ProteinVariant (de.charite.compbio:jannovar-hgvs 0.41 API)

java.lang.Object
- de.charite.compbio.jannovar.hgvs.HGVSVariant
- - de.charite.compbio.jannovar.hgvs.protein.variant.ProteinVariant

All Implemented Interfaces:

ConvertibleToHGVSString

Direct Known Subclasses:

MultiAlleleProteinVariant, SingleAlleleProteinVariant
```
public abstract class ProteinVariant
extends HGVSVariant
```
Base class for protein changes.

Author:

Manuel Holtgrewe

Field Summary

Fields
Modifier and Type Field Description

static int NO_PROTEIN_ISOFORM

Constructor Summary

Constructors
Constructor	Description
`ProteinVariant(String refID)`	Set variant's reference ID, protein ID is null, isoform is `NO_PROTEIN_ISOFORM`.
`ProteinVariant(String refID, String proteinID, int proteinIsoform)`	Set variant's reference ID, protein ID, and protein isoform to the given value

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`equals(Object obj)`
`String`	`getProteinID()`
`String`	`getSequenceNamePrefix()`
`int`	`hashCode()`
`String`	`toHGVSString()`	Return HGVS representation in three-letter amino acid code.
`String`	`toString()`

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

Methods inherited from interface de.charite.compbio.jannovar.hgvs.ConvertibleToHGVSString
toHGVSString

- Field Detail
  - NO_PROTEIN_ISOFORM
```
public static final int NO_PROTEIN_ISOFORM
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - ProteinVariant
```
public ProteinVariant(String refID)
```
    Set variant's reference ID, protein ID is null, isoform is NO_PROTEIN_ISOFORM.
  - ProteinVariant
```
public ProteinVariant(String refID,
                      String proteinID,
                      int proteinIsoform)
```
    Set variant's reference ID, protein ID, and protein isoform to the given value
- Method Detail
  - toHGVSString
```
public String toHGVSString()
```
    Description copied from interface: ConvertibleToHGVSString
    
    Return HGVS representation in three-letter amino acid code.
    
    Returns:
    
    HGVS representation, e.g. "133L" for an ProteinPointLocation
  - getProteinID
```
public String getProteinID()
```
    Returns:
    
    the protein ID
  - getSequenceNamePrefix
```
public String getSequenceNamePrefix()
```
    Returns:
    
    sequence name prefix, e.g. "NM_000109.3(DMD_v2)", or "NM_000109.3".
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object
  - equals
```
public boolean equals(Object obj)
```
    Overrides:
    
    equals in class Object