with the contents of a boolean vector
@since JRI 0.3-2
@param val contents */
public REXP(boolean[] val) {
Xt = XT_ARRAY_BOOL_INT;
if (val==null) { cont = new int[0]; } else {
int [] ic = new int[val.length];
int i=0;
while (inull if there is none associated
@since JRI 0.3, replaces getAttribute() but should be avoided if possible - use {@link #getAttribute(String)} instead.
*/
public REXP getAttributes() {
return attr;
}
/** retrieve a specific attribute.
Note: the current representation fetches the attribute ad-hoc, so it breaks the assumption that the expression is no longer accessed after the constructor was called. This should change in the future.
@param name name of the attribute
@return REXP containing the attribute or null if the attribute doesn't exist. The conversion flag is inherited from this REXP.
@since JRI 0.3
*/
public REXP getAttribute(String name) {
// FIXME: we could do some caching if attr is not null ...
long aref = eng.rniGetAttr(xp, name);
if (aref==0) return null;
return new REXP(eng, aref, (Xt != XT_NONE));
}
/**
* get raw content. Use as... methods to retrieve contents of known type.
*
* @return content of the REXP
*/
public Object getContent() {
return cont;
}
/**
* get xpression type (see XT_.. constants) of the content. It defines the
* type of the content object.
*
* @return xpression type
*/
public int getType() {
return Xt;
}
/**
* Obtains R engine object which supplied this REXP.
*
* @returns {@link Rengine} object
*/
Rengine getEngine() {
return eng;
};
/** return the first element of a character vector if this REXP is a character vector of length 1 or more, return null otherwise */
public String asString() {
if (cont == null)
return null;
if (Xt == XT_STR)
return (String) cont;
if (Xt == XT_ARRAY_STR) {
String[] sa = (String[]) cont;
return (sa.length > 0) ? sa[0] : null;
}
return null;
}
/** return the name of the symbol represented by this REXP if is it a symbol or null otherwise */
public String asSymbolName() {
return (Xt == XT_SYM)?((String) cont):null;
}
/** return the contents of this REXP as an array of strings if this REXP is a character vector, return null otherwise */
public String[] asStringArray() {
if (cont == null)
return null;
if (Xt == XT_STR) {
String[] sa = new String[1];
sa[0] = (String) cont;
return sa;
}
if (Xt == XT_ARRAY_STR)
return (String[]) cont;
return null;
}
/**
* get content of the REXP as int (if it is one)
*
* @return int content or 0 if the REXP is no integer
*/
public int asInt() {
if (Xt == XT_ARRAY_INT) {
int i[] = (int[]) cont;
if (i != null && i.length > 0)
return i[0];
}
return (Xt == XT_INT) ? ((Integer) cont).intValue() : 0;
}
/**
* get content of the REXP as double (if it is one)
*
* @return double content or 0.0 if the REXP is no double
*/
public double asDouble() {
if (Xt == XT_ARRAY_DOUBLE) {
double d[] = (double[]) cont;
if (d != null && d.length > 0)
return d[0];
}
return (Xt == XT_DOUBLE) ? ((Double) cont).doubleValue() : 0.0;
}
/**
* get content of the REXP as {@link Vector} (if it is one)
*
* @return Vector content or null if the REXP is no Vector
*/
public RVector asVector() {
return (Xt == XT_VECTOR) ? (RVector) cont : null;
}
/**
* get content of the REXP as {@link RFactor} (if it is one)
*
* @return {@link RFactor} content or null if the REXP is no
* factor
*/
public RFactor asFactor() {
return (Xt == XT_FACTOR) ? (RFactor) cont : null;
}
/**
* get content of the REXP as {@link RList} if the contents is a list or a generic vector
*
* @return {@link RList} content or null if the REXP is neither a list nor a generic vector
*/
public RList asList() {
return (Xt == XT_LIST) ?
(RList) cont :
( // for compatibility with Rserve we convert vectors to lists
(Xt == XT_VECTOR) ? new RList((RVector)cont) : null
);
}
/**
* get content of the REXP as {@link RBool} (if it is one)
*
* @return {@link RBool} content or null if the REXP is no
* logical value
*/
public RBool asBool() {
if (Xt == XT_ARRAY_BOOL_INT) {
int [] ba = (int[]) cont;
return (ba!=null && ba.length>0)?new RBool(ba[0]):null;
}
return (Xt == XT_BOOL) ? (RBool) cont : null;
}
/**
* get content of the REXP as an array of doubles. Array of integers, single
* double and single integer are automatically converted into such an array
* if necessary.
*
* @return double[] content or null if the REXP is not a
* array of doubles or integers
*/
public double[] asDoubleArray() {
if (Xt == XT_ARRAY_DOUBLE)
return (double[]) cont;
if (Xt == XT_DOUBLE) {
double[] d = new double[1];
d[0] = asDouble();
return d;
}
if (Xt == XT_INT) {
double[] d = new double[1];
d[0] = ((Integer) cont).doubleValue();
return d;
}
if (Xt == XT_ARRAY_INT) {
int[] i = asIntArray();
if (i == null)
return null;
double[] d = new double[i.length];
int j = 0;
while (j < i.length) {
d[j] = (double) i[j];
j++;
}
return d;
}
return null;
}
/**
* get content of the REXP as an array of integers. Unlike
* {@link #asDoubleArray} NO automatic conversion is done if the
* content is not an array of the correct type, because there is no
* canonical representation of doubles as integers. A single integer is
* returned as an array of the length 1. This method can be also used
* to access a logical array in its integer form (0=FALSE, 1=TRUE, 2=NA).
*
* @return int[] content or null if the REXP is not a
* array of integers
*/
public int[] asIntArray() {
if (Xt == XT_ARRAY_INT || Xt == XT_ARRAY_BOOL_INT)
return (int[]) cont;
if (Xt == XT_INT) {
int[] i = new int[1];
i[0] = asInt();
return i;
}
return null;
}
/**
* returns the content of the REXP as a matrix of doubles (2D-array:
* m[rows][cols]). This is the same form as used by popular math packages
* for Java, such as JAMA. This means that following leads to desired
* results:
* Matrix m=new Matrix(c.eval("matrix(c(1,2,3,4,5,6),2,3)").asDoubleMatrix());
*
* @return 2D array of doubles in the form double[rows][cols] or
* null if the contents is no 2-dimensional matrix of
* doubles
*/
public double[][] asDoubleMatrix() {
double[] ct = asDoubleArray();
if (ct==null) return null;
REXP dim = getAttribute("dim");
if (dim == null || dim.Xt != XT_ARRAY_INT)
return null; // we need dimension attr
int[] ds = dim.asIntArray();
if (ds == null || ds.length != 2)
return null; // matrix must be 2-dimensional
int m = ds[0], n = ds[1];
double[][] r = new double[m][n];
if (ct == null)
return null;
// R stores matrices as matrix(c(1,2,3,4),2,2) = col1:(1,2), col2:(3,4)
// we need to copy everything, since we create 2d array from 1d array
int i = 0, k = 0;
while (i < n) {
int j = 0;
while (j < m) {
r[j++][i] = ct[k++];
}
i++;
}
return r;
}
/** this is just an alias for {@link #asDoubleMatrix()}. */
public double[][] asMatrix() {
return asDoubleMatrix();
}
/**
* displayable contents of the expression. The expression is traversed
* recursively if aggregation types are used (Vector, List, etc.)
*
* @return String descriptive representation of the xpression
*/
public String toString() {
StringBuffer sb = new StringBuffer("[" + xtName(Xt) + " ");
if (attr != null)
sb.append("\nattr=" + attr + "\n ");
if (Xt == XT_DOUBLE)
sb.append((Double) cont);
if (Xt == XT_INT)
sb.append((Integer) cont);
if (Xt == XT_BOOL)
sb.append((RBool) cont);
if (Xt == XT_FACTOR)
sb.append((RFactor) cont);
if (Xt == XT_ARRAY_DOUBLE) {
double[] d = (double[]) cont;
sb.append("(");
for (int i = 0; i < d.length; i++) {
sb.append(d[i]);
if (i < d.length - 1)
sb.append(", ");
if (i == 99) {
sb.append("... (" + (d.length - 100)
+ " more values follow)");
break;
}
}
sb.append(")");
}
if (Xt == XT_ARRAY_INT) {
int[] d = (int[]) cont;
sb.append("(");
for (int i = 0; i < d.length; i++) {
sb.append(d[i]);
if (i < d.length - 1)
sb.append(", ");
if (i == 99) {
sb.append("... (" + (d.length - 100)
+ " more values follow)");
break;
}
}
sb.append(")");
}
if (Xt == XT_ARRAY_BOOL) {
RBool[] d = (RBool[]) cont;
sb.append("(");
for (int i = 0; i < d.length; i++) {
sb.append(d[i]);
if (i < d.length - 1)
sb.append(", ");
}
sb.append(")");
}
if (Xt == XT_ARRAY_STR) {
String[] d = (String[]) cont;
sb.append("(");
for (int i = 0; i < d.length; i++) {
sb.append((d[i] == null) ? "NA" : ("\"" + d[i] + "\""));
if (i < d.length - 1)
sb.append(", ");
if (i == 10 && d.length > 14) {
sb.append("... (" + (d.length - 10) + " more values follow)");
break;
}
}
sb.append(")");
}
if (Xt == XT_VECTOR) {
Vector v = (Vector) cont;
sb.append("(");
for (int i = 0; i < v.size(); i++) {
sb.append(((REXP) v.elementAt(i)).toString());
if (i < v.size() - 1)
sb.append(", ");
}
sb.append(")");
}
if (Xt == XT_STR) {
if (cont == null)
sb.append("NA");
else {
sb.append("\"");
sb.append((String) cont);
sb.append("\"");
}
}
if (Xt == XT_SYM) {
sb.append((String) cont);
}
if (Xt == XT_LIST || Xt == XT_LANG) {
RList l = (RList) cont;
sb.append(l.head);
sb.append(":");
sb.append(l.tag);
sb.append(",(");
sb.append(l.body);
sb.append(")");
}
if (Xt == XT_NONE) {
sb.append("{"+rtype+"}");
}
if (Xt == XT_UNKNOWN)
sb.append((Integer) cont);
sb.append("]");
return sb.toString();
}
public static String quoteString(String s) {
// this code uses API introdiced in 1.4 so it needs to be re-written for
// earlier JDKs
if (s.indexOf('\\') >= 0)
s.replaceAll("\\", "\\\\");
if (s.indexOf('"') >= 0)
s.replaceAll("\"", "\\\"");
return "\"" + s + "\"";
}
/** returns human-readable name of the xpression type as string. Arrays are denoted by a trailing asterisk (*).
@param xt xpression type
@return name of the xpression type */
public static String xtName(int xt) {
if (xt==XT_NULL) return "NULL";
if (xt==XT_INT) return "INT";
if (xt==XT_STR) return "STRING";
if (xt==XT_DOUBLE) return "REAL";
if (xt==XT_BOOL) return "BOOL";
if (xt==XT_ARRAY_INT) return "INT*";
if (xt==XT_ARRAY_STR) return "STRING*";
if (xt==XT_ARRAY_DOUBLE) return "REAL*";
if (xt==XT_ARRAY_BOOL) return "BOOL*";
if (xt==XT_ARRAY_BOOL_INT) return "BOOLi*";
if (xt==XT_SYM) return "SYMBOL";
if (xt==XT_LANG) return "LANG";
if (xt==XT_LIST) return "LIST";
if (xt==XT_CLOS) return "CLOS";
if (xt==XT_VECTOR) return "VECTOR";
if (xt==XT_FACTOR) return "FACTOR";
if (xt==XT_UNKNOWN) return "UNKNOWN";
if (xt==XT_NONE) return "(SEXP)";
return "";
}
}