Hgvs (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.snpEffect.Hgvs

Direct Known Subclasses:

HgvsDna, HgvsProtein
```
public class Hgvs
extends java.lang.Object
```
HGSV notation References: http://www.hgvs.org/

Author:

pcingola

Field Summary

Fields
Modifier and Type	Field	Description
`protected boolean`	`duplication`
`protected Genome`	`genome`
`protected boolean`	`hgvsTrId`
`protected Marker`	`marker`
`static int`	`MAX_SEQUENCE_LEN_HGVS`
`protected boolean`	`strandMinus`
`protected boolean`	`strandPlus`
`protected Transcript`	`tr`
`protected Variant`	`variant`
`protected VariantEffect`	`variantEffect`

Constructor Summary

Constructors
Constructor Description

Hgvs(VariantEffect variantEffect)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`initStrand()`
`static java.lang.String`	`parseTranscript(java.lang.String hgvs)`
`static java.lang.String`	`removeTranscript(java.lang.String hgvs)`

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

Field Detail

MAX_SEQUENCE_LEN_HGVS
```
public static final int MAX_SEQUENCE_LEN_HGVS
```
See Also:

Constant Field Values

variantEffect
```
protected VariantEffect variantEffect
```

variant
```
protected Variant variant
```

marker
```
protected Marker marker
```

tr
```
protected Transcript tr
```

genome
```
protected Genome genome
```

duplication
```
protected boolean duplication
```

strandPlus
```
protected boolean strandPlus
```

strandMinus
```
protected boolean strandMinus
```

hgvsTrId
```
protected boolean hgvsTrId
```

Constructor Detail

Hgvs

public Hgvs(VariantEffect variantEffect)

Method Detail

parseTranscript

public static java.lang.String parseTranscript(java.lang.String hgvs)

removeTranscript

public static java.lang.String removeTranscript(java.lang.String hgvs)

initStrand
```
protected void initStrand()
```