SeqCoder3

java.lang.Object
- bref.SeqCoder3

```
public class SeqCoder3
extends java.lang.Object
```
Class SeqCoder3 compresses a sequence of allele-coded RefGTRec objects. The class is designed for use with brev v3 format. Compression is performed by storing the list of distinct allele sequences and the allele sequence carried by each haplotype.

Class SeqCoder3 is not thread-safe.

Field Summary

Fields
Modifier and Type	Field	Description
`static float`	`COMPRESS_FREQ_THRESHOLD`	The major allele frequency threshold for allele coding.
`static int`	`MAX_NALLELES`	The maximum number of alleles are that permitted in order for the `add()` method to return `true`

Constructor Summary

Constructors
Constructor	Description
`SeqCoder3(Samples samples)`	Constructs a new `SeqCoder3` for the specified samples.
`SeqCoder3(Samples samples, int maxNSeq)`	Constructs a new `SeqCoder3` for the specified samples.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`add(RefGTRec rec)`	Attempts to add the specified `RefGTRec` object to the list of compressed `RefGTRec` objects, and returns `true` if the `RefGTRec` object was added.
`static int`	`defaultMaxNSeq(int nSamples)`	Returns the default maximum number of sequences for the specified number of samples.
`java.util.List<RefGTRec>`	`getCompressedList()`	Returns and clears the stored list of compressed `RefGTRec` objects.
`int`	`maxNSeq()`	Returns the maximum number of distinct allele sequences.
`int`	`nRecs()`	Returns the number of compressed `RefGTRec` objects.
`Samples`	`samples()`	Returns the list of samples whose phased genotype data will be compressed.

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

- Field Detail
  - MAX_NALLELES
```
public static final int MAX_NALLELES
```
    The maximum number of alleles are that permitted in order for the add() method to return true
    
    See Also:
    
    Constant Field Values
  - COMPRESS_FREQ_THRESHOLD
```
public static final float COMPRESS_FREQ_THRESHOLD
```
    The major allele frequency threshold for allele coding. Sequence coding should only be applied if the major allele frequency less than or equal to this threshold.
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - SeqCoder3
```
public SeqCoder3(Samples samples)
```
    Constructs a new SeqCoder3 for the specified samples.
    
    Parameters:
    
    samples - the list of samples whose data will be compressed
    
    Throws:
    
    java.lang.NullPointerException - if samples == null
  - SeqCoder3
```
public SeqCoder3(Samples samples,
                 int maxNSeq)
```
    Constructs a new SeqCoder3 for the specified samples.
    
    Parameters:
    
    samples - the list of samples whose data will be compressed
    
    maxNSeq - the maximum number of distinct allele sequences permitted if the add() method returns true
    
    Throws:
    
    java.lang.NullPointerException - if samples == null
    
    java.lang.IllegalArgumentException - maxNSeq < 0 || maxNSeq >= Chracter.MAX_VALUE
- Method Detail
  - defaultMaxNSeq
```
public static int defaultMaxNSeq(int nSamples)
```
    Returns the default maximum number of sequences for the specified number of samples. The default value is equal to (int) Math.min((long) Math.pow(2, 2*Math.log10(nSamples) + 1), Character.MAX_VALUE)
    
    Parameters:
    
    nSamples - the number of samples
    
    Returns:
    
    the default maximum number of sequences for the specified number of samples
    
    Throws:
    
    java.lang.IllegalArgumentException - if nSamples < 1
  - samples
```
public Samples samples()
```
    Returns the list of samples whose phased genotype data will be compressed.
    
    Returns:
    
    the list of samples whose phased genotype data will be compressed
  - nRecs
```
public int nRecs()
```
    Returns the number of compressed RefGTRec objects.
    
    Returns:
    
    the number of compressed RefGTRec objects
  - maxNSeq
```
public int maxNSeq()
```
    Returns the maximum number of distinct allele sequences.
    
    Returns:
    
    the maximum number of distinct allele sequences
  - add
```
public boolean add(RefGTRec rec)
```
    Attempts to add the specified RefGTRec object to the list of compressed RefGTRec objects, and returns true if the RefGTRec object was added.
    
    Parameters:
    
    rec - reference genotypes for a marker
    
    Returns:
    
    true if the specified RefGTRec object was added to the list of compressed markers
    
    Throws:
    
    java.lang.IllegalArgumentException - if em.samples().equals(this.samples()) == false
    
    java.lang.IllegalArgumentException - if rec.isAlleleCoded() == false
    
    java.lang.NullPointerException - if em == null
  - getCompressedList
```
public java.util.List<RefGTRec> getCompressedList()
```
    Returns and clears the stored list of compressed RefGTRec objects.
    
    Returns:
    
    the list of compressed RefGTRec objects

Class SeqCoder3

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MAX_NALLELES

COMPRESS_FREQ_THRESHOLD

Constructor Detail

SeqCoder3

SeqCoder3

Method Detail

defaultMaxNSeq

samples

nRecs

maxNSeq

add

getCompressedList