Index

A C D E I L M O R S T W
All Classes|All Packages

A

alternate - Variable in class org.monarchinitiative.vmvt.cli.commands.SequenceComparisonCommand

C

call() - Method in class org.monarchinitiative.vmvt.cli.commands.DeltaCommand

call() - Method in class org.monarchinitiative.vmvt.cli.commands.EseCommand

call() - Method in class org.monarchinitiative.vmvt.cli.commands.LogoCommand

call() - Method in class org.monarchinitiative.vmvt.cli.commands.RulerCommand

call() - Method in class org.monarchinitiative.vmvt.cli.commands.TrekCommand

call() - Method in class org.monarchinitiative.vmvt.cli.commands.WalkerCommand

call() - Method in class org.monarchinitiative.vmvt.cli.Main

D

DeltaCommand - Class in org.monarchinitiative.vmvt.cli.commands

DeltaCommand() - Constructor for class org.monarchinitiative.vmvt.cli.commands.DeltaCommand

E

EseCommand - Class in org.monarchinitiative.vmvt.cli.commands

Create an SVG representing the distribution of ESE scores

EseCommand() - Constructor for class org.monarchinitiative.vmvt.cli.commands.EseCommand

eseLength - Variable in class org.monarchinitiative.vmvt.cli.commands.EseCommand

Length, either 6 (hexamer) or 7 (heptameter)

I

infile - Variable in class org.monarchinitiative.vmvt.cli.commands.SequenceComparisonCommand

initSequences() - Method in class org.monarchinitiative.vmvt.cli.commands.SequenceComparisonCommand

Users are allowed t pass both sequences on the command line or to pass the path to a file that contains ref on the first line and alt on the second line.

isAcceptor - Variable in class org.monarchinitiative.vmvt.cli.commands.LogoCommand

isDonor - Variable in class org.monarchinitiative.vmvt.cli.commands.LogoCommand

L

LogoCommand - Class in org.monarchinitiative.vmvt.cli.commands

Print an SVG with the donor or acceptor logo.

LogoCommand() - Constructor for class org.monarchinitiative.vmvt.cli.commands.LogoCommand

M

main(String[]) - Static method in class org.monarchinitiative.vmvt.cli.Main

Main - Class in org.monarchinitiative.vmvt.cli

Main entry point to the command-line interface of vmvt.

Main() - Constructor for class org.monarchinitiative.vmvt.cli.Main

O

org.monarchinitiative.vmvt.cli - module org.monarchinitiative.vmvt.cli

org.monarchinitiative.vmvt.cli - package org.monarchinitiative.vmvt.cli

org.monarchinitiative.vmvt.cli.commands - package org.monarchinitiative.vmvt.cli.commands

outname - Variable in class org.monarchinitiative.vmvt.cli.commands.LogoCommand

outname - Variable in class org.monarchinitiative.vmvt.cli.commands.SequenceComparisonCommand

R

readInputFile() - Method in class org.monarchinitiative.vmvt.cli.commands.SequenceComparisonCommand

reference - Variable in class org.monarchinitiative.vmvt.cli.commands.SequenceComparisonCommand

RulerCommand - Class in org.monarchinitiative.vmvt.cli.commands

Print an SVG with the donor or acceptor ruler.

RulerCommand() - Constructor for class org.monarchinitiative.vmvt.cli.commands.RulerCommand

S

seqlen - Variable in class org.monarchinitiative.vmvt.cli.commands.SequenceComparisonCommand

Length of the sequences.

SequenceComparisonCommand - Class in org.monarchinitiative.vmvt.cli.commands

SequenceComparisonCommand() - Constructor for class org.monarchinitiative.vmvt.cli.commands.SequenceComparisonCommand

T

TrekCommand - Class in org.monarchinitiative.vmvt.cli.commands

TrekCommand() - Constructor for class org.monarchinitiative.vmvt.cli.commands.TrekCommand

W

WalkerCommand - Class in org.monarchinitiative.vmvt.cli.commands

WalkerCommand() - Constructor for class org.monarchinitiative.vmvt.cli.commands.WalkerCommand

A C D E I L M O R S T W
All Classes|All Packages