MarkerInfo Class Reference

Collaboration diagram for MarkerInfo:

Public Member Functions
	MarkerInfo (String &string)
bool	AdjustFrequencies ()
String	GetAlleleLabel (int allele)
int	GetAlleleNumber (char label) const
int	GetAlleleNumber (const String &label) const
int	NewAllele (char label)
int	NewAllele (const String &label)
void	UpdateSerial ()
void	IndexAlleles ()
int	CountAlleles ()

Static Public Member Functions
static int	ComparePosition (MarkerInfo **left, MarkerInfo **right)

Public Attributes
int	chromosome
double	position
double	positionMale
double	positionFemale
Vector	freq
String	name
StringArray	alleleLabels
StringIntHash	alleleNumbers

Detailed Description

Definition at line 29 of file PedigreeGlobals.h.

Constructor & Destructor Documentation

MarkerInfo()

MarkerInfo::MarkerInfo ( String &  string )

inline

Definition at line 45 of file PedigreeGlobals.h.

    {
        serial = count++;
        name = string;
        chromosome = -1;
        position = 0.0;
        positionMale = 0.0;
        positionFemale = 0.0;
    }

Member Function Documentation

AdjustFrequencies()

bool MarkerInfo::AdjustFrequencies

(

)

Definition at line 80 of file PedigreeGlobals.cpp.

{
    if (freq.Length() <= 1)
    {
        freq.Clear();
        return false;
    }
 
    if (freq.Min() < 0.0)
        error("Locus %s has negative allele frequencies\n", (const char *) name);
 
    double sum = freq.Sum();
 
    if (sum <= 0.0)
        error("Locus %s frequencies sum to %f, which doesn't make sense\n",
              (const char *) name, sum);
 
    if (sum != 1.0)
        freq *= 1.0 / sum;
 
    if (fabs(sum - 1.0) > 1.2e-5)
    {
        printf("Locus %s frequencies sum to %f, adjusted to 1.0\n",
               (const char *) name, sum);
        return true;
    }
 
    return false;
}

ComparePosition()

int MarkerInfo::ComparePosition ( MarkerInfo **  left, MarkerInfo **  right  )

static

Definition at line 56 of file PedigreeGlobals.cpp.

{
    if ((*left)->chromosome != (*right)->chromosome)
        return (*left)->chromosome - (*right)->chromosome;
 
    double difference = (*left)->position - (*right)->position;
 
    if (difference >  0.0)
        return 1;
    else if (difference == 0.0)
        return (*left)->serial - (*right)->serial;
    else
        return -1;
}

CountAlleles()

int MarkerInfo::CountAlleles ( )

inline

Definition at line 89 of file PedigreeGlobals.h.

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

GetAlleleLabel()

String MarkerInfo::GetAlleleLabel

(

int

allele

)

Definition at line 71 of file PedigreeGlobals.cpp.

{
    if (alleleLabels.Length() > allele && alleleLabels[allele].Length())
        return alleleLabels[allele];
    else if (alleleLabels.Length() <= allele)
        alleleLabels.Dimension(allele + 1);
    return alleleLabels[allele] = allele;
}

GetAlleleNumber() [1/2]

int MarkerInfo::GetAlleleNumber ( char  label ) const

inline

Definition at line 60 of file PedigreeGlobals.h.

    {
        String labelString;
        labelString = label;
        return(GetAlleleNumber(labelString));
    }

GetAlleleNumber() [2/2]

int MarkerInfo::GetAlleleNumber ( const String &  label ) const

inline

Definition at line 66 of file PedigreeGlobals.h.

    {
        return label == "0" ? 0 : alleleNumbers.Integer(label);
    }

IndexAlleles()

void MarkerInfo::IndexAlleles

(

)

Definition at line 110 of file PedigreeGlobals.cpp.

{
    if (alleleLabels.Length() >= 255)
        error("Marker %s has more than 254 distinct alleles\n",
              (const char *) name);
 
    alleleNumbers.Clear();
 
    for (int i = 1; i < alleleLabels.Length(); i++)
        alleleNumbers.SetInteger(alleleLabels[i], i);
}

NewAllele() [1/2]

int MarkerInfo::NewAllele ( char  label )

inline

Definition at line 71 of file PedigreeGlobals.h.

    {
        String labelString;
        labelString = label;
        return(NewAllele(labelString));
    }

NewAllele() [2/2]

int MarkerInfo::NewAllele

(

const String &

label

)

Definition at line 122 of file PedigreeGlobals.cpp.

{
    if (alleleLabels.Length() == 0)
        alleleLabels.Push("");
 
    if (alleleLabels.Length() >= 255)
        error("Marker %s has more than 254 distinct alleles\n",
              (const char *) name);
 
    alleleNumbers.SetInteger(label, alleleLabels.Length());
    alleleLabels.Push(label);
 
    return alleleLabels.Length() - 1;
}

UpdateSerial()

void MarkerInfo::UpdateSerial ( )

inline

Definition at line 82 of file PedigreeGlobals.h.

    {
        serial = count++;
    }

Member Data Documentation

alleleLabels

StringArray MarkerInfo::alleleLabels

Definition at line 42 of file PedigreeGlobals.h.

alleleNumbers

StringIntHash MarkerInfo::alleleNumbers

Definition at line 43 of file PedigreeGlobals.h.

chromosome

int MarkerInfo::chromosome

Definition at line 33 of file PedigreeGlobals.h.

freq

Vector MarkerInfo::freq

Definition at line 40 of file PedigreeGlobals.h.

name

String MarkerInfo::name

Definition at line 41 of file PedigreeGlobals.h.

position

double MarkerInfo::position

Definition at line 36 of file PedigreeGlobals.h.

positionFemale

double MarkerInfo::positionFemale

Definition at line 38 of file PedigreeGlobals.h.

positionMale

double MarkerInfo::positionMale

Definition at line 37 of file PedigreeGlobals.h.

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The documentation for this class was generated from the following files:

• general/PedigreeGlobals.h
• general/PedigreeGlobals.cpp