A B C D E F G H I K L M N O P Q R S T U V W X Y

A

Amber - Static variable in class kea.programs.pintail.TrafficLightSetting
Amber light on, all others off.

B

BACKGROUND_COLOUR - Static variable in interface kea.programs.pintail.Constants
 
badSequences(String, String) - Method in class kea.programs.pintail.MainClass
 
badSequences(String, String) - Method in class kea.programs.pintail.MainPanel
 
badSequences(Window, String, String) - Static method in class kea.programs.pintail.PintailUtil
 
BOLD_FONT - Static variable in interface kea.programs.pintail.Constants
 

C

clear() - Method in class kea.programs.pintail.GraphPanel
Clears graph.
clear() - Method in class kea.programs.pintail.InformationPanel1
 
clear() - Method in class kea.programs.pintail.InformationPanel2
 
clear() - Method in class kea.programs.pintail.MessagePanel
Clears text.
clear() - Method in class kea.programs.pintail.ResultsPanel
 
clear() - Method in class kea.programs.pintail.TablePanel
 
ColouredNumberField - Class in kea.programs.pintail
Component for displaying numerical data.
ColouredNumberField(double, Color, int) - Constructor for class kea.programs.pintail.ColouredNumberField
Creates a new instance of ColouredNumberField.
Constants - Interface in kea.programs.pintail
Constants used by various classes within pintail package.
convertToSimpleConsensusString(String) - Static method in class kea.programs.pintail.PintailUtil
 
CUT_OFF_TYPE - Static variable in interface kea.programs.pintail.Constants
 
CutOffType - Class in kea.programs.pintail
 
CV_UPPER_LIMIT - Static variable in interface kea.programs.pintail.Constants
 

D

DEFAULT_STEP_SIZE - Static variable in interface kea.programs.pintail.Constants
 
DEFAULT_WINDOW_SIZE - Static variable in interface kea.programs.pintail.Constants
 

E

ECOLI - Static variable in interface kea.programs.pintail.Constants
 
ECOLI_LABEL - Static variable in interface kea.programs.pintail.Constants
 
editConsensusString(String, String) - Static method in class kea.programs.pintail.PintailUtil
 
ERROR_BAR_SIZE - Static variable in interface kea.programs.pintail.Constants
 
ERROR_Y_AXIS_END - Static variable in interface kea.programs.pintail.Constants
 
ERROR_Y_AXIS_START - Static variable in interface kea.programs.pintail.Constants
 

F

FIRST_SEQUENCE_NAME - Static variable in interface kea.programs.pintail.Constants
 
FOREGROUND_COLOUR - Static variable in interface kea.programs.pintail.Constants
 

G

generateExpectedScores(float[], int, int, float, int, int) - Static method in class kea.programs.pintail.PintailUtil
 
generateObservedScores(int, int, String) - Static method in class kea.programs.pintail.PintailUtil
 
getGraphPanel() - Method in class kea.programs.pintail.ResultsPanel
 
getPrintGraphAction() - Method in class kea.programs.pintail.GraphPanel
Returns the 'Print graph' action associated with panel.
getSaveGraphAction() - Method in class kea.programs.pintail.GraphPanel
Returns the 'Save graph' action associated with panel.
getShowDataAction() - Method in class kea.programs.pintail.GraphPanel
Returns the 'show data' action associated with panel.
getStandardError(double, QuantileType, CutOffType) - Static method in class kea.programs.pintail.Model
Returns standard error of model data.
getTrafficLightSetting() - Method in class kea.programs.pintail.TrafficLight
 
getValue() - Method in class kea.programs.pintail.ColouredNumberField
Returns value currently displayed (i.e., raw value, not rounded).
GraphPanel - Class in kea.programs.pintail
Graph panel component.
GraphPanel(JFrame, int, int) - Constructor for class kea.programs.pintail.GraphPanel
Creates a new instance of GraphPanel.
GraphPanel(JFrame, int, int, boolean) - Constructor for class kea.programs.pintail.GraphPanel
Creates a new instance of GraphPanel.
GREATER_THAN - Static variable in interface kea.programs.pintail.Constants
 
Green - Static variable in class kea.programs.pintail.TrafficLightSetting
Green light on, all others off.

H

HEADING_FONT - Static variable in interface kea.programs.pintail.Constants
 
HIGH_MEAN - Static variable in interface kea.programs.pintail.Constants
 
HTML_END - Static variable in interface kea.programs.pintail.Constants
 
HTML_START - Static variable in interface kea.programs.pintail.Constants
 

I

InformationPanel - Class in kea.programs.pintail
 
InformationPanel() - Constructor for class kea.programs.pintail.InformationPanel
Creates a new instance of InformationPanel.
InformationPanel1 - Class in kea.programs.pintail
 
InformationPanel1() - Constructor for class kea.programs.pintail.InformationPanel1
Creates a new instance of InformationPanel1.
InformationPanel2 - Class in kea.programs.pintail
 
InformationPanel2() - Constructor for class kea.programs.pintail.InformationPanel2
Creates a new instance of InformationPanel2.

K

kea.programs.pintail - package kea.programs.pintail
 

L

LARGE_BOLD_FONT - Static variable in interface kea.programs.pintail.Constants
 
LESS_THAN - Static variable in interface kea.programs.pintail.Constants
 
LinearFunction - Static variable in class kea.programs.pintail.CutOffType
 
LOW_MEAN - Static variable in interface kea.programs.pintail.Constants
 

M

MAC_OSX_CLUSTAL_PATH - Static variable in interface kea.programs.pintail.Constants
 
main(String[]) - Static method in class kea.programs.pintail.MainClass
Entry point for program.
main(String[]) - Static method in class kea.programs.pintail.OLD_MainClass
Entry point for program.
MainClass - Class in kea.programs.pintail
Main class for Pintail - a program for comparing two 16S rRNA gene sequences.
MainClass() - Constructor for class kea.programs.pintail.MainClass
Creates a new instance of MainClass.
MainPanel - Class in kea.programs.pintail
Main panel for Pintail - a panel version of MainClass - for use my other programs.
MainPanel(JFrame) - Constructor for class kea.programs.pintail.MainPanel
 
MAX_STEP_SIZE - Static variable in interface kea.programs.pintail.Constants
 
MAX_WINDOW_SIZE - Static variable in interface kea.programs.pintail.Constants
 
MessagePanel - Class in kea.programs.pintail
Component for displaying summary message.
MessagePanel(CutOffType, boolean) - Constructor for class kea.programs.pintail.MessagePanel
Creates a new instance of MessagePanel.
MessagePanel(CutOffType) - Constructor for class kea.programs.pintail.MessagePanel
Creates a new instance of MessagePanel.
MIN_STEP_SIZE - Static variable in interface kea.programs.pintail.Constants
 
MIN_WINDOW_SIZE - Static variable in interface kea.programs.pintail.Constants
 
MODEL - Static variable in interface kea.programs.pintail.Constants
 
Model - Class in kea.programs.pintail
Supplies information on expected scores line.

N

NoFunction - Static variable in class kea.programs.pintail.CutOffType
 
NoFunctionSmoothed - Static variable in class kea.programs.pintail.CutOffType
 
NULL_VALUE - Static variable in interface kea.programs.pintail.Constants
 

O

OBSERVED_SCORES_MEAN_CUT_OFF - Static variable in interface kea.programs.pintail.Constants
 
Off - Static variable in class kea.programs.pintail.TrafficLightSetting
All lights off.
OLD_MainClass - Class in kea.programs.pintail
Main class for Pintail - a chimera detecting program.
OLD_MainClass() - Constructor for class kea.programs.pintail.OLD_MainClass
Creates a new instance of MainClass.

P

PintailUtil - Class in kea.programs.pintail
 
PolynomialFunction - Static variable in class kea.programs.pintail.CutOffType
 
processWindowEvent(WindowEvent) - Method in class kea.programs.pintail.MainClass
Overrides base class method if the WINDOW_CLOSING window event is fired.
processWindowEvent(WindowEvent) - Method in class kea.programs.pintail.OLD_MainClass
Overrides base class method if the WINDOW_CLOSING window event is fired.

Q

QUANTILE_TYPE - Static variable in interface kea.programs.pintail.Constants
 

R

RC_LOWER_LIMIT - Static variable in interface kea.programs.pintail.Constants
 
RC_UPPER_LIMIT - Static variable in interface kea.programs.pintail.Constants
 
Red - Static variable in class kea.programs.pintail.TrafficLightSetting
Red light on, all others off.
ResultsPanel - Class in kea.programs.pintail
 
ResultsPanel(JFrame, CutOffType, int, int) - Constructor for class kea.programs.pintail.ResultsPanel
Creates a new instance of ResultsPanel.
ResultsTableDialog - Class in kea.programs.pintail
Displays data for lines plotted on graph.
ResultsTableDialog(Frame, String, String, String, String, String, String, CoordinateCollection, CoordinateCollection, CoordinateCollection, CoordinateCollection) - Constructor for class kea.programs.pintail.ResultsTableDialog
Creates a new instance of ResultsTableDialog.

S

scoresCoordinateCollection(float[], int, int, String, int) - Static method in class kea.programs.pintail.PintailUtil
 
SD_UPPER_LIMIT - Static variable in interface kea.programs.pintail.Constants
 
SECOND_SEQUENCE_NAME - Static variable in interface kea.programs.pintail.Constants
 
setConsensus(String) - Method in class kea.programs.pintail.MainPanel
 
setQuerySequence(NucleicAcidSequence) - Method in class kea.programs.pintail.MainPanel
 
setSeqs(String, String, String) - Method in class kea.programs.pintail.MainPanel
 
setSubjectSequence(NucleicAcidSequence) - Method in class kea.programs.pintail.MainPanel
 
setTrafficLight(TrafficLightSetting) - Method in class kea.programs.pintail.TrafficLight
 
setValue(double, Color) - Method in class kea.programs.pintail.ColouredNumberField
Sets value to be displayed.
showDialog() - Method in class kea.programs.pintail.SimpleTableDialog
Displays dialog.
SigmaFunction - Static variable in class kea.programs.pintail.CutOffType
 
SimpleTableDialog - Class in kea.programs.pintail
Simple dialog component for displaying data in table format.
SimpleTableDialog(Frame, String, String, String, CoordinateCollection) - Constructor for class kea.programs.pintail.SimpleTableDialog
Creates a new instance of SimpleTableDialog.
STEP_SIZE_USED_TO_CALCULATE_MODEL - Static variable in interface kea.programs.pintail.Constants
 
straightLineCoordinateCollection(float, float, String) - Static method in class kea.programs.pintail.PintailUtil
 

T

TablePanel - Class in kea.programs.pintail
 
TablePanel(CutOffType) - Constructor for class kea.programs.pintail.TablePanel
Creates a new instance of TablePanel.
TEXT_FONT - Static variable in interface kea.programs.pintail.Constants
 
TITLE_FONT - Static variable in interface kea.programs.pintail.Constants
 
TOO_HIGH_MEAN_FOR_ACCURATE_CONCLUSION - Static variable in interface kea.programs.pintail.Constants
 
toString() - Method in class kea.programs.pintail.CutOffType
Returns a string representation of CutOffType.
toString() - Method in class kea.programs.pintail.TrafficLightSetting
Returns a string representation of TrafficLightSetting.
TrafficLight - Class in kea.programs.pintail
Traffic light component.
TrafficLight(TrafficLightSetting) - Constructor for class kea.programs.pintail.TrafficLight
Creates a new instance of TrafficLight.
TrafficLightSetting - Class in kea.programs.pintail
Enum respresenting the different types of display available with an instance of TrafficLight class.

U

UNUSUALLY_HIGH_MEAN - Static variable in interface kea.programs.pintail.Constants
 
UNUSUALLY_LARGE_SEQUENCE - Static variable in interface kea.programs.pintail.Constants
 
update(int, int, int, int, double, CoordinateCollection, CoordinateCollection, CoordinateCollection, CoordinateCollection) - Method in class kea.programs.pintail.GraphPanel
Update display.
update(double, double, int, int) - Method in class kea.programs.pintail.InformationPanel
 
update(String, String) - Method in class kea.programs.pintail.InformationPanel1
 
update(int, int, double, double) - Method in class kea.programs.pintail.InformationPanel2
 
update(int, int, double, double) - Method in class kea.programs.pintail.MessagePanel
Updates display.
update(int, int, String, String, CoordinateCollection, CoordinateCollection, CoordinateCollection, CoordinateCollection, double, double) - Method in class kea.programs.pintail.ResultsPanel
 
update(int, int, double, double) - Method in class kea.programs.pintail.TablePanel
 

V

VALUE_FONT - Static variable in class kea.programs.pintail.ColouredNumberField
Text font.

W

WIN_CLUSTAL_PATH - Static variable in interface kea.programs.pintail.Constants
 
WIN_XP_CLUSTAL_PATH - Static variable in interface kea.programs.pintail.Constants
 
WINDOW_SIZE_USED_TO_CALCULATE_MODEL - Static variable in interface kea.programs.pintail.Constants
 

X

X_AXIS_END - Static variable in interface kea.programs.pintail.Constants
 
X_AXIS_START - Static variable in interface kea.programs.pintail.Constants
 

Y

Y_AXIS_END - Static variable in interface kea.programs.pintail.Constants
 
Y_AXIS_START - Static variable in interface kea.programs.pintail.Constants
 

A B C D E F G H I K L M N O P Q R S T U V W X Y