tree.h

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#ifndef __TREE_H__
#define __TREE_H__

#include<utils.h>
#include<stdarg.h>
#include<utils_string.h>

typedef struct tagTree* pTree;
typedef struct tagTreeNode* pTreeNode;

typedef struct tagTree
{
    pTreeNode    root;
    void*        data;
    int          size;
    int*         count;
    pArrayList   nlist;
    pArrayList   postfix, prefix;
}Tree;

typedef struct tagTreeNode 
{
    pTreeNode   parent;
    pVector     children;
    int         reg;
    int         id;
}TreeNode;

/****************************************************************************
 * Tree
****************************************************************************/

typedef pTreeNode (*tree_func_node_new)(pTree ptree);
typedef pTree (*tree_func_new)(tree_func_node_new nfunc, int size);
typedef void (*tree_func_node)(pTree ptree, pTreeNode pnode, va_list ap);
typedef void (*tree_func_node_copy)(pTreeNode psrc, pTreeNode pdest );

extern pTree tree_new(tree_func_node_new nfunc, int size);
extern void tree_new_fill(pTree ptree, tree_func_node_new nfunc ) ;
extern void tree_free(pTree ptree);
extern pTreeNode tree_new_empty_node();
extern int tree_is_leaf(pTreeNode pnode);
extern int tree_is_root(pTree ptree, pTreeNode pnode);
extern void tree_add_child_to_node(pTreeNode parent, pTreeNode child);
extern void tree_traveral_prefix(pTree ptree, tree_func_node func, ...);
extern void tree_traveral_postfix(pTree ptree, tree_func_node func, ...);
extern void tree_traveral_infix(pTree ptree, tree_func_node func, ... );
extern void tree_clear_reg(pTree ptree);
extern void* tree_get_child(pTreeNode ptnode, int idx);
extern pTree tree_copy(pTree psrc, tree_func_node_new new_node_func, tree_func_node_copy copy);
extern void tree_build_node_list(pTree ptree);

typedef enum
{
    PHYLOGENY_SPECIATION_NOT_DECIDED = 0,
    PHYLOGENY_SPECIATION_DUPLICATED,
    PHYLOGENY_SPECIATION_SPECIES 
}enumPhylogeny_speciation ;

typedef struct tagPhylogenyNode* pPhylogenyNode;
typedef struct tagPhylogenyNode
{
    TreeNode super;
    char*   name;   
    double  branchlength;
    char*   species;
    char*   gene;
    int     duplicated;
    int     bootstrap;
    int     taxaid;
}PhylogenyNode;

/****************************************************************************
 * Phylogeny
****************************************************************************/

typedef void (*phylogeny_func_parse_node)(pTree ptree, pTreeNode pnode);
typedef void (*phylogeny_func_name_modify)(pString str, pPhylogenyNode pnode);

extern pTree phylogeny_split_tree(pTree ptree, int idx, tree_func_node freenode );
extern pString phylogeny_string(pTree ptree, phylogeny_func_name_modify fmod);
extern void phylogeny_node_copy(pTreeNode psrc, pTreeNode pdest );
extern pTree phylogeny_load_from_string(char* sztree, 
                                 tree_func_new new_tree_func, 
                                 tree_func_node_new new_tree_node_func, 
                                 phylogeny_func_parse_node parsefunc, int size);
extern pTree phylogeny_root_tree(pTree ptree, 
                            tree_func_node_new new_tree_node_func, 
                            phylogeny_func_parse_node parsefunc, ... );
extern pTree phylogeny_load_from_file(char* sztree, 
                                 tree_func_new new_tree_func, 
                                 tree_func_node_new new_tree_node_func, 
                                 phylogeny_func_parse_node parsefunc );
extern void phylogeny_free(pTree ptree);

extern pTreeNode phylogeny_new_empty_node(pTree ptree);
extern void phylogeny_clear_node(pPhylogenyNode pnode);
extern pTree phylogeny_copy(pTree psrc);
extern pTree phylogeny_new(char* sztree, phylogeny_func_parse_node parsefunc );
extern int phylogeny_delete_nodes_by_index(pTree ptree, int idx, tree_func_node freenode );
extern int phylogeny_delete_nodes_by_reg(pTree ptree, tree_func_node freenode );
extern int phylogeny_delete_nodes_by_func(pTree ptree, tree_func_node filter ,tree_func_node freenode );
extern pTreeNode phylogeny_get_sibling(pTree ptree, pTreeNode ptnode );

extern pString phylogeny_string_nhx(pTree ptree, phylogeny_func_name_modify fmod, int opts);
extern pString phylogeny_string_newick(pTree ptree, phylogeny_func_name_modify fmod, int opts);


#define PS_SKIP_BL  0x1000
#define PS_NWICK    0x0000
#define PS_NHX      0x0FFE

/****************************************************************************
 * MetaPhost Config
****************************************************************************/
typedef enum
{
    MP_UNIT_IN = 0,
    MP_UNIT_MM, 
    MP_UNIT_CM
}tagMPUnitList;

typedef enum
{
    MP_DIR_HORIZONTAL = 0,
    MP_DIR_VERTICAL 
}tagMPDirectionList;

typedef enum
{
    MP_SHAPE_RECT = 1,
    MP_SHAPE_TRI = 2,
    MP_SHAPE_MASK = 3,
    MP_SHAPE_MOST_CENTER = 4,
    MP_SHAPE_LEAST_CENTER = 8,
}tagMPShapeList;

typedef struct tagMetapostConfig* pMetapostConfig;
typedef double (*metapost_remark)(pString str, pTree ptree, pMetapostConfig  pmc, va_list ap);
typedef double (*metapost_annotation_func)(pString str, pTreeNode pnode, pMetapostConfig pmc, va_list ap);

typedef struct tagMetapostConfig
{
    int id;
    int unit;
    int dir;
    int shape;
    metapost_remark fremark;
    metapost_annotation_func fmod;
    double width, height;
}MetapostConfig;


pString phylogeny_to_mp(pTree ptree, pMetapostConfig pmc, ... );

#define TREE_DEBUG 1

#endif