newick.java

生物物种进化历程的演示

/* Generated By:JavaCC: Do not edit this line. Newick.java */
package Parser;
//import Parse.*;
import AccordionTreeDrawer.Tree;
import AccordionTreeDrawer.TreeNode;

/** 
 * A static class used for parsing a Newick format file containing just one tree 
 * @author Yunhong Zhou, Tamara Munzner
 */

public class Newick implements NewickConstants {

  /** the tree to be generated from this parser */
  private static Tree tree;

  /** the current TreeNode that the parser is visiting and initiating */
  private static TreeNode current_node;

  /** a helper TreeNode field */
  private static TreeNode tn;

  /** 
   * function parseTree initiates field tree, call function Input to parse the input.
   * @param t Tree t will be initiated throught the parsing process 
   * @author Yunhong Zhou
   */
  public void parseTree(Tree t) {
    tree = t;
    try{ Input(); }
    catch( ParseException e ){
        if(t.getName() == null)
          System.out.println("Parsing error with input!");
        else
          System.out.println("Parsing error with input file " + t.getName());
        e.printStackTrace();
    }
  }
  
//  WTF!!?!!?
//  public void close(){
//		tree=null;
//		current_node=null;
//		tn=null;	
//		for (int i = 0; i < jj_2_rtns.length; i++) jj_2_rtns[i] = null;
//		System.out.println("clean Parser");
//	}
//
//	protected void finalize() throws Throwable {
//		 
//				 try {
//					 close();
//				 }
//				 finally {
//					 super.finalize();     
//				 }
//	 }
 

  static final public void Input() throws ParseException {
  String s;
  double len;
    current_node = tree.getRoot();
    descendant_list();
    if (jj_2_1(2)) {
      s = label();
                  current_node.setName(s);
                  //System.out.println("Name: " + s);

    } else {
      ;
    }
    if (jj_2_2(2)) {
      jj_consume_token(7);
      len = branch_length();
                                current_node.setWeight(len);
                                //System.out.println("weight: " + len); 

    } else {
      ;
    }
    jj_consume_token(8);
    jj_consume_token(0);
  }

  static final public void descendant_list() throws ParseException {
    jj_consume_token(9);
        tn = new TreeNode();
        current_node.addChild(tn);
        current_node = tn;
    subtree();
    label_1:
    while (true) {
      if (jj_2_3(2)) {
        ;
      } else {
        break label_1;
      }
      jj_consume_token(10);
          tn = new TreeNode();
          current_node.addChild(tn);
          current_node = tn;
      subtree();
    }
    jj_consume_token(11);
  }

/** function subtree will set name, length and weight for each tree node */
  static final public void subtree() throws ParseException {
  String s;
  double len;
    if (jj_2_8(2)) {
      descendant_list();

      if (jj_2_4(2)) {
        s = label();
                  current_node.setName(s);
                  //System.out.println("Name: " + s); 

      } else {
        ;
      }
      if (jj_2_5(2)) {
        jj_consume_token(7);
        len = branch_length();
                                current_node.setWeight(len);
                                //System.out.println("Weight: " + len);

      } else {
        ;
      }
         current_node = current_node.parent();
    } else {
      if (jj_2_6(2)) {
        s = label();
                  current_node.setName(s);
                  //System.out.println("Name: " + s); 

      } else {
        ;
      }
      if (jj_2_7(2)) {
        jj_consume_token(7);
        len = branch_length();
                                current_node.setWeight(len);
                                //System.out.println("Weight: " + len);

      } else {
        ;
      }
         current_node = current_node.parent();
    }
  }

  static final public String label() throws ParseException {
  String s;
    if (jj_2_9(2)) {
      s = unquoted_label();
                         {if (true) return s;}
    } else if (jj_2_10(2)) {
      s = quoted_label();
                       {if (true) return s;}
    } else {
      jj_consume_token(-1);
      throw new ParseException();
    }
    throw new Error("Missing return statement in function");
  }

/** for each unquoted label, we need to replace '_' by ' ' */
  static final public String unquoted_label() throws ParseException {
  Token t;
    if (jj_2_11(2)) {
      t = jj_consume_token(unquoted_string);
                          String s = new String(t.toString());
                          {if (true) return s.replace('_', ' ');}
    } else if (jj_2_12(2)) {
      t = jj_consume_token(double_number);
                        {if (true) return new String(t.toString());}
    } else {
      jj_consume_token(-1);
      throw new ParseException();
    }
    throw new Error("Missing return statement in function");
  }

/** for each quoted label, we remove double quotes from the string */
  static final public String quoted_label() throws ParseException {
  Token t;
    t = jj_consume_token(quoted_string);
                        String s = new String(t.toString());
                        {if (true) return s.substring(1, s.length()-1);}
    throw new Error("Missing return statement in function");
  }

  static final public double branch_length() throws ParseException {
  Token t;
    t = jj_consume_token(double_number);
                        {if (true) return Double.parseDouble(t.toString());}
    throw new Error("Missing return statement in function");
  }

  static final private boolean jj_2_1(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_1();
    jj_save(0, xla);
    return retval;
  }

  static final private boolean jj_2_2(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_2();
    jj_save(1, xla);
    return retval;
  }

  static final private boolean jj_2_3(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_3();
    jj_save(2, xla);
    return retval;
  }

  static final private boolean jj_2_4(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_4();
    jj_save(3, xla);
    return retval;
  }

  static final private boolean jj_2_5(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_5();
    jj_save(4, xla);
    return retval;
  }

  static final private boolean jj_2_6(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_6();
    jj_save(5, xla);
    return retval;
  }

  static final private boolean jj_2_7(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_7();
    jj_save(6, xla);
    return retval;
  }

  static final private boolean jj_2_8(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_8();
    jj_save(7, xla);
    return retval;
  }

  static final private boolean jj_2_9(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_9();
    jj_save(8, xla);
    return retval;
  }

  static final private boolean jj_2_10(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_10();
    jj_save(9, xla);
    return retval;
  }

  static final private boolean jj_2_11(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_11();
    jj_save(10, xla);
    return retval;
  }

  static final private boolean jj_2_12(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    boolean retval = !jj_3_12();
    jj_save(11, xla);
    return retval;
  }

  static final private boolean jj_3R_7() {
    if (jj_scan_token(quoted_string)) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    return false;
  }

  static final private boolean jj_3_12() {
    if (jj_scan_token(double_number)) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    return false;
  }

  static final private boolean jj_3_3() {
    if (jj_scan_token(10)) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    if (jj_3R_4()) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    return false;
  }

  static final private boolean jj_3_11() {
    if (jj_scan_token(unquoted_string)) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    return false;
  }

  static final private boolean jj_3R_6() {
    Token xsp;
    xsp = jj_scanpos;
    if (jj_3_11()) {
    jj_scanpos = xsp;
    if (jj_3_12()) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    } else if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    return false;
  }

  static final private boolean jj_3R_5() {
    if (jj_scan_token(9)) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    if (jj_3R_4()) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    Token xsp;
    while (true) {
      xsp = jj_scanpos;
      if (jj_3_3()) { jj_scanpos = xsp; break; }
      if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    }
    if (jj_scan_token(11)) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    return false;
  }

  static final private boolean jj_3_10() {
    if (jj_3R_7()) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    return false;
  }

  static final private boolean jj_3_9() {
    if (jj_3R_6()) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    return false;
  }

  static final private boolean jj_3R_2() {
    Token xsp;
    xsp = jj_scanpos;
    if (jj_3_9()) {
    jj_scanpos = xsp;
    if (jj_3_10()) return true;
    if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    } else if (jj_la == 0 && jj_scanpos == jj_lastpos) return false;
    return false;
  }

  static final private boolean jj_3_7() {
    if (jj_scan_token(7)) return true;