Java Code Examples for org.rosuda.REngine.REXP#asInteger()
The following examples show how to use
org.rosuda.REngine.REXP#asInteger() .
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Example 1
| Source File: Rsession.java From mzmine3 with GNU General Public License v2.0 | 6 votes |
|
/**
* Check for package loaded in R environment.
*
* @param pack R package name
* @return package loading status
*/
public boolean isPackageLoaded(String pack) {
silentlyVoidEval(loadedpacks + "<-.packages()", false);
boolean isloaded = false;
try {
REXP i = silentlyEval("is.element(set=" + loadedpacks + ",el='" + pack + "')");
if (i != null) {
isloaded = i.asInteger() == 1;
}
} catch (REXPMismatchException ex) {
log(HEAD_ERROR + ex.getMessage() + "\n isPackageLoaded(String pack=" + pack + ")",
Level.ERROR);
}
if (isloaded) {
log(_PACKAGE_ + pack + " is loaded.", Level.INFO);
} else {
log(_PACKAGE_ + pack + " is not loaded.", Level.INFO);
}
// silentlyEval("rm(" + loadedpacks + ")");
return isloaded;
}
Example 2
| Source File: Rsession.java From mzmine3 with GNU General Public License v2.0 | 6 votes |
|
/**
*
* @param robject R object name
* @return R type of object
*/
public String typeOf(String robject) {
if (robject == null) {
return "NULL";
}
for (String t : types) {
REXP is = silentlyEval("is." + t + "(" + robject + ")");
try {
if (is != null && is.asInteger() == 1) {
return t;
}
} catch (REXPMismatchException ex) {
log(HEAD_ERROR + "[typeOf] " + robject + " type unknown.", Level.ERROR);
return null;
}
}
return "unknown";
}
Example 3
| Source File: Rsession.java From mzmine2 with GNU General Public License v2.0 | 6 votes |
|
/**
* Check for package loaded in R environment.
*
* @param pack R package name
* @return package loading status
*/
public boolean isPackageLoaded(String pack) {
silentlyVoidEval(loadedpacks + "<-.packages()", false);
boolean isloaded = false;
try {
REXP i = silentlyEval("is.element(set=" + loadedpacks + ",el='" + pack + "')");
if (i != null) {
isloaded = i.asInteger() == 1;
}
} catch (REXPMismatchException ex) {
log(HEAD_ERROR + ex.getMessage() + "\n isPackageLoaded(String pack=" + pack + ")",
Level.ERROR);
}
if (isloaded) {
log(_PACKAGE_ + pack + " is loaded.", Level.INFO);
} else {
log(_PACKAGE_ + pack + " is not loaded.", Level.INFO);
}
// silentlyEval("rm(" + loadedpacks + ")");
return isloaded;
}
Example 4
| Source File: Rsession.java From mzmine2 with GNU General Public License v2.0 | 6 votes |
|
/**
*
* @param robject R object name
* @return R type of object
*/
public String typeOf(String robject) {
if (robject == null) {
return "NULL";
}
for (String t : types) {
REXP is = silentlyEval("is." + t + "(" + robject + ")");
try {
if (is != null && is.asInteger() == 1) {
return t;
}
} catch (REXPMismatchException ex) {
log(HEAD_ERROR + "[typeOf] " + robject + " type unknown.", Level.ERROR);
return null;
}
}
return "unknown";
}
Example 5
| Source File: RSessionWrapper.java From mzmine3 with GNU General Public License v2.0 | 4 votes |
|
public void loadPackage(String packageName) throws RSessionWrapperException {
String loadCode = "library(" + packageName + ", logical.return = TRUE)";
if (TRY_MODE)
loadCode = "try(" + loadCode + ", silent=TRUE)";
String errorMsg = "The \"" + this.callerFeatureName + "\" requires " + "the \"" + packageName
+ "\" R package, which couldn't be loaded - is it installed in R?";
if (this.rEngineType == REngineType.RSERVE) {
if (this.session != null && !this.userCanceled) {
logger.log(logLvl, "Loading package '" + packageName + "'...");
int loaded = 0;
try {
REXP r = ((RConnection) this.rEngine).eval(loadCode);
if (r.inherits("try-error")) {
logger.severe("R Error [0]: " + r.asString());
logger.severe("R eval attempt [0]: " + loadCode);
}
loaded = r.asInteger();
logger.log(logLvl, "Load status: '" + (loaded != 0) + "'.");
} catch (RserveException | REXPMismatchException e) {
logger.log(logLvl, "Loaded package KO: '" + e.getMessage() + "'.");
// Remain silent if eval KO ("server down").
loaded = Integer.MIN_VALUE;
}
// Throw loading failure only if eval OK, but return FALSE
// (package not loaded).
// ("server down" case will be handled soon enough).
if (loaded == 0)
if (!this.userCanceled)
throw new RSessionWrapperException(errorMsg);
logger.log(logLvl, "Loaded package: '" + packageName + "'.");
}
} else { // RCaller
((RCaller) rEngine).getRCode().addRCode(loadCode);
// try {
//
// ((RCallerScriptEngine2) rEngine).eval(loadCode);
// } catch (ScriptException e) {
//
// if (!this.userCanceled)
// throw new RSessionWrapperException(errorMsg);
// }
}
}
Example 6
| Source File: Rsession.java From mzmine3 with GNU General Public License v2.0 | 4 votes |
|
/**
* cast R object in java object
*
* @param eval REXP R object
* @return java object
* @throws org.rosuda.REngine.REXPMismatchException
*/
public static Object cast(REXP eval) throws REXPMismatchException {
if (eval == null) {
return null;
}
/*
* int[] dim = eval.dim(); String dims = "["; if (dim == null) { dims = "NULL"; } else { for
* (int i : dim) { dims += (i + " "); } dims += "]"; }
*
* System.out.println(eval.toString() + "\n isComplex= " + (eval.isComplex() ? "TRUE" :
* " false") + "\n isEnvironment= " + (eval.isEnvironment() ? "TRUE" : " false") +
* "\n isExpression= " + (eval.isExpression() ? "TRUE" : " false") + "\n isFactor= "
* + (eval.isFactor() ? "TRUE" : " false") + "\n isFactor= " + (eval.isFactor() ?
* "TRUE" : " false") + "\n isInteger= " + (eval.isInteger() ? "TRUE" : " false") +
* "\n isLanguage= " + (eval.isLanguage() ? "TRUE" : " false") + "\n isList= " +
* (eval.isList() ? "TRUE" : " false") + "\n isLogical= " + (eval.isLogical() ? "TRUE" :
* " false") + "\n isNull= " + (eval.isNull() ? "TRUE" : " false") +
* "\n isNumeric= " + (eval.isNumeric() ? "TRUE" : " false") + "\n isRaw= " +
* (eval.isRaw() ? "TRUE" : " false") + "\n isRecursive= " + (eval.isRecursive() ? "TRUE"
* : " false") + "\n isString= " + (eval.isString() ? "TRUE" : " false") +
* "\n isSymbol= " + (eval.isSymbol() ? "TRUE" : " false") + "\n isVector= " +
* (eval.isVector() ? "TRUE" : " false") + "\n length= " + (eval.length()) + "\n dim= " +
* dims);
*/
if (eval.isNumeric()) {
if (eval.dim() == null || eval.dim().length == 1) {
double[] array = eval.asDoubles();
if (array.length == 0) {
return null;
}
if (array.length == 1) {
return array[0];
}
return array;
} else {
// System.err.println("eval.dim()="+eval.dim()+"="+cat(eval.dim()));
double[][] mat = eval.asDoubleMatrix();
if (mat.length == 0) {
return null;
} else if (mat.length == 1) {
if (mat[0].length == 0) {
return null;
} else if (mat[0].length == 1) {
return mat[0][0];
} else {
return mat[0];
}
} else {
if (mat[0].length == 0) {
return null;
} else if (mat[0].length == 1) {
double[] dmat = new double[mat.length];
for (int i = 0; i < dmat.length; i++) {
dmat[i] = mat[i][0];
}
return dmat;
} else {
return mat;
}
}
}
}
if (eval.isString()) {
String[] s = eval.asStrings();
if (s.length == 1) {
return s[0];
} else {
return s;
}
}
if (eval.isLogical()) {
return eval.asInteger() == 1;
}
if (eval.isList()) {
return eval.asList();
}
if (eval.isNull()) {
return null;
} else {
System.err.println("Unsupported type: " + eval.toDebugString());
}
return eval.toString();
}
Example 7
| Source File: RSessionWrapper.java From mzmine2 with GNU General Public License v2.0 | 4 votes |
|
public void loadPackage(String packageName) throws RSessionWrapperException {
String loadCode = "library(" + packageName + ", logical.return = TRUE)";
if (TRY_MODE)
loadCode = "try(" + loadCode + ", silent=TRUE)";
String errorMsg = "The \"" + this.callerFeatureName + "\" requires " + "the \"" + packageName
+ "\" R package, which couldn't be loaded - is it installed in R?";
if (this.rEngineType == REngineType.RSERVE) {
if (this.session != null && !this.userCanceled) {
LOG.log(logLvl, "Loading package '" + packageName + "'...");
int loaded = 0;
try {
REXP r = ((RConnection) this.rEngine).eval(loadCode);
if (r.inherits("try-error")) {
LOG.severe("R Error [0]: " + r.asString());
LOG.severe("R eval attempt [0]: " + loadCode);
}
loaded = r.asInteger();
LOG.log(logLvl, "Load status: '" + (loaded != 0) + "'.");
} catch (RserveException | REXPMismatchException e) {
LOG.log(logLvl, "Loaded package KO: '" + e.getMessage() + "'.");
// Remain silent if eval KO ("server down").
loaded = Integer.MIN_VALUE;
}
// Throw loading failure only if eval OK, but return FALSE
// (package not loaded).
// ("server down" case will be handled soon enough).
if (loaded == 0)
if (!this.userCanceled)
throw new RSessionWrapperException(errorMsg);
LOG.log(logLvl, "Loaded package: '" + packageName + "'.");
}
} else { // RCaller
((RCaller) rEngine).getRCode().addRCode(loadCode);
// try {
//
// ((RCallerScriptEngine2) rEngine).eval(loadCode);
// } catch (ScriptException e) {
//
// if (!this.userCanceled)
// throw new RSessionWrapperException(errorMsg);
// }
}
}
Example 8
| Source File: Rsession.java From mzmine2 with GNU General Public License v2.0 | 4 votes |
|
/**
* cast R object in java object
*
* @param eval REXP R object
* @return java object
* @throws org.rosuda.REngine.REXPMismatchException
*/
public static Object cast(REXP eval) throws REXPMismatchException {
if (eval == null) {
return null;
}
/*
* int[] dim = eval.dim(); String dims = "["; if (dim == null) { dims = "NULL"; } else { for
* (int i : dim) { dims += (i + " "); } dims += "]"; }
*
* System.out.println(eval.toString() + "\n isComplex= " + (eval.isComplex() ? "TRUE" :
* " false") + "\n isEnvironment= " + (eval.isEnvironment() ? "TRUE" : " false") +
* "\n isExpression= " + (eval.isExpression() ? "TRUE" : " false") + "\n isFactor= "
* + (eval.isFactor() ? "TRUE" : " false") + "\n isFactor= " + (eval.isFactor() ?
* "TRUE" : " false") + "\n isInteger= " + (eval.isInteger() ? "TRUE" : " false") +
* "\n isLanguage= " + (eval.isLanguage() ? "TRUE" : " false") + "\n isList= " +
* (eval.isList() ? "TRUE" : " false") + "\n isLogical= " + (eval.isLogical() ? "TRUE" :
* " false") + "\n isNull= " + (eval.isNull() ? "TRUE" : " false") +
* "\n isNumeric= " + (eval.isNumeric() ? "TRUE" : " false") + "\n isRaw= " +
* (eval.isRaw() ? "TRUE" : " false") + "\n isRecursive= " + (eval.isRecursive() ? "TRUE"
* : " false") + "\n isString= " + (eval.isString() ? "TRUE" : " false") +
* "\n isSymbol= " + (eval.isSymbol() ? "TRUE" : " false") + "\n isVector= " +
* (eval.isVector() ? "TRUE" : " false") + "\n length= " + (eval.length()) + "\n dim= " +
* dims);
*/
if (eval.isNumeric()) {
if (eval.dim() == null || eval.dim().length == 1) {
double[] array = eval.asDoubles();
if (array.length == 0) {
return null;
}
if (array.length == 1) {
return array[0];
}
return array;
} else {
// System.err.println("eval.dim()="+eval.dim()+"="+cat(eval.dim()));
double[][] mat = eval.asDoubleMatrix();
if (mat.length == 0) {
return null;
} else if (mat.length == 1) {
if (mat[0].length == 0) {
return null;
} else if (mat[0].length == 1) {
return mat[0][0];
} else {
return mat[0];
}
} else {
if (mat[0].length == 0) {
return null;
} else if (mat[0].length == 1) {
double[] dmat = new double[mat.length];
for (int i = 0; i < dmat.length; i++) {
dmat[i] = mat[i][0];
}
return dmat;
} else {
return mat;
}
}
}
}
if (eval.isString()) {
String[] s = eval.asStrings();
if (s.length == 1) {
return s[0];
} else {
return s;
}
}
if (eval.isLogical()) {
return eval.asInteger() == 1;
}
if (eval.isList()) {
return eval.asList();
}
if (eval.isNull()) {
return null;
} else {
System.err.println("Unsupported type: " + eval.toDebugString());
}
return eval.toString();
}
