Homology (biojava-legacy 1.9.5 API)

All Known Implementing Classes:

SimpleHomology
```
public interface Homology
```
Signifies that two or more features are homologous.

Blast hits or local multiple-sequence alignments can be represented as a set of features on sequences that have an alignment. The features will probably implement HomologyFeature.

Since:

1.2

Author:

Matthew Pocock, Keith James

Field Summary

Fields
Modifier and Type Field Description

static ChangeType ALIGNMENT
Signals that the alignment describing the homologous sequences has changed.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`Alignment`	`getAlignment()`	Retrieve the Alignment that specifies how the homologous regions are aligned.
`FeatureHolder`	`getFeatures()`	Retrieve the set of features that mark homologous regions.

- Field Detail
  - ALIGNMENT
```
static final ChangeType ALIGNMENT
```
    Signals that the alignment describing the homologous sequences has changed. For implementations which implement Changeable.
- Method Detail
  - getFeatures
```
FeatureHolder getFeatures()
```
    Retrieve the set of features that mark homologous regions.
    
    Returns:
    
    the FeatureHolder containing each homologous region
  - getAlignment
```
Alignment getAlignment()
```
    Retrieve the Alignment that specifies how the homologous regions are aligned. The labels of the alignment are the HomologyFeature objects.
    
    Returns:
    
    the Alignment between the HomologyFeatures