Question

嗨，我正在尝试实现一种算法并实现该功能：当一个分子编号变为0时，整个while循环将结束，并使用JFreeChart自动进行下一个图表绘制步骤。现在，使用“ return”后，eclipse不会显示任何错误并完全处理主要方法。但是，我看不到我的图表显示出来。想知道是否有任何步骤出错。我想显示不同物种在不同时间的分子数量。每个物种将代表一个新行。所以我创建了一个新的图表

static JPanel chartPanel;

然后在构造函数中设置类似（只需遵循在线教程）

super("Line Chart of molecule numbers at different times");
     add(chartPanel, BorderLayout.CENTER);
        setSize(640, 480);
        setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
        setLocationRelativeTo(null);

在主要方法中，我想显示折线图中输入并计算的数字（因为害怕空指针异常，所以没有创建另一个类）

public static void main(String args[]) throws Exception {

    //input the number of species
    System.out.println("Enter the number of species:");
    int n = sc.nextInt();

    //input the number of reactions
    System.out.println("Enter the number of reactions:");
    int m = sc.nextInt();



    //
    int[][]matrixPre = new int[m][n];
    enterMatrixDataPre(sc, matrixPre, m, n);
    printMatrixPre(matrixPre, m, n);

    //convert the 2d int to 2d double
    double [][] matrixPre2 = new double[m][n];
    for(int i = 0; i <m; i++)
    {
        for(int j = 0; j < n; j++)
            matrixPre2[i][j] = (double) matrixPre[i][j];
    }

    RealMatrix PreMatrix = new Array2DRowRealMatrix(matrixPre2);


    // remember to add space key when doing the typing
    int[][]matrixPost = new int[m][n];
    enterMatrixDataPost(sc, matrixPost, m, n);
    printMatrixPost(matrixPost, m, n);

    //convert the 2d int to 2d double
        double [][] matrixPost2 = new double[m][n];
        for(int i = 0; i <m; i++)
        {
            for(int j = 0; j < n; j++)
                matrixPost2[i][j] = (double) matrixPost[i][j];
        }

    RealMatrix PostMatrix = new Array2DRowRealMatrix(matrixPost2);


     //
    RealMatrix matrixSubtract = PreMatrix.subtract(PostMatrix);
    System.out.println("So the transpose matrix after subtraction is:\t"+matrixSubtract.transpose());

     //input the default maxium time of the whole reaction
    System.out.println("Enter the maxium time of the whole reaction:");
    double Tmax =sc.nextDouble();

    //input the name of all the species
    System.out.println("Enter the name of all species");
    String[] strs=new String[n];
    for(int i = 0; i< n; i++) {
        strs[i]=sc.nextLine();  
    }


    //input the rate constant of all the reactions(the coefficient), must be a double
    System.out.println("Enter the rate constant of each reaction:");
    Double[] rate=new Double[m];
    for(int r = 0; r< m; r++) {     
        rate[r]=sc.nextDouble();
    }


    //   
    Vector<Double> timeList = new Vector<Double>(0); 
    Vector<int[]> allStateList = new Vector<int[]>(0);
    timeList.add(newTime);

    //input the initial states of numbers of molecules
    System.out.println("Enter the initial molecule numbers of all species:");
    int[]state = new int[n];
    for (int i = 0; i< n; i++)
   {
       state[i]=sc.nextInt();
   }

   allStateList.add(state);

    while(newTime<Tmax) {

        for(int loopIndex =0; loopIndex<allStateList.size(); loopIndex++)  {            
   //  calculate the hazard for each reaction and the general hazard
    double[] h = new double[m];
    H = 0;
  try {
      for(int i =0; i<m; i++) {
          for(int j =0; j<n; j++) { 
          h[i]=rate[i]*CombinatoricsUtils.binomialCoefficientDouble(allStateList.get(loopIndex)[j],(int)(PreMatrix.getRowVector(i).toArray()[j]));
          H +=h[i];
          }
        }
      }

  catch(NumberIsTooLargeException exceptionn) {
      System.out.println("One of the species has been exhausted and there is no next firing");
      return;
  }
    System.out.println("So the general hazard is:"+H);


     // select a random reaction time
     Random random = new Random(); 
    double tau = (1*Math.log(1/random.nextDouble()))/H;
     System.out.println("So the random reaction time is"+tau);

    //put the newTime
     newTime = timeList.get(loopIndex)+tau;
     System.out.println("So the new reaction time is:" + newTime);
     timeList.add(newTime);

    //select a random reaction j
     Random random2 = new Random(); 
     int index =0;
     for (int i=0; i<m; i++) { 
        if(h[i]>random2.nextDouble()*H) 
            index =i;
  }
  System.out.println("So the next simulated event is:"+index);


      //Update the state
     double[] vectorDoubleArray = matrixSubtract.transpose().getColumnVector(index).toArray();
     int[] intArray = new int[n];
     for (int i=0; i<n; i++) {
              intArray[i] = (int) vectorDoubleArray[i];
     }
     int[] newState = new int[n];
     int newS =0;
     for (int p =0; p<n; p++){
     newS= intArray[p]+allStateList.get(loopIndex)[p];
           newState[p]=newS;           
         }
     System.out.println("Right now the molecule number of all species are:"+Arrays.toString(newState));
     allStateList.add(newState);
   }  

        //close the scanner 
     sc.close();
     }

}

所有准备工作完成后，我想使用jfreechart打印两个向量列表的数量，timeList和allStateList

String chartTitle = "Line chart of molecule numbers";
    String categoryAxisLabel = "time";
    String valueAxisLabel = "molecule numbers";

    DefaultCategoryDataset dataset = new DefaultCategoryDataset();
    int[] eachSpecieState = new int[allStateList.size()]; 
    for (int i =0; i<n; i++) {
        for (int j=0; j<allStateList.size(); j++) {
            eachSpecieState[i]=allStateList.get(j)[i];
        }
    }

    for (int i =0; i<m;i++) {
        String series[]= new String[m];
        series[i]=""+strs[i];
    for(int k =0; k<n;k++) {    
        for (int j=0; j<allStateList.size(); j++) {
            eachSpecieState[k]=allStateList.get(j)[k];
            dataset.addValue(eachSpecieState[k],series[i+1],""+timeList.get(j));
        }
    }   
}
    JFreeChart chart = ChartFactory.createLineChart(chartTitle,
            categoryAxisLabel, valueAxisLabel, dataset);

    chartPanel = new ChartPanel(chart);

    SwingUtilities.invokeLater(new Runnable() {
        public void run() {
           new StochasticProcess().setVisible(true);
        }
    });

但是没有图表显示。由于我的摇摆语言不太好，有人可以帮我指出是否有任何部分出错？（代码的最后一个绘图和图表部分）谢谢〜

Answer 1

最简单的解决方案之一就是将中断条件添加到一个简单的<!DOCTYPE HTML> <html ng-app="todoApp"> <head> <script src="https://ajax.googleapis.com/ajax/libs/angularjs/1.6.4/angular.min.js"></script> </head> <body> <div ng-controller="todoList" class="jumbotron"> <h2><strong>To-Do List</strong></h2> <br/> <form ng-submit="addTodo()"> <input type="text" ng-model="todoText" placeholder="Add new task" size="30"> <button type="submit" class="btn btn-primary glyphicon glyphicon-plus">Add</button> </form> <br/> <ul> <li ng-repeat="todo in todos"> <label class="checkbox"> <input type="checkbox" ng-model="todo.done"> <span class="done-{{todo.done}}">{{todo.text}}</span> <span class="glyphicon glyphicon-trash" ng-click="removeTodo()"></span> </label> </li> </ul> </div> <script> var app = angular.module('todoApp', []); app.controller('todoList', function ($scope, $localStorage) { $scope.getTodos = function() { var str = $localStorage.getItem("todos"); $scope.todos = JSON.parse(str); if (!todos) { $scope.todos = [{ text: 'Feed the cat', done: true }, { text: 'Mow the lawn', done: false }]; } } $scope.saveToDos = function() { var str = JSON.stringify(todos); $localStorage.SetItem("todos", str); } $scope.addTodo = function () { if($scope.todoText !== '') { $scope.todos.push({text:$scope.todoText, done:false}); $scope.todoText = ''; saveToDos(); } }; $scope.removeToDo = function() { todos.splice($index, 1); saveToDos(); } }); </script> </body> </html>循环中

for

Answer 2

我不得不承认，在没有特定知识的情况下，要理解和调试整个代码并不容易。但是，总的来说，我看到了，在一定程度上，您写道：

      ***while(allStateList.get(loopIndex)[j]==0) {
          break;
      }***

我认为，作为一般规则，如果要检查条件，则必须使用IF语句，例如：if（condition == true）{break; }

我认为这对您有用。

Answer 3

因此，为了解决该问题，我创建了XYSeries列表，并为循环内的每个XYSeries添加了新名称。在为每个XYSeries添加值之后，使用另一个循环将其添加到XYCollection中。问题是在一周前提出的，对许多部分进行了修改以获取最终结果。我将在下面发布整个代码的新版本以将其设置为例。

import java.util.*;
import java.awt.BasicStroke;
import java.awt.Color;
import java.awt.Font;
import java.lang.Math;

import org.apache.commons.math3.exception.NumberIsTooLargeException;
import org.apache.commons.math3.linear.Array2DRowRealMatrix;
import org.apache.commons.math3.linear.RealMatrix;
import org.apache.commons.math3.util.CombinatoricsUtils;

import javax.swing.BorderFactory;
import javax.swing.JFrame;
import javax.swing.SwingUtilities;

import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.block.BlockBorder;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.chart.plot.XYPlot;
import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
import org.jfree.chart.title.TextTitle;
import org.jfree.data.xy.XYSeries;
import org.jfree.data.xy.XYSeriesCollection;

主要方法部分在这里：

public class StochasticSimulationProcess extends JFrame {
    /**
     * 
     */
    private static final long serialVersionUID = 1L;
    static int matrixPre[][];
    static int matrixPost[][];
    static int m;// the number of reactions
    static int n;// the number of species
    static double[] h;// the hazard for each reaction
    static double[] rate;
    static int[] state;
    static double newTime;
    static int max;
    static double Tmax;// the overall reaction time
    Vector<Double> timeList;
    static double H;
    Vector<int[]> allStateList;
    static String[] strs;
    XYSeriesCollection dataset;


    public StochasticSimulationProcess(String s) {
        super(s);
        newTime = 0;

    }

    static Scanner sc = new Scanner(System.in);

    public static void main(String args[]) throws Exception {

        // input the number of species
        System.out.println("Enter the number of species:");
        int n = sc.nextInt();

        // input the number of reactions
        System.out.println("Enter the number of reactions:");
        int m = sc.nextInt();

        //
        int[][] matrixPre = new int[m][n];
        enterMatrixDataPre(sc, matrixPre, m, n);
        printMatrixPre(matrixPre, m, n);

        // convert the 2d int to 2d double
        double[][] matrixPre2 = new double[m][n];
        for (int i = 0; i < m; i++) {
            for (int j = 0; j < n; j++)
                matrixPre2[i][j] = (double) matrixPre[i][j];
        }

        RealMatrix PreMatrix = new Array2DRowRealMatrix(matrixPre2);

        // remember to add space key when doing the typing
        int[][] matrixPost = new int[m][n];
        enterMatrixDataPost(sc, matrixPost, m, n);
        printMatrixPost(matrixPost, m, n);

        // convert the 2d int to 2d double
        double[][] matrixPost2 = new double[m][n];
        for (int i = 0; i < m; i++) {
            for (int j = 0; j < n; j++)
                matrixPost2[i][j] = (double) matrixPost[i][j];
        }

        RealMatrix PostMatrix = new Array2DRowRealMatrix(matrixPost2);

        //
        RealMatrix matrixSubtract = PreMatrix.subtract(PostMatrix);
        System.out.println("So the transpose matrix after subtraction is:\t" + matrixSubtract.transpose());

        // input the default maxium time of the whole reaction
        System.out.println("Enter the maxium time of the whole reaction:");
        double Tmax = sc.nextDouble();

        // input the name of all the species
        System.out.println("Enter the name of all species");
        String[] strs = new String[n];
        for (int i = 0; i < n; i++) {
            strs[i] = sc.nextLine();
        }

        // input the rate constant of all the reactions(the coefficient), must be a
        // double
        System.out.println("Enter the rate constant of each reaction:");
        Double[] rate = new Double[m];
        for (int r = 0; r < m; r++) {
            rate[r] = sc.nextDouble();
        }

        //
        Vector<Double> timeList = new Vector<Double>(0);
        Vector<int[]> allStateList = new Vector<int[]>(0);
        timeList.add(newTime);

        // input the initial states of numbers of molecules
        System.out.println("Enter the initial molecule numbers of all species:");
        int[] state = new int[n];
        for (int i = 0; i < n; i++) {
            state[i] = sc.nextInt();
        }

        allStateList.add(state);
        timeLoop:
        while (newTime < Tmax) {
            for (int loopIndex = 0; loopIndex < allStateList.size(); loopIndex++) {
                // calculate the hazard for each reaction and the general hazard
                double[] h = new double[m];
                H = 0;
                try {
                    for (int i = 0; i < m; i++) {
                        for (int j = 0; j < n; j++) {
                            h[i] = rate[i] * CombinatoricsUtils.binomialCoefficientDouble(
                                    allStateList.get(loopIndex)[j], (int) (PreMatrix.getRowVector(i).toArray()[j]));
                            H += h[i];
                        }
                    }
                }

                catch (NumberIsTooLargeException exceptionn) {
                    System.out.println("One of the species has been exhausted and there is no next firing");
                    break timeLoop;
                }
                System.out.println("So the general hazard is:" + H);

                // select a random reaction time
                Random random = new Random();
                double tau = (1 * Math.log(1 / random.nextDouble())) / H;
                System.out.println("So the random reaction time is" + tau);

                // put the newTime
                newTime = timeList.get(loopIndex) + tau;
                System.out.println("So the new reaction time is:" + newTime);
                timeList.add(newTime);

                // select a random reaction j
                Random random2 = new Random();
                int index = 0;
                double hi =0;
                for (int i = 0; i < m; i++) {
                    hi +=h[i];
                    if (hi >= random2.nextDouble() * H) {
                        index = i;
                        break;
                    }
                }
                System.out.println("So the next simulated event is:" + index);

                // Update the state
                double[] vectorDoubleArray = matrixSubtract.transpose().getColumnVector(index).toArray();
                int[] intArray = new int[n];
                for (int i = 0; i < n; i++) {
                    intArray[i] = (int) vectorDoubleArray[i];
                }
                int[] newState = new int[n];
                int newS = 0;
                for (int p = 0; p < n; p++) {
                    newS = intArray[p] + allStateList.get(loopIndex)[p];
                    newState[p] = newS;
                }
                System.out.println("Right now the molecule number of all species are:" + Arrays.toString(newState));
                allStateList.add(newState);
            }

            // close the scanner
            sc.close();
        }


        XYSeriesCollection dataset = new XYSeriesCollection();
        XYSeries[] species = new XYSeries[n];
        for (int j =0; j<n; j++) {
            species[j]=new XYSeries(""+strs[j]+Integer.toString(j));
        }


        for (int j =0; j<n; j++) {
            for (int k=0; k< allStateList.size();k++) {
            species[j].add(timeList.get(k).doubleValue(), allStateList.get(k)[j]);
        }
            dataset.addSeries(species[j]);
    }

        // plot out the graph
        System.out.println("TEST");

        JFreeChart chart = ChartFactory.createXYLineChart(
                "SSA Modeling", 
                "time", 
                "Number of Molecules", 
                dataset, 
                PlotOrientation.VERTICAL,
                true, 
                true, 
                false
        );

         ChartPanel chartPanel = new ChartPanel(chart);
            chartPanel.setBorder(BorderFactory.createEmptyBorder(15, 15, 15, 15));
            chartPanel.setBackground(Color.white);
           XYPlot plot = chart.getXYPlot();


            XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer();

            for (int j =0; j<n;j++){
             renderer.setSeriesPaint(j, Color.RED);
             renderer.setSeriesStroke(j, new BasicStroke(2.0f));
            }


            plot.setRenderer(renderer);
            plot.setBackgroundPaint(Color.white);

            plot.setRangeGridlinesVisible(false);
            plot.setDomainGridlinesVisible(false);


           chart.getLegend().setFrame(BlockBorder.NONE);

            chart.setTitle(new TextTitle("Stochastic Simulation Algorithm",
                            new Font("Serif", Font.BOLD, 18)
                    )
            );

        SwingUtilities.invokeLater(() -> {
            StochasticSimulationProcess ex = new StochasticSimulationProcess("SSA");
            ex.setContentPane(chartPanel);
            ex.pack();
            ex.setLocationRelativeTo(null);
            ex.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);  
            ex.setVisible(true);

        });
    }

    public static void enterMatrixDataPre(Scanner sc, int[][] matrixPre, int m, int n) {
        System.out.println("Enter Matrix pre data");
        for (int i = 0; i < m; i++) {
            for (int j = 0; j < n; j++) {
                matrixPre[i][j] = sc.nextInt();
            }
        }
    }

    public static void printMatrixPre(int[][] matrixPre, int m, int n) {
        System.out.println("Matrix pre is:");
        for (int i = 0; i < m; i++) {
            for (int j = 0; j < n; j++) {
                System.out.print(matrixPre[i][j] + "\t");
            }
            System.out.println();
        }
    }

    public static void enterMatrixDataPost(Scanner sc, int[][] matrixPost, int m, int n) {
        System.out.println("Enter Matrix post data");
        for (int i = 0; i < m; i++) {
            for (int j = 0; j < n; j++) {
                matrixPost[i][j] = sc.nextInt();
            }
        }
    }

    public static void printMatrixPost(int[][] matrixPost, int m, int n) {
        System.out.println("Matrix post is:");
        for (int i = 0; i < m; i++) {
            for (int j = 0; j < n; j++) {
                System.out.print(matrixPost[i][j] + "\t");
            }
            System.out.println();
        }
    }
}

随机更改颜色，因为表示物种的XYSeries的数量是不确定的，所以我选择了随机设置hgb方法，因为只要值在0-255之间，它们就可以随机组合，因此我更改了代码为：

renderer.setSeriesPaint(j, Color.getHSBColor(0 + (float)(Math.random() * ((255 - 0) + 1)), 0 + (float)(Math.random() * ((255 - 0) + 1)), 0 + (float)(Math.random() * ((255 - 0) + 1))));

如何在jfreechart

3 个答案: