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## calhoun.seq
Interface FastaSequence

All Known Implementing Classes:
  FastaIterator.ReaderSequence, SimpleFastaSequence

    public interface FastaSequence

Represents a generic sequence in a fasta file. FastaIterator and FastaReader have different classes that they store the result in, but these methods are common. Unifies the Fasta classes so you can more easily intermix them.

Method Summary
`java.lang.String` | `getHeader()` Gets the fasta header (with leading and trailing spaces trimmed)
`int` | `getLength()` The number of sequence characters
`byte[]` | `getQuality()` Returns the quality scores for this sequence.
`java.lang.String` | `getSequence()` Returns the entire sequence.
`java.lang.String` | `getSequence(int start, int stop)` Returns a portions of the sequence.

Method Detail

### getLength

    int getLength()

  The number of sequence characters

### getHeader

    java.lang.String getHeader()

  Gets the fasta header (with leading and trailing spaces trimmed)

### getSequence

    java.lang.String getSequence()

  Returns the entire sequence.

### getSequence

    java.lang.String getSequence(int start,
                                 int stop)

  Returns a portions of the sequence.

  Parameters:
    `start` - 1-based index of the first character to return. Can be from 1 to the length of the sequence.
    `stop` - 1-based index of the last charater to return. Can be from 1 to the length of the sequence.

### getQuality

    byte[] getQuality()

  Returns the quality scores for this sequence. May be null if no quality is present.

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