All Known Subinterfaces:

DotBracketFromPdb, Strand

All Known Implementing Classes:

AbstractCombinedStrand, CombinedStrand, CombinedStrandFromPdb, DefaultDotBracket, DefaultDotBracketFromPdb, DefaultStrand, ImmutableCombinedStrand, ImmutableCombinedStrandFromPdb, ImmutableDefaultDotBracket, ImmutableDefaultDotBracketFromPdb, ImmutableDefaultStrand, ImmutableStrandView, StrandView
```
public interface DotBracket
```
An RNA structure encoded in dot-bracket format.

Method Summary

All Methods Instance Methods Abstract Methods Default 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.
`default boolean`	`containsMissing()`
`default Strand`	`findStrand(DotBracketSymbol symbol)`	Finds a strand which contains the given symbol.
`default int`	`length()`
`default List<DotBracketSymbol>`	`missingInternal()`
`default List<TerminalMissing>`	`missingTerminal()`
`default int`	`originalIndex(DotBracketSymbol symbol)`	Returns the index of a dot-bracket symbol according to some external source like PDB numbering.
`default Map<DotBracketSymbol,DotBracketSymbol>`	`pairs()`
`default int`	`pseudoknotOrder()`
`default String`	`sequence()`
`default String`	`sequence(boolean separateStrands)`	Creates a string representation of nucleotide sequence, where strands may be separated with ampersand `&` or not.
`default List<Strand>`	`strands()`
`default String`	`structure()`
`default String`	`structure(boolean separateStrands)`	Creates a string of dots and brackets which represents base pairing, where strands may be separated with ampersand `&` or not.
`List<DotBracketSymbol>`	`symbols()`
`default String`	`toStringWithStrands()`

- Method Detail
  - symbols
```
List<DotBracketSymbol> symbols()
```
    Returns:
    
    The list of dot-bracket symbols.
  - combineStrands
```
List<DotBracket> combineStrands()
```
    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.
  - originalIndex
```
default int originalIndex(DotBracketSymbol symbol)
```
    Returns the index of a dot-bracket symbol according to some external source like PDB numbering.
    
    Parameters:
    
    symbol - Dot-bracket symbol for which the original index is sought.
    
    Returns:
    
    An index which reflects the numbering in real structure (e.g. PDB).
  - strands
```
default List<Strand> strands()
```
    Returns:
    
    The list of strands.
  - sequence
```
default String sequence()
```
    Returns:
    
    The sequence of nucleotides.
  - structure
```
default String structure()
```
    Returns:
    
    The sequence of dots and brackets representing paired and unpaired residues.
  - pairs
```
default Map<DotBracketSymbol,DotBracketSymbol> pairs()
```
  - toStringWithStrands
```
default String toStringWithStrands()
```
    Returns:
    
    A string representation of this dot-bracket, where every strand is written out separately.
  - length
```
default int length()
```
    Returns:
    
    The number of nucleotides in this structure.
  - containsMissing
```
default boolean containsMissing()
```
    Returns:
    
    True, if at least one symbol represents a missing residue.
  - missingTerminal
```
default List<TerminalMissing> missingTerminal()
```
    Returns:
    
    The list of missing symbols at 5' and 3' ends of all strands.
  - missingInternal
```
default List<DotBracketSymbol> missingInternal()
```
    Returns:
    
    The list of missing symbols which are not at 5' or 3' ends of any strand.
  - pseudoknotOrder
```
default int pseudoknotOrder()
```
    Returns:
    
    The pseudoknot order of this structure.
  - findStrand
```
default Strand findStrand(DotBracketSymbol symbol)
```
    Finds a strand which contains the given symbol.
    
    Parameters:
    
    symbol - The symbol to look for.
    
    Returns:
    
    The strand containing the symbol.
  - sequence
```
default String sequence(boolean separateStrands)
```
    Creates a string representation of nucleotide sequence, where strands may be separated with ampersand & or not.
    
    Parameters:
    
    separateStrands - If true, the result will contain ampersand between strands.
    
    Returns:
    
    The string representation of nucleotide sequence.
  - structure
```
default String structure(boolean separateStrands)
```
    Creates a string of dots and brackets which represents base pairing, where strands may be separated with ampersand & or not.
    
    Parameters:
    
    separateStrands - If true, the result will contain ampersand between strands.
    
    Returns:
    
    The string representation of this structure.

Interface DotBracket

Method Summary

Method Detail

symbols

combineStrands

originalIndex

strands

sequence

structure

pairs

toStringWithStrands

length

containsMissing

missingTerminal

missingInternal

pseudoknotOrder

findStrand

sequence

structure