RepeatScan (Gemma 1.31.2-SNAPSHOT API)

java.lang.Object
- ubic.gemma.core.analysis.sequence.RepeatScan

```
public class RepeatScan
extends Object
```
Scan sequences for repeats

Author:

pavlidis

Constructor Summary

Constructors
Constructor Description

RepeatScan()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`Collection<BioSequence>`	`processRepeatMaskerOutput(Collection<BioSequence> sequences, String outputSequencePath)`
`Collection<BioSequence>`	`repeatScan(Collection<BioSequence> sequences)`	Run repeatmasker on the sequences.

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

- Constructor Detail
  - RepeatScan
```
public RepeatScan()
```
- Method Detail
  - processRepeatMaskerOutput
```
public Collection<BioSequence> processRepeatMaskerOutput(Collection<BioSequence> sequences,
                                                         String outputSequencePath)
```
    Parameters:
    
    sequences - sequences
    
    outputSequencePath - in FASTA format
    
    Returns:
    
    Sequences which were updated.
  - repeatScan
```
public Collection<BioSequence> repeatScan(Collection<BioSequence> sequences)
```
    Run repeatmasker on the sequences. The sequence will be updated with the masked (lower-case) sequences and the fraction of masked bases will be filled in.
    
    Parameters:
    
    sequences - sequences
    
    Returns:
    
    sequences that had repeats.