B D G N P S T

B

BiojavaDNA - Class in net.bioclipse.biojava.domain

BiojavaDNA(Sequence) - Constructor for class net.bioclipse.biojava.domain.BiojavaDNA

BiojavaDNA() - Constructor for class net.bioclipse.biojava.domain.BiojavaDNA

BiojavaManager - Class in net.bioclipse.managers

Bioclipse manager that provides BioJava functionality.

BiojavaManager(String) - Constructor for class net.bioclipse.managers.BiojavaManager

Creates a new BiojavaManager.

BiojavaProtein - Class in net.bioclipse.biojava.domain

BiojavaProtein(Sequence) - Constructor for class net.bioclipse.biojava.domain.BiojavaProtein

BiojavaProtein() - Constructor for class net.bioclipse.biojava.domain.BiojavaProtein

BiojavaSequence - Class in net.bioclipse.biojava.domain

BiojavaSequence(Sequence) - Constructor for class net.bioclipse.biojava.domain.BiojavaSequence

Create a BiojavaSequence from a RichSequence

BiojavaSequence() - Constructor for class net.bioclipse.biojava.domain.BiojavaSequence

D

DNAfromPlainSequence(String) - Method in class net.bioclipse.managers.BiojavaManager

DNAfromPlainSequence(String, String) - Method in class net.bioclipse.managers.BiojavaManager

doi() - Method in class net.bioclipse.managers.BiojavaManager

G

getAdapter(Class) - Method in class net.bioclipse.biojava.domain.BiojavaSequence

getManagerName() - Method in class net.bioclipse.managers.BiojavaManager

getName() - Method in class net.bioclipse.biojava.domain.BiojavaSequence

getParsedResource() - Method in class net.bioclipse.biojava.domain.BiojavaSequence

Returns the RichSequence

getPlainSequence() - Method in class net.bioclipse.biojava.domain.BiojavaSequence

N

net.bioclipse.biojava.domain - package net.bioclipse.biojava.domain

net.bioclipse.managers - package net.bioclipse.managers

P

proteinFromPlainSequence(String) - Method in class net.bioclipse.managers.BiojavaManager

proteinFromPlainSequence(String, String) - Method in class net.bioclipse.managers.BiojavaManager

S

setRichSequence(RichSequence) - Method in class net.bioclipse.biojava.domain.BiojavaSequence

T

toFasta() - Method in class net.bioclipse.biojava.domain.BiojavaSequence

Convert RichSequence to FASTA and return as String

toString() - Method in class net.bioclipse.biojava.domain.BiojavaDNA

toString() - Method in class net.bioclipse.biojava.domain.BiojavaProtein

B D G N P S T