InvalidNewickException
extends InvalidArgumentException
in package
Class InvalidNewickException
Tags
Table of Contents
Methods
- emptyString() : InvalidNewickException
- Builds the exception raised when the input string is empty or made of whitespace only.
- invalidBranchLength() : InvalidNewickException
- Builds the exception raised when a branch length (the text following ":") is not a valid number.
- missingTerminator() : InvalidNewickException
- Builds the exception raised when the input does not end with the ";" every Newick tree description must be terminated with.
- trailingContent() : InvalidNewickException
- Builds the exception raised when characters remain after the subtree that starts right after the opening of the string has been fully parsed, i.e. the string describes more than one tree.
- unbalancedParentheses() : InvalidNewickException
- Builds the exception raised when a "(" opened for a subtree is never matched by a ")", or a ")" is encountered with no matching "(" still open.
- unexpectedCharacter() : InvalidNewickException
- Builds the exception raised when a character can follow neither a node nor its branch length, most often the second word of an unquoted label holding a blank.
- unnamedLeaf() : InvalidNewickException
- Builds the exception raised when a leaf has no name : valid Newick ("(,A);"), but a PhylogeneticNode leaf is named.
- unterminatedComment() : InvalidNewickException
- Builds the exception raised when a comment ([...]) is never closed.
- unterminatedQuotedLabel() : InvalidNewickException
- Builds the exception raised when a quoted label ('...') is never closed.
Methods
emptyString()
Builds the exception raised when the input string is empty or made of whitespace only.
public
static emptyString() : InvalidNewickException
Return values
InvalidNewickExceptioninvalidBranchLength()
Builds the exception raised when a branch length (the text following ":") is not a valid number.
public
static invalidBranchLength(string $sValue, int $iPosition) : InvalidNewickException
Parameters
- $sValue : string
- $iPosition : int
Return values
InvalidNewickExceptionmissingTerminator()
Builds the exception raised when the input does not end with the ";" every Newick tree description must be terminated with.
public
static missingTerminator() : InvalidNewickException
Return values
InvalidNewickExceptiontrailingContent()
Builds the exception raised when characters remain after the subtree that starts right after the opening of the string has been fully parsed, i.e. the string describes more than one tree.
public
static trailingContent(int $iPosition) : InvalidNewickException
Parameters
- $iPosition : int
Return values
InvalidNewickExceptionunbalancedParentheses()
Builds the exception raised when a "(" opened for a subtree is never matched by a ")", or a ")" is encountered with no matching "(" still open.
public
static unbalancedParentheses(int $iPosition) : InvalidNewickException
Parameters
- $iPosition : int
-
Zero-based character position where parsing failed
Return values
InvalidNewickExceptionunexpectedCharacter()
Builds the exception raised when a character can follow neither a node nor its branch length, most often the second word of an unquoted label holding a blank.
public
static unexpectedCharacter(string $sCharacter, int $iPosition) : InvalidNewickException
Parameters
- $sCharacter : string
- $iPosition : int
Return values
InvalidNewickExceptionunnamedLeaf()
Builds the exception raised when a leaf has no name : valid Newick ("(,A);"), but a PhylogeneticNode leaf is named.
public
static unnamedLeaf(int $iPosition) : InvalidNewickException
Parameters
- $iPosition : int
-
Where the leaf ends
Return values
InvalidNewickExceptionunterminatedComment()
Builds the exception raised when a comment ([...]) is never closed.
public
static unterminatedComment(int $iPosition) : InvalidNewickException
Parameters
- $iPosition : int
-
Where the comment opens
Return values
InvalidNewickExceptionunterminatedQuotedLabel()
Builds the exception raised when a quoted label ('...') is never closed.
public
static unterminatedQuotedLabel(int $iPosition) : InvalidNewickException
Parameters
- $iPosition : int
-
Where the label opens