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JSci is a set of open source Java packages. The aim is to encapsulate scientific methods/principles in the most natural way possible. As such they should greatly aid the development of scientific based software. It offers: abstract math interfaces, linear algebra (support for various matrix and vector types), statistics (including probability distributions), wavelets, newtonian mechanics, chart/graph components (AWT and Swing), MathML DOM implementation, ... Note: some packages, like javax.comm, for the astro and instruments package aren't listed as dependencies (not available).

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package JSci.io;

import java.lang.Comparable;
import java.util.List;
import java.util.Map;
import java.util.ArrayList;
import JSci.maths.*;
import JSci.maths.matrices.*;
import JSci.maths.vectors.*;
import JSci.maths.groups.AbelianGroup;
import JSci.maths.algebras.*;
import JSci.maths.fields.*;

/**
* The MathMLExpression class is used by the MathMLParser to
* encapsulate math expressions described by the <apply> tag.
* @version 0.8
* @author Mark Hale
*/
public final class MathMLExpression extends Object {
        private String operation;
        private List args=new ArrayList();

        /**
        * Constructs a MathML expression.
        */
        public MathMLExpression() {}
        /**
        * Set the operation to be applied to the arguments.
        * @param op a MathML tag name
        * (plus, minus, times, divide, etc).
        */
        public void setOperation(String op) {
                operation=op;
        }
        /**
        * Returns the operation to be applied to the arguments.
        * @return a MathML tag name.
        */
        public String getOperation() {
                return operation;
        }
        /**
        * Adds an argument to this expression.
        */
        public void addArgument(Object obj) {
                args.add(obj);
        }
        /**
        * Returns an argument from this expression.
        */
        public Object getArgument(int n) {
                return args.get(n);
        }
        /**
        * Returns the number of arguments.
        */
        public int length() {
                return args.size();
        }
        /**
        * Substitutes a value for a variable in this expression.
        * @param var the variable to substitute for.
        * @param value the value of the variable.
        * @return the expression after substitution.
        */
        public MathMLExpression substitute(String var,Object value) {
                MathMLExpression subExpr=new MathMLExpression();
                subExpr.operation=operation;
                Object arg;
                for(int i=0;i=0.0)
                                        value=RealField.ZERO;
                                else
                                        value=RealField.PI;
                        } else if(value instanceof Complex) {
                                value=new MathDouble(((Complex)value).arg());
                        } else
                                value = "arg("+value+")";
                } else if(operation.equals("real")) {
                        if(value instanceof Complex)
                                value=new MathDouble(((Complex)value).real());
                        else if(value instanceof AbstractComplexVector)
                                value=((AbstractComplexVector)value).real();
                        else if(value instanceof AbstractComplexMatrix)
                                value=((AbstractComplexMatrix)value).real();
                        else
                                value = "re("+value+")";
                } else if(operation.equals("imaginary")) {
                        if(value instanceof Complex)
                                value=new MathDouble(((Complex)value).imag());
                        else if(value instanceof AbstractComplexVector)
                                value=((AbstractComplexVector)value).imag();
                        else if(value instanceof AbstractComplexMatrix)
                                value=((AbstractComplexMatrix)value).imag();
                        else
                                value = "im("+value+")";
                } else if(operation.equals("conjugate")) {
                        if(value instanceof Complex)
                                value=((Complex)value).conjugate();
                        else if(value instanceof AbstractComplexVector)
                                value=((AbstractComplexVector)value).conjugate();
                        else if(value instanceof AbstractComplexMatrix)
                                value=((AbstractComplexMatrix)value).conjugate();
                        else
                                value = "("+value+")*";
                } else if(operation.equals("transpose")) {
                        if(value instanceof Matrix)
                                value=((Matrix)value).transpose();
                        else
                                value = "("+value+")^T";
                } else if(operation.equals("exp")) {
                        if(value instanceof Number)
                                value=MathDouble.exp((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.exp((Complex)value);
                        else
                                value = "exp("+value+")";
                } else if(operation.equals("ln")) {
                        if(value instanceof Number)
                                value=MathDouble.log((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.log((Complex)value);
                        else
                                value = "log("+value+")";
                } else if(operation.equals("sin")) {
                        if(value instanceof Number)
                                value=MathDouble.sin((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.sin((Complex)value);
                        else
                                value = "sin("+value+")";
                } else if(operation.equals("cos")) {
                        if(value instanceof Number)
                                value=MathDouble.cos((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.cos((Complex)value);
                        else
                                value = "cos("+value+")";
                } else if(operation.equals("tan")) {
                        if(value instanceof Number)
                                value=MathDouble.tan((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.tan((Complex)value);
                        else
                                value = "tan("+value+")";
                } else if(operation.equals("arcsin")) {
                        if(value instanceof Number)
                                value=MathDouble.asin((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.asin((Complex)value);
                        else
                                value = "arcsin("+value+")";
                } else if(operation.equals("arccos")) {
                        if(value instanceof Number)
                                value=MathDouble.acos((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.acos((Complex)value);
                        else
                                value = "arccos("+value+")";
                } else if(operation.equals("arctan")) {
                        if(value instanceof Number)
                                value=MathDouble.atan((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.atan((Complex)value);
                        else
                                value = "arctan("+value+")";
                } else if(operation.equals("sinh")) {
                        if(value instanceof Number)
                                value=MathDouble.sinh((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.sinh((Complex)value);
                        else
                                value = "sinh("+value+")";
                } else if(operation.equals("cosh")) {
                        if(value instanceof Number)
                                value=MathDouble.cosh((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.cosh((Complex)value);
                        else
                                value = "cosh("+value+")";
                } else if(operation.equals("tanh")) {
                        if(value instanceof Number)
                                value=MathDouble.tanh((Number)value);
                        else if(value instanceof Complex)
                                value=Complex.tanh((Complex)value);
                        else
                                value = "tanh("+value+")";
                } else if(operation.equals("factorial")) {
                        if(value instanceof Number)
                                value=new MathDouble(ExtraMath.factorial(((Number)value).doubleValue()));
                        else
                                value = "("+value+")!";
                } else if(operation.equals("not")) {
                        if(value instanceof Boolean)
                                value=new Boolean(!((Boolean)value).booleanValue());
                        else
                                value = "!("+value+")";
                }
                return value;
        }
        /**
        * Evaluates binary expressions.
        */
        private Object binaryEvaluate() {
                Object value=getArgument(0);
                if(value instanceof MathMLExpression)
                        value=((MathMLExpression)value).evaluate();
                Object next=getArgument(1);
                if(next instanceof MathMLExpression)
                        next=((MathMLExpression)next).evaluate();
                if(operation.equals("minus")) {
                        if(value instanceof AbelianGroup.Member && next instanceof AbelianGroup.Member)
                                value=((AbelianGroup.Member)value).subtract((AbelianGroup.Member)next);
                        else
                                value = "("+value+")-("+next+")";
                } else if(operation.equals("divide")) {
                        if(next instanceof Field.Member) {
                                if(value instanceof Field.Member)
                                        value=((Field.Member)value).divide((Field.Member)next);
                                else if(value instanceof VectorSpace.Member)
                                        value=((VectorSpace.Member)value).scalarDivide((Field.Member)next);
                                else
                                    value = "("+value+")/("+next+")";
                        } else
                                value = "("+value+")/("+next+")";
                } else if(operation.equals("scalarproduct")) {
                        if(value instanceof AbstractDoubleVector && next instanceof AbstractDoubleVector)
                                value=new MathDouble(((AbstractDoubleVector)value).scalarProduct((AbstractDoubleVector)next));
                        else if(value instanceof AbstractComplexVector && next instanceof AbstractComplexVector)
                                value=((AbstractComplexVector)value).scalarProduct((AbstractComplexVector)next);
                        else
                                value = "("+value+").("+next+")";
                } else if(operation.equals("vectorproduct")) {
                        if(value instanceof Double3Vector && next instanceof Double3Vector)
                                value=((Double3Vector)value).multiply((Double3Vector)next);
                        else if(value instanceof Complex3Vector && next instanceof Complex3Vector)
                                value=((Complex3Vector)value).multiply((Complex3Vector)next);
                        else
                                value = "("+value+")x("+value+")";
                } else if(operation.equals("power")) {
                    if(value instanceof Number && next instanceof Number)
                        value=new MathDouble(Math.pow(((Number)value).doubleValue(),((Number)next).doubleValue()));
                        else
                                value = "("+value+")^("+value+")";
                } else if(operation.equals("neq")) {
                        value=new Boolean(!value.equals(next));
                } else
                        return nAryEvaluate();
                return value;
        }
        /**
        * Evaluates n-ary expressions.
        */
        private Object nAryEvaluate() {
                Object value=getArgument(0);
                if(value instanceof MathMLExpression)
                        value=((MathMLExpression)value).evaluate();
                if(operation.equals("plus")) {
                        for(int i=1;i0)
                                            value=next;
                                }
                        }
                } else if(operation.equals("max")) {
                        for(int i=1;i0;
                                        if(arg2 instanceof Comparable)
                                                arg1=(Comparable)arg2;
                                }
                                value=new Boolean(ans);
                        }
                } else if(operation.equals("geq")) {
                        if(value instanceof Comparable) {
                                Comparable arg1=(Comparable)value;
                                boolean ans=true;
                                for(int i=1;i=0;
                                        if(arg2 instanceof Comparable)
                                                arg1=(Comparable)arg2;
                                }
                                value=new Boolean(ans);
                        }
                }
                return value;
        }
        /**
        * Calculates the mean for this expression.
        */
        private double mean() {
                double sum=((Number)getArgument(0)).doubleValue();
                for(int i=1;i




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