ChromInterval

java.lang.Object
- beagleutil.ChromInterval

All Implemented Interfaces:

IntInterval, java.lang.Comparable<ChromInterval>
```
public final class ChromInterval
extends java.lang.Object
implements IntInterval, java.lang.Comparable<ChromInterval>
```
Class ChromInterval represents a chromosome interval whose end points are genome coordinates.
Instances of class ChromInterval are immutable.

Constructor Summary

Constructors
Constructor and Description
`ChromInterval(Marker start, Marker end)` Constructs a new `ChromInterval` instance.
`ChromInterval(java.lang.String chrom, int start, int end)` Constructs a new `ChromInterval` instance.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`java.lang.String`	`chrom()` Returns the chromosome identifier.
`int`	`chromIndex()` Returns the chromosome index.
`int`	`compareTo(ChromInterval o)` Compares this `ChromInteval` with the specified `ChromInterval` instance for order, and returns -1, 0, or 1 depending on whether `this` is less than, equal or greater than the specified instance.
`int`	`end()` Returns the last genome coordinate in this chromosome interval.
`boolean`	`equals(java.lang.Object obj)` Returns `true` if the specified object is a `ChromInterval` instance representing the same interval of genome coordinates as `this`, and returns `false` otherwise.
`int`	`hashCode()` Returns a hash code value for the object.
`static ChromInterval`	`merge(ChromInterval a, ChromInterval b)` Returns the union of the specified overlapping chromosome intervals.
`static boolean`	`overlap(ChromInterval a, ChromInterval b)` Returns `true` if the specified chromosome intervals have non-empty intersection and returns `false` otherwise.
`static ChromInterval`	`parse(java.lang.String str)` Returns a `ChromInterval` instance corresponding to the specified string, or returns `null` if the specified string does not represent a valid chromosome interval or if the specified string is `null`.
`int`	`start()` Returns the first genome coordinate in this chromosome interval.
`java.lang.String`	`toString()` Returns the string: `this.chrom() + ":" + this.start() + "-" + this.end()`

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

- Constructor Detail
  - ChromInterval
```
public ChromInterval(Marker start,
                     Marker end)
```
    Constructs a new ChromInterval instance.
    
    Parameters:
    
    start - the first marker in the interval.
    
    end - the last marker in the interval.
    
    Throws:
    
    java.lang.IllegalArgumentException - if start.chromIndex()!=end.chromIndex() || start.pos()<0 || start.pos()>end.pos().
    
    java.lang.NullPointerException - if start==null || end==null.
  - ChromInterval
```
public ChromInterval(java.lang.String chrom,
                     int start,
                     int end)
```
    Constructs a new ChromInterval instance.
    
    Parameters:
    
    chrom - the chromosome,
    
    start - the first genome coordinate in the interval.
    
    end - the last genome coordinate in the interval.
    
    Throws:
    
    java.lang.IllegalArgumentException - if start<0 || start>end || chrom.isEmpty().
    
    java.lang.NullPointerException - if chrom==null.
- Method Detail
  - parse
```
public static ChromInterval parse(java.lang.String str)
```
    Returns a ChromInterval instance corresponding to the specified string, or returns null if the specified string does not represent a valid chromosome interval or if the specified string is null.
    The string representation of the chromosome interval must have one of the following forms:
```
 [chrom]:[start]-[end]
 [chrom]
 [chrom]:
 [chrom]:[start]-
 [chrom]:-end
 
```
    where
    
    [chrom] is a chromosome identifier, and [start] and [end] are non-negative integers satisfying [start]<=[end]. If the specified string does not contain a start position, the start() method of the returned ChromInterval instance returns 0. If no end position is specified, the end() method of the returned ChromInterval instance returns Integer.MAX_VALUE.
    Parameters:
    
    str - a chromosome interval.
    
    Returns:
    
    a ChromInterval instance corresponding to the specified string, or returns null if the specified string does not represent a valid chromosome interval or if the specified string is null.
  - chromIndex
```
public int chromIndex()
```
    Returns the chromosome index. The chromosome index is equal to ChromIds.indexOf(this.chrom()).
    
    Returns:
    
    the chromosome index.
  - chrom
```
public java.lang.String chrom()
```
    Returns the chromosome identifier.
    
    Returns:
    
    the chromosome identifier.
  - start
```
public int start()
```
    Returns the first genome coordinate in this chromosome interval.
    
    Specified by:
    
    start in interface IntInterval
    
    Returns:
    
    the first genome coordinate in this chromosomet interval.
  - end
```
public int end()
```
    Returns the last genome coordinate in this chromosome interval.
    
    Specified by:
    
    end in interface IntInterval
    
    Returns:
    
    the last genome coordinate in this chromosome interval.
  - compareTo
```
public int compareTo(ChromInterval o)
```
    Compares this ChromInteval with the specified ChromInterval instance for order, and returns -1, 0, or 1 depending on whether this is less than, equal or greater than the specified instance.
    ChromInterval objects are ordered first by this.chromIndex(), then by this.start(), and finally by this.end(). All fields are ordered in ascending order.
    
    Specified by:
    
    compareTo in interface java.lang.Comparable<ChromInterval>
    
    Parameters:
    
    o - the ChromInterval to be compared with this.
    
    Returns:
    
    -1, 0, or 1 depending on whether this is less than, equal or greater than the specified instance.
  - hashCode
```
public int hashCode()
```
    Returns a hash code value for the object.
    
    The hash code is defined by the following calculation:
```
        int hash = 7;
        hash = 67 * hash + this.chromIndex();
        hash = 67 * hash + this.start();
        hash = 67 * hash + this.end();
 
```
    Overrides:
    
    hashCode in class java.lang.Object
    
    Returns:
    
    a hash code value for the object.
  - equals
```
public boolean equals(java.lang.Object obj)
```
    Returns true if the specified object is a ChromInterval instance representing the same interval of genome coordinates as this, and returns false otherwise.
    
    Overrides:
    
    equals in class java.lang.Object
    
    Parameters:
    
    obj - the object to be compared with this for equality.
    
    Returns:
    
    true if the specified object is a ChromInterval instance representing the same interval of genome coordinates as this, and returns false otherwise.
  - toString
```
public java.lang.String toString()
```
    Returns the string: this.chrom() + ":" + this.start() + "-" + this.end()
    
    Overrides:
    
    toString in class java.lang.Object
    
    Returns:
    
    this.chrom() + ":" + this.start() + "-" + this.end()
  - overlap
```
public static boolean overlap(ChromInterval a,
                              ChromInterval b)
```
    Returns true if the specified chromosome intervals have non-empty intersection and returns false otherwise.
    
    Parameters:
    
    a - a chromosome interval.
    
    b - a chromosome interval.
    
    Returns:
    
    true if the specified chromosome intervals have non-empty intersection and returns false otherwise.
  - merge
```
public static ChromInterval merge(ChromInterval a,
                                  ChromInterval b)
```
    Returns the union of the specified overlapping chromosome intervals.
    
    Parameters:
    
    a - a chromosome interval.
    
    b - a chromosome interval.
    
    Returns:
    
    the union of the specified overlapping chromosome intervals.
    
    Throws:
    
    java.lang.IllegalArgumentException - if ChromInterval.overlap(a, b)==false.

Class ChromInterval

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ChromInterval

ChromInterval

Method Detail

parse

chromIndex

chrom

start

end

compareTo

hashCode

equals

toString

overlap

merge