Constant Field Values

Contents

• phylosort.*

phylosort.*

phylosort.TreeCluster

public static final int

DEFAULT_MINIMUM_OVERLAP

1

phylosort.TreeNode

public static final float	DEFAULT_BRANCH_LENGTH	0.0f
public static final int	DEFAULT_ROOT_ID	0
public static final int	DEFAULT_ROOT_LEVEL	0
public static final int	INVALID_NODE_ID	-1

phylosort.util.*

phylosort.util.Commons

public static final java.lang.String	COMMENT_STARTER	"#"
public static final java.lang.String	DELIMITERS	" \t,;"
public static final java.lang.String	TAB	"\t"

phylosort.util.Config

public static final float	DEFAULT_MAXIMUM_AVERAGE_NUMBER_OF_COPIES	-1.0f
public static final int	DEFAULT_MAXIMUM_NUMBER_OF_TAXA	-1
public static final float	DEFAULT_MINIMUM_BOOTSTRAP_SUPPORT	-1.0f
public static final int	DEFAULT_MINIMUM_NUMBER_OF_TAXA	-1
public static final java.lang.String	DEFAULT_MODE	"inclusive"
public static final java.lang.String	DEFAULT_ON_MATCH_ACTION	"count"
public static final java.lang.String	DEFAULT_PHYLOSORT_FILE_NAME	"phylosort.config"
public static final java.lang.String	DEFAULT_REGEXP	"(.+)"
public static final java.lang.String	DEFAULT_ROOT	"yes"
public static final java.lang.String	PROPERTY_MAXIMUM_AVERAGE_NUMBER_OF_COPIES	"phylosort.maximum.average.number.copies"
public static final java.lang.String	PROPERTY_MAXIMUM_NUMBER_OF_TAXA	"phylosort.maximum.number.taxa"
public static final java.lang.String	PROPERTY_MINIMUM_BOOTSTRAP_SUPPORT	"phylosort.minimum.bootstrap.support"
public static final java.lang.String	PROPERTY_MINIMUM_NUMBER_OF_TAXA	"phylosort.minimum.number.taxa"
public static final java.lang.String	PROPERTY_MODE	"phylosort.mode"
public static final java.lang.String	PROPERTY_MODE_EXCLUSIVE	"exclusive"
public static final java.lang.String	PROPERTY_MODE_INCLUSIVE	"inclusive"
public static final java.lang.String	PROPERTY_ON_MATCH_ACTION	"phylosort.on.match.action"
public static final java.lang.String	PROPERTY_ON_MATCH_ACTION_COPY	"copy"
public static final java.lang.String	PROPERTY_ON_MATCH_ACTION_COUNT	"count"
public static final java.lang.String	PROPERTY_ON_MATCH_ACTION_MOVE	"move"
public static final java.lang.String	PROPERTY_REGEXP	"phylosort.pattern"
public static final java.lang.String	PROPERTY_ROOT	"phylosort.root.outgroup"
public static final java.lang.String	PROPERTY_ROOT_OUTGROUP_NO	"no"
public static final java.lang.String	PROPERTY_ROOT_OUTGROUP_YES	"yes"
public static final java.lang.String	SYSTEM_PROPERTY_PHYLOSORT_CONFIG	"phylosort.config"

phylosort.util.NewickConstants

public static final char	COLON	58
public static final char	COMMA	44
public static final char	LEFT_PARENTHESIS	41
public static final char	RIGHT_PARENTHESIS	40
public static final char	SEMI_COLON	59
public static final char	SINGLE_QUOTE	39