Package phase
Class SampleSeg
- java.lang.Object
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- phase.SampleSeg
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- All Implemented Interfaces:
IntInterval
,java.lang.Comparable<SampleSeg>
public class SampleSeg extends java.lang.Object implements java.lang.Comparable<SampleSeg>, IntInterval
Class
Instances of classSampleSeg
represents a haplotype shared with a sample.SampleSeg
are immutable.
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Constructor Summary
Constructors Constructor Description SampleSeg(int sample, int start, int end)
Constructs a newSampleSeg
instance from the specified data.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description int
compareTo(SampleSeg hs)
Compares this object with the specified object for order.boolean
equals(java.lang.Object o)
Compares the specified object with thisSampleSeg
for equality.int
hashCode()
Returns the hash code value for this object.int
inclEnd()
Returns the end of the segment (inclusive).int
sample()
Returns the sample index.static java.util.Comparator<SampleSeg>
sampleComp()
Returns a comparator that orders first bythis.sample()
, then bythis.start()
, and finally bythis.end()
.int
start()
Returns the start of the segment (inclusive).java.lang.String
toString()
Returns a string representation ofthis
.
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Constructor Detail
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SampleSeg
public SampleSeg(int sample, int start, int end)
Constructs a newSampleSeg
instance from the specified data.- Parameters:
sample
- the sample indexstart
- the start of the segment (inclusive)end
- the end of the segment (inclusive)- Throws:
java.lang.IllegalArgumentException
- ifstart > end
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Method Detail
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sample
public int sample()
Returns the sample index.- Returns:
- the sample index
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start
public int start()
Returns the start of the segment (inclusive).- Specified by:
start
in interfaceIntInterval
- Returns:
- the start of the segment (inclusive)
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inclEnd
public int inclEnd()
Returns the end of the segment (inclusive).- Specified by:
inclEnd
in interfaceIntInterval
- Returns:
- the end of the segment (inclusive)
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toString
public java.lang.String toString()
Returns a string representation ofthis
. The exact details of the representation are unspecified and subject to change.- Overrides:
toString
in classjava.lang.Object
- Returns:
- a string representation of
this
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hashCode
public int hashCode()
Returns the hash code value for this object. The hash code is defined by the following calculation:
int hash = 5; hash = 89 * hash + this.hap(); hash = 89 * hash + this.start(); hash = 89 * hash + this.end();
- Overrides:
hashCode
in classjava.lang.Object
- Returns:
- the hash code value for this object
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equals
public boolean equals(java.lang.Object o)
Compares the specified object with thisSampleSeg
for equality. Returnstrue
if the specified object is aSampleSeg
instance and if thisSampleSeg
is equal to the specifiedSampleSeg
, and returnsfalse
otherwise. TwoSampleSeg
instances are equal if they have equal haplotype indices, equal starting marker indices, and equal ending marker indices.- Overrides:
equals
in classjava.lang.Object
- Parameters:
o
- the reference object with which to compare.- Returns:
true
if the specified object is anSampleSeg
instance and if thisSampleSeg
is equal to the specifiedSampleSeg
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compareTo
public int compareTo(SampleSeg hs)
Compares this object with the specified object for order. Returns a negative integer, zero, or a positive integer as this object is less than, equal to, or greater than the specified object.SampleSeg
instances are ordered first bythis.start()
, then bythis.end()
, and finally bythis.sample()
.- Specified by:
compareTo
in interfacejava.lang.Comparable<SampleSeg>
- Parameters:
hs
- theSampleSeg
to be compared- Returns:
- a negative integer, zero, or a positive integer as this
SampleSeg
is less than, equal to, or greater than the specifiedSampleSeg
- Throws:
java.lang.NullPointerException
- ifo == null
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sampleComp
public static java.util.Comparator<SampleSeg> sampleComp()
Returns a comparator that orders first bythis.sample()
, then bythis.start()
, and finally bythis.end()
.- Returns:
- a comparator that orders first by
this.sample()
, then bythis.start()
, and finally bythis.end()
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