Needleman-Wunsch算法是一种经典的全局序列比对方法，用于比较DNA或蛋白质序列的同源性。它通过二维表格计算最佳比对，考虑匹配、不匹配和空格的情况。算法初始填充第二行和第二列，然后逐个填充其余单元格，选择得分最高的路径。最终从右下角单元格回溯得到比对字符串和得分。
Needleman Wusch算法
是经典的全局比对算法，用于比对两条DNA序列或者蛋白质序列的同源性或者说相似性；
全局序列比对： 尝试找到两个完整的序列 S1 和 S2 之间的最佳比对。如S1=GCCCTAGCG S2=GCGCAATG 如果设定每个匹配字符为1分，每个空格为-2分，每个不匹配为-1分，则下面的比对就是全局最优比对：S1'=GCCCTAGCG S2'=GCGC_AATG,连字符“_”代表空格。在 S2' 中有五个匹配字符，一个空格（或者反过来说，在 S1' 中有一个插入项），有三个不匹配字符。这样得到的分数是 (5×1) + (1×-2) + (3×-1) = 0，这是能够实现的最佳结果。
局部序列比对： 不必对两个完整的序列进行比对；可以在每个序列中使用某些部分来获得最大得分。使用同样的序列 S1 和 S2，以及同样的得分方案，可以得到以下局部最优比对 S1'' 和 S2''：S1=GCCCTAGCG S2=GCGCAATG S1''=GCG S2''=GCG，虽然这个局部比对恰好没有不匹配字符或空格，但是一般情况下，局部比对可能存在不匹配字符或空格。这个局部比对的得分是 (3×1) + (0×-2) + (0×-1) = 3。（最佳局部比对的得分要大于或等于最佳全局比对的得分，这是因为全局比对也属于局部比对)
百度经验：https://jingyan.baidu.com/article/358570f6b545cace4724fcbb.html
该算法用来计算全局比对。它的思路与 LCS 算法相似。这个算法也使用二维表格，一个序列沿顶部展开，一个序列沿左侧展开。而且也能通过以下三个途径到达每个单元格：1.来自上面的单元格，代表将左侧的字符与空格比对。2.来自左侧的单元格，代表将上面的字符与空格比对。3.来自左上侧的单元格，代表与左侧和上面的字符比对（可能匹配也可能不匹配）。该单元格的值来自于一下3个中的最大值：（1）上方的值-2 （2）左边的值-2 （3）如果该单元格所在的行于所在的列对应的字符相等，则为左上值加1，否则为左上值-1。
首先，必须初始化表格。这意味着填充第二行和第二列的分数和指针。填充第二行的操作意味着使用位于顶部的第一个序列中的字符，并使用空格，而不是使用左侧从上到下的序列中的第一个字符。空格的扣分是 -2，所以每次使用空格的时候，就给以前的单元格加了 -2 分。以前的单元格是左侧的单元格。这就说明了在第二行中为什么得到了 0, -2, -4, -6, ... 这样的序列。用相似的方式得到第二列的得分和指针.
接下来，需要填充余下的单元格。同 LCS 算法一样，对于每个单元格，都有三个选择，要从中选择最大的。可以从上面、左侧、左上侧到达每个单元格。假设 S1 和 S2 是要比对的字符串，S1' 和 S2' 是生成的比对中的字符串。从上面到达单元格相当于将左面的字符从 S2 加入 S2'，跳过上面的 S1 中的当前字符，并在 S1'中加入一个空格。因为一个空格的分数是 -2，所以当前单元格的得分要从上面的单元格得分减 2 得到。类似的，将左边的单元格得分减 2，可以从左侧到达空单元格。
最后，可以将上面的字符加入到 S1' 中，将左边的字符加入到 S2' 中。这就相当于从左上侧进入空白单元格。这两个字符将会匹配，在这种情况下，新的得分就是左上侧单元格的得分减 1。在这三种可能性当中，选择得分最大的一个（如果得分相等，可以从得分高的单元格中从任选一个）。接下来，需要得到实际的比对字符串S1' 和S2'以及比对的得分。右下角单元格中的得分包含 S1 和 S2 的最大比对得分，就像在 LCS 算法中包含 LCS 的长度一样。而且，与 LCS 算法类似，要获得 S1' 和 S2'，要从右下角单元格开始沿着指针回溯，反向构建 S1' 和 S2'。从表格的构建过程可知，从上向下对应着将左侧字符从 S2 加入到 S2' 中，将空格加入 S1' 中；从左向右对应着将上面的字符从 S1 加入到 S1' 中，将空格加入 S2' 中；而向下和向右移动意味着分别将来自S1 和 S2 的字符加入 S1' 和 S2'
代码：
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import javax.swing.JScrollPane;
import javax.swing.JTree;
import javax.swing.table.DefaultTableModel;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.DefaultTreeModel;
import org.dom4j.Attribute;
import org.dom4j.Document;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
import com.highgo.Test.XMLDemo1;
import java.io.InputStream;
import java.util.Iterator;
import org.dom4j.Attribute;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
/**
*
* @author Highgo
*/
public class CheckboxSwing extends javax.swing.JFrame {
/**
*
*/
private static final long serialVersionUID = 1L;
/**
* Creates new form CheckboxSwing
*
* @throws IOException
*/
public CheckboxSwing() throws IOException {
this.setTitle("CheckboxSwing");
initComponents();
inittable();
this.setLocationRelativeTo(null);
}
private CheckboxSwing getThis() {
return this;
}
private String filepath = null;
private String comppath = null;
private String resultpath = null;
private void dathinit() {
jTabcheckbox.getModel();
getXml();
jTextArea1.append(filepath);
if (filepath == null || filepath.trim().equals("")) {
}
else {
traverseFolder(filepath,0);
}
}
private void getXml() {
SAXReader reader = new SAXReader();
try {
InputStream is = new FileInputStream("../filedath.xml");
Document doc= null;
doc = reader.read(is);
Element root = doc.getRootElement();
int i = 0;
Iterator<Element> it = root.elementIterator();
while(it.hasNext()){
Element e = it.next();//获取子元素
//Attribute idAttr = e.attribute("id");
//String id = idAttr.getValue();
//System.out.println(id);
//通过元素对象获取子元素对象
Element nameElement = e.element("name");
//获取元素中的文本内容
if(i == 0) {
filepath = nameElement.getText();
//System.out.println(filepath);
}
if(i == 1) {
comppath = nameElement.getText();
}
if(i == 2) {
resultpath = nameElement.getText();
}
i++;
}
} catch (DocumentException | FileNotFoundException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
}
private DefaultMutableTreeNode traverseFolder(String path,int n) {
DefaultMutableTreeNode temp;
DefaultTableModel model = (DefaultTableModel) jTabcheckbox.getModel();
DefaultMutableTreeNode fujiedian = new DefaultMutableTreeNode(new File(path).getName());
File file = new File(path);
if (file.exists()) {
if(file.isDirectory()) {
File[] files = file.listFiles();
if (files.length == 0) {
if(file.isDirectory()) {//如果是空文件夹
DefaultMutableTreeNode dn = new DefaultMutableTreeNode(file.getName(), false);
return dn;
}
}else{
for (File file2 : files) {
if (file2.isDirectory()) {
//是目录的话，生成节点，并添加里面的节点
if( n < 5) {
n++;
fujiedian.add(traverseFolder(file2.getAbsolutePath(),n));
}
}else{
//是文件的话直接生成节点，并把该节点加到对应父节点上
try {
String fileName = file2.getName();
String fapat = file2.getCanonicalPath();
model.addRow(new Object[] { true, model.getRowCount() + 1 ,fileName,fapat});
temp = new DefaultMutableTreeNode(file2.getName());
fujiedian.add(temp);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
javax.swing.tree.DefaultTreeModel dm = new DefaultTreeModel(fujiedian);
// 将模型设给树,树上显示的将上前面所加载的节点
jTree.setModel(dm);
}
}
} else {
//model.addRow(new Object[] { true, model.getRowCount() + 1 ,file.getName()});
}
} else {//文件不存在
return null;
}
return fujiedian;
}
private void inittable() {
DefaultTableModel model = (DefaultTableModel) jTabcheckbox.getModel();
jTree.setModel(null);
jBAll.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
for (int i = 0; i < model.getRowCount(); i++) {
model.setValueAt(Boolean.valueOf(true), i, 0);
}
}
});
jBAllNot.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
for (int i = 0; i < model.getRowCount(); i++) {
model.setValueAt(Boolean.valueOf(false), i, 0);
}
}
});
jBClear.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
model.setRowCount(0);
}
});
jBDelete.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
int sum = model.getRowCount();
for(int i = sum - 1; i >=0; i--) {
if((boolean) model.getValueAt(i, 0) == true) {
model.removeRow(i);
}
}
}
});
getRootPane().setDefaultButton(jBOK);
jBOK.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
Boolean str = null;
String[] mojdlogName = new String[model.getRowCount()];
String[] mojdlogPath = new String[model.getRowCount()];
int mi = 0;
for (int i = 0; i < model.getRowCount(); i++) {
str = (Boolean) model.getValueAt(i, 0);
if (str.equals(true)) {
mojdlogName[mi] = (String) model.getValueAt(i, 2);
mojdlogPath[mi] = (String) model.getValueAt(i, 3);
System.out.println(mojdlogName[mi]);
System.out.println(mojdlogPath[mi]);
mi++;
System.out.println("true" + (i + 1));
} else {
System.out.println("false" + (i + 1));
}
}
System.out.println(mojdlogName);
new NewJDialog(getThis(), true, mojdlogName,mojdlogPath,comppath,resultpath);
}
});
jBDath.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
dathinit();
}
});
}
/**
* This method is called from within the constructor to initialize the form.
* WARNING: Do NOT modify this code. The content of this method is always
* regenerated by the Form Editor.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
jBAllNot = new javax.swing.JButton();
jBAll = new javax.swing.JButton();
jSPTabel = new javax.swing.JScrollPane();
jTabcheckbox = new javax.swing.JTable();
jBOK = new javax.swing.JButton();
jSPArea = new javax.swing.JScrollPane();
jTextArea1 = new javax.swing.JTextArea();
jBDath = new javax.swing.JButton();
jBClear = new javax.swing.JButton();
jBDelete = new javax.swing.JButton();
jSPTree = new javax.swing.JScrollPane();
jTree = new javax.swing.JTree();
setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
jBAllNot.setText("ANOT");
jBAll.setText("ALL");
jTabcheckbox.setModel(new javax.swing.table.DefaultTableModel(
new Object [][] {
},
new String [] {
"Choose", "line", "Name", "path"
}
) {
Class[] types = new Class [] {
java.lang.Boolean.class, java.lang.Integer.class, java.lang.Object.class, java.lang.Object.class
};
public Class getColumnClass(int columnIndex) {
return types [columnIndex];
}
});
jSPTabel.setViewportView(jTabcheckbox);
if (jTabcheckbox.getColumnModel().getColumnCount() > 0) {
jTabcheckbox.getColumnModel().getColumn(0).setMinWidth(30);
jTabcheckbox.getColumnModel().getColumn(0).setPreferredWidth(60);
jTabcheckbox.getColumnModel().getColumn(0).setMaxWidth(200);
jTabcheckbox.getColumnModel().getColumn(1).setMinWidth(30);
jTabcheckbox.getColumnModel().getColumn(1).setPreferredWidth(50);
jTabcheckbox.getColumnModel().getColumn(1).setMaxWidth(200);
jTabcheckbox.getColumnModel().getColumn(3).setMinWidth(30);
jTabcheckbox.getColumnModel().getColumn(3).setPreferredWidth(30);
}
jBOK.setText("OK");
jTextArea1.setColumns(20);
jTextArea1.setRows(5);
jSPArea.setViewportView(jTextArea1);
jBDath.setText("Dath");
jBClear.setText("Clear");
jBDelete.setText("Delete");
jSPTree.setViewportView(jTree);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGap(39, 39, 39)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addComponent(jBAllNot, javax.swing.GroupLayout.PREFERRED_SIZE, 68, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jBAll, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addGap(18, 18, 18)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addComponent(jBDelete, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(jBClear, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 66, Short.MAX_VALUE)
.addComponent(jSPArea, javax.swing.GroupLayout.PREFERRED_SIZE, 428, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jBDath, javax.swing.GroupLayout.PREFERRED_SIZE, 69, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(26, 26, 26))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addGap(162, 162, 162)
.addComponent(jBOK, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGap(169, 169, 169))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addComponent(jSPTabel, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jSPTree)
.addContainerGap())
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(jSPArea, javax.swing.GroupLayout.PREFERRED_SIZE, 63, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGroup(layout.createSequentialGroup()
.addContainerGap()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jBAll)
.addComponent(jBClear))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jBAllNot)
.addComponent(jBDelete)))
.addComponent(jBDath))
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addComponent(jSPTabel, javax.swing.GroupLayout.DEFAULT_SIZE, 437, Short.MAX_VALUE)
.addGap(3, 3, 3))
.addGroup(layout.createSequentialGroup()
.addGap(6, 6, 6)
.addComponent(jSPTree)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)))
.addComponent(jBOK)
.addGap(6, 6, 6))
);
pack();
}// </editor-fold>//GEN-END:initComponents
/**
* @param args the command line arguments
*/
public static void main(String args[]) {
/* Set the Nimbus look and feel */
// <editor-fold defaultstate="collapsed" desc=" Look and feel setting code
// (optional) ">
/*
* If Nimbus (introduced in Java SE 6) is not available, stay with the default
* look and feel. For details see
* http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html
*/
try {
for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
if ("Nimbus".equals(info.getName())) {
javax.swing.UIManager.setLookAndFeel(info.getClassName());
break;
}
}
} catch (ClassNotFoundException ex) {
java.util.logging.Logger.getLogger(CheckboxSwing.class.getName()).log(java.util.logging.Level.SEVERE, null,
ex);
} catch (InstantiationException ex) {
java.util.logging.Logger.getLogger(CheckboxSwing.class.getName()).log(java.util.logging.Level.SEVERE, null,
ex);
} catch (IllegalAccessException ex) {
java.util.logging.Logger.getLogger(CheckboxSwing.class.getName()).log(java.util.logging.Level.SEVERE, null,
ex);
} catch (javax.swing.UnsupportedLookAndFeelException ex) {
java.util.logging.Logger.getLogger(CheckboxSwing.class.getName()).log(java.util.logging.Level.SEVERE, null,
ex);
}
// </editor-fold>
/* Create and display the form */
java.awt.EventQueue.invokeLater(new Runnable() {
public void run() {
try {
new CheckboxSwing().setVisible(true);
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
});
}
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JButton jBAll;
private javax.swing.JButton jBAllNot;
private javax.swing.JButton jBClear;
private javax.swing.JButton jBDath;
private javax.swing.JButton jBDelete;
private javax.swing.JButton jBOK;
private javax.swing.JScrollPane jSPArea;
private javax.swing.JScrollPane jSPTabel;
private javax.swing.JScrollPane jSPTree;
private javax.swing.JTable jTabcheckbox;
private javax.swing.JTextArea jTextArea1;
private javax.swing.JTree jTree;
// End of variables declaration//GEN-END:variables
}
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.IOException;
import javax.swing.table.DefaultTableModel;
import javax.swing.text.BadLocationException;
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
/**
*
* @author Highgo
*/
public class NewJDialog extends javax.swing.JDialog {
/**
*
*/
private static final long serialVersionUID = 1L;
private boolean compbl;
// private String RESULT_FILE_PATH = "src/result.txt";
private String[] path;
private String comppath;
private String resultpath;
public NewJDialog(java.awt.Frame parent, boolean modal, String[] mojdlogName, String[] mojdlogPath, String comp_path, String result_path) {
super(parent, modal);
initComponents();
path = mojdlogPath;
comppath = comp_path;
resultpath = result_path;
String file_path = null;
DefaultTableModel model = (DefaultTableModel) jTable1.getModel();
for(int i = 0 ; i < mojdlogName.length; i++) {
if(mojdlogName[i] != null) {
file_path = mojdlogPath[i];
compare(file_path,comp_path);
model.addRow(new Object[] { model.getRowCount() + 1 ,mojdlogName[i], compbl});
}
}
// System.out.println(path);
initAction();
this.setTitle("NewjDialog");
this.setLocationRelativeTo(null);
this.setVisible(true);
}
private void compare(String file_path,String comp_path) {
try {
BufferedReader br = new BufferedReader(new FileReader(file_path));
BufferedReader cbr = new BufferedReader(new FileReader(comp_path));
compbl = false;
String brStr = null;
String cbrStr = null;
while((brStr = br.readLine()) != null && (cbrStr = cbr.readLine()) != null) {
if (brStr.equals(cbrStr)) {
compbl = true;
} else {
compbl = false;
break;
}
}
if(compbl = true) {
while ((cbrStr = cbr.readLine()) != null)
{
compbl = false;
}
while((brStr = br.readLine()) != null )
{
compbl = false;
}
}
try {
br.close();
cbr.close();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
private void initAction() {
DefaultTableModel model = (DefaultTableModel) jTable1.getModel();
jTable1.addMouseListener(new MouseAdapter() {
@Override
public void mouseClicked(MouseEvent e) {
int clickCount = e.getClickCount();
if ( clickCount == 2 ) {
int numac = jTable1.getSelectedRow();
System.out.println(numac);
if (model.getValueAt(numac, 2).equals(false)) {
String file_name = (String)model.getValueAt(numac, 1);
new JDiaComp( null, true, numac, path,comppath,resultpath,file_name);
}
}
}
});
}
/**
* This method is called from within the constructor to initialize the form.
* WARNING: Do NOT modify this code. The content of this method is always
* regenerated by the Form Editor.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
jScrollPane1 = new javax.swing.JScrollPane();
jTable1 = new javax.swing.JTable();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
jTable1.setModel(new javax.swing.table.DefaultTableModel(
new Object [][] {
},
new String [] {
"Line", "Name", "Boolean"
}
) {
boolean[] canEdit = new boolean [] {
false, false, false
};
public boolean isCellEditable(int rowIndex, int columnIndex) {
return canEdit [columnIndex];
}
});
jScrollPane1.setViewportView(jTable1);
if (jTable1.getColumnModel().getColumnCount() > 0) {
jTable1.getColumnModel().getColumn(0).setMinWidth(30);
jTable1.getColumnModel().getColumn(0).setPreferredWidth(60);
jTable1.getColumnModel().getColumn(0).setMaxWidth(150);
}
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addContainerGap()
.addComponent(jScrollPane1)
.addContainerGap())
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addContainerGap()
.addComponent(jScrollPane1)
.addContainerGap())
);
pack();
}// </editor-fold>//GEN-END:initComponents
/**
* @param args the command line arguments
*/
public static void main(String args[]) {
/* Set the Nimbus look and feel */
//<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
/* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
* For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html
*/
try {
for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
if ("Nimbus".equals(info.getName())) {
javax.swing.UIManager.setLookAndFeel(info.getClassName());
break;
}
}
} catch (ClassNotFoundException ex) {
java.util.logging.Logger.getLogger(NewJDialog.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (InstantiationException ex) {
java.util.logging.Logger.getLogger(NewJDialog.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (IllegalAccessException ex) {
java.util.logging.Logger.getLogger(NewJDialog.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (javax.swing.UnsupportedLookAndFeelException ex) {
java.util.logging.Logger.getLogger(NewJDialog.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
}
//</editor-fold>
/* Create and display the dialog */
java.awt.EventQueue.invokeLater(new Runnable() {
public void run() {
NewJDialog dialog = new NewJDialog(new javax.swing.JFrame(), true, null,null,null,null);
dialog.addWindowListener(new java.awt.event.WindowAdapter() {
@Override
public void windowClosing(java.awt.event.WindowEvent e) {
System.exit(0);
}
});
dialog.setVisible(true);
}
});
}
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JScrollPane jScrollPane1;
private javax.swing.JTable jTable1;
// End of variables declaration//GEN-END:variables
}
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
import com.highgo.Test.*;
import java.awt.Color;
import java.awt.HeadlessException;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import javax.swing.text.AttributeSet;
import javax.swing.text.BadLocationException;
import javax.swing.text.Document;
import javax.swing.text.SimpleAttributeSet;
import javax.swing.text.StyleConstants;
/**
*
* @author Highgo
*/
public class JDiaComp extends javax.swing.JDialog {
/**
* Creates new form JDiaComp
*
*
*/
public JDiaComp(java.awt.Frame parent, boolean modal, int num,Object[] Path,String comppath,String resultpath,String file_name) {
super(parent, modal);
initComponents();
//compare(filepath,comppath,resultpath,num);
String result = resultpath + "//result_" + (num + 1) + file_name+ ".txt";
compareDNA(num, Path, comppath, result);
this.setTitle("JDiaComp");
this.setLocationRelativeTo(null);
this.setVisible(true);
}
private void compareDNA(int num,Object[] Path,String comppath,String resultpath) {
String filepath ;
String dnas1,dnas2;
filepath = (String) Path[num];
//String result = resultpath + "//result_" + (num + 1) + file_name+ ".txt";
try {
BufferedWriter rbw = new BufferedWriter(new FileWriter(resultpath));
new Read_File(filepath);
String File1= Read_File.getFile();
new Read_File(comppath);
String File2= Read_File.getFile();
DNASequence dna = new DNASequence(File1,File2);
dna.runAnalysis();
dna.traceback();
dnas1=dna.getString1();//获取处理后的字符串
dnas2=dna.getString2();
Document docs1=jTextPane1.getDocument();
Document docs2=jTextPane2.getDocument();
char[] s = dnas1.toCharArray();//字符串转Char数组
char[] p = dnas2.toCharArray();
int len=dnas1.length();
SimpleAttributeSet set2 = new SimpleAttributeSet();//设置一个属性
StyleConstants.setFontSize(set2,16);//设置字号
for(int i=0;i<len;i++){
if(s[i]=='~'){
StyleConstants.setForeground(set2,Color.BLUE);//设置文字颜色
docs2.insertString(docs2.getLength(),String.valueOf(p[i]), set2);
}else if(p[i]=='~'){
StyleConstants.setForeground(set2,Color.BLUE);//设置文字颜色
docs1.insertString(docs1.getLength(),String.valueOf(s[i]), set2);
}else if(s[i]==p[i]){
StyleConstants.setForeground(set2,Color.black);//设置文字颜色
docs1.insertString(docs1.getLength(),String.valueOf(s[i]), set2);
docs2.insertString(docs2.getLength(),String.valueOf(p[i]), set2);
}else if(s[i]!=p[i]){
StyleConstants.setForeground(set2,Color.red);//设置文字颜色
docs1.insertString(docs1.getLength(),String.valueOf(s[i]), set2);
docs2.insertString(docs2.getLength(),String.valueOf(p[i]), set2);
}else{
System.out.print("考虑更多颜色");
}
}
rbw.write(dnas1 + "\r\n" + dnas2);
rbw.close();
//jTextPane1.setText(dnas1);
// jTextPane2.setText(dnas2);
} catch (IOException | BadLocationException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
private void compare(String file_path, String comp_path,String result_path,int num) {
try {
String result = result_path + "//result_" + (num + 1) + ".txt";
BufferedReader br = new BufferedReader(new FileReader(file_path));
BufferedReader cbr = new BufferedReader(new FileReader(comp_path));
BufferedWriter rbw = new BufferedWriter(new FileWriter(result));
try {
int lineNum = 0;
String lineStr = null;
String TlineStr = null;
String brStr = null;
String cbrStr = null;
while((brStr = br.readLine()) != null &&(cbrStr = cbr.readLine()) != null)
{
lineNum++;
if (brStr.equals(cbrStr)) {
lineStr = brStr + "\n";
setDocs(brStr, Color.black,true,13);
rbw.write(" EQUAL Line " + lineNum + " : " + lineStr);
} else
{
lineStr = brStr + "\n";
//jTextPane1.setText(jTextPane1.getText() + lineStr);
setDocs(brStr, Color.red,true,13);
rbw.write("NOT EQUAL Line " + lineNum + " : " + lineStr);
}
TlineStr = cbrStr + "\n";
// jTextPane2.setText(jTextPane2.getText() + TlineStr);
setDocs2(cbrStr, Color.black,true,13);
}
while ((cbrStr = cbr.readLine()) != null )
{
lineStr = cbrStr + "\n";
// jTextPane2.setText(jTextPane2.getText() + lineStr);
// jTextPane1.setText(jTextPane1.getText() + " NULL " + "\n");
setDocs(" NULL ", Color.black,true,13);
setDocs2(cbrStr, Color.black,true,13);
lineNum++;
rbw.write("br NULL Line: " + lineNum + "\n");
}
while ((brStr = br.readLine()) != null )
{
lineStr = brStr + "\n";
// jTextPane1.setText(jTextPane1.getText() + lineStr);
// jTextPane2.setText(jTextPane2.getText() + " NULL " + "\n");
setDocs(brStr, Color.black,true,13);
setDocs2(" NULL ", Color.black,true,13);
lineNum++;
rbw.write("Cbr NULL Line: " + lineNum + "\n");
}
} catch (Exception e) {
e.printStackTrace();
} finally {
br.close();
cbr.close();
rbw.close();
}
} catch (IOException e) {
e.printStackTrace();
}
}
private void insert(String str, AttributeSet attrSet) {
Document doc = jTextPane1.getDocument();
str = "\n " + str;
try {
doc.insertString(doc.getLength(), str, attrSet);
}
catch (BadLocationException e) {
System.out.println( "BadLocationException: " + e);
}
}
private void setDocs(String str,Color col,boolean bold,int fontSize) {
SimpleAttributeSet attrSet = new SimpleAttributeSet();
StyleConstants.setForeground(attrSet, col);
if(bold==true){
StyleConstants.setBold(attrSet, true);
}
StyleConstants.setFontSize(attrSet, fontSize);
insert(str, attrSet);
}
private void insert2(String str, AttributeSet attrSet) {
Document doc = jTextPane2.getDocument();
str = "\n " + str;
try {
doc.insertString(doc.getLength(), str, attrSet);
}
catch (BadLocationException e) {
System.out.println( "BadLocationException: " + e);
}
}
private void setDocs2(String str,Color col,boolean bold,int fontSize) {
SimpleAttributeSet attrSet = new SimpleAttributeSet();
StyleConstants.setForeground(attrSet, col);
if(bold==true){
StyleConstants.setBold(attrSet, true);
}
StyleConstants.setFontSize(attrSet, fontSize);
insert2(str, attrSet);
}
/**
* This method is called from within the constructor to initialize the form.
* WARNING: Do NOT modify this code. The content of this method is always
* regenerated by the Form Editor.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
jScrollPane1 = new javax.swing.JScrollPane();
jTextPane1 = new javax.swing.JTextPane();
jScrollPane3 = new javax.swing.JScrollPane();
jTextPane2 = new javax.swing.JTextPane();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
jScrollPane1.setViewportView(jTextPane1);
jScrollPane3.setViewportView(jTextPane2);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addComponent(jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 249, Short.MAX_VALUE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(jScrollPane3, javax.swing.GroupLayout.DEFAULT_SIZE, 245, Short.MAX_VALUE)
.addContainerGap())
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(jScrollPane3)
.addComponent(jScrollPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 376, Short.MAX_VALUE))
.addContainerGap())
);
pack();
}// </editor-fold>//GEN-END:initComponents
/**
* @param args the command line arguments
*/
public static void main(String args[]) {
/* Set the Nimbus look and feel */
//<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
/* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
* For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html
*/
try {
for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
if ("Nimbus".equals(info.getName())) {
javax.swing.UIManager.setLookAndFeel(info.getClassName());
break;
}
}
} catch (ClassNotFoundException ex) {
java.util.logging.Logger.getLogger(JDiaComp.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (InstantiationException ex) {
java.util.logging.Logger.getLogger(JDiaComp.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (IllegalAccessException ex) {
java.util.logging.Logger.getLogger(JDiaComp.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
} catch (javax.swing.UnsupportedLookAndFeelException ex) {
java.util.logging.Logger.getLogger(JDiaComp.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
}
//</editor-fold>
/* Create and display the dialog */
java.awt.EventQueue.invokeLater(new Runnable() {
public void run() {
JDiaComp dialog;
try {
dialog = new JDiaComp(new javax.swing.JFrame(), true, 0, null,null,null,null);
dialog.addWindowListener(new java.awt.event.WindowAdapter() {
@Override
public void windowClosing(java.awt.event.WindowEvent e) {
System.exit(0);
}
});
dialog.setVisible(true);
} catch (HeadlessException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
}
});
}
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JScrollPane jScrollPane1;
private javax.swing.JScrollPane jScrollPane3;
private javax.swing.JTextPane jTextPane1;
private javax.swing.JTextPane jTextPane2;
// End of variables declaration//GEN-END:variables
}
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.InputStreamReader;
public class Read_File {
static String fileName;
public Read_File(String str){
fileName=str;
}
public static String getFile(){
BufferedReader br = null;
StringBuffer sb = null;
try {
br = new BufferedReader(new InputStreamReader(new FileInputStream(fileName),"utf-8")); //这里可以控制编码
sb = new StringBuffer();
String line = null;
while((line = br.readLine()) != null) {
sb.append(line + "\r\n");
}
} catch (Exception e) {
e.printStackTrace();
} finally {
try {
br.close();
} catch (Exception e) {
e.printStackTrace();
}
}
String data = new String(sb); //StringBuffer ==> String
System.out.println("数据为==> " + data);
return data;
}
// public static void main(String[] args) {
// new Read_File("1");
// }
}
//https://codereview.stackexchange.com/questions/182601/optimizing-needleman-wunsch-algorithm-in-java
public class DNASequence {
protected final String seq_1, seq_2; //要分析的两个序列
public int alignmentScore; //使用Needleman-Wunsch算法
protected Node[][] matrix; //存储分数和缩进
protected final int matchScore, mismatchScore, indel;
//用于打印DNA序列分析的字符串
String top = ""; // Sequence 1
String bottom = ""; // Sequence 2
public DNASequence(String s1, String s2) {
//我使用一个■作为缓冲,这样序列字符串正确对齐
// 在矩阵中使用缩进和分数。
ScoreScheme s = new ScoreScheme(2, -1, -2);
seq_1 = "\u25A0" + s1;
seq_2 = "\u25A0" + s2;
matchScore = s.matchScore;
mismatchScore = s.mismatchScore;
indel = s.indel;
matrix = new Node[seq_1.length()][seq_2.length()];
for (int i = 0; i < seq_1.length(); i++)
matrix[i][0] = new Node(i * indel, i, 0);
for (int i = 0; i < seq_2.length(); i++)
matrix[0][i] = new Node(i * indel, 0, i);
}
//辅助方法，帮助决定使用哪种匹配/不匹配得分。
protected int score(int i, int j) {
if (seq_1.charAt(i) == seq_2.charAt(j))
return matchScore;
else
return mismatchScore;
}
//在本地级别上实现Needleman-Wunsch algo的Helper方法。
protected Node match(int i, int j) {
Node s1,s2,s3;
s1 = new Node(matrix[i-1][j-1].score + score(i, j), i, j);
s2 = new Node(matrix[i-1][j].score + indel, i, j);
s3 = new Node(matrix[i][j-1].score + indel, i, j);
Node largest = new Node(Math.max(s1.score, Math.max(s2.score, s3.score)), i, j);
if (s1.compareTo(largest) == 0)
largest.prev = matrix[i-1][j-1];
else if(s2.compareTo(largest) == 0)
largest.prev = matrix[i-1][j];
else
largest.prev = matrix[i][j-1];
return largest;
}
public Node runAnalysis() {
for (int i = 1; i < seq_1.length(); i++) {
for (int j = 1; j < seq_2.length(); j++){
matrix[i][j] = match(i, j);
}
}
alignmentScore = matrix[seq_1.length()-1][seq_2.length()-1].score;
return matrix[seq_1.length()-1][seq_2.length()-1];
}
//辅助方法，逐步构建分析结果。它将返回
//“尾巴”，因为我们可能还需要做一些工作。
protected Node traceHelper(Node curr) {
while (curr.prev != null) {
if (curr.i - curr.prev.i == 1 && curr.j - curr.prev.j == 1){ // If the path leads diagonal
boolean x = seq_1.charAt(curr.i) == seq_2.charAt(curr.j) ? true : false;
if(x){
top = seq_1.charAt(curr.i) +top;
bottom = seq_2.charAt(curr.j) +bottom;
}else{
top = seq_1.charAt(curr.i) + top;
bottom = seq_2.charAt(curr.j) + bottom;
}
}else if (curr.i - curr.prev.i == 1){ //如果这条路通向山顶
top = seq_1.charAt(curr.i) + top;
bottom = "~" + bottom; //如果这条路通向左边
}else if (curr.j - curr.prev.j == 1){
top = " " + top;
bottom = seq_2.charAt(curr.j) + bottom;
}
curr = curr.prev;
}
return curr;
}
//从矩阵的最后一个节点回溯到第一个索引节点。
public void traceback() {
Node curr = matrix[seq_1.length()-1][seq_2.length()-1];
curr = traceHelper(curr);
while (curr.i != 0 || curr.j != 0) {
if (curr.i != 0 && curr.j == 0){
curr.prev = matrix[curr.i-1][curr.j];
curr = traceHelper(curr);
}else if (curr.i == 0 && curr.j != 0) {
curr.prev = matrix[curr.i][curr.j-1];
curr = traceHelper(curr);
}
}
//打印DNA序列分析
System.out.println(top);
System.out.println(bottom);
}
public String getString1(){
return top;
}
public String getString2(){
return bottom;
}
}
class Node implements Comparable<Node>{
int i, j;
int score;
Node prev;
public Node(int score, int x, int y) {
this.i = x;
this.j = y;
this.score = score;
this.prev = null;
}
public int compareTo(Node n) {
return this.score - n.score;
}
public String toString() {
return ""+score;
}
}
class ScoreScheme {
int matchScore, mismatchScore, indel;
public ScoreScheme(int m1, int m2, int i) {
matchScore = m1;
mismatchScore = m2;
indel = i;
}
}<?xml version="1.0" encoding="UTF-8"?>
<companys>
<company id="1001">
<name>D:\\测试目录</name>
</company>
<company id="1002">
<name>../File101.txt</name>
</company>
<company id="1003">
<name>../result101</name>
</company>
</companys>
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