DnaSequenceId (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.binseq.BinarySequence
- - org.snpeff.binseq.DnaSequence
  - - org.snpeff.binseq.DnaSequenceId

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<BinarySequence>
```
public class DnaSequenceId
extends DnaSequence
```
Binary packed DNA sequence with an ID (long)

Author:

pcingola

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor	Description
`DnaSequenceId(long id, int length, long[] codes)`
`DnaSequenceId(long id, java.lang.String seqStr)`
`DnaSequenceId(java.lang.String seqStr)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static DnaSequenceId`	`empty()`	Empty sequence singleton
`protected DnaSequence`	`factory()`	Create sequences
`long`	`getId()`
`BinarySequence`	`read(java.io.DataInputStream dataInStream)`	Read data in binary format
`protected void`	`readDataStream(java.io.DataInputStream dataInStream)`	Read data in binary format
`java.lang.String`	`toString()`
`void`	`write(java.io.DataOutputStream dataOutStream)`	Write data in binary format

Methods inherited from class org.snpeff.binseq.DnaSequence
clone, compareTo, getBase, getBases, getCode, getCoder, getCodes, getSequence, hashCode, isEmpty, length, overlap, reverseWc, set, set, setBase, setCodes

Methods inherited from class org.snpeff.binseq.BinarySequence
setQuality

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

Constructor Detail

DnaSequenceId

public DnaSequenceId(long id,
                     int length,
                     long[] codes)

DnaSequenceId

public DnaSequenceId(long id,
                     java.lang.String seqStr)

DnaSequenceId

public DnaSequenceId(java.lang.String seqStr)

Method Detail
- empty
```
public static DnaSequenceId empty()
```
  Empty sequence singleton
  
  Returns:
- factory
```
protected DnaSequence factory()
```
  Create sequences
  
  Overrides:
  
  factory in class DnaSequence
  
  Returns:
- getId
```
public long getId()
```
- read
```
public BinarySequence read(java.io.DataInputStream dataInStream)
                    throws java.io.IOException
```
  Read data in binary format
  
  Overrides:
  
  read in class DnaSequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  java.io.IOException
- readDataStream
```
protected void readDataStream(java.io.DataInputStream dataInStream)
                       throws java.io.IOException
```
  Read data in binary format
  
  Overrides:
  
  readDataStream in class DnaSequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  java.io.IOException
- toString
```
public java.lang.String toString()
```
  Overrides:
  
  toString in class DnaSequence
- write
```
public void write(java.io.DataOutputStream dataOutStream)
           throws java.io.IOException
```
  Write data in binary format
  
  Overrides:
  
  write in class DnaSequence
  
  Parameters:
  
  dataOutStream -
  
  Throws:
  
  java.io.IOException