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PedigreeDescription.h
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __PEDDESCRIBE_H__
#define __PEDDESCRIBE_H__
#include "PedigreeGlobals.h"
#include "PedigreePerson.h"
#include "StringArray.h"
#include "IntArray.h"
#include <stdio.h>
// Possible pedigree columns
#define pcSkip 0
#define pcMarker 1
#define pcTrait 2
#define pcAffection 3
#define pcCovariate 4
#define pcString 5
#define pcZygosity 6
#define pcEnd 7
// Undocumented pedigree column types -- not recommended
#define pcUndocumentedTraitCovariate 1001
class PedigreeDescription : public PedigreeGlobals
{
public:
int columnCount;
IntArray columns, columnHash;
PedigreeDescription();
~PedigreeDescription();
void Load(IFILE & Input, bool warnIfLinkage = false);
void Load(const char * filename, bool warnIfLinkage = false);
void LoadLinkageDataFile(IFILE & input);
void LoadLinkageDataFile(const char * filename);
void LoadMendelDataFile(IFILE & input);
void LoadMendelDataFile(const char * filename);
void LoadMap(IFILE & Input);
void LoadMap(const char * filename);
PedigreeDescription & operator = (PedigreeDescription & rhs);
int CountTextColumns();
// returns a string summarizing column contents
const char * ColumnSummary(String & string);
// Flag specifying Mendel format
bool mendelFormat;
String filename;
void AddMarkerColumn(const char * markerName);
void AddTraitColumn(const char * traitName);
void AddAffectionColumn(const char * affectionName);
void AddCovariateColumn(const char * covariateName);
void AddStringColumn(const char * stringName);
void AddZygosityColumn();
void AddSkippedColumn();
private:
int ReadLineHelper(IFILE & input, String & buffer, StringArray & tokens);
int CountColumns(int type);
void UpdateSummary(String & string, int type, const char * label);
};
#endif
IFILE
InputFile * IFILE
Define IFILE as a pointer to an InputFile object.
Definition InputFile.h:551
IntArray
Definition IntArray.h:24
StringArray
Definition StringArray.h:24
String
Definition StringBasics.h:39