edu.rit.compbio.seq

Class ProteinSequence

java.lang.Object

edu.rit.compbio.seq.Sequence

edu.rit.compbio.seq.ProteinSequence

public class ProteinSequence
extends Sequence

Class ProteinSequence encapsulates a protein sequence. A protein sequence object may be constructed from a string or read from a file. Protein sequence objects may also be read from a protein sequence database using class ProteinDatabase.

In a file, a protein sequence is stored in FASTA format. A FASTA format protein sequence consists of one description line and one or more sequence lines. The description line consists of an initial '>' character followed by zero or more characters (the protein's description). A sequence line consists of one or more characters 'A' through 'Z', 'a' through 'z', '*', or '-'.

In a program, a protein sequence is represented as a byte array (type byte[]). For a protein sequence of length L, the byte array contains L+1 bytes. The byte at index 0 is unused and contains a value of -1. The bytes at indexes 1 through L contain the amino acids. Amino acids 'A' through 'Z' (case insensitive) are represented by the values 0 through 25; '*' is represented as 26; '-' is represented as 27.

The amino acid letters and values are:

Letter	Value	Amino Acid
A	0	Alanine
B	1	Aspartate or asparagine
C	2	Cysteine
D	3	Aspartate
E	4	Glutamate
F	5	Phenylalanine
G	6	Glycine
H	7	Histidine
I	8	Isoleucine
J	9	unused
K	10	Lysine
L	11	Leucine
M	12	Methionine
N	13	Asparagine
O	14	unused
P	15	Proline
Q	16	Glutamine
R	17	Arginine
S	18	Serine
T	19	Threonine
U	20	Selenocysteine
V	21	Valine
W	22	Tryptophan
X	23	Any, unknown
Y	24	Tyrosine
Z	25	Glutamate or glutamine
*	26	Translation stop
-	27	Gap of indeterminate length

Constructor Summary

Constructors

Constructor and Description
ProteinSequence(java.io.File file) Construct a new protein sequence read from the given file.
ProteinSequence(java.lang.String description, java.lang.String sequence) Construct a new protein sequence from the given string.

Method Summary

Modifier and Type	Method and Description
char	charAt(int i) Returns a character version of this protein sequence's element at the given index.
java.lang.String	toString() Returns a string version of this protein sequence.

Methods inherited from class edu.rit.compbio.seq.Sequence

description, elementsToString, equals, hashCode, length, sequence

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

ProteinSequence

public ProteinSequence(java.lang.String description,
                       java.lang.String sequence)

Construct a new protein sequence from the given string.

Parameters:

description - Description string. Must start with a '>' character.

sequence - Sequence string. Must consist of the characters 'A' through 'Z', 'a' through 'z', '*', and '-'.

ProteinSequence

public ProteinSequence(java.io.File file)
                throws java.io.IOException

Construct a new protein sequence read from the given file.

Parameters:

file - File.

Throws:

java.io.IOException - Thrown if an I/O error occurred.

Method Detail

charAt

public char charAt(int i)

Returns a character version of this protein sequence's element at the given index.

Specified by:

charAt in class Sequence

Parameters:

i - Index in the range 1 .. L.

Returns:

Character corresponding to element i.

toString

public java.lang.String toString()

Returns a string version of this protein sequence. The string is "ProteinSequence(description)".

Overrides:

toString in class java.lang.Object

Returns:

String version.