PedigreeGlobals.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 __PEDGLOBALS_H__
#define __PEDGLOBALS_H__

#include "Constant.h"
#include "StringArray.h"
#include "StringHash.h"
#include "IntArray.h"
#include "MathVector.h"

#include <iostream>

class MarkerInfo
{
public:
    // Chromosome number
    int    chromosome;

    // Position along chromosome in morgans
    double position;
    double positionMale;
    double positionFemale;

    Vector         freq;
    String         name;
    StringArray    alleleLabels;
    StringIntHash  alleleNumbers;

    MarkerInfo(String & string)
    {
        serial = count++;
        name = string;
        chromosome = -1;
        position = 0.0;
        positionMale = 0.0;
        positionFemale = 0.0;
    }

    bool AdjustFrequencies();

    static int ComparePosition(MarkerInfo ** left, MarkerInfo ** right);

    String GetAlleleLabel(int allele);
    int    GetAlleleNumber(const String & label) const
    {
        return label == "0" ? 0 : alleleNumbers.Integer(label);
    }

    int  NewAllele(const String & label);

    // Calling update serial for a series of markers ensures they are
    // clustered in a particular order
    void UpdateSerial()
    {
        serial = count++;
    }

    void IndexAlleles();

    int CountAlleles()
    {
        return alleleLabels.Length() ? alleleLabels.Length() - 1 : 0;
    }

private:
    // How many marker info structures have we created?
    static int count;
    static String label;

    // When sorting markers, use serial_no to break ties, so
    // markers we saw first in the map file / datafile come
    // first
    int serial;
};

std::ostream &operator << (std::ostream &stream, MarkerInfo &m);

class PedigreeGlobals
{
public:
    static int traitCount;
    static int markerCount;
    static int affectionCount;
    static int covariateCount;
    static int stringCount;

    // Should be set to true if handling X-linked data
    static bool chromosomeX;
    // Set to true when map file includes position info
    // based on sex-specific recombination fractions
    static bool sexSpecificMap;

    static StringArray   traitNames;
    static StringArray   covariateNames;
    static StringArray   affectionNames;
    static StringArray   markerNames;
    static StringArray   stringNames;
    static StringIntHash markerLookup;
    static StringIntHash traitLookup;
    static StringIntHash affectionLookup;
    static StringIntHash covariateLookup;
    static StringIntHash stringLookup;

    // These functions are guaranteed to return a valid ID
    // If no matching attribute exists, one is created
    //

    static int GetTraitID(const char * name);
    static int GetMarkerID(const char * name);
    static int GetCovariateID(const char * name);
    static int GetAffectionID(const char * name);
    static int GetStringID(const char * name);

    // These functions return a matching ID or -1 if none is found
    //

    static int LookupTrait(const char * name)
    {
        return traitLookup.Integer(name);
    }
    static int LookupMarker(const char * name)
    {
        return markerLookup.Integer(name);
    }
    static int LookupCovariate(const char * name)
    {
        return covariateLookup.Integer(name);
    }
    static int LookupAffection(const char * name)
    {
        return affectionLookup.Integer(name);
    }
    static int LookupString(const char * name)
    {
        return stringLookup.Integer(name);
    }

    static int markerInfoCount;
    static int markerInfoSize;
    static MarkerInfo ** markerInfo;
    static StringHash    markerInfoByName;
    static MarkerInfo ** markerInfoByInteger;

    static void GrowMarkerInfo();
    static MarkerInfo * GetMarkerInfo(String & name);
    static MarkerInfo * GetMarkerInfo(int marker);

    static int  SortMarkersInMapOrder(IntArray & markers, int chromosome = -1);
    static void GetOrderedMarkers(IntArray & markers);
    static void FlagMissingMarkers(IntArray & missingMarkers);

    static bool MarkerPositionsAvailable();
    static bool AlleleFrequenciesAvailable();

    static void VerifySexSpecificOrder();

    static void LoadAlleleFrequencies(const char * filename, bool required = false);
    static void LoadAlleleFrequencies(IFILE & file);

    static void LoadMarkerMap(const char * filename, bool filter = false);
    static void LoadMarkerMap(IFILE & file, bool filter = false);

    static void LoadBasepairMap(const char * filename);
    static void LoadBasepairMap(IFILE & file);

    static void WriteMapFile(const char * filename);
    static void WriteMapFile(FILE * file);

    static void WriteFreqFile(const char * filename, bool old_format = false);
    static void WriteFreqFile(FILE * file, bool old_format = false);

    static int  LoadAllele(int marker, String & label);          // Read an allele
    static int  LoadAllele(MarkerInfo * info, String & label);

    PedigreeGlobals()
    {
        instanceCount++;
    }
    ~PedigreeGlobals();

private:
    static int  instanceCount;

};

#endif