nexus.java

生物物种进化历程的演示

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

/** 
 * A static class used for parsing a Nexus format file containing multiple trees.
 * Given a Nexus tree file and an index number, the parser will find the corresponding 
 * tree with the given index number and initiate a tree object for it. 
 * @author Yunhong Zhou
 */

public class Nexus implements NexusConstants {

  /** the target tree to be initiated by the 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;

  /** the index of the tree to be initiated from the collection of trees in the nexus file */
  private static int index;

  /** flag is true if the parser is visiting the target tree */
  private static boolean flag;

  private static int cnt;

  /** 
   * transflag is true if the nexus file has a translation header. 
   * If transflag is true, then we need to translate the leaf label to its real name.
   */
  private static boolean transflag = false;

  /** the hashtable ht_trans stores entries for label translation process */
  private static Hashtable ht_trans;

  /** 
   * function parseTree initiates field tree, call function Input to parse the input.
   * @param t Tree t will be initiated throught the parsing process 
   * @param index The index of the tree to be initiated from parsing 
   * @author Yunhong Zhou
   */
  public void parseTree(Tree t, int index) {
    tree = t;
    this.index = index;
    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();
    }
  }

  static final public void Input() throws ParseException {
  cnt = 0;
    label_1:
    while (true) {
      if (jj_2_1(2)) {
        jj_consume_token(token_tree);
        tree_newick();
      } else if (jj_2_2(2)) {
        jj_consume_token(translate);
        trans_statement();
      } else if (jj_2_3(2)) {
        jj_consume_token(unquoted_string);
        other_statement();
      } else {
        jj_consume_token(-1);
        throw new ParseException();
      }
      if (jj_2_4(2)) {
        ;
      } else {
        break label_1;
      }
    }
    jj_consume_token(0);
  }

  static final public void other_statement() throws ParseException {
    label_2:
    while (true) {
      if (jj_2_5(2)) {
        ;
      } else {
        break label_2;
      }
      if (jj_2_6(2)) {
        jj_consume_token(unquoted_string);
      } else if (jj_2_7(2)) {
        jj_consume_token(quoted_string);
      } else if (jj_2_8(2)) {
        jj_consume_token(double_number);
      } else if (jj_2_9(2)) {
        jj_consume_token(token_tree);
      } else if (jj_2_10(2)) {
        jj_consume_token(equal);
      } else if (jj_2_11(2)) {
        jj_consume_token(lparen);
      } else if (jj_2_12(2)) {
        jj_consume_token(rparen);
      } else if (jj_2_13(2)) {
        jj_consume_token(comma);
      } else if (jj_2_14(2)) {
        jj_consume_token(colon);
      } else {
        jj_consume_token(-1);
        throw new ParseException();
      }
    }
    jj_consume_token(semicolon);
  }

/** 
 * function trans_statement generates a hash table for label translation
 */
  static final public void trans_statement() throws ParseException {
  String s_key, s_value;
  transflag = true;
  ht_trans = new Hashtable();
  Hashtable ht_values = new Hashtable();
    label_3:
    while (true) {
      s_key = label_text();
      s_value = label_text();
      if (jj_2_15(2)) {
        jj_consume_token(comma);
      } else {
        ;
      }
      String prev_key = (String)(ht_values.get(s_value));
      if(prev_key != null){
        StringBuffer sb = new StringBuffer(s_value);
        sb.append(" ").append(s_key);
        ht_trans.put(s_key, sb.toString());

        if(!prev_key.equals("-1")){
          sb = new StringBuffer(s_value);
          sb.append(" ").append(prev_key);
          ht_trans.put(prev_key, sb.toString());
          ht_values.put(s_value, "-1");
        }

      }else{
        ht_trans.put(s_key, s_value);
        ht_values.put(s_value, s_key);
      }
      if (jj_2_16(2)) {
        ;
      } else {
        break label_3;
      }
    }
    jj_consume_token(semicolon);
    ht_values = null;
  }

/** this function is responsible for parsing one tree */
  static final public void tree_newick() throws ParseException {
  String s;
  double len;
    jj_consume_token(unquoted_string);
    jj_consume_token(equal);
    cnt++; flag = (cnt == index)?true:false;
    if(flag)current_node = tree.getRoot();
    descendant_list();
    if (jj_2_17(2)) {
      s = label();
                  if(flag)current_node.setName(s);
                  //System.out.println("Name: " + s);

    } else {
      ;
    }
    if (jj_2_18(2)) {
      jj_consume_token(colon);
      len = branch_length();
                                    if(flag)current_node.setWeight(len);
                                //System.out.println("weight: " + len); 

    } else {
      ;
    }
    jj_consume_token(semicolon);
  }

  static final public void descendant_list() throws ParseException {
    jj_consume_token(lparen);
             if(flag){
        tn = new TreeNode();
        current_node.addChild(tn);
        current_node = tn;
        }
    subtree();
    label_4:
    while (true) {
      if (jj_2_19(2)) {
        ;
      } else {
        break label_4;
      }
      jj_consume_token(comma);
              if(flag){
          tn = new TreeNode();
          current_node.addChild(tn);
          current_node = tn;
          }
      subtree();
    }
    jj_consume_token(rparen);
  }

/** 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_24(2)) {
      descendant_list();

      if (jj_2_20(2)) {
        s = label();
                  if(flag)current_node.setName(s);
                  //System.out.println("Name: " + s); 

      } else {
        ;
      }
      if (jj_2_21(2)) {
        jj_consume_token(colon);
        len = branch_length();
                                    if(flag)current_node.setWeight(len);
                                //System.out.println("Weight: " + len);

      } else {
        ;
      }
         if(flag)current_node = current_node.parent();
    } else {
      if (jj_2_22(2)) {
        s = label();
                  if(flag)current_node.setName(s);
                  //System.out.println("Name: " + s); 

      } else {
        ;
      }
      if (jj_2_23(2)) {
        jj_consume_token(colon);
        len = branch_length();
                                    if(flag)current_node.setWeight(len);
                                //System.out.println("Weight: " + len);

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

/** get the real name for each label, translate if necessary */
  static final public String label() throws ParseException {
  String s, s_trans = null; Token t;
    s = label_text();
                     if(transflag && flag){
                       s_trans = (String)ht_trans.get(s);
                       if(s_trans != null){
                         {if (true) return s_trans;}
                       }else {if (true) return s;}

                     }else {if (true) return s;}
                     // TODO : integer index

    throw new Error("Missing return statement in function");
  }

/** 
 * for each unquoted label, we need to replace '_' by ' '.
 * for each quoted label, we remove double quotes from the string.
 */
  static final public String label_text() throws ParseException {
  String s; Token t;
    if (jj_2_25(2)) {
      t = jj_consume_token(unquoted_string);
                          s = new String(t.toString());
                          {if (true) return s.replace('_', ' ');}
    } else if (jj_2_26(2)) {
      t = jj_consume_token(quoted_string);
                        s = new String(t.toString());
                        {if (true) return s.substring(1, s.length()-1).replaceAll("[\n\r\f]", "");}
    } else if (jj_2_27(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");
  }

  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;
    try { return !jj_3_1(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(0, xla); }
  }

  static final private boolean jj_2_2(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_2(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(1, xla); }
  }

  static final private boolean jj_2_3(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_3(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(2, xla); }
  }

  static final private boolean jj_2_4(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_4(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(3, xla); }
  }

  static final private boolean jj_2_5(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_5(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(4, xla); }
  }

  static final private boolean jj_2_6(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_6(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(5, xla); }
  }

  static final private boolean jj_2_7(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_7(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(6, xla); }
  }

  static final private boolean jj_2_8(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_8(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(7, xla); }
  }

  static final private boolean jj_2_9(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_9(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(8, xla); }
  }

  static final private boolean jj_2_10(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_10(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(9, xla); }
  }

  static final private boolean jj_2_11(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_11(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(10, xla); }
  }

  static final private boolean jj_2_12(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_12(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(11, xla); }
  }

  static final private boolean jj_2_13(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_13(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(12, xla); }
  }

  static final private boolean jj_2_14(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_14(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(13, xla); }
  }

  static final private boolean jj_2_15(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_15(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(14, xla); }
  }

  static final private boolean jj_2_16(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_16(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(15, xla); }
  }

  static final private boolean jj_2_17(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_17(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(16, xla); }
  }

  static final private boolean jj_2_18(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_18(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(17, xla); }
  }

  static final private boolean jj_2_19(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_19(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(18, xla); }
  }

  static final private boolean jj_2_20(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_20(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(19, xla); }
  }

  static final private boolean jj_2_21(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_21(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(20, xla); }
  }

  static final private boolean jj_2_22(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_22(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(21, xla); }
  }

  static final private boolean jj_2_23(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_23(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(22, xla); }
  }

  static final private boolean jj_2_24(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_24(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(23, xla); }
  }

  static final private boolean jj_2_25(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_25(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(24, xla); }
  }

  static final private boolean jj_2_26(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_26(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(25, xla); }
  }

  static final private boolean jj_2_27(int xla) {
    jj_la = xla; jj_lastpos = jj_scanpos = token;
    try { return !jj_3_27(); }
    catch(LookaheadSuccess ls) { return true; }
    finally { jj_save(26, xla); }
  }

  static final private boolean jj_3_18() {
    if (jj_scan_token(colon)) return true;
    if (jj_3R_10()) return true;
    return false;
  }

  static final private boolean jj_3_17() {
    if (jj_3R_9()) return true;
    return false;
  }

  static final private boolean jj_3_9() {
    if (jj_scan_token(token_tree)) return true;
    return false;
  }

  static final private boolean jj_3R_10() {
    if (jj_scan_token(double_number)) return true;
    return false;
  }

  static final private boolean jj_3R_5() {
    if (jj_scan_token(unquoted_string)) return true;
    return false;
  }

  static final private boolean jj_3_27() {
    if (jj_scan_token(double_number)) return true;
    return false;
  }

  static final private boolean jj_3_26() {
    if (jj_scan_token(quoted_string)) return true;
    return false;
  }