BioSequence (com.hfg API Documentation)

All Superinterfaces:

Cloneable, Comparable, Matter

All Known Subinterfaces:

BioSequencePlus

All Known Implementing Classes:

BioSequenceImpl, BioSequencePlusImpl, DigestFragment, Intron, NucleicAcid, Protein
```
public interface BioSequence
extends Cloneable, Comparable, Matter
```
Interface for a biological Protein, DNA, or RNA sequence.

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Default Methods
Modifier and Type	Method and Description
`BioSequence`	`clone()`
`Object`	`getAttribute(String inName)`
`Collection<String>`	`getAttributeNames()`
`String`	`getDescription()`
`String`	`getID()`
`byte[]`	`getMD5Checksum()`
`String`	`getSequence()`
`Reader`	`getSequenceReader()`
`InputStream`	`getSequenceStream()`
`byte[]`	`getSHA1Checksum()`
`String`	`getSubSequence(SeqLocation inSeqLocation)`
`Reader`	`getSubSequenceReader(SeqLocation inSeqLocation)`
`BioSequenceType`	`getType()`
`boolean`	`hasAttribute(String inName)`
`static BioSequence`	`instantiate(XMLNode inXMLNode)`
`int`	`length()`
`Object`	`removeAttribute(String inName)`
`char`	`residueAt(int inIndex)` Returns the residue character at the specified (1-based) sequence location.
`void`	`setAttribute(String inName, Object inValue)`
`BioSequence`	`setDescription(CharSequence inValue)`
`BioSequence`	`setID(String inValue)` Sets the id or name for the sequence.
`BioSequence`	`setSequence(CharSequence inValue)`
`BioSequence`	`setSequence(Reader inReader)`
`XMLNode`	`toXMLNode()`

Methods inherited from interface java.lang.Comparable
compareTo

Methods inherited from interface com.hfg.chem.Matter
getAverageMass, getChemicalFormula, getElementalComposition, getMonoisotopicMass, getOrganicAverageMass

Method Detail

clone
```
BioSequence clone()
```

setID
```
BioSequence setID(String inValue)
```
Sets the id or name for the sequence. Returns 'this' which can be useful for method chaining.

Parameters:

inValue - the id to use for this sequence

Returns:

this BioSequence to enable method chaining

getID
```
String getID()
```

getType
```
BioSequenceType getType()
```

setDescription

BioSequence setDescription(CharSequence inValue)

getDescription
```
String getDescription()
```

setSequence

BioSequence setSequence(CharSequence inValue)

setSequence

BioSequence setSequence(Reader inReader)

getSequence
```
String getSequence()
```

getSubSequence

String getSubSequence(SeqLocation inSeqLocation)

length
```
int length()
```

residueAt
```
char residueAt(int inIndex)
```
Returns the residue character at the specified (1-based) sequence location.

Parameters:

inIndex - the 1-based sequence location at which to retrieve the residue

Returns:

the residue at the specified index

getSequenceReader
```
Reader getSequenceReader()
```

getSubSequenceReader

Reader getSubSequenceReader(SeqLocation inSeqLocation)

getSequenceStream
```
InputStream getSequenceStream()
```

getMD5Checksum
```
byte[] getMD5Checksum()
```

getSHA1Checksum
```
byte[] getSHA1Checksum()
```

setAttribute

void setAttribute(String inName,
                  Object inValue)

getAttribute
```
Object getAttribute(String inName)
```

hasAttribute
```
boolean hasAttribute(String inName)
```

getAttributeNames
```
Collection<String> getAttributeNames()
```

removeAttribute
```
Object removeAttribute(String inName)
```

toXMLNode
```
XMLNode toXMLNode()
```

instantiate

static BioSequence instantiate(XMLNode inXMLNode)

Interface BioSequence

Method Summary

Methods inherited from interface java.lang.Comparable

Methods inherited from interface com.hfg.chem.Matter

Method Detail

clone

setID

getID

getType

setDescription

getDescription

setSequence

setSequence

getSequence

getSubSequence

length

residueAt

getSequenceReader

getSubSequenceReader

getSequenceStream

getMD5Checksum

getSHA1Checksum

setAttribute

getAttribute

hasAttribute

getAttributeNames

removeAttribute

toXMLNode

instantiate