IubString (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.util.IubString

All Implemented Interfaces:

java.lang.Iterable<java.lang.String>, java.util.Iterator<java.lang.String>
```
public class IubString
extends java.lang.Object
implements java.lang.Iterable<java.lang.String>, java.util.Iterator<java.lang.String>
```
Find all bases combinations from a string containing IUB codes

Author:

pcingola

Field Summary

Fields
Modifier and Type Field Description

static int MAX_IUB_BASES

Constructor Summary

Constructors
Constructor Description

IubString(java.lang.String str)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static int`	`countIUB(java.lang.String str)`	How many IUB bases are in this string?
`static boolean`	`hasIUB(java.lang.String str)`	Does the string have ANY IUB base?
`static boolean`	`hasIUBMax(java.lang.String str)`	Does the string have at most 'MAX_IUB_BASES' IUB bases?
`boolean`	`hasNext()`
`static boolean`	`isUIB(char base)`
`java.util.Iterator<java.lang.String>`	`iterator()`
`static char[]`	`iub2bases(char alt)`	Convert a single IUB code to the corresponding bases IUB codes: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T, K=G/T and N=A/C/G/T
`java.lang.String`	`next()`
`void`	`remove()`

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

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Methods inherited from interface java.util.Iterator
forEachRemaining

- Field Detail
  - MAX_IUB_BASES
```
public static final int MAX_IUB_BASES
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - IubString
```
public IubString(java.lang.String str)
```
- Method Detail
  - countIUB
```
public static int countIUB(java.lang.String str)
```
    How many IUB bases are in this string?
  - hasIUB
```
public static boolean hasIUB(java.lang.String str)
```
    Does the string have ANY IUB base?
  - hasIUBMax
```
public static boolean hasIUBMax(java.lang.String str)
```
    Does the string have at most 'MAX_IUB_BASES' IUB bases?
  - isUIB
```
public static boolean isUIB(char base)
```
  - iub2bases
```
public static char[] iub2bases(char alt)
```
    Convert a single IUB code to the corresponding bases IUB codes: M=A/C, R=A/G, W=A/T, S=C/G, Y=C/T, K=G/T and N=A/C/G/T
  - hasNext
```
public boolean hasNext()
```
    Specified by:
    
    hasNext in interface java.util.Iterator<java.lang.String>
  - iterator
```
public java.util.Iterator<java.lang.String> iterator()
```
    Specified by:
    
    iterator in interface java.lang.Iterable<java.lang.String>
  - next
```
public java.lang.String next()
```
    Specified by:
    
    next in interface java.util.Iterator<java.lang.String>
  - remove
```
public void remove()
```
    Specified by:
    
    remove in interface java.util.Iterator<java.lang.String>