Uses of Class
org.mathIT.genes.ORF

Packages that use ORF

Package	Description
org.mathIT.genes	Provides classes to simulate biological amino acid sequences and to use the genetic code

Uses of ORF in org.mathIT.genes

Methods in org.mathIT.genes that return types with arguments of type ORF

Modifier and Type	Method and Description
static ArrayList<ORF>	ORF.decode(CharSequence string) Factory method producing a list of genes from a specified DNA base sequence of the letters A, C, G, T.
static ArrayList<ORF>	ORF.loadFASTA(boolean completeGenome) Returns a genome after opening a file in FASTA format, determined by a file chooser dialog.
static ArrayList<ORF>	ORF.loadORFs() Returns a genome after opening a file in GNOM format, found by a file chooser dialog.

Method parameters in org.mathIT.genes with type arguments of type ORF

Modifier and Type	Method and Description
static double	ORF.entropy(ArrayList<ORF> orfs) Returns the entropy of the frequency distribution of this gene.
static String	ORF.getFrequencyAsHTMLGraph(ArrayList<ORF> orfs) Returns the frequency distribution of the codons in the specified list of ORF's as HTML graph.
static String	ORF.getFrequencyAsHTMLTable(ArrayList<ORF> genes) Returns the frequency distribution of the codons in the specified list of genes as HTML table.
static void	ORF.save(ArrayList<ORF> orfs) Saves this genome in GENE format.