NuclideChart.java

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import java.io.*;
import java.awt.*;
import java.awt.geom.*;
import java.text.*;
import java.awt.image.*;
import java.awt.font.*;
import javax.imageio.*;
import javax.swing.ImageIcon;
import javax.swing.*;
import java.util.ArrayList;

public class NuclideChart
{    
    public static void main(String[] args)
    {
        if(args.length == 0)
            {
                printHelp();
                System.exit(0);
            }
        
        IndataParameters myParameters = new IndataParameters(args);
        
        ArrayList<JIsotope> isotopeList  = readJIsotopeList(myParameters.getJIsotopeFiles(), myParameters.getRGBVectorList());

        EPSCreator myEPSCreator;
        if(!myParameters.getSectionSpecified())
            myEPSCreator = new EPSCreator(isotopeList);
        else
            {
                NuclideSquare mySquare = myParameters.getSection();
                myEPSCreator = new EPSCreator(isotopeList, mySquare.bottomLeftZ, mySquare.bottomLeftA, mySquare.upperRightZ, mySquare.upperRightA);
            }

        myEPSCreator.createEPSDocument(myParameters.getFilename());             
    }
    

    public static ArrayList<JIsotope> readJIsotopeList(ArrayList<String> iLists, ArrayList<RGBVector> rgbVec)
    {
        ArrayList<JIsotope> isotopeList = new ArrayList<JIsotope>();
        //      isotopeLists.add(new ArrayList<JIsotope>());    
        for(int i=0; i<iLists.size(); i++)
            {
                
                int listIndex = 0;
                
                try
                    {
                        BufferedReader in = new BufferedReader(new FileReader(iLists.get(i)));  
                        String input = in.readLine();
                        
                        // read all lines and create an isotope object from each of them
                        // and add it to the last isotopeList in isotopeLists
                        // that is, the list in isotopeLists with index (isotopeLists.size()-1)
                        while (input != null && input.length()>0)
                            {
                                
                                JIsotope localJIsotope;
                                boolean isInList = false;
                                
                                
                                int index1 = 0, index2 = 0;                     // indices of the first and second whitespace in the string
                                
                                // find the first and second whitespaces
                                for (int j = 0; j < input.length(); j++)
                                    {
                                        if (input.charAt(j) == ' ' && index1 == 0)
                                            index1 = j;                 
                                        else if (input.charAt(j) == ' ' && index1 != 0)
                                            {
                                                index2 = j;
                                                break;
                                            }
                                    }
                                
                                // set the member variables
                                int Z = Integer.parseInt(input.substring(0, index1));
                                int A = Integer.parseInt(input.substring(index1+1, index2));
                                int N = A-Z;
                                
                                String name = input.substring(index2+1);
                                
                                
                                for(int k=0; k<isotopeList.size(); k++)
                                    {
                                        if(name.equals(isotopeList.get(k).getName()) && A == isotopeList.get(k).getA())
                                            {
                                                isInList = true;
                                                listIndex = k;
                                                break;
                                            }
                                    }
                                
                                if(isInList)
                                    {
                                        isotopeList.get(listIndex).addColor(rgbVec.get(i));
                                    }

                                else
                                    {
                                        localJIsotope = new JIsotope(Z, A, name, rgbVec.get(i));
                                        isotopeList.add(localJIsotope);
                                    }
                                input = in.readLine();
                            }
                    }
                
                catch (IOException e)
                    {
                        System.out.println("Error reading file:" + listIndex);
                    }
            }
        return isotopeList;
    }

    /*
    public static void printAllJIsotopeList()
    {
    for (int i = 0; i < isotopeList.size(); i++)
            {
                System.out.println("JIsotope number " + i + ": " +isotopeList.get(i).getZ() +" "+ isotopeList.get(i).getA() + isotopeList.get(i).getName() + " " + isotopeList.get(i).getColorList().get(0).getR()+ " " + isotopeList.get(i).getColorList().get(0).getG()+ " " + isotopeList.get(i).getColorList().get(0).getB());
            }
    }
    */


    private static void printHelp()
    {
        System.out.println("Program to draw a nuclide chart from given input nuclide lists.");
        System.out.println("Usage: java NuclideChart <Output file> [-n BottomLeftZ BottomLeftA UpperRightZ UpperRightA] [allNuclidesFile R1 G1 B1] [stableJIsotopes R2 G2 B2] n*[additionalNuclideList Ri Gi Bi]");
        System.out.println("Parameters:");
        System.out.println("<Output file>: EPS file to print to. Will be overwritten if it exists.");
        System.out.println("-n BottomLeftZ BottomLeftA UpperRightZ UpperRightA: plot only the square between the nuclide with A and Z as BottomLeftA and BottomLeftZ, and A and Z as UpperRightZ and UpperRightA.");
        System.out.println("allNuclidesFile: File containing all nuclides for the chart.");
        System.out.println("Ri, Gi, Bi: R, G and B components of coloring for that specific isotope list.");
        System.out.println("stableJIsotopes: File containing all stable isotopes.");
        System.out.println("additionalNuclideList: list containing additional nuclear data for coloring purposes.");
        /*
        System.out.println("In order to plot the entire nuclide chart, type the following command line arguments in the given order and press \"Enter\":");
        System.out.println();
        System.out.println("1 Type the name of the .txt file containing ALL nuclides, followed by its RGB coloring code on the form \"R G B\".");
        System.out.println();
        System.out.println("2 (Optional) Enter the name of the .txt file containing all stable isotopes, followed by its RGB coloring code on the form \"R G B\".");
        System.out.println();
        System.out.println("3 Type the names of all remaining .txt files to be plotted, each followed by its respective RGB coloring code on the form \"R G B\".");     
        System.out.println();
        System.out.println("In order to plot a specific region of the nuclide chart, BEFORE the above mentioned, also type:");
        System.out.println();
        System.out.println("\"-n BottomLeftZ BottomLeftA UpperRightZ UpperRightA\", where the last four arguments specify the specific region to be viewed in the way that their names indicate.");
        */
    }
}
    
class IndataParameters
{
    private String filename;
    public String getFilename(){return filename;}
    private boolean sectionSpecified;
    public boolean getSectionSpecified(){return sectionSpecified;}
    private NuclideSquare section;
    public NuclideSquare getSection(){return new NuclideSquare(section);}
    private ArrayList<RGBVector> rgbVectorList;
    public ArrayList<RGBVector> getRGBVectorList(){ return new ArrayList<RGBVector>(rgbVectorList);}
    private ArrayList<String> isotopeFiles;
    public ArrayList<String> getJIsotopeFiles(){ return new ArrayList<String>(isotopeFiles);}


    public IndataParameters(String[] args)
    {
        rgbVectorList = new ArrayList<RGBVector>();
        isotopeFiles = new ArrayList<String>();

        filename = args[0];
        int ptr = 1; 

        if (args[ptr].equalsIgnoreCase("-n"))
            {
                sectionSpecified = true;
                ptr=6;
                section = new NuclideSquare();
                try
                    {
                        section.bottomLeftZ = Integer.parseInt(args[2]);
                        section.bottomLeftA = Integer.parseInt(args[3]);
                        section.upperRightZ = Integer.parseInt(args[4]);
                        section.upperRightA = Integer.parseInt(args[5]);
                    }
                catch(NumberFormatException ex)
                    {
                        System.out.println("Error in parsing limits.");
                        System.exit(1);
                    }
            }
        else
            {
                sectionSpecified = false;
            }

        for (int i=ptr; i < args.length; i=i+4) //Var fjärde härifrån är en xxx.txt-fil
            {
                isotopeFiles.add(args[i]);
            }
        
        for (int i=ptr+1; i < args.length; i=i+4) //överväg i+4
            {
                int r, g, b;
                try
                    {
                        rgbVectorList.add(new RGBVector(Integer.parseInt(args[i]),Integer.parseInt(args[i+1]),Integer.parseInt(args[i+2])));
                    }
                catch(NumberFormatException ex)
                    {
                        System.out.println("Error in parsing rgb vectors.");
                        System.exit(1);
                    }
            }
        
    }
}

class NuclideSquare
{
    public int bottomLeftZ;
    public int bottomLeftA;
    public int upperRightZ;
    public int upperRightA;
    
    public NuclideSquare()
    {
        bottomLeftZ = 0;
        bottomLeftA = 0;
        upperRightZ = 0;
        upperRightA = 0;
    }

    public NuclideSquare(NuclideSquare toCopy)
    {
        this.bottomLeftZ = toCopy.bottomLeftZ;
        this.bottomLeftA = toCopy.bottomLeftA;
        this.upperRightZ = toCopy.upperRightZ;
        this.upperRightA = toCopy.upperRightA;
    }
}