CombinedStrand (BioCommons 3.0.4 API)

java.lang.Object
- pl.poznan.put.structure.formats.AbstractCombinedStrand
- - pl.poznan.put.structure.formats.CombinedStrand

All Implemented Interfaces:

DotBracket

Direct Known Subclasses:

ImmutableCombinedStrand
```
@Immutable
public abstract class CombinedStrand
extends AbstractCombinedStrand
```
A dot-bracket encoded structure made from combining one or more strands.

Constructor Summary

Constructors
Constructor Description

CombinedStrand()

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`List<DotBracket>`	`combineStrands()`	Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
`protected abstract List<Strand>`	`inputStrands()`
`Map<DotBracketSymbol,DotBracketSymbol>`	`pairs()`
`List<Strand>`	`strands()`
`List<DotBracketSymbol>`	`symbols()`
`String`	`toString()`

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

Methods inherited from interface pl.poznan.put.structure.formats.DotBracket
containsMissing, findStrand, length, missingInternal, missingTerminal, originalIndex, pseudoknotOrder, sequence, sequence, structure, structure, toStringWithStrands

- Constructor Detail
  - CombinedStrand
```
public CombinedStrand()
```
- Method Detail
  - inputStrands
```
@Parameter(order=1)
protected abstract List<Strand> inputStrands()
```
    Specified by:
    
    inputStrands in class AbstractCombinedStrand
    
    Returns:
    
    The list of input strands.
  - symbols
```
@Lazy
@Auxiliary
public List<DotBracketSymbol> symbols()
```
    Specified by:
    
    symbols in interface DotBracket
    
    Overrides:
    
    symbols in class AbstractCombinedStrand
    
    Returns:
    
    The list of dot-bracket symbols.
  - strands
```
@Lazy
@Auxiliary
public List<Strand> strands()
```
    Specified by:
    
    strands in interface DotBracket
    
    Overrides:
    
    strands in class AbstractCombinedStrand
    
    Returns:
    
    The list of strands.
  - toString
```
public final String toString()
```
    Overrides:
    
    toString in class Object
  - combineStrands
```
public final List<DotBracket> combineStrands()
```
    Description copied from interface: DotBracket
    
    Combines strands which share a base pair into a new dot-bracket instance and returns a list of those.
    
    Returns:
    
    The list of dot-bracket instances, each containing strands which only pair with each other.
  - pairs
```
@Lazy
@Auxiliary
public Map<DotBracketSymbol,DotBracketSymbol> pairs()
```