BasicMarker

java.lang.Object
- vcf.BasicMarker

All Implemented Interfaces:

java.lang.Comparable<Marker>, Marker
```
public class BasicMarker
extends java.lang.Object
implements Marker
```
Class BasicMarker represents a genetic marker.

Instances of class BasicMarker are immutable.

Constructor Summary

Constructors
Constructor and Description
`BasicMarker(int chrom, int pos, java.lang.String[] ids, java.lang.String[] alleles)` Constructs a new `BasicMarker` instance from the specified data.
`BasicMarker(int chrom, int pos, java.lang.String[] ids, java.lang.String[] alleles, int end)` Constructs a new `BasicMarker` instance from the specified data.
`BasicMarker(java.lang.String vcfRecord)` Constructs a new `BasicMarker` instance from the specified string VCF record.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.lang.String`	`allele(int index)` Returns the specified allele.
`java.lang.String[]`	`alleles()` Returns the alleles.
`java.lang.String`	`chrom()` Returns the chromosome.
`int`	`chromIndex()` Returns the chromosome index.
`int`	`compareTo(Marker other)` Compares this marker with the specified marker for order, and returns a negative integer, 0, or a positive integer depending on whether this marker is less than, equal to, or greater than the specified marker.
`int`	`end()` Returns the INFO END field, or -1 if there is no INFO END field.
`boolean`	`equals(java.lang.Object obj)` Returns `true` if the specified object is a `Marker` with the same chromosome, position, allele lists, and INFO END field, and returns `false` otherwise.
`static Marker`	`flipStrand(Marker marker)` Constructs and returns a new marker obtained from the specified marker by changing the marker's non-symbolic alleles to the alleles on the opposite chromosome strand.
`int`	`hashCode()` Returns the hash code value for this object.
`java.lang.String`	`id()` Returns the first marker identifier if there is at least one identifier in the VCF record ID field, and returns `this.chr() + ":" + this.pos()` otherwise.
`java.lang.String`	`id(int index)` Returns the specified marker identifier.
`int`	`nAlleles()` Returns the number of alleles for the marker, including the REF allele.
`int`	`nGenotypes()` Returns the number of distinct genotypes, which equals `this.nAlleles()*(1 + this.nAlleles())/2`.
`int`	`nIds()` Returns the number of marker identifiers.
`int`	`pos()` Returns the chromosome position coordinate.
`java.lang.String`	`toString()` Returns a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker.

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - BasicMarker
```
public BasicMarker(int chrom,
                   int pos,
                   java.lang.String[] ids,
                   java.lang.String[] alleles)
```
    Constructs a new BasicMarker instance from the specified data. The end() method of the new instance will return -1. The JVM will exit with an error message if any marker identifier in the specifiedids array or if any allele identifier in the specified alleles array does not conform to the VCF specification.
    
    Parameters:
    
    chrom - a chromosome index
    
    pos - the marker position
    
    ids - a list of marker identifiers
    
    alleles - a list of alleles beginning with the reference allele
    
    Throws:
    
    java.lang.IllegalArgumentException - if chrom < 0 || chrom >= ChromIds.instance().size()
    
    java.lang.NullPointerException - if ids == null or if any element of ids is null
    
    java.lang.NullPointerException - if alleles == null or if any element of alleles is null
  - BasicMarker
```
public BasicMarker(int chrom,
                   int pos,
                   java.lang.String[] ids,
                   java.lang.String[] alleles,
                   int end)
```
    Constructs a new BasicMarker instance from the specified data. The JVM will exit with an error message if any marker identifier in the specified ids array does not conform to the VCF specification, if any allele identifier in the specified alleles array does not conform to the VCF specification, or if (end != -1 && end < pos).
    
    Parameters:
    
    chrom - a chromosome index
    
    pos - the marker position
    
    ids - a list of marker identifiers
    
    alleles - a list of alleles beginning with the reference allele
    
    end - the INFO END field, or -1 if there is no INFO END field
    
    Throws:
    
    java.lang.IllegalArgumentException - if chrom < 0 || chrom >= ChromIds.instance().size()
    
    java.lang.NullPointerException - if ids == null or if any element of ids is null
    
    java.lang.NullPointerException - if alleles == null or if any element of alleles is null
  - BasicMarker
```
public BasicMarker(java.lang.String vcfRecord)
```
    Constructs a new BasicMarker instance from the specified string VCF record.
    
    Parameters:
    
    vcfRecord - a VCF record
    
    Throws:
    
    java.lang.IllegalArgumentException - if the specified VCF record has fewer than 8 tab-delimited fields, or if a format error is detected in the specified VCF record
    
    java.lang.NullPointerException - if vcfRecord == null
- Method Detail
  - flipStrand
```
public static Marker flipStrand(Marker marker)
```
    Constructs and returns a new marker obtained from the specified marker by changing the marker's non-symbolic alleles to the alleles on the opposite chromosome strand.
    
    Parameters:
    
    marker - a marker
    
    Returns:
    
    the equivalent marker on the opposite chromosome strand
    
    Throws:
    
    java.lang.NullPointerException - if marker == null
  - chrom
```
public java.lang.String chrom()
```
    Description copied from interface: Marker
    
    Returns the chromosome.
    
    Specified by:
    
    chrom in interface Marker
    
    Returns:
    
    the chromosome
  - chromIndex
```
public int chromIndex()
```
    Description copied from interface: Marker
    
    Returns the chromosome index.
    
    Specified by:
    
    chromIndex in interface Marker
    
    Returns:
    
    the chromosome index
  - pos
```
public int pos()
```
    Description copied from interface: Marker
    
    Returns the chromosome position coordinate.
    
    Specified by:
    
    pos in interface Marker
    
    Returns:
    
    the chromosome position coordinate
  - nIds
```
public int nIds()
```
    Description copied from interface: Marker
    
    Returns the number of marker identifiers.
    
    Specified by:
    
    nIds in interface Marker
    
    Returns:
    
    the number of marker identifiers
  - id
```
public java.lang.String id(int index)
```
    Description copied from interface: Marker
    
    Returns the specified marker identifier.
    
    Specified by:
    
    id in interface Marker
    
    Parameters:
    
    index - a marker identifier index
    
    Returns:
    
    the specified marker identifier
  - id
```
public java.lang.String id()
```
    Description copied from interface: Marker
    
    Returns the first marker identifier if there is at least one identifier in the VCF record ID field, and returns this.chr() + ":" + this.pos() otherwise.
    
    Specified by:
    
    id in interface Marker
    
    Returns:
    
    a marker identifier
  - nAlleles
```
public int nAlleles()
```
    Description copied from interface: Marker
    
    Returns the number of alleles for the marker, including the REF allele.
    
    Specified by:
    
    nAlleles in interface Marker
    
    Returns:
    
    the number of alleles for the marker, including the REF allele
  - allele
```
public java.lang.String allele(int index)
```
    Description copied from interface: Marker
    
    Returns the specified allele. The reference allele has index 0.
    
    Specified by:
    
    allele in interface Marker
    
    Parameters:
    
    index - an allele index
    
    Returns:
    
    the specified allele
  - alleles
```
public java.lang.String[] alleles()
```
    Description copied from interface: Marker
    
    Returns the alleles. The k-th element of the returned array is equal to this.allele(k).
    
    Specified by:
    
    alleles in interface Marker
    
    Returns:
    
    the alleles
  - nGenotypes
```
public int nGenotypes()
```
    Description copied from interface: Marker
    
    Returns the number of distinct genotypes, which equals this.nAlleles()*(1 + this.nAlleles())/2.
    
    Specified by:
    
    nGenotypes in interface Marker
    
    Returns:
    
    the number of distinct genotypes
  - end
```
public int end()
```
    Description copied from interface: Marker
    
    Returns the INFO END field, or -1 if there is no INFO END field.
    
    Specified by:
    
    end in interface Marker
    
    Returns:
    
    the INFO END field, or -1 if there is no INFO END field
  - toString
```
public java.lang.String toString()
```
    Description copied from interface: Marker
    
    Returns a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker.
    
    Specified by:
    
    toString in interface Marker
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    a string equal to the first five tab-delimited fields of a VCF record corresponding to this marker
  - hashCode
```
public int hashCode()
```
    Description copied from interface: Marker
    Returns the hash code value for this object. The hash code does not depend on value of the VCF record ID field. The hash code is defined by the following calculation:
```
   int hash = 5;
   hash = 29 * hash + this.chromIndex();
   hash = 29 * hash + this.pos();
   for (int j=0, n=this.nAlleles(); j<n; ++j) {
       hash = 29 * hash + alleles[j].hashCode();
   }
   hash = 29 * hash + end();
 
```
    Specified by:
    
    hashCode in interface Marker
    
    Overrides:
    
    hashCode in class java.lang.Object
    
    Returns:
    
    the hash code value for this marker
  - equals
```
public boolean equals(java.lang.Object obj)
```
    Description copied from interface: Marker
    
    Returns true if the specified object is a Marker with the same chromosome, position, allele lists, and INFO END field, and returns false otherwise. Equality does not depend on value of the VCF record ID field.
    
    Specified by:
    
    equals in interface Marker
    
    Overrides:
    
    equals in class java.lang.Object
    
    Parameters:
    
    obj - object to be compared with this for equality
    
    Returns:
    
    true if the specified object is a Marker with the same chromosome, position, and allele lists, and INFO END field
  - compareTo
```
public int compareTo(Marker other)
```
    Description copied from interface: Marker
    
    Compares this marker with the specified marker for order, and returns a negative integer, 0, or a positive integer depending on whether this marker is less than, equal to, or greater than the specified marker. Comparison is on chromosome index, position, allele identifier lists, and end value in that order. Allele identifier lists are compared for lexicographical order, and alleles are compared using the String compareTo() method.
    
    Specified by:
    
    compareTo in interface java.lang.Comparable<Marker>
    
    Specified by:
    
    compareTo in interface Marker
    
    Parameters:
    
    other - the Marker to be compared
    
    Returns:
    
    a negative integer, 0, or a positive integer depending on whether this marker is less than, equal, or greater than the specified marker

Class BasicMarker

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

BasicMarker

BasicMarker

BasicMarker

Method Detail

flipStrand

chrom

chromIndex

pos

nIds

id

id

nAlleles

allele

alleles

nGenotypes

end

toString

hashCode

equals

compareTo