rmodel.java

化学图形处理软件

    /**
     * Get the instance of the <code>Rengine</code>.
     * <p/>
     * In case the R engine has not been initialized, it is initialized before
     * returning the object.
     *
     * @return The Rengine object
     */
    public static Rengine getRengine() {
        return rengine;
    }

    /**
     * Get the actual model object.
     *
     * @return An <code>RList</code> object representation of the model.
     */
    public RList getModelObject() {
        return modelObject;
    }

    /**
     * Get a unique String value.
     * <p/>
     * This method can be used to get unique variable names for use in an R session. The
     * String is generated from a combination of the prefix, the system time and a random
     * portion.
     *
     * @param prefix Any value. If empty or null, <code>"var"</code> is used.
     * @return A unique String value
     */
    public String getUniqueVariableName(String prefix) {
        if (prefix == null || prefix.equals("")) prefix = "var";
        Random rnd = new Random();
        long uid = ((System.currentTimeMillis() >>> 16) << 16) + rnd.nextLong();
        return prefix + String.valueOf(Math.abs(uid)).trim();
    }

    /**
     * Loads the parameters for a model into a <code>list</code> object in the R session.
     * <p/>
     * The method assigns the list to a (relatively) unique variable name and returns
     * the variable name to the caller so that the list can be accessed later on.
     *
     * @return
     * @throws QSARModelException if there are any problems within the R session.
     */
    protected String loadParametersIntoRSession() throws QSARModelException {
        REXP result;
        Set keys = params.keySet();
        String paramVariableName = getUniqueVariableName("param");

        for (Iterator iterator = keys.iterator(); iterator.hasNext();) {
            String name = (String) iterator.next();
            Object value = params.get(name);

            if (value instanceof Integer) {
                logger.debug("Assigning a Integer");
                Integer tmp1 = (Integer) value;
                int[] tmp2 = new int[]{tmp1.intValue()};
                rengine.assign(name, tmp2);
            } else if (value instanceof String) {
                logger.debug("Assigning a String");
                rengine.assign(name, (String) value);
            } else if (value instanceof Boolean) {
                logger.debug("Assigning a Boolean");
                Boolean tmp1 = (Boolean) value;
                if (tmp1.booleanValue()) result = rengine.eval(name + "<- TRUE");
                else result = rengine.eval(name + "<- FALSE");
                if (result == null) throw new QSARModelException("Error assigning a boolean");
            } else if (value instanceof Double) {
                logger.debug("Assigning a Double");
                Double tmp1 = (Double) value;
                double[] tmp2 = new double[]{tmp1.doubleValue()};
                rengine.assign(name, tmp2);
            } else if (value instanceof Integer[]) {
                logger.debug("Assigning a Integer[]");
                Integer[] tmp1 = (Integer[]) value;
                int[] tmp2 = new int[tmp1.length];
                for (int i = 0; i < tmp1.length; i++) tmp2[i] = tmp1[i].intValue();
                rengine.assign(name, tmp2);
            } else if (value instanceof Double[]) {
                logger.debug("Assigning a Double[]");
                Double[] tmp1 = (Double[]) value;
                double[] tmp2 = new double[tmp1.length];
                for (int i = 0; i < tmp1.length; i++) tmp2[i] = tmp1[i].doubleValue();
                rengine.assign(name, tmp2);
            } else if (value instanceof Integer[][]) {
                logger.debug("Assigning a Integer[][]");
                Integer[][] tmp1 = (Integer[][]) value;
                int nrow = tmp1.length;
                int ncol = tmp1[0].length;
                int[] tmp2 = new int[nrow * ncol];
                for (int i = 0; i < ncol; i++) {
                    for (int j = 0; j < nrow; j++) {
                        tmp2[i * nrow + j] = (tmp1[j][i]).intValue();
                    }
                }
                rengine.assign(name, tmp2);
                result = rengine.eval(name + "<- matrix(" + name + ", nrow=" + nrow + ")");
                if (result == null) throw new QSARModelException("Error assigning a int[][]");
            } else if (value instanceof Double[][]) {
                logger.debug("Assigning a Double[][]");
                Double[][] tmp1 = (Double[][]) value;
                int nrow = tmp1.length;
                int ncol = tmp1[0].length;
                double[] tmp2 = new double[nrow * ncol];
                for (int i = 0; i < ncol; i++) {
                    for (int j = 0; j < nrow; j++) {
                        tmp2[i * nrow + j] = (tmp1[j][i]).doubleValue();
                    }
                }
                rengine.assign(name, tmp2);
                result = rengine.eval(name + "<- matrix(" + name + ", nrow=" + nrow + ")");
                if (result == null) throw new QSARModelException("Error assigning a double[][]");
            }
        }

        // make the list command
        String cmd = paramVariableName + " <- list(";
        for (Iterator iterator = keys.iterator(); iterator.hasNext();) {
            String name = (String) iterator.next();
            cmd = cmd + name + " = " + name + ", ";
        }
        cmd = cmd + ")";

        // now eval the command
        result = rengine.eval(cmd);
        if (result == null) throw new QSARModelException("Error making the parameter list");

        // now lets remove all the variables we had assigned
        for (Iterator iterator = keys.iterator(); iterator.hasNext();) {
            String name = (String) iterator.next();
            rengine.eval("rm(" + name + ")");
        }

        return paramVariableName;
    }

    /**
     * Checks whether the class of a named object is of the specified class.
     * <p/>
     *
     * @param objectName  The name of the R variable holding the object to check
     * @param objectClass The class to check for
     * @return true if the object is of the specified class, false if the object is not
     *         of the specified class or the R command to obtain the class failed
     */
    public boolean isOfClass(String objectName, String objectClass) {
        REXP klass = rengine.eval("class(" + objectName + ")");
        if (klass == null) {
            return false;
        }
        return klass.asString().equals(objectClass);
    }

    /**
     * Removes an object from the R session.
     *
     * @param objectName The name of the R variable to remove
     * @throws QSARModelException if the <code>'rm'</code> command failed
     */
    public void removeObject(String objectName) throws QSARModelException {
        REXP ret = rengine.eval("rm(\"" + objectName + "\")");
        if (ret == null) throw new QSARModelException("Error removing \'" + objectName + "\'");
    }

    /**
     * Abstract method to handle loading R models.
     * <p/>
     * This method can be used to load a previously saved R model object. Since
     * the user can save any arbitrary R object, checks must be made that the
     * object being returned is an instance of one of the current modeling classes.
     * <p/>
     * This is best achieved by forcing each modeling class to write its own loader.
     *
     * @param fileName The file containing the R object to load
     * @throws org.openscience.cdk.qsar.model.QSARModelException
     *          if the R session could not load the object or if the loaded model
     *          does not correspond to the class that it was loaded from
     * @see #saveModel
     */
    abstract public void loadModel(String fileName) throws QSARModelException;

    /**
     * Abstract method to handle loading R models that were previously serialized.
     * <p/>
     * This method can be used to load a previously serialized R model object (usinging
     * serialize()). Since
     * the user can save any arbitrary R object, checks must be made that the
     * object being returned is an instance of one of the current modeling classes.
     * This is best achieved by forcing each modeling class to write its own loader.
     * <p/>
     * In addition
     * objects saved using serialize() do not have a name. As a result a name for the object must
     * be specified when using this method.
     *
     * @param serializedModel A String containing the ASCII sreialized R object
     * @param modelName       The name of the model. (Within the R session, the model will be assigned to
     *                        a variable of this name)
     * @throws QSARModelException if the R session could not load the object or if the loaded model
     *                            does not correspond to the class that it was loaded from
     * @see #saveModel
     */
    abstract public void loadModel(String serializedModel, String modelName) throws QSARModelException;

    /**
     * Specifies the parameters value.
     *
     * @param key A String representing the name of the parameter (corresponding to the
     *            name described in the R manpages)
     * @param obj The value of the parameter
     * @throws QSARModelException if the parameters are of the wrong type for the given modeling function
     */
    abstract public void setParameters(String key, Object obj) throws QSARModelException;

    abstract public void build() throws QSARModelException;

    abstract public void predict() throws QSARModelException;

    protected void finalize() {
        rengine.eval("rm(\"" + getModelName() + "\",pos=1)");
    }

    ;


    class TextConsole implements RMainLoopCallbacks {
        public void rWriteConsole(Rengine re, String text) {
            System.out.print(text);
        }

        public void rBusy(Rengine re, int which) {
            System.out.println("rBusy(" + which + ")");
        }

        public String rReadConsole(Rengine re, String prompt, int addToHistory) {
            System.out.print(prompt);
            try {
                BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
                String s = br.readLine();
                return (s == null || s.length() == 0) ? s : s + "\n";
            } catch (Exception e) {
                System.out.println("jriReadConsole exception: " + e.getMessage());
            }
            return null;
        }

        public void rShowMessage(Rengine re, String message) {
            System.out.println("rShowMessage \"" + message + "\"");
        }

        public String rChooseFile(Rengine re, int newFile) {
            FileDialog fd = new FileDialog(new Frame(), (newFile == 0) ? "Select a file" : "Select a new file", (newFile == 0) ? FileDialog.LOAD : FileDialog.SAVE);
            fd.pack();
            fd.setVisible(true);
            String res = null;
            if (fd.getDirectory() != null) res = fd.getDirectory();
            if (fd.getFile() != null) res = (res == null) ? fd.getFile() : (res + fd.getFile());
            return res;
        }

        public void rFlushConsole(Rengine re) {
        }

        public void rLoadHistory(Rengine re, String filename) {
        }

        public void rSaveHistory(Rengine re, String filename) {
        }
    }

}