Sequence (nthash-java 0.0.4 API)

All Known Implementing Classes:

DiskSequence, MemorySequence
```
public interface Sequence
```

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`void`	`buildIndex(long k)`	Builds the index based on the length of the k-mer.
`Base`	`getBase(long position)`
`List<Long>`	`getMatchingPositions(Sequence kmer)`	Gets positions of the sequence that matches with k-mer.
`long`	`getSize()`

- Method Detail
  - buildIndex
```
void buildIndex(long k)
         throws Exception
```
    Builds the index based on the length of the k-mer.
    
    Parameters:
    
    k - length of the k-mer
    
    Throws:
    
    Exception - throws exception when errors occur on database end
  - getMatchingPositions
```
List<Long> getMatchingPositions(Sequence kmer)
                         throws Exception
```
    Gets positions of the sequence that matches with k-mer. If an index has been built, then this method tries to use that index to perform faster look-up.
    
    Parameters:
    
    kmer - sub-sequence to search for
    
    Returns:
    
    list of matching starting positions in this sequence
    
    Throws:
    
    Exception - throws exception
  - getSize
```
long getSize()
```
    Returns:
    
    size of the sequence
  - getBase
```
Base getBase(long position)
```
    Parameters:
    
    position - the position of the sequence
    
    Returns:
    
    the base at the position provided