newick.ypp

ncbi源码

%{
/*  $Id: newick.ypp,v 1000.1 2004/06/01 18:09:36 gouriano Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Authors:  Josh Cherry
 *
 * File Description:  bison parser for Newick format phylogenetic trees
 *
 */


/*
 * Meant to be used in conjunction with flex lexer defined
 * by newick.lpp.  Generate code using (essentially)
 *   flex -olex.newick.cpp newick.lpp
 *   bison -d -p newick newick.ypp
 * The line '#include <unistd.h>' must be removed from the flex-generated
 * code for it to compile on some platforms.
 */


#include <ncbi_pch.hpp>
#include <algo/phy_tree/phy_node.hpp>
USING_SCOPE(ncbi);
static int nodecount = 0;
static TPhyTreeNode *g_Tree = 0;
void yyerror(const char *error);
int yylex(void);
CNcbiIstream *g_NewickIstr;
// a list of all allocated nodes so they can be deleted on error
vector<TPhyTreeNode*> g_NodeList;
%}

%union {
    char *strval;
    double dblval;
    TPhyTreeNode *nodeval;
}

%token <strval> LABEL
%token <dblval> NUM
%type  <nodeval> node
%type  <nodeval> nodelist

%%


tree:	node ';' { 
    g_Tree = $1;
}
;


node:	'(' nodelist ')' ':' NUM { 
    $$ = $2;
    $$->GetValue().SetDist($5);
    $$->GetValue().SetId(nodecount);
    nodecount++; 
}

|  '(' nodelist ')' { 
    $$ = $2;
    $$->GetValue().SetId(nodecount);
    nodecount++; 
}

|	LABEL	':' NUM		{ 
    $$ = new TPhyTreeNode;
    $$->GetValue().SetLabel($1);
    $$->GetValue().SetDist($3);
    $$->GetValue().SetId(nodecount);
    nodecount++; 
}

|	LABEL			{ 
    $$ = new TPhyTreeNode;
    $$->GetValue().SetLabel($1);
    $$->GetValue().SetId(nodecount);
    nodecount++; 
}
;


nodelist:  node {
    $$ = new TPhyTreeNode;
    $$->AddNode($1);
}

| nodelist ',' node {
    $$ = $1;
    $$->AddNode($3);
}
;


%%

void yyerror(const char *s)
{
    if (g_Tree) {
        delete g_Tree;
    } else {
        // delete only those nodes that are nobody's children
        vector<TPhyTreeNode*> del_list;
        ITERATE (vector<TPhyTreeNode*>, iter, g_NodeList) {
            if (!(*iter)->GetParent()) {
                del_list.push_back(*iter);
            }
        }
        ITERATE (vector<TPhyTreeNode*>, iter, del_list) {
            delete *iter;
        }
    }
    g_NodeList.clear();
    throw runtime_error(string("error parsing Newick format tree file:  ")
                        + s);
}

void newick_flex_reset(void);

BEGIN_NCBI_SCOPE

TPhyTreeNode *ReadNewickTree(CNcbiIstream& is)
{
    g_NewickIstr = &is;
    g_Tree = 0;
    g_NodeList.clear();
    newick_flex_reset();
    yyparse();
    if (!g_Tree) {
        yyerror("unknown");
    }
    g_NodeList.clear();
    return g_Tree;
}

END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: newick.ypp,v $
 * Revision 1000.1  2004/06/01 18:09:36  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
 *
 * Revision 1.2  2004/05/25 14:42:45  jcherry
 * #include <ncbi_pch.hpp>
 *
 * Revision 1.1  2004/02/11 17:40:56  jcherry
 * Initial version
 *
 * ===========================================================================
 */