A B C F G H I L M N O P R S T U V Z

A

aa - Static variable in class org.biojava.nbio.phylo.ResidueProperties

aa2Triplet - Static variable in class org.biojava.nbio.phylo.ResidueProperties

aa3Hash - Static variable in class org.biojava.nbio.phylo.ResidueProperties

aaIndex - Static variable in class org.biojava.nbio.phylo.ResidueProperties

addProgessListener(NJTreeProgressListener) - Method in class org.biojava.nbio.phylo.TreeConstructor

Ala - Static variable in class org.biojava.nbio.phylo.ResidueProperties

aliphatic - Static variable in class org.biojava.nbio.phylo.ResidueProperties

Arg - Static variable in class org.biojava.nbio.phylo.ResidueProperties

aromatic - Static variable in class org.biojava.nbio.phylo.ResidueProperties

Asn - Static variable in class org.biojava.nbio.phylo.ResidueProperties

Asp - Static variable in class org.biojava.nbio.phylo.ResidueProperties

B

broadcastComplete() - Method in class org.biojava.nbio.phylo.TreeConstructor

buried - Static variable in class org.biojava.nbio.phylo.ResidueProperties

buriedmax - Static variable in class org.biojava.nbio.phylo.ResidueProperties

buriedmin - Static variable in class org.biojava.nbio.phylo.ResidueProperties

C

cancel() - Method in class org.biojava.nbio.phylo.TreeConstructor

canceled(Object) - Method in interface org.biojava.nbio.phylo.NJTreeProgressListener

canceled(Object) - Method in class org.biojava.nbio.phylo.ProgressListenerStub

charged - Static variable in class org.biojava.nbio.phylo.ResidueProperties

CheckTreeAccuracy - Class in org.biojava.nbio.phylo

CheckTreeAccuracy() - Constructor for class org.biojava.nbio.phylo.CheckTreeAccuracy

codonHash - Static variable in class org.biojava.nbio.phylo.ResidueProperties

codonHash2 - Static variable in class org.biojava.nbio.phylo.ResidueProperties

codonTranslate(String) - Static method in class org.biojava.nbio.phylo.ResidueProperties

Comparison - Class in org.biojava.nbio.phylo

Comparison() - Constructor for class org.biojava.nbio.phylo.Comparison

complete(Object) - Method in interface org.biojava.nbio.phylo.NJTreeProgressListener

complete(Object) - Method in class org.biojava.nbio.phylo.ProgressListenerStub

copyMatrix(DistanceMatrix) - Static method in class org.biojava.nbio.phylo.CheckTreeAccuracy

Cys - Static variable in class org.biojava.nbio.phylo.ResidueProperties

F

findCommonParent(PhylogenyNode, Set<PhylogenyNode>) - Method in class org.biojava.nbio.phylo.CheckTreeAccuracy

G

getAA3Hash() - Static method in class org.biojava.nbio.phylo.ResidueProperties

getBLOSUM62() - Static method in class org.biojava.nbio.phylo.ResidueProperties

getBLOSUM62(char, char) - Static method in class org.biojava.nbio.phylo.ResidueProperties

getCodons(String) - Static method in class org.biojava.nbio.phylo.ResidueProperties

getDefaultDnaMatrix() - Static method in class org.biojava.nbio.phylo.ResidueProperties

getDefaultPeptideMatrix() - Static method in class org.biojava.nbio.phylo.ResidueProperties

getDistanceMatrix() - Method in class org.biojava.nbio.phylo.TreeConstructor

getDNA() - Static method in class org.biojava.nbio.phylo.ResidueProperties

getDssp3state(String) - Static method in class org.biojava.nbio.phylo.ResidueProperties

translate from other dssp secondary structure alphabets to 3-state

getHyd() - Static method in class org.biojava.nbio.phylo.ResidueProperties

getHydmax() - Static method in class org.biojava.nbio.phylo.ResidueProperties

getHydmin() - Static method in class org.biojava.nbio.phylo.ResidueProperties

getMatrix() - Method in class org.biojava.nbio.phylo.ScoreMatrix

getNewickString(boolean, boolean) - Method in class org.biojava.nbio.phylo.TreeConstructor

getNodeDistance(PhylogenyNode, PhylogenyNode) - Method in class org.biojava.nbio.phylo.CheckTreeAccuracy

getPairwiseScore(String, String) - Method in class org.biojava.nbio.phylo.ScoreMatrix

getPairwiseScore(char, char) - Method in class org.biojava.nbio.phylo.ScoreMatrix

getPAM250(String, String) - Static method in class org.biojava.nbio.phylo.ResidueProperties

getPAM250(char, char) - Static method in class org.biojava.nbio.phylo.ResidueProperties

getScoreMatrix(String) - Static method in class org.biojava.nbio.phylo.ResidueProperties

get a ScoreMatrix based on its string name

Gln - Static variable in class org.biojava.nbio.phylo.ResidueProperties

Glu - Static variable in class org.biojava.nbio.phylo.ResidueProperties

Gly - Static variable in class org.biojava.nbio.phylo.ResidueProperties

H

helix - Static variable in class org.biojava.nbio.phylo.ResidueProperties

helixmax - Static variable in class org.biojava.nbio.phylo.ResidueProperties

helixmin - Static variable in class org.biojava.nbio.phylo.ResidueProperties

His - Static variable in class org.biojava.nbio.phylo.ResidueProperties

hyd - Static variable in class org.biojava.nbio.phylo.ResidueProperties

hyd2 - Static variable in class org.biojava.nbio.phylo.ResidueProperties

hydmax - Static variable in class org.biojava.nbio.phylo.ResidueProperties

hydmin - Static variable in class org.biojava.nbio.phylo.ResidueProperties

hydrophobic - Static variable in class org.biojava.nbio.phylo.ResidueProperties

I

Ile - Static variable in class org.biojava.nbio.phylo.ResidueProperties

isDNA() - Method in class org.biojava.nbio.phylo.ScoreMatrix

isGap(char) - Static method in class org.biojava.nbio.phylo.Comparison

DOCUMENT ME!

isProtein() - Method in class org.biojava.nbio.phylo.ScoreMatrix

L

Leu - Static variable in class org.biojava.nbio.phylo.ResidueProperties

Lys - Static variable in class org.biojava.nbio.phylo.ResidueProperties

M

main(String[]) - Static method in class org.biojava.nbio.phylo.ResidueProperties

main(String[]) - Static method in class org.biojava.nbio.phylo.TreeConstructor

markPathToRoot(PhylogenyNode, Set<PhylogenyNode>) - Method in class org.biojava.nbio.phylo.CheckTreeAccuracy

Met - Static variable in class org.biojava.nbio.phylo.ResidueProperties

midBlue - Static variable in class org.biojava.nbio.phylo.ResidueProperties

N

negative - Static variable in class org.biojava.nbio.phylo.ResidueProperties

NJTreeProgressListener - Interface in org.biojava.nbio.phylo

nucleotide - Static variable in class org.biojava.nbio.phylo.ResidueProperties

nucleotideIndex - Static variable in class org.biojava.nbio.phylo.ResidueProperties

nucleotideName - Static variable in class org.biojava.nbio.phylo.ResidueProperties

O

org.biojava.nbio.phylo - package org.biojava.nbio.phylo

outputPhylipDistances(String) - Method in class org.biojava.nbio.phylo.TreeConstructor

P

Phe - Static variable in class org.biojava.nbio.phylo.ResidueProperties

PID(String, String) - Static method in class org.biojava.nbio.phylo.Comparison

this is a gapped PID calculation

PID(String, String, int, int) - Static method in class org.biojava.nbio.phylo.Comparison

pidColours - Static variable in class org.biojava.nbio.phylo.ResidueProperties

pidThresholds - Static variable in class org.biojava.nbio.phylo.ResidueProperties

polar - Static variable in class org.biojava.nbio.phylo.ResidueProperties

positive - Static variable in class org.biojava.nbio.phylo.ResidueProperties

Pro - Static variable in class org.biojava.nbio.phylo.ResidueProperties

process(Phylogeny, DistanceMatrix) - Method in class org.biojava.nbio.phylo.CheckTreeAccuracy

process() - Method in class org.biojava.nbio.phylo.TreeConstructor

progress(Object, String, int) - Method in interface org.biojava.nbio.phylo.NJTreeProgressListener

progress(Object, String, int, int) - Method in interface org.biojava.nbio.phylo.NJTreeProgressListener

progress(Object, String, int) - Method in class org.biojava.nbio.phylo.ProgressListenerStub

progress(Object, String, int, int) - Method in class org.biojava.nbio.phylo.ProgressListenerStub

ProgressListenerStub - Class in org.biojava.nbio.phylo

ProgressListenerStub() - Constructor for class org.biojava.nbio.phylo.ProgressListenerStub

proline - Static variable in class org.biojava.nbio.phylo.ResidueProperties

propHash - Static variable in class org.biojava.nbio.phylo.ResidueProperties

R

removeProgessListener(NJTreeProgressListener) - Method in class org.biojava.nbio.phylo.TreeConstructor

ResidueProperties - Class in org.biojava.nbio.phylo

run() - Method in class org.biojava.nbio.phylo.TreeConstructor

S

scaleColours - Static variable in class org.biojava.nbio.phylo.ResidueProperties

scoreMatrices - Static variable in class org.biojava.nbio.phylo.ResidueProperties

ScoreMatrix - Class in org.biojava.nbio.phylo

Ser - Static variable in class org.biojava.nbio.phylo.ResidueProperties

small - Static variable in class org.biojava.nbio.phylo.ResidueProperties

ssHash - Static variable in class org.biojava.nbio.phylo.ResidueProperties

STOP - Static variable in class org.biojava.nbio.phylo.ResidueProperties

strand - Static variable in class org.biojava.nbio.phylo.ResidueProperties

strandmax - Static variable in class org.biojava.nbio.phylo.ResidueProperties

strandmin - Static variable in class org.biojava.nbio.phylo.ResidueProperties

T

taylor - Static variable in class org.biojava.nbio.phylo.ResidueProperties

Thr - Static variable in class org.biojava.nbio.phylo.ResidueProperties

tiny - Static variable in class org.biojava.nbio.phylo.ResidueProperties

toDssp3State - Static variable in class org.biojava.nbio.phylo.ResidueProperties

TreeConstructionAlgorithm - Enum in org.biojava.nbio.phylo

TreeConstructor<C extends AbstractSequence<D>,D extends Compound> - Class in org.biojava.nbio.phylo

Tree constructor uses the forrester tree library to build phylogenetic trees using neighbor joining algorithm.

TreeConstructor(MultipleSequenceAlignment<C, D>, TreeType, TreeConstructionAlgorithm, NJTreeProgressListener) - Constructor for class org.biojava.nbio.phylo.TreeConstructor

TreeConstructor(BasicSymmetricalDistanceMatrix, TreeType, TreeConstructionAlgorithm, NJTreeProgressListener) - Constructor for class org.biojava.nbio.phylo.TreeConstructor

TreeType - Enum in org.biojava.nbio.phylo

Trp - Static variable in class org.biojava.nbio.phylo.ResidueProperties

turn - Static variable in class org.biojava.nbio.phylo.ResidueProperties

turnmax - Static variable in class org.biojava.nbio.phylo.ResidueProperties

turnmin - Static variable in class org.biojava.nbio.phylo.ResidueProperties

Tyr - Static variable in class org.biojava.nbio.phylo.ResidueProperties

U

updateProgress(String, int) - Method in class org.biojava.nbio.phylo.TreeConstructor

updateProgress(String, int, int) - Method in class org.biojava.nbio.phylo.TreeConstructor

V

Val - Static variable in class org.biojava.nbio.phylo.ResidueProperties

valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeConstructionAlgorithm

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.biojava.nbio.phylo.TreeType

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.biojava.nbio.phylo.TreeConstructionAlgorithm

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.biojava.nbio.phylo.TreeType

Returns an array containing the constants of this enum type, in the order they are declared.

Z

zappo - Static variable in class org.biojava.nbio.phylo.ResidueProperties

A B C F G H I L M N O P R S T U V Z