GapPenalty (biojava 6.1.0 API)

All Known Implementing Classes:

SimpleGapPenalty
```
public interface GapPenalty
```
Defines a data structure for the gap penalties used during a sequence alignment routine.

Author:

Mark Chapman

Nested Class Summary

Nested Classes
Modifier and Type Interface Description

static class GapPenalty.Type
Defines the possible types of gap penalties.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`int`	`getExtensionPenalty()`	Returns penalty given when an already open gap elongates by a single element
`int`	`getOpenPenalty()`	Returns penalty given when a deletion or insertion gap first opens
`GapPenalty.Type`	`getType()`	Returns `GapPenalty.Type` stored.
`void`	`setExtensionPenalty(int gep)`	Sets penalty given when an already open gap elongates by a single element
`void`	`setOpenPenalty(int gop)`	Sets penalty given when a deletion or insertion gap first opens

- Method Detail
  - getExtensionPenalty
```
int getExtensionPenalty()
```
    Returns penalty given when an already open gap elongates by a single element
    
    Returns:
    
    gap extension penalty
  - getOpenPenalty
```
int getOpenPenalty()
```
    Returns penalty given when a deletion or insertion gap first opens
    
    Returns:
    
    gap open penalty
  - getType
```
GapPenalty.Type getType()
```
    Returns GapPenalty.Type stored.
    
    Returns:
    
    gap penalty type
  - setExtensionPenalty
```
void setExtensionPenalty(int gep)
```
    Sets penalty given when an already open gap elongates by a single element
    
    Parameters:
    
    gep - gap extension penalty
  - setOpenPenalty
```
void setOpenPenalty(int gop)
```
    Sets penalty given when a deletion or insertion gap first opens
    
    Parameters:
    
    gop - gap open penalty