RemotePairwiseAlignmentProperties (biojava 5.2.0 API)

All Superinterfaces:

Serializable

All Known Implementing Classes:

NCBIQBlastAlignmentProperties
```
public interface RemotePairwiseAlignmentProperties
extends Serializable
```
RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties. Ideally, one would extend this class if creating a service by creating wrapper methods that actually call either getAlignementOption or setAlignementOption with specific values for parameter names and checking values for options. For an example, go see NCBIQBlastProperties

Since:

Biojava 3

Author:

Sylvain Foisy, Diploide BioIT

Field Summary

Fields
Modifier and Type Field Description

static long serialVersionUID

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`String`	`getAlignmentOption(String key)`	Method that returns the value associated with the key given in parameter.
`Set<String>`	`getAlignmentOptions()`	Method to get all keys to the information stored in this object.
`void`	`setAlignementOption(String key, String val)`	Method to set the value for a specific alignment parameter using a key to store in a map.

- Field Detail
  - serialVersionUID
```
static final long serialVersionUID
```
    See Also:
    
    Constant Field Values
- Method Detail
  - getAlignmentOption
```
String getAlignmentOption(String key)
                   throws Exception
```
    Method that returns the value associated with the key given in parameter.
    
    Parameters:
    
    key - :a String with the required key for this map.
    
    Returns:
    
    a String with the value associated with this key
    
    Throws:
    
    Exception - if key is not in the map of output options.
  - setAlignementOption
```
void setAlignementOption(String key,
                         String val)
```
    Method to set the value for a specific alignment parameter using a key to store in a map.
    
    Parameters:
    
    key - :the key use to designate the value to be stored
    
    val - :the actual value matched to key
  - getAlignmentOptions
```
Set<String> getAlignmentOptions()
```
    Method to get all keys to the information stored in this object.
    
    Returns:
    
    a Set with all keys held in this instance of the object