Constant Field Values

Contents

• statalign.*

statalign.*

statalign.StatAlign

public static final int	majorVersion	3
public static final int	minorVersion	1
public static final java.lang.String	version	"v3.1"
public static final java.lang.String	webPageURL	"http://statalign.github.io/"

statalign.base.*

statalign.base.AutomateParameters

public static final double

PERCENT_CONST

0.998

statalign.base.Utils

public static final boolean	DOWNWEIGHT_INDEL_LIKELIHOOD	false
public static final double	log0	-1d/0d
public static final double	LOW_COUNT_MULTIPLIER	0.999
public static final int	LOW_COUNT_THRESHOLD	10
public static final double	MAX_ACCEPTANCE	0.4
public static final int	MAX_SILENT_LENGTH	10
public static final double	MIN_ACCEPTANCE	0.2
public static final double	MIN_EDGE_LENGTH	0.01
public static final double	MIN_SAMPLES_FOR_ACC_ESTIMATE	10.0
public static final int	MIN_SEQ_LENGTH	1
public static final boolean	SHAKE_IF_STUCK	true
public static final double	SILENT_INSERT_PROB	0.5
public static final double	SPAN_MULTIPLIER	0.7
public static final boolean	USE_INDEL_CORRECTION_FACTOR	true

statalign.base.mcmc.AlignmentMove

public static final double	MAX_WINDOW_MULTIPLIER	1.5
public static final double	MIN_WINDOW_MULTIPLIER	0.5

statalign.model.*

statalign.model.ext.plugins.StructAlign

public final double	angleP	1000.0
public final double	xlatP	0.1

statalign.model.ext.plugins.structalign.AlignmentMove

public static final double	MAX_WINDOW_MULTIPLIER	1.5
public static final double	MIN_WINDOW_MULTIPLIER	0.5

statalign.model.subst.plugins.AminoAcidModel

public static final java.lang.String

type

"protein"

statalign.model.subst.plugins.Blosum

public static final java.lang.String

menuName

"Blosum rate"

statalign.model.subst.plugins.Dayhoff

public static final java.lang.String

menuName

"Dayhoff"

statalign.model.subst.plugins.Felsenstein81

public static final java.lang.String

menuName

"Felsenstein 1981"

statalign.model.subst.plugins.Felsenstein84

public static final java.lang.String

menuName

"Felsenstein 1984"

statalign.model.subst.plugins.HKY85

public static final java.lang.String

menuName

"Hasegawa/Kishino/Yano 1985"

statalign.model.subst.plugins.Jones

public static final java.lang.String

menuName

"Jones"

statalign.model.subst.plugins.JukesCantor

public static final java.lang.String

menuName

"Jukes-Cantor"

statalign.model.subst.plugins.Kimura3

public static final java.lang.String

menuName

"Kimura 3 parameters"

statalign.model.subst.plugins.MtMam

public static final java.lang.String

menuName

"Mammalian mitochondrial"

statalign.model.subst.plugins.MtREV

public static final java.lang.String

menuName

"Mitochondrial REV"

statalign.model.subst.plugins.ReversibleNucleotide

public static final java.lang.String

menuName

"General Reversible (Nucl.)"

statalign.model.subst.plugins.RtREV

public static final java.lang.String

menuName

"Retrovirus"

statalign.model.subst.plugins.Tamura92

public static final java.lang.String

menuName

"Tamura 1992"

statalign.model.subst.plugins.TamuraNei

public static final java.lang.String

menuName

"Tamura/Nei"

statalign.model.subst.plugins.Vt

public static final java.lang.String

menuName

"Muller-Vingron"

statalign.model.subst.plugins.Wag

public static final java.lang.String

menuName

"WAG"

statalign.postprocess.*

statalign.postprocess.gui.CNetworkView

public final int

zoomDivisor

20

statalign.postprocess.gui.DistanceGUI

public static final int	OFFSET_X	50
public static final int	TITLE_X	100
public static final int	TITLE_Y	30

statalign.postprocess.gui.EntropyGUI

public static final int	OFFSET_X	50
public static final int	TITLE_X	100
public static final int	TITLE_Y	30

statalign.postprocess.gui.PPFoldGUI

public static final int

OFFSET

5

statalign.postprocess.gui.treeviews.NetworkTreeView

public final int

zoomDivisor

20

statalign.postprocess.utils.RNAFoldingTools

public static final double

emptyValue

1.7976931348623157E308

statalign.ui.*

statalign.ui.MainFrame

public static final java.lang.String	DEV_MANUAL	"doc/developer_manual.html"
public static final java.lang.String	IDLE_STATUS_MESSAGE	" StatAlign :: Ready"
public static final java.lang.String	JAVADOCS	"doc/javadoc/index.html"
public static final java.lang.String	USER_MANUAL	"doc/user_manual.html"
public static final java.lang.String	WELCOME_MSG	"<html><div style=\'padding: 20px 20px 20px 20px; font-family: Arial; font-size: 12px\'><h2>Welcome to StatAlign!</h2><br><p>To get started, please <a href=\'http://add\'>add sequences</a> (and optionally structures) to analyse.<p>If you need any help along the way, please refer to the <a href=\'http://doc\'>manual</a>, which is available from the <b>Help menu.</b><br><br><p>Happy StatAligning!</div></html>"

statalign.utils.*

statalign.utils.BetaDistribution

public static final double

DEFAULT_INVERSE_ABSOLUTE_ACCURACY

1.0E-9

statalign.utils.GammaDistribution

public static final double

DEFAULT_INVERSE_ABSOLUTE_ACCURACY

1.0E-9

statalign.utils.NormalDistribution

public static final double

DEFAULT_INVERSE_ABSOLUTE_ACCURACY

1.0E-9