org.biojava3.alignment.template
Interface GapPenalty

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
static class GapPenalty.Type
          Defines the possible types of gap penalties.
 
Method Summary
 short getExtensionPenalty()
          Returns penalty given when an already open gap elongates by a single element
 short getOpenPenalty()
          Returns penalty given when a deletion or insertion gap first opens
 GapPenalty.Type getType()
          Returns GapPenalty.Type stored.
 void setExtensionPenalty(short gep)
          Sets penalty given when an already open gap elongates by a single element
 void setOpenPenalty(short gop)
          Sets penalty given when a deletion or insertion gap first opens
 

Method Detail

getExtensionPenalty

short getExtensionPenalty()
Returns penalty given when an already open gap elongates by a single element

Returns:
gap extension penalty

getOpenPenalty

short 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(short gep)
Sets penalty given when an already open gap elongates by a single element

Parameters:
gep - gap extension penalty

setOpenPenalty

void setOpenPenalty(short gop)
Sets penalty given when a deletion or insertion gap first opens

Parameters:
gop - gap open penalty