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Class diana.sequence.AminoAcidSequence

java.lang.Object
   |
   +----diana.sequence.AminoAcidSequence

public class AminoAcidSequence

extends Object

Version:

$Id: AminoAcidSequence.java,v 1.24 2003/11/18 14:38:16 kmr Exp $

amino_acid_symbol_count

The number of amino acid symbols, not including stop codons: 20.

codon_translation_array

This table is used for fast lookup of codon translations by getCodonTranslation ().

HYDROPHOBIC_AA

Used by getAminoAcidType ().

ILLEGAL_AA

Used by getAminoAcidType ().

NEGATIVELY_CHARGED_AA

Used by getAminoAcidType ().

POLAR_UNCHARGED_AA

Used by getAminoAcidType ().

POSITIVELY_CHARGED_AA

Used by getAminoAcidType ().

SPECIAL_AA

Used by getAminoAcidType ().

STOP_AA

Used by getAminoAcidType ().

symbol_count

The number of amino acid symbols, including stop codons and a symbol for unknown (---): 23.

UNKNOWN_AA

Used by getAminoAcidType ().

AminoAcidSequence(String)

Create a new AminoAcidSequence object from a string containing single character amino acids symbols.

checkForMatch(AminoAcidSequence)

Search the subject_sequence for this AminoAcidSequence as a substring.

containsStopCodon()

Return true if and only if this sequence contains a stop codon.

elementAt(int)

Return the one letter codon code of the codon at the given index (counting from zero).

findMatch(Bases, Marker, boolean)

Find the next occurrence of this seqeuence on either Strand of the given Bases object.

getAminoAcidType(char)

Returns one of POLAR_UNCHARGED_AA, POSITIVELY_CHARGED_AA, NEGATIVELY_CHARGED_AA, HYDROPHOBIC_AA, SPECIAL_AA or STOP_AA depending on the aa_char argument.

getCodonTranslation(char, char, char)

Translate a single codon into the corresponding single letter amino acid code.

getCodonTranslation(String)

Translate a single codon into the corresponding single letter amino acid code.

getMolecularWeight()

Return the total molecular weight of the amino acids in this AminoAcidSequence..

getOneLetterCode(String)

Return the one letter abbreviation for the given three letter amino acid name.

getSymbolFromIndex(int)

Given an index return a one letter codon symbol.

getSymbolIndex(char)

Return an integer from 0 to 22 representing the index of a codon symbol.

getThreeLetterAbbreviation(char)

Return the three letter abbreviation for the given one letter amino acid code.

getThreeLetterAbbreviation(int)

Return the three letter abbreviation for the given index code.

getTranslation(String, boolean)

Translate a sequence of bases into the corresponding single letter amino acid codes.

isLegalCodon(char)

Return true if and only if the given one letter code symbol is the a legal amino acid or stop symbol.

isStopCodon(char)

Return true if and only if the given amino acid symbol is the translation of a stop codon.

length()

Return the number of units in this amino acid sequence.

reverseComplementSearchBackwardFor(String, int)

Search backward for this AminoAcidSequence in the reverse complement of the given String of bases.

reverseComplementSearchFor(String, int, boolean)

Search for this AminoAcidSequence in the reverse complement of the given String of bases.

reverseComplementSearchForwardFor(String, int)

Search forward for this AminoAcidSequence in the reverse complement of the given String of bases.

searchBackwardFor(String, int)

Search backward for this AminoAcidSequence in the given String of bases.

searchFor(String, int, boolean)

Search for this AminoAcidSequence in the given String of bases.

searchForwardFor(String, int)

Search forward for this AminoAcidSequence in the given String of bases.

toString()

Return a string representation of this object.

 public static final char codon_translation_array[]

This table is used for fast lookup of codon translations by getCodonTranslation (). There is one entry for each codon and the entries are in this order: TTT, TTC, TTA, TTG, TCT, TCC, ...

 public static final int POLAR_UNCHARGED_AA

Used by getAminoAcidType ().

 public static final int POSITIVELY_CHARGED_AA

Used by getAminoAcidType ().

 public static final int NEGATIVELY_CHARGED_AA

Used by getAminoAcidType ().

 public static final int HYDROPHOBIC_AA

Used by getAminoAcidType ().

 public static final int SPECIAL_AA

Used by getAminoAcidType ().

 public static final int STOP_AA

Used by getAminoAcidType ().

 public static final int UNKNOWN_AA

Used by getAminoAcidType ().

 public static final int ILLEGAL_AA

Used by getAminoAcidType ().

 public static final int symbol_count

The number of amino acid symbols, including stop codons and a symbol for unknown (---): 23.

 public static final int amino_acid_symbol_count

The number of amino acid symbols, not including stop codons: 20.

 public AminoAcidSequence(String amino_acid_string)

Create a new AminoAcidSequence object from a string containing single character amino acids symbols.

 public static AminoAcidSequence getTranslation(String bases,
                                                boolean unknown_is_x)

Translate a sequence of bases into the corresponding single letter amino acid codes.

Parameters:

bases - The bases to translated. If the string length is not a multiple of three the last codon is incomplete and will not be translated.

unknown_is_x - If this parameter is true codons that contain ambiguous bases will be translated as 'x', if false they will be translated as '.'

Returns:

The translated sequence in one letter abbreviated form.

 public static char getCodonTranslation(String codon_string)

Translate a single codon into the corresponding single letter amino acid code.

Parameters:

codon_string - A three character lowercase String containing the bases to translate.

Returns:

The translated sequence in one letter abbreviated form. The return value will be '.' if the codon_string isn't a codon (eg. it contains more or less than three letters or the letters aren't from "CTAG")

 public static char getCodonTranslation(char first_letter,
                                        char second_letter,
                                        char third_letter)

Translate a single codon into the corresponding single letter amino acid code.

Parameters:

first_letter - The first base of the codon.

second_letter - The second base of the codon.

third_letter - The third base of the codon.

Returns:

The translated sequence in one letter abbreviated form. The return value will be '.' if the letters do not form a codon.

 public int length()

Return the number of units in this amino acid sequence.

 public char elementAt(int index)

Return the one letter codon code of the codon at the given index (counting from zero).

 public float getMolecularWeight()

Return the total molecular weight of the amino acids in this AminoAcidSequence..

 public String toString()

Return a string representation of this object. This string will contain the one character amino acid codes for each acid in sequence.

Overrides:

toString in class Object

 public boolean checkForMatch(AminoAcidSequence subject_sequence)

Search the subject_sequence for this AminoAcidSequence as a substring. 'X' AAs are treated as wildcards in both sequences.

 public MarkerRange findMatch(Bases bases,
                              Marker search_start_marker,
                              boolean search_backwards)

Find the next occurrence of this seqeuence on either Strand of the given Bases object. This method searches both strands simultaneously by searching the underlying Bases object directly.

Parameters:

bases - This holds the Strand objects to search.

search_start_marker - The match that will be returned will be after this base Marker position. Position 1 on the reverse strand is considered to be after position 1 on the forward strand, forward position 2 is after reverse position 1, reverse position 2 is after forward position 2, etc. This scheme allows the caller to iterate through all matches.

search_end_position - The search will not extend past this position.

search_backwards - If true the search will move from last base to first base, otherwise first to last.

Returns:

A MarkerRange covering the matching bases or null if there is no match in the given range.

 public int searchFor(String bases_string,
                      int start_index,
                      boolean search_backwards)

Search for this AminoAcidSequence in the given String of bases. The String is treated as a sequence of bases and this AminoAcidSequence is searched for in each of the three reading frames.

Parameters:

bases_string - Search this String for the amino acid sequence.

start_index - This is the index in bases_string where the search should start.

search_backwards - If true the search will move from last base to first base, otherwise first to last.

Returns:

The index of the match or -1 if there is no match.

 public int searchForwardFor(String bases_string,
                             int start_index)

Search forward for this AminoAcidSequence in the given String of bases. The String is treated as a sequence of bases and this AminoAcidSequence is searched for in each of the three reading frames.

Parameters:

bases_string - Search this String for the amino acid sequence.

start_index - This is the index in bases_string where the search should start.

Returns:

The index of the match or -1 if there is no match.

 public int searchBackwardFor(String bases_string,
                              int start_index)

Search backward for this AminoAcidSequence in the given String of bases. The String is treated as a sequence of bases and this AminoAcidSequence is searched for in each of the three reading frames.

Parameters:

bases_string - Search this String for the amino acid sequence.

start_index - This is the index in bases_string where the search should start.

Returns:

The index of the match or -1 if there is no match.

 public int reverseComplementSearchFor(String bases_string,
                                       int start_index,
                                       boolean search_backwards)

Search for this AminoAcidSequence in the reverse complement of the given String of bases. The String is treated as a sequence of bases and this AminoAcidSequence is searched for in each of the three reading frames.

Parameters:

bases_string - Search this String for the amino acid sequence.

start_index - This is the index in bases_string where the search should start.

search_backwards - If true the search will move from last base to first base, otherwise first to last.

Returns:

The index of the match or -1 if there is no match.

 public int reverseComplementSearchForwardFor(String bases_string,
                                              int start_index)

Search forward for this AminoAcidSequence in the reverse complement of the given String of bases. The String is treated as a sequence of bases and this AminoAcidSequence is searched for in each of the three reading frames.

Parameters:

bases_string - Search this String for the amino acid sequence.

start_index - This is the index in bases_string where the search should start.

Returns:

The index of the match or -1 if there is no match.

 public int reverseComplementSearchBackwardFor(String bases_string,
                                               int start_index)

Search backward for this AminoAcidSequence in the reverse complement of the given String of bases. The String is treated as a sequence of bases and this AminoAcidSequence is searched for in each of the three reading frames.

Parameters:

bases_string - Search this String for the amino acid sequence.

start_index - This is the index in bases_string where the search should start.

Returns:

The index of the match or -1 if there is no match.

 public boolean containsStopCodon()

Return true if and only if this sequence contains a stop codon.

 public static boolean isStopCodon(char amino_acid_char)

Return true if and only if the given amino acid symbol is the translation of a stop codon. ie #, * or +.

 public static boolean isLegalCodon(char one_letter_code)

Return true if and only if the given one letter code symbol is the a legal amino acid or stop symbol.

 public static int getAminoAcidType(char aa_char)

Returns one of POLAR_UNCHARGED_AA, POSITIVELY_CHARGED_AA, NEGATIVELY_CHARGED_AA, HYDROPHOBIC_AA, SPECIAL_AA or STOP_AA depending on the aa_char argument.

 public static char getOneLetterCode(String three_letter_code)

Return the one letter abbreviation for the given three letter amino acid name.

Returns:

A one letter code or -1 if three_letter_code can't be understood.

 public static String getThreeLetterAbbreviation(char one_letter_code)

Return the three letter abbreviation for the given one letter amino acid code.

 public static String getThreeLetterAbbreviation(int index)

Return the three letter abbreviation for the given index code.

 public static int getSymbolIndex(char one_letter_code)

Return an integer from 0 to 22 representing the index of a codon symbol.

 public static char getSymbolFromIndex(int index)

Given an index return a one letter codon symbol. This method is the inverse of getSymbolIndex ().

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