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///////////////////////////////////////////////////////////////////////////////////////////////////
// File : PNode.h
// Purpose : Phylogenetic Tree Node
//
// Developer : David Knox (david.knox@colorado.edu) Jan 2011
// Copyright : Copyright (C) 2007-2011 David Knox
//
// Web site : http://parsinsert.sourceforge.net/
//
///////////////////////////////////////////////////////////////////////////////////////////////////
// This file is part of ParsInsert.
//
// ParsInsert is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// ParsInsert is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with ParsInsert. If not, see <http://www.gnu.org/licenses/>.
///////////////////////////////////////////////////////////////////////////////////////////////////
#if !defined(__PNODE_H__)
#define __PNODE_H__
#include "Knox_Stddef.h"
#include "AttrList.h"
#include "ParsimonySet.h"
#include <string>
#include <map>
#include <vector>
using namespace std;
extern LPCSTR globalAttrs[];
extern LPCSTR treeAttrs[];
extern LPCSTR branchAttrs[];
extern LPCSTR branchAttrs2[];
extern LPCSTR applyAttrs[];
///////////////////////////////////////////////////////////////////////////////////////////////////
extern BOOL ValidRegEx(LPCSTR expr);
extern BOOL MatchRegEx(LPCSTR expr, LPCSTR text);
///////////////////////////////////////////////////////////////////////////////////////////////////
///////////////////////////////////////////////////////////////////////////////////////////////////
class CPNode;
class CPTree;
typedef vector<CPNode*> CPNodeList;
typedef vector<CPNode*>::iterator CPNodeListIter;
class CPNode
{
public:
string title; // name of the node
int id; // internal id
CPTree *tree; // tree the node belongs to
CPNode *parent; // parent node of this node
CPNodeList edges; // children
CAttrList attrs; // list of attributes assigned to this node
public:
CPNode(CPTree *ptree, LPCSTR v="");
~CPNode();
void AddEdge(CPNode *other);
CPNode* FindEdgeNode(int e);
void InvertEdges(BOOL recurse=FALSE); // invert the edge list
inline BOOL IsBranchNode() {return (edges.size() > 0); }
BOOL GetComment(LPCSTR attr, string& str, LPCSTR _default=NULL);
void SetAttr(LPCSTR k, string& v);
void SetAttr(LPCSTR k, LPCSTR v);
void AddAttrs(LPCSTR v);
BOOL ReadAttrs(LPCSTR filename);
BOOL WriteAttrs(FILE *f);
BOOL Display(LPCSTR key);
BOOL WriteNode(FILE *f, int indent=0, BOOL includeAttrs=FALSE, BOOL withComment=FALSE);
string& CleanString(string& s, BOOL searchForBootstrap=FALSE);
void ResetParent(CPNode *p);
// traverse the tree setting parent to correct items
// used by tree inversion
int GetAncestors(CPNodeList &list, BOOL fromBottom=TRUE);
// return the ancestors in an ordered list
// fromBottom - if TRUE, inserts each parent at end of list
int GetDecendants(CPNodeList &list, BOOL leafOnly=TRUE);
// return the nodes the decendants
// leafOnly - if TRUE, only add the leaf id's to list
};
///////////////////////////////////////////////////////////////////////////////
typedef BOOL (* ProgressFunction)(LPCSTR msg, int curInProcess, int totalToProcess, PVOID data);
class CPTree
{
public:
string filename; // file tree read from or wriiten to
CPNode *root; // root node of the tree
CAttrList attrs; // list of attributes for tree
int internal; // internal id number for last created node
CPNodeList nodeList; // list of nodes in the tree
/// map<string,CPNode*> nameTable; // lookup table for node names
//
// Variables for parsing
//
LPCSTR buffer; // points to current location in the buffer to get chars
FILE *bufFile; // file to read from
int lineCount; // current position in lines of the file
int colCount; // Current column within the line
char errorReason[2048];
// Status reporting
ProgressFunction Progress;
int totalProcess;
int nProcess;
LPCSTR endParseStr; // str position when parsing complete
//
// Class variables
//
static int PRECISION; // number of decimal points to use when printing
public:
CPTree();
~CPTree();
void ShowError(int codeline, LPCSTR msg);
BOOL WriteNewickTree(LPCSTR filename, CPNode *base, BOOL withComment=FALSE);
CPNode * Decode(LPCSTR &str); // Decode encoded node description
void Parse(LPCSTR str);
CPNode* ParseTree(LPCSTR &str);
void ReadComment(LPCSTR &v, string &s);
static string& QuoteString(string& comment, char quote='\"');
void GetQuotedString(LPCSTR &str, string &v);
void ReadToken(LPCSTR &str, string &v);
BOOL ReadTreeAttrs();
BOOL ReadNodeAttrs();
BOOL WriteAttrs();
void SetAttr(LPCSTR k, LPCSTR v);
BOOL RemoveAttribute(LPCSTR attr, BOOL all);
// Remove the given attribute.
// all - if TRUE, remove from all nodes,
// otherwise from only from global TREE attrs
void ProcessAttrList(LPCSTR str, CPNode *node);
CPNode* Find(LPCSTR v);
CPNode* FindCommonAncestor(CPNode *n1, CPNode *n2);
// returns the nearest common ancestor to given nodes
// Progress Functions Access
BOOL SetProgressFunction(ProgressFunction callBack);
BOOL ClearProgressFunction();
BOOL ShowProgress(LPCSTR msg, int n, int total, PVOID data);
};
#endif
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