apollo.seq
Class ResidueProperties

java.lang.Object
  apollo.seq.ResidueProperties

public class ResidueProperties
extends java.lang.Object

DELETE THIS - was only used by apollo.gui.SeqMatchPanel, but that now uses org.bdgp.util.DNAUtils which is redundant with this class, and now takes into account genetic code (which this doesnt), so this class has been basically replaced by DNAUtils

Field Summary

static java.util.Vector	Ala
static java.util.Vector	Arg
static java.util.Vector	Asn
static java.util.Vector	Asp
static java.util.Hashtable	codonHash
static java.util.Hashtable	compressedCodonHash
static java.util.Vector	Cys
static java.util.Vector	Gln
static java.util.Vector	Glu
static java.util.Vector	Gly
static int	HIGH_AFFINITY
static java.util.Vector	His
static java.util.Vector	Ile
static java.util.Vector	Leu
static java.util.Vector	Lys
static java.util.Vector	Met
static int	NO_AFFINITY
protected static java.util.Hashtable	pamHash
static int	PERFECT_AFFINITY
static java.util.Vector	Phe
static java.util.Vector	Pro
static java.util.Vector	Ser
static int	SOME_AFFINITY
static java.util.Vector	STOP
static java.util.Vector	Thr
static java.util.Vector	Trp
static java.util.Vector	Tyr
static int	UNRECOGNIZED_VALUES
static java.util.Vector	Val

Constructor Summary

ResidueProperties()

Method Summary

protected static void	buildPAM()
static java.lang.String	codonTranslate(java.lang.String codon)
static int	getAARelationshipType(java.lang.String acid1, java.lang.String acid2)
static java.lang.String	getCodon(java.lang.String res)
static java.util.Vector	getCodons(java.lang.String res)
static java.lang.Integer	getDistance(java.lang.String acid1, java.lang.String acid2)
static boolean	isStop(java.lang.String codon)
static java.lang.String	reverseComplement(java.lang.String dna)
static java.lang.String	translate(java.lang.String dna, int phase)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

codonHash

public static java.util.Hashtable codonHash

compressedCodonHash

public static java.util.Hashtable compressedCodonHash

pamHash

protected static java.util.Hashtable pamHash

UNRECOGNIZED_VALUES

public static final int UNRECOGNIZED_VALUES

See Also:

Constant Field Values

NO_AFFINITY

public static final int NO_AFFINITY

See Also:

Constant Field Values

SOME_AFFINITY

public static final int SOME_AFFINITY

See Also:

Constant Field Values

HIGH_AFFINITY

public static final int HIGH_AFFINITY

See Also:

Constant Field Values

PERFECT_AFFINITY

public static final int PERFECT_AFFINITY

See Also:

Constant Field Values

Lys

public static java.util.Vector Lys

Asn

public static java.util.Vector Asn

Gln

public static java.util.Vector Gln

His

public static java.util.Vector His

Glu

public static java.util.Vector Glu

Asp

public static java.util.Vector Asp

Tyr

public static java.util.Vector Tyr

Thr

public static java.util.Vector Thr

Pro

public static java.util.Vector Pro

Ala

public static java.util.Vector Ala

Ser

public static java.util.Vector Ser

Arg

public static java.util.Vector Arg

Gly

public static java.util.Vector Gly

Trp

public static java.util.Vector Trp

Cys

public static java.util.Vector Cys

Ile

public static java.util.Vector Ile

Met

public static java.util.Vector Met

Leu

public static java.util.Vector Leu

Val

public static java.util.Vector Val

Phe

public static java.util.Vector Phe

STOP

public static java.util.Vector STOP

Constructor Detail

ResidueProperties

public ResidueProperties()

Method Detail

translate

public static java.lang.String translate(java.lang.String dna,
                                         int phase)

isStop

public static boolean isStop(java.lang.String codon)

reverseComplement

public static java.lang.String reverseComplement(java.lang.String dna)

getCodons

public static java.util.Vector getCodons(java.lang.String res)

getCodon

public static java.lang.String getCodon(java.lang.String res)

codonTranslate

public static java.lang.String codonTranslate(java.lang.String codon)

getDistance

public static java.lang.Integer getDistance(java.lang.String acid1,
                                            java.lang.String acid2)

getAARelationshipType

public static int getAARelationshipType(java.lang.String acid1,
                                        java.lang.String acid2)

buildPAM

protected static void buildPAM()