Interval (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.util.Interval

All Implemented Interfaces:

Locatable, java.lang.Cloneable, java.lang.Comparable<Interval>
```
public class Interval
extends java.lang.Object
implements java.lang.Comparable<Interval>, java.lang.Cloneable, Locatable
```
Represents a simple interval on a sequence. Coordinates are 1-based closed ended.

Constructor Summary

Constructors
Constructor and Description
`Interval(java.lang.String sequence, int start, int end)` Constructs an interval with the supplied sequence and start and end.
`Interval(java.lang.String sequence, int start, int end, boolean negative, java.lang.String name)` Constructs an interval with the supplied sequence and start, end, strand and name.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`boolean`	`abuts(Interval other)` Returns true if this interval overlaps the other interval, otherwise false.
`Interval`	`clone()`
`int`	`compareTo(Interval that)` Sort based on sequence.compareTo, then start pos, then end pos with null objects coming lexically last
`static long`	`countBases(java.util.Collection<Interval> intervals)` Counts the total number of bases a collection of intervals.
`boolean`	`equals(java.lang.Object other)` Equals method that agrees with `compareTo(Interval)`.
`java.lang.String`	`getContig()` Gets the contig name for the contig this is mapped to.
`int`	`getEnd()`
`int`	`getIntersectionLength(Interval other)`
`java.lang.String`	`getName()` Returns the name of the interval, possibly null.
`java.lang.String`	`getSequence()` Deprecated. use getContig() instead
`int`	`getStart()`
`int`	`hashCode()`
`Interval`	`intersect(Interval that)` Returns a new Interval that represents the intersection between the two intervals.
`boolean`	`intersects(Interval other)` Returns true if this interval overlaps the other interval, otherwise false.
`boolean`	`isNegativeStrand()` Returns true if the interval is on the negative strand, otherwise false.
`boolean`	`isPositiveStrand()` Returns true if the interval is on the positive strand, otherwise false.
`int`	`length()` Gets the length of this interval.
`Interval`	`pad(int left, int right)` Returns a new interval that is padded by the amount of bases specified on either side.
`java.lang.String`	`toString()`

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

- Constructor Detail
  - Interval
```
public Interval(java.lang.String sequence,
                int start,
                int end)
```
    Constructs an interval with the supplied sequence and start and end. If the end position is less than the start position an exception is thrown.
    
    Parameters:
    
    sequence - the name of the sequence
    
    start - the start position of the interval on the sequence
    
    end - the end position of the interval on the sequence
  - Interval
```
public Interval(java.lang.String sequence,
                int start,
                int end,
                boolean negative,
                java.lang.String name)
```
    Constructs an interval with the supplied sequence and start, end, strand and name. If the end position is less than the start position an exception is thrown.
    
    Parameters:
    
    sequence - the name of the sequence
    
    start - the start position of the interval on the sequence
    
    end - the end position of the interval on the sequence
    
    negative - true to indicate negative strand, false otherwise
    
    name - the name (possibly null) of the interval
- Method Detail
  - getSequence
```
@Deprecated
public java.lang.String getSequence()
```
    Deprecated. use getContig() instead
    
    Gets the name of the sequence on which the interval resides. This is a simple alias of getContig()
  - isNegativeStrand
```
public boolean isNegativeStrand()
```
    Returns true if the interval is on the negative strand, otherwise false.
  - isPositiveStrand
```
public boolean isPositiveStrand()
```
    Returns true if the interval is on the positive strand, otherwise false.
  - getName
```
public java.lang.String getName()
```
    Returns the name of the interval, possibly null.
  - intersects
```
public boolean intersects(Interval other)
```
    Returns true if this interval overlaps the other interval, otherwise false.
  - getIntersectionLength
```
public int getIntersectionLength(Interval other)
```
  - intersect
```
public Interval intersect(Interval that)
```
    Returns a new Interval that represents the intersection between the two intervals.
  - abuts
```
public boolean abuts(Interval other)
```
    Returns true if this interval overlaps the other interval, otherwise false.
  - length
```
public int length()
```
    Gets the length of this interval.
  - pad
```
public Interval pad(int left,
                    int right)
```
    Returns a new interval that is padded by the amount of bases specified on either side.
  - countBases
```
public static long countBases(java.util.Collection<Interval> intervals)
```
    Counts the total number of bases a collection of intervals.
  - compareTo
```
public int compareTo(Interval that)
```
    Sort based on sequence.compareTo, then start pos, then end pos with null objects coming lexically last
    
    Specified by:
    
    compareTo in interface java.lang.Comparable<Interval>
  - equals
```
public boolean equals(java.lang.Object other)
```
    Equals method that agrees with compareTo(Interval).
    
    Overrides:
    
    equals in class java.lang.Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - clone
```
public Interval clone()
```
    Overrides:
    
    clone in class java.lang.Object
  - getContig
```
public java.lang.String getContig()
```
    Description copied from interface: Locatable
    
    Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.
    
    Specified by:
    
    getContig in interface Locatable
    
    Returns:
    
    name of the contig this is mapped to, potentially null
  - getStart
```
public int getStart()
```
    Specified by:
    
    getStart in interface Locatable
    
    Returns:
    
    1-based start position, undefined if getContig() == null
  - getEnd
```
public int getEnd()
```
    Specified by:
    
    getEnd in interface Locatable
    
    Returns:
    
    1-based closed-ended position, undefined if getContig() == null

Class Interval

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Interval

Interval

Method Detail

getSequence

isNegativeStrand

isPositiveStrand

getName

intersects

getIntersectionLength

intersect

abuts

length

pad

countBases

compareTo

equals

hashCode

toString

clone

getContig

getStart

getEnd