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/*
* #%L
* Nuiton Java-2-R
* %%
* Copyright (C) 2006 - 2012 CodeLutin
* %%
* This program 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 3 of the
* License, or (at your option) any later version.
*
* This program 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 this program. If not, see
* .
* #L%
*/
package org.nuiton.j2r;
import java.io.File;
/**
* Abstract REngine that provides utility R methods (such as clear session, set
* working directory, import data, ...) for all R engines.
*
* @author couteau
*/
public abstract class REngineAbstract implements REngine {
/**
* If true, commit each R instruction on the fly, if false, commit only when
* the commit() method is called.
*/
protected Boolean autocommit = true;
/**
* Load a specific R session :
* Load .RData file located in directory
*
* @param directory
* directory where the .RData file is located
* @throws RException if an error occur while loading the R session file
*/
@Override
public void loadRData(File directory) throws RException {
setwd(directory);
voidEval(RInstructions.LOAD_RDATA);
}
/**
* Load a specific R session :
* Load the "fileName.RData" file located in directory.
*
* @param directory directory where the ".RData" file is located
* @param fileName name of the file to load (will load the fileName.RData
* file)
* @throws org.nuiton.j2r.RException if an error occur while loading the R
* session file.
*/
@Override
public void loadRData(File directory, String fileName) throws RException {
setwd(directory);
voidEval(String.format(RInstructions.LOAD_RDATA_FILE, fileName));
}
/**
* Load the "fileName.RData" file located in current working directory.
*
* @param fileName name of the file to load (will load the fileName.RData
* file)
* @throws org.nuiton.j2r.RException if an error occur while loading the R
* session file.
*/
@Override
public void loadRData(String fileName) throws RException {
voidEval(String.format(RInstructions.LOAD_RDATA_FILE, fileName));
}
/**
* Save the session in a .RData file in directory
*
* @param directory
* where the .RData file will be saved
* @throws RException if an error occur while saving the R
* session.
*/
@Override
public void saveRData(File directory) throws RException {
setwd(directory);
voidEval(RInstructions.SAVE_IMAGE);
}
/**
* Save the session in a .RData file in current working directory
*
* @param filename
* the .RData filename (will be followed by .RData)
* @throws RException if an error occur while saving the R
* session.
*/
@Override
public void saveRData(String filename) throws RException {
voidEval(String.format(RInstructions.SAVE_IMAGE_FILE, filename));
}
/**
* Save a R session in a fileName.RData file located in directory.
*
* @param directory where the ".RData" file will be located
* @param fileName name of the file to save (will save in the fileName.RData
* file)
* @throws org.nuiton.j2r.RException if an error occur while saving the R
* session.
*/
@Override
public void saveRData(File directory, String fileName) throws RException {
setwd(directory);
voidEval(String.format(RInstructions.SAVE_IMAGE_FILE, fileName));
}
/**
* Set the R working directory
*
* @param directory
* to set
* @throws RException
*/
@Override
public void setwd(File directory) throws RException {
voidEval(String.format(RInstructions.SET_WORKING_DIRECTORY,
directory.getAbsolutePath().replaceAll("\\\\", "/")));
}
/**
* Get the actual R session working directory
*
* @return a File that is the actual R session working directory
* @throws RException
*/
@Override
public File getwd() throws RException {
String directory = (String) eval(RInstructions.GET_WORKING_DIRECTORY);
return new File(directory);
}
/**
* Use the dput R instruction to store the content of a R object to a file.
* The file created will be in the working directory
*
* @param rObject
* name of the R object to save
* @param outputFileName
* name of the file to save
* @throws RException
*/
@Override
public void dput(String rObject, String outputFileName) throws RException {
voidEval(String.format(RInstructions.DPUT, rObject, outputFileName));
}
/**
* Use the dget rInstruction to store the content of a file (created with
* the dput instruction) into a R object. The file used have to be in the
* working directory
*
* @param rObject
* name of the R object created
* @param inputFileName
* name of the file to load
* @throws RException
*/
@Override
public void dget(String rObject, String inputFileName) throws RException {
voidEval(String.format(RInstructions.DGET, rObject, inputFileName));
}
/**
* Use the dput R instruction to store the content of a R object to a file.
*
* @param rObject
* R object to save
* @param outputFile
* the file to save
* @throws RException
*/
@Override
public void dput(String rObject, File outputFile) throws RException {
//Store the previous working directory
File workingdir = getwd();
//Set the destination working directory
setwd(outputFile.getParentFile());
//Save the R object.
voidEval(String.format(RInstructions.DPUT, rObject, outputFile.getName()));
//Go back to previous working directory
setwd(workingdir);
}
/**
* Use the dget rInstruction to store the content of a file (created with
* the dput instruction) into a R object.
*
* @param rObject
* name of the R object created
* @param inputFile
* file to load
* @throws RException
*/
@Override
public void dget(String rObject, File inputFile) throws RException {
//Store the previous working directory
File workingdir = getwd();
//Set the source working directory
setwd(inputFile.getParentFile());
//Load the inputFile
voidEval(String.format(RInstructions.DGET, rObject, inputFile.getName()));
//Go back to the previous working directory
setwd(workingdir);
}
/**
* Remove a R object from the R session using the R method : remove(rObject).
*
* @param rObject name of the R object to be removed.
* @throws org.nuiton.j2r.RException if an error occur while trying to
* remove the R object.
*/
@Override
public void remove(String rObject) throws RException {
voidEval(String.format(RInstructions.REMOVE, rObject));
}
/**
* Method similar to the linux mv instruction : move an object to a
* destination, or in this case, rename a R object.
* Does :
* destination<-source
* remove(source)
*
* @param source source R object name
* @param destination destination R object name
* @throws org.nuiton.j2r.RException if an error occur while trying to move
* the R object.
*/
@Override
public void mv(String source, String destination) throws RException {
cp(source, destination);
remove(source);
}
/**
* Copy a R Object into another one (similar to the linux cp instruction).
* Does :
* destination<-source
*
* @param source source R object name
* @param destination destination R object name
* @throws org.nuiton.j2r.RException if an error occur while trying to
* assign the source to the destination
*/
@Override
public void cp(String source, String destination) throws RException {
voidEval(destination + "<-" + source);
}
/**
* Method to get all the R object in session. Return the result of the R ls()
* function.
*
* @return the names of the R objects present in session as a String[]. The
* order of the names is given by their order given by the R ls() method,
* e.g. alphabetic order.
* @throws org.nuiton.j2r.RException if an error occur while trying to list
* the R objects in session.
*/
@Override
public String[] ls() throws RException {
String[] rObjects = (String[]) eval(RInstructions.LS);
return rObjects;
}
/**
* Method to clear the R session. Does : rm(list=ls())
*
* @throws org.nuiton.j2r.RException if an error occur while trying to clear
* the session
*/
@Override
public void clearSession() throws RException {
voidEval(RInstructions.CLEAR_SESSION);
}
/**
* Change the autocommit mode of the engine. If switching from no-autocommit
* to autocommit mode, does a commit of all R instructions stored.
*
* @param autocommit true for autocommit mode, false for no-autocommit mode.
* @throws org.nuiton.j2r.RException if an error occur while commiting all
* the R instructions stored.
*/
@Override
public void setAutoCommit(Boolean autocommit) throws RException {
if ((!this.autocommit) && (autocommit)) {
commit();
}
this.autocommit = autocommit;
}
/**
* Method to know if engine is in autocommit mode.
*
* @return true if in autocommit mode, false otherwise.
*/
@Override
public Boolean isAutoCommit() {
return this.autocommit;
}
/**
* @param filename
* @param x
* @param y
* @param type
* @param main
* @param sub
* @param xlab
* @param ylab
* @param asp
*/
public void plot(String filename, String x, String y, String type,
String main, String sub, String xlab, String ylab,
String asp) throws RException {
eval("jpeg(\"" + filename + ".jpg\")");
StringBuilder rinstruction = new StringBuilder("plot(");
if ((x != null) && (!x.isEmpty())) {
rinstruction.append(x);
} else {
throw new IllegalArgumentException("x argument must be filled");
}
if ((y != null) && (!y.isEmpty())) {
rinstruction.append(",y=");
rinstruction.append(y);
}
if (type != null) {
rinstruction.append(",type=\"");
rinstruction.append(type);
rinstruction.append("\"");
}
if (main != null) {
rinstruction.append(",main=\"");
rinstruction.append(main);
rinstruction.append("\"");
}
if (sub != null) {
rinstruction.append(",sub=\"");
rinstruction.append(sub);
rinstruction.append("\"");
}
if (xlab != null) {
rinstruction.append(",xlab=\"");
rinstruction.append(xlab);
rinstruction.append("\"");
}
if (ylab != null) {
rinstruction.append(",ylab=\"");
rinstruction.append(ylab);
rinstruction.append("\"");
}
if (asp != null) {
rinstruction.append(",asp=");
rinstruction.append(asp);
rinstruction.append("\"");
}
rinstruction.append(")");
eval(rinstruction.toString());
eval("dev.off()");
}
}
