package org.rosuda.JGR;
//JGR - Java Gui for R, see http://www.rosuda.org/JGR/
//Copyright (C) 2003 - 2005 Markus Helbig
//--- for licensing information see LICENSE file in the original JGR distribution ---
import java.io.*;
import java.util.*;
import org.rosuda.ibase.*;
import org.rosuda.util.Global;
import org.rosuda.JRI.*;
import org.rosuda.JGR.robjects.*;
import org.rosuda.JGR.toolkit.Editor;
/**
* RController - implementations of an interface between JGR and Rengine, providing all needed functions for working with R.
*
* @author Markus Helbig
*
* RoSuDa 2003 - 2005
*/
public class RController {
/**
* dummy object.
*/
public static Object dummy = new Object();
/**
* Get R_HOME.
* @return R_HOME path
*/
public static String getRHome() {
REXP x = JGR.R.eval("R.home()");
if (x != null && x.asStringArray()!=null) return x.asStringArray()[0];
return "";
}
/**
* Get R_LIBS.
* @return R_LIBS paths
*/
public static String[] getRLibs() {
REXP x = JGR.R.eval(".libPaths()");
if (x != null && x.asStringArray()!=null) return x.asStringArray();
return null;
}
/**
* Get R prompt
* @return prompt
*/
public static String getRPrompt() {
REXP x = JGR.R.eval("try(as.character(options('prompt')),silent=TRUE)");
if (x != null && x.asStringArray()!=null) return x.asStringArray()==null?"> ":x.asStringArray()[0];
return "> ";
}
/**
* Get R continue
* @return continue
*/
public static String getRContinue() {
REXP x = JGR.R.eval("try(as.character(options('continue')),silent=TRUE)");
if (x != null && x.asStringArray()!=null) return x.asStringArray()==null?"> ":x.asStringArray()[0];
return "> ";
}
/**
* Get R_DEFAULT_PACKAGES.
* @return default packages
*/
public static String getCurrentPackages() {
REXP x = JGR.R.eval(".allpkg <- (.packages(all=T));.p <- NULL;for (i in 1:length(.allpkg)) .p <- paste(.p,as.character(.allpkg[i]),sep=\",\");substring(.p,2)");
if (x != null && x.asStringArray()!=null) {
String p = "";
for (int i = 0; i < x.asStringArray().length-1; i++)
p += x.asStringArray()[i]+",";
return p+=x.asStringArray()[x.asStringArray().length-1];
}
return null;
}
/**
* Get current installed packages
* @return installed packages
*/
public static String[] getDefaultPackages() {
REXP x = JGR.R.eval("getOption(\"defaultPackages\")");
if (x != null && x.asStringArray()!=null) return x.asStringArray();
return new String[] {};
}
/**
* Show all posibilities to complete your given part of a command.
* @param partOfCmd part which you want to complete
* @return possible completions
*/
public static String[] completeCommand(String partOfCmd) {
if (!JGR.STARTED) return null;
int s = partOfCmd.length()-1;
if (partOfCmd.trim().length() == 0) return null;
partOfCmd = partOfCmd.replaceAll("\\.","\\\\."); //replace real . with their equivalent regex
REXP cmds = JGR.R.idleEval(".completeCommand(\""+partOfCmd+"\")");
String[] c = null;
if (cmds != null && (c=cmds.asStringArray()) != null) return c;
return null;
}
/**
* Completetion of a file (doesn't supports multiple fils yet).
* @param part of file to complete
* @return file
*/
public static String completeFile(String part) {
part = part.replaceFirst("~",System.getProperty("user.home"));
int tl = part.length();
int ls = tl - 1, fb = 0;
if (tl == 0) ls = 0;
String dir = null;
boolean working = false;
String fn = null;
if (System.getProperty("os.name").startsWith("Windows")) part = part.replaceAll(":/","://");
while (ls > 0 && part.charAt(ls) != '/') {
ls--;
}
if (ls == 0 && (tl == 0 || part.charAt(ls) != '/'))
working = true;
dir = working ? "." : ( (ls == 0) ? "/" : (part.substring(0, ls)));
fb = ls;
if (fb < tl && part.charAt(fb) == '/')
fb++;
fn = (fb < tl) ? part.substring(fb) : "";
File directory = null;
String[] cont = null;
if ( (directory = new File(dir)).exists())
cont = directory.list();
if (cont == null)
return null;
int firstMatch = -1, matches = 0;
String common = null;
for (int i = 0; i < cont.length; i++) {
String sx = cont[i];
if (sx.startsWith(fn)) {
if (matches == 0) {
firstMatch = i;
common = sx;
}
else {
common = commonWithPrefix(common, sx);
}
matches++;
}
}
if (common != null) {
String fnp = common.replace('\\','/');
File tfile = null;
boolean isDir = false;
fnp = ( (dir == ".") ? fnp :
( (dir == "/") ? ("/" + fnp) :
(dir + "/") + fnp));
if ( (tfile = new File(fnp)).exists() && (isDir = tfile.isDirectory()))
fnp = fnp + "/";
if (fnp.endsWith("//"))
fnp = "";
return fnp.replaceFirst(part, "");
}
return null;
}
/**
* Get all keywords for syntaxhighlighting.
* @return keywords
*/
public static String[] getKeyWords() {
REXP x = JGR.R.idleEval(".refreshKeyWords()");
String[] r = null;
if (x != null && (r=x.asStringArray()) != null) return r;
return r;
}
/**
* Get object names used for syntaxhighlighting.
* @return objects
*/
public static String[] getObjects() {
REXP x = JGR.R.idleEval(".refreshObjects()");
String[] r = null;
if (x != null && (r=x.asStringArray()) != null) return r;
return r;
}
/**
* Browse the workspace for objects and put them in JGR.MODELS, JGR.DATA, JGR.OTHER and JGR.FUNCTIONS.
* currently only these things which are provided by R-command: ls(pos=1).
*/
public static void refreshObjects() {
JGR.DATA.clear();
JGR.OTHERS.clear();
JGR.MODELS.clear();
JGR.FUNCTIONS.clear();
String models[];
REXP x = JGR.R.idleEval(".getModels()");
if (x != null && (models = x.asStringArray()) != null) {
for (int i = 0; i < models.length; i++)
JGR.MODELS.add(createRModel(models[i],models[++i]));
}
x = JGR.R.idleEval(".getDataObjects()");
String[] data;
if (x != null && (data = x.asStringArray()) != null) {
int a = 1;
for (int i = 0; i < data.length; i++) {
boolean b = (data[i].equals("null")||data[i].trim().length()==0);
String name = b?a+"":data[i];
JGR.DATA.add(createRObject(name,data[++i],null,(!b)));
a++;
}
}
x = JGR.R.idleEval(".getOtherObjects()");
String[] other;
if (x != null && (other = x.asStringArray()) != null) {
int a = 1;
for (int i = 0; i < other.length; i++) {
boolean b = (other[i].equals("null")||other[i].trim().length()==0);
String name = b?a+"":other[i];
JGR.OTHERS.add(createRObject(name,other[++i],null,(!b)));
a++;
}
}
x = JGR.R.idleEval(".getFunctionsInWS()");
String[] functions;
if (x != null && (functions = x.asStringArray()) != null) {
int a = 1;
for (int i = 0; i < functions.length; i++) {
JGR.FUNCTIONS.add(createRObject(functions[i],"function",null,true));
a++;
}
}
}
/**
* Get information about all packages (loaded, undloaded, defaults ...).
* @return package information
*/
public static Object[][] refreshPackages() {
Object[][] pkg = null;
Hashtable loadedP = new Hashtable();
REXP x = JGR.R.eval("sort(.packages(all.available=T))");
String[] res;
if (x != null && x.asStringArray() != null) {
REXP y = JGR.R.eval("(.packages())");
if (y != null && (res=y.asStringArray()) != null) {
for (int i = 0; i < res.length; i++) loadedP.put(res[i],dummy);
}
res = x.asStringArray();
pkg = new Object[res.length][4];
for (int i = 0; i < res.length; i++) {
pkg[i][2]=new String(res[i]);
try {
pkg[i][3]=JGR.R.eval("packageDescription(\""+res[i]+"\",fields=\"Title\")").asString();
} catch (Exception e) { pkg[i][1] = "";}
pkg[i][0]= loadedP.containsKey(res[i])?(new Boolean(true)):(new Boolean(false));
pkg[i][1]= new Boolean(false);
for (int d = 0; d < JGRPackageManager.defaultPackages.length; d++) {
if (res[i].equals(JGRPackageManager.defaultPackages[d]) || JGRPackageManager.neededPackages.containsKey(res[i])) pkg[i][1] = new Boolean(true);
}
}
}
return pkg;
}
/**
* Get the content of an {@seeRObjects} (list, data.frame, table, matrix).
* @param o {@seeRObjects}
* @param c all found objects are collected in c (currently disabled)
* @return vector of {@seeRObjects}
*/
public static Vector createContent(RObject o, Collection c) {
Vector cont = new Vector();
String p = "";
if (o.getParent() != null && o.getParent().getType().equals("table"))
p = ","+o.getParent().getRName();
REXP x = JGR.R.eval("suppressWarnings(try(.getContent("+(o.getRName())+p+"),silent=TRUE))");
String[] res;
if (x != null && (res = x.asStringArray()) != null && !res[0].startsWith("Error")) {
int a = 1;
for (int i = 0; i < res.length; i++) {
boolean b = (res[i].equals("null")||res[i].trim().length()==0);
String name = b?a+"":res[i];
RObject ro = createRObject(name,res[++i],o,(!b));
//if (c != null) c.add(ro);
if (ro != null) cont.add(ro);
a++;
}
}
return cont;
}
/**
* Ceates an {@seeRObjects} (java-side) out of R
* @param sx name
* @param type type
* @param parent parent {@seeRObjects}
* @param b names(..) provides real names or not
* @return new RObject
*/
public static RObject createRObject(String sx, String type, RObject parent, boolean b)
{
RObject ro = new RObject(sx,type, parent, b);
REXP y;
if (type.equals("data.frame")) {
y = JGR.R.eval("dim("+(ro.getRName())+")");
if (y!=null && y.asIntArray()!=null) {
ro.setInfo("dim("+y.asIntArray()[0]+":"+y.asIntArray()[1]+")");
}
}
else if (type.equals("matrix")) {
y = JGR.R.eval("dim("+(ro.getRName())+")");
if (y!=null && y.asIntArray()!=null) {
ro.setInfo("dim("+y.asIntArray()[0]+":"+y.asIntArray()[1]+")");
}
}
else if (type.equals("factor")) {
y = JGR.R.eval("length(levels("+(ro.getRName())+"))");
if (y!=null && y.asIntArray() != null) ro.setInfo("levels: "+y.asIntArray()[0]);
}
else if (type.equals("list")) {
y = JGR.R.eval("length("+(ro.getRName())+")");
if (y!=null && y.asIntArray() != null) ro.setInfo("length: "+y.asIntArray()[0]);
}
else if (type.equals("table")) {
y = JGR.R.eval("length(dim("+(ro.getRName())+"))");
if (y!=null && y.asIntArray() != null) ro.setInfo("dim: "+y.asIntArray()[0]);
}
else if (type.equals("function")) {
ro.setInfo("arguments: "+getFunHelp(ro.getRName()).replaceFirst(ro.getRName(),"").replaceAll("
",""));
}
else if (parent != null && parent.getType().equals("table")) {
y = JGR.R.eval("length(dimnames("+parent.getRName()+")[[\""+ro.getName()+"\"]])");
if (y!=null && y.asIntArray() != null) ro.setInfo("cats: "+y.asIntArray()[0]);
}
return ro;
}
/**
* Create {@see RModel} (java-side) out of R
* @param sx name
* @param type type (currently only lm and glm is supported
* @return new {@see RModel}
*/
public static RModel createRModel(String sx, String type) {
RModel m = new RModel(sx,type);
REXP y = JGR.R.eval("summary("+sx+")[[\"r.squared\"]]");
double[] res;
if (y != null && (res = y.asDoubleArray()) != null) m.setRsquared(res[0]);
y = JGR.R.eval("AIC("+sx+")");
if (y != null && (res = y.asDoubleArray()) != null) m.setAic(res[0]);
y = JGR.R.eval("deviance("+sx+")");
if (y != null && (res = y.asDoubleArray()) != null) m.setDeviance(res[0]);
int[] res1;
y = JGR.R.eval("summary("+sx+")[[\"df\"]]");
if (y != null && (res1 = y.asIntArray()) != null) m.setDf(res1[0]);
String[] res2;
y = JGR.R.eval("family("+sx+")[[\"family\"]]");
if (y != null && (res2 = y.asStringArray()) != null) m.setFamily(res2[0]);
y = JGR.R.eval("suppressWarnings(try(capture.output("+sx+"[[\"call\"]][[\"formula\"]])))"); //as.character((cm$call))
if (y != null && (res2 = y.asStringArray()) != null) {
String call = "";
for (int i = 0; i < res2.length; i++) {
call += res2[i];
}
m.setCall(call);
}
y = JGR.R.eval("suppressWarnings(try(capture.output("+sx+"[[\"call\"]][[\"data\"]])))"); //as.character((cm$call))
if (y != null && (res2 = y.asStringArray()) != null) {
String data = "";
for (int i = 0; i < res2.length; i++) {
data += res2[i];
}
if (!data.trim().equals("NULL")) m.setData(data);
}
return m;
}
public static String getFunHelpTip(String s) {
String tip = getFunHelp(s);
return tip!=null?""+tip+"
":null;
}
/**
* Get argumentes for function
* @param s function name
* @return arguments
*/
private static String getFunHelp(String s) {
if (s==null) return null;
String tip = null;
String res[] = null;
REXP x;
try { x = JGR.R.idleEval("try(deparse(args("+s+")),silent=T)"); } catch (Exception e) { return null;}
if (x!=null && (res = x.asStringArray()) != null) {
tip = "";
int l = -1;
for (int i = 0; i < (l=res.length); i++) {
if ((l-2)==i && !res[i].trim().equals("NULL")) tip += res[i].replaceFirst("function",s);
else if (!res[i].trim().equals("NULL")) tip += res[i].replaceFirst("function",s)+ "
";
}
tip += "";
}
else return null;
if (tip.trim().length() == 0) return null;
return (tip.indexOf("Error")>=0)?null:tip;
}
/**
* Get summary of an {@see RObject}, R-command summary(...).
* @param o {@see RObject}
* @return summary of object
*/
public static String getSummary(RObject o) {
if (o.getType().equals("function")) return ""+getFunHelp(o.getRName())+"
";
String tip = "";
String res[] = null;
REXP x;
try { x = JGR.R.idleEval("suppressWarnings(try(capture.output(summary("+(o.getRName())+")),silent=TRUE))"); } catch (Exception e) { return null;}
if (x!=null && (res = x.asStringArray()) != null && !res[0].startsWith("Error")) {
//tip = "";
int l = -1;
for (int i = ((l = res.length) > 10?10:l)-1; i >= 0; i--) {
if (i < l-1) tip = res[i] +"
"+ tip;
else tip = res[i]+" ";
}
tip = ""+tip+(l > 10?"...":"")+"
";
}
else return null;
return tip.startsWith("Error")?null:tip;
}
public static void newFunction(RObject o) {
REXP x = JGR.R.eval("suppressWarnings(try(capture.output("+o.getRName()+"),silent=TRUE))");
String[] res;
if (x != null && (res = x.asStringArray()) != null) {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < res.length; i++) {
if (i==0) sb.append(o.getRName()+" <- "+res[i]+"\n");
else sb.append(res[i]+"\n");
}
if (sb.length() > 0) new Editor().setText(sb);
}
}
/**
* Create a new {@see SVarSet} of the specified {@see RObject}.
* @param o {@see RObject} which should be parsed into the dataset
* @return new dataset
*/
public static SVarSet newSet(RObject o) {
SVarSet cvs=new SVarSet();
cvs.setName(o.getRName());
if (o.getType().equals("function")) {
//thats not really the best way to do this but the easiest
REXP x = JGR.R.eval("suppressWarnings(try(capture.output("+o.getRName()+"),silent=TRUE))");
String[] res;
if (x != null && (res = x.asStringArray()) != null) {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < res.length; i++) {
if (i==0) sb.append(o.getRName()+" <- "+res[i]+"\n");
else sb.append(res[i]+"\n");
}
if (sb.length() > 0) new Editor().setText(sb);
}
return null;
}
else {
REXP x = JGR.R.eval("suppressWarnings(try(attributes("+o.getRName()+")[[\"row.names\"]],silent=TRUE))");
String[] res;
if (x != null && (res = x.asStringArray()) != null && !res[0].startsWith("Error")) {
SVar v = newVar(cvs,"row.names",x.asStringArray());
cvs.add(v);
}
Iterator i = createContent(o,null).iterator();
if (!i.hasNext()) {
cvs.add(createSVar(cvs,o));
}
while (i.hasNext()) {
RObject o2 = (RObject) i.next();
cvs.add(createSVar(cvs,o2));
}
}
return cvs;
}
/**
* Create SVar out of an {@see RObject}.
* @param cvs destination SVarSet
* @param o {@see RObject}
* @return new SVar
*/
private static SVar createSVar(SVarSet cvs, RObject o) {
REXP x = JGR.R.eval("suppressWarnings(try("+o.getRName()+",silent=TRUE))");
if (x !=null && x.asStringArray() != null && x.asStringArray().length > 0 && x.asStringArray()[0].startsWith("Error"))
return null;
SVar v = null;
if (o.getType().equals("factor")) {
REXP y = JGR.R.eval("suppressWarnings(try(levels("+o.getRName()+"),silent=TRUE))");
if (y != null && x != null && y.asStringArray() != null && x.asIntArray() != null) {
v = newVar(cvs,o.getName(),x.asIntArray(),y.asStringArray());
}
}
else if (o.getType().equals("character")) {
if (x != null && x.asStringArray() != null) {
v = newVar(cvs,o.getName(),x.asStringArray());
}
}
else if (x != null && x.asIntArray() != null) {
v = newVar(cvs,o.getName(),x.asIntArray());
}
else if (x!= null && x.asDoubleArray() != null) {
v = newVar(cvs,o.getName(),x.asDoubleArray());
}
return v;
}
/**
* Construct a new numerical variable from supplied array of doubles.
* @param name variable name
* @param d array of doubles
* @return SVar
*/
public static SVar newVar(SVarSet cvs, String name, double[] d) {
if (d==null) return null;
if (Global.DEBUG>0)
System.out.println("newVar: double["+d.length+"]");
if (cvs.count()>0 && cvs.at(0).size()!=d.length) {
double[] n = new double[cvs.at(0).size()];
for (int i = 0; i < d.length && i < n.length; i++)
n[i] = d[i];
d = n;
}
SVar v=new SVarDouble(name,d);
return v;
}
/**
* Construct a new numerical variable from supplied array of integers.
* @param name variable name
* @param d array of integers
* @return SVar
*/
public static SVar newVar(SVarSet cvs, String name, int[] d) {
if (d==null) return null;
if (Global.DEBUG>0)
System.out.println("newVar: int["+d.length+"]");
if (cvs.count()>0 && cvs.at(0).size()!=d.length) {
int[] n = new int[cvs.at(0).size()];
for (int i = 0; i < d.length && i < n.length; i++)
n[i] = d[i];
d = n;
}
SVar v=new SVarInt(name,d);
return v;
};
/**
* Construct a new categorical variable from supplied array of strings.
* @param name variable name
* @param d array of strings
* @return SVar
*/
public static SVar newVar(SVarSet cvs, String name, String[] d) {
if (d==null) return null;
if (Global.DEBUG>0)
System.out.println("newVar: String[]");
if (cvs.count()>0 && cvs.at(0).size()!=d.length) {
String[] n = new String[cvs.at(0).size()];
for (int i = 0; i < d.length && i < n.length; i++)
n[i] = d[i];
d = n;
}
SVar v=new SVarObj(name);
int i=0; while(ilength(d)) are treated as missing values
* @param d levels (d[0]=ID 1, d[1]=ID 2, ...)
* @return SVar
*/
public static SVar newVar(SVarSet cvs, String name, int[] ix, String[] d) {
if (ix==null) return null;
if (d==null) return newVar(cvs, name,ix);
if (Global.DEBUG>0)
System.out.println("newVar: int["+ix.length+"] + levels["+d.length+"]");
if (cvs.count()>0 && cvs.at(0).size()!=ix.length) {
int[] n = new int[cvs.at(0).size()];
for (int i = 0; i < d.length && i < n.length; i++)
n[i] = ix[i];
ix = n;
}
int j=0;
while (j 1) return false;
long v = JGR.R.rniPutDoubleArray(((SVarDouble) vs.at(0)).cont);
System.out.println(vs.getName());
JGR.R.rniAssign("jgrtemp",v,0);
return setName(vs.getName());
}
catch (Exception e) {
e.printStackTrace();
return false;
}
}
/**
* Export r-integer.
* @param vs dataset
* @return true if successful, false if not
*/
private static boolean exportInteger(SVarSet vs) {
try {
if (vs.count() > 1) return false;
long v = JGR.R.rniPutIntArray(((SVarInt) vs.at(0)).cont);
JGR.R.rniAssign("jgrtemp",v,0);
return setName(vs.getName());
}
catch (Exception e) {
e.printStackTrace();
return false;
}
}
/**
* Export r-factor.
* @param vs dataset
* @return true if successful, false if not
*/
private static boolean exportFactor(SVarSet vs) {
try {
if (vs.count() > 1) return false;
int[] ids = new int[((SVarFact) vs.at(0)).cont.length];
for (int z = 0; z < ids.length; z++)
ids[z] = ((SVarFact) vs.at(0)).cont[z]+1;
long v = JGR.R.rniPutIntArray(ids);
long c = JGR.R.rniPutString("factor");
JGR.R.rniSetAttr(v,"class",c);
long levels = JGR.R.rniPutStringArray(((SVarFact) vs.at(0)).cats);
JGR.R.rniSetAttr(v,"levels",levels);
JGR.R.rniAssign("jgrtemp",v,0);
return setName(vs.getName());
}
catch (Exception e) {
e.printStackTrace();
return false;
}
}
/**
* Export r-character.
* @param vs dataset
* @return true if successful, false if not
*/
private static boolean exportCharacter(SVarSet vs) {
try {
if (vs.count() > 1) return false;
long v = JGR.R.rniPutStringArray(((SVarObj) vs.at(0)).getContent());
JGR.R.rniAssign("jgrtemp",v,0);
return setName(vs.getName());
}
catch (Exception e) {
e.printStackTrace();
return false;
}
}
/**
* Export r-data.frame.
* @param vs dataset
* @return true if successful, false if not
*/
private static boolean exportDataFrame(SVarSet vs) {
try {
boolean rnames = false;
String[] rownames = new String[vs.length()];
SVar rn = null;
int rnn = 0;
for (int i = 0; i< vs.count(); i++) {
if (vs.at(i).getName().equals("row.names")) {
int length = rownames.length;
for (int a = 0; a < rownames.length; a++) {
Object o = ((SVarObj) vs.at(i)).at(a);
if (o != null) rownames[a] = o.toString();
else {
rownames[a] = (length-1)+""; //Just a workaround to avoid duplicate row.names
length++;
}
}
rnames = true;
rnn = i;
rn = vs.at(i);
vs.remove(i);
break;
}
}
System.out.println("Export data.frame with length: "+vs.count());
long contlist[] = new long[vs.count()];
String[] names = new String[vs.count()];
for (int i = 0; i< vs.count(); i++) {
names[i] = vs.at(i).getName();
if (vs.at(i).getClass().getName().equals("org.rosuda.ibase.SVarDouble")) {
long v = JGR.R.rniPutDoubleArray(((SVarDouble) vs.at(i)).cont);
contlist[i] = v;
}
else if (vs.at(i).getClass().getName().equals("org.rosuda.ibase.SVarInt")) {
long v = JGR.R.rniPutIntArray(((SVarInt) vs.at(i)).cont);
contlist[i] = v;
}
else if (vs.at(i).getClass().getName().equals("org.rosuda.ibase.SVarFact")) {
int[] ids = new int[((SVarFact) vs.at(i)).cont.length];
String[] cats = ((SVarFact) vs.at(i)).cats;
boolean NAS = false;
for (int z = 0; z < ids.length; z++) {
ids[z] = ((SVarFact) vs.at(i)).cont[z]+1;
//Detect missingCats
if (ids[z] == 0) {
NAS = true;
ids[z] = cats.length+1;
}
}
//Add missing cats
if (NAS) {
String[] newcats = new String[cats.length+1];
System.arraycopy(cats,0,newcats,0,cats.length);
newcats[newcats.length-1] = "NA";
cats = newcats;
NAS = false;
}
long v = JGR.R.rniPutIntArray(ids);
long c = JGR.R.rniPutString("factor");
JGR.R.rniSetAttr(v,"class",c);
long levels = JGR.R.rniPutStringArray(cats);
JGR.R.rniSetAttr(v,"levels",levels);
contlist[i] = v;
}
else if (vs.at(i).getClass().getName().equals("org.rosuda.ibase.SVarObj")) {
long v = JGR.R.rniPutStringArray(((SVarObj) vs.at(i)).getContent());
contlist[i] = v;
}
}
long xp1 = JGR.R.rniPutVector(contlist);
long xp2 = JGR.R.rniPutStringArray(names);
JGR.R.rniSetAttr(xp1,"names",xp2);
if (!rnames) for (int i = 1; i <= rownames.length; i++) rownames[i-1] = i+"";
long xp3 = JGR.R.rniPutStringArray(rownames);
JGR.R.rniSetAttr(xp1,"row.names",xp3);
long c = JGR.R.rniPutString("data.frame");
JGR.R.rniSetAttr(xp1,"class",c);
JGR.R.rniAssign("jgrtemp",xp1,0);
if (rnames) vs.insert(rnn,rn);
return setName(vs.getName());
}
catch (Exception e) {
e.printStackTrace();
return false;
}
}
/**
* Export r-matrix.
* @param vs dataset
* @return true if successful, false if not
*/
private static boolean exportMatrix(SVarSet vs) {
try {
String[] names = new String[vs.count()];
Object mcont;
int vlength = vs.at(0).size();
boolean isInt = false;
if (vs.at(0).getClass().getName().equals("org.rosuda.ibase.SVarDouble")) {
mcont = new double[vs.count()*vlength];
}
else if (vs.at(0).getClass().getName().equals("org.rosuda.ibase.SVarInt")) {
mcont = new int[vs.count()*vlength];
isInt = true;
}
else return false;
for (int i = 0; i< vs.count(); i++) {
names[i] = vs.at(i).getName();
if (isInt) System.arraycopy(((SVarInt) vs.at(i)).cont,0,mcont,i*vlength,vlength);
else System.arraycopy(((SVarDouble) vs.at(i)).cont,0,mcont,i*vlength,vlength);
}
long xp1;
if (isInt) xp1 = JGR.R.rniPutIntArray((int[]) mcont);
else xp1 = JGR.R.rniPutDoubleArray((double[]) mcont);
long[] dimnames = new long[2];
long xp2 = JGR.R.rniPutStringArray(names);
String[] rownames = new String[vs.length()];
for (int i = 1; i <= rownames.length; i++) rownames[i-1] = i+"";
long xp3 = JGR.R.rniPutStringArray(rownames);
dimnames[0] = xp3;
dimnames[1] = xp2;
long xp4 = JGR.R.rniPutVector(dimnames);
double[] dim = new double[] {vlength,vs.count()};
long xp5 = JGR.R.rniPutDoubleArray(dim);
JGR.R.rniSetAttr(xp1,"dim",xp5);
JGR.R.rniSetAttr(xp1,"dimnames",xp4);
long c = JGR.R.rniPutString("matrix");
JGR.R.rniSetAttr(xp1,"class",c);
JGR.R.rniAssign("jgrtemp",xp1,0);
return setName(vs.getName());
}
catch (Exception e) {
e.printStackTrace();
return false;
}
}
/**
* Export r-list.
* @param vs dataset
* @return true if successful, false if not
*/
private static boolean exportList(SVarSet vs) {
try {
long contlist[] = new long[vs.count()];
String[] names = new String[vs.count()];
for (int i = 0; i< vs.count(); i++) {
names[i] = vs.at(i).getName();
if (vs.at(i).getClass().getName().equals("org.rosuda.ibase.SVarDouble")) {
long v = JGR.R.rniPutDoubleArray(((SVarDouble) vs.at(i)).cont);
contlist[i] = v;
}
else if (vs.at(i).getClass().getName().equals("org.rosuda.ibase.SVarInt")) {
long v = JGR.R.rniPutIntArray(((SVarInt) vs.at(i)).cont);
contlist[i] = v;
}
else if (vs.at(i).getClass().getName().equals("org.rosuda.ibase.SVarFact")) {
int[] ids = new int[((SVarFact) vs.at(i)).cont.length];
for (int z = 0; z < ids.length; z++)
ids[z] = ((SVarFact) vs.at(i)).cont[z]+1;
long v = JGR.R.rniPutIntArray(ids);
long c = JGR.R.rniPutString("factor");
JGR.R.rniSetAttr(v,"class",c);
long levels = JGR.R.rniPutStringArray(((SVarFact) vs.at(i)).cats);
JGR.R.rniSetAttr(v,"levels",levels);
contlist[i] = v;
}
else if (vs.at(i).getClass().getName().equals("org.rosuda.ibase.SVarObj")) {
long v = JGR.R.rniPutStringArray(((SVarObj) vs.at(i)).getContent());
contlist[i] = v;
}
}
long xp1 = JGR.R.rniPutVector(contlist);
long xp2 = JGR.R.rniPutStringArray(names);
JGR.R.rniSetAttr(xp1,"names",xp2);
JGR.R.rniAssign("jgrtemp",xp1,0);
return setName(vs.getName());
}
catch (Exception e) {
e.printStackTrace();
return false;
}
}
/**
* Compare to string and return the common prefix.
* @param str1 String 1
* @param str2 String 2
* @return common prefix
*/
public static String commonWithPrefix(String str1, String str2) {
int min = Math.min(str1.length(),str2.length());
String result = "";
String s = "";
for (int i = 0; i < min; i++) {
if ((s=str1.substring(i,i+1)).equals(str2.substring(i,i+1))) result += s;
else break;
}
return result;
}
}