MultiLineDotBracket (BioCommons 3.0.4 API)

java.lang.Object
- pl.poznan.put.structure.formats.MultiLineDotBracket

Direct Known Subclasses:

ImmutableMultiLineDotBracket
```
@Immutable
public abstract class MultiLineDotBracket
extends Object
```
An extended secondary structure, which contains also non-canonical base pairs.

Constructor Summary

Constructors
Constructor Description

MultiLineDotBracket()

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`abstract Collection<? extends ClassifiedBasePair>`	`basePairs()`
`protected Collection<ClassifiedBasePair>`	`basePairs5to3()`
`static MultiLineDotBracket`	`fromString(String input)`	Creates an instance by reading a set of lines in dot-bracket notation.
`abstract String`	`sequence()`
`String`	`toString()`

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

- Constructor Detail
  - MultiLineDotBracket
```
public MultiLineDotBracket()
```
- Method Detail
  - fromString
```
public static MultiLineDotBracket fromString(String input)
```
    Creates an instance by reading a set of lines in dot-bracket notation. Each line begins with a Leontis-Westhof notation shortand (e.g. cWW, tSH, etc.), a whitespace, and a dot-bracket. One line contains 'seq' instead of LW notation and it is followed by the sequence. For example:
    seq AGGGCGGGU cWW (.......) cWH .([{.}]).
    Parameters:
    
    input - A string containing input in the format specified above.
    
    Returns:
    
    An instance of this class.
  - sequence
```
@Parameter(order=1)
public abstract String sequence()
```
    Returns:
    
    The sequence of nucleotides.
  - basePairs
```
@Parameter(order=2)
public abstract Collection<? extends ClassifiedBasePair> basePairs()
```
    Returns:
    
    The list of base pairs.
  - toString
```
public final String toString()
```
    Overrides:
    
    toString in class Object
  - basePairs5to3
```
@Lazy
protected Collection<ClassifiedBasePair> basePairs5to3()
```