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

A

about_menuitem - Variable in class neobio.gui.NeoBio

AboutDialog - class neobio.gui.AboutDialog.

About screen.

AboutDialog(Frame) - Constructor for class neobio.gui.AboutDialog

Creates a new instance of the About screen.

aboutMenuItemActionPerformed(ActionEvent) - Method in class neobio.gui.NeoBio

add(JComponent, JComponent, GridBagConstraints, int, int) - Method in class neobio.gui.PairwiseAlignmentFrame

add(Object, char) - Method in class neobio.alignment.Trie

Adds a new child to this node.

addSibling(Object, char) - Method in class neobio.alignment.Trie

Adds a sibling to this node.

algorithm - Variable in class neobio.gui.PairwiseAlignmentFrame

algorithm_combo - Variable in class neobio.gui.PairwiseAlignmentFrame

algorithm_name - Variable in class neobio.gui.PairwiseAlignmentFrame

algorithm_panel - Variable in class neobio.gui.PairwiseAlignmentFrame

alignment - Variable in class neobio.alignment.PairwiseAlignmentAlgorithm

Stores the product of the last pairwise alignment performed.

alignment_button - Variable in class neobio.gui.NeoBio

AlignmentBlock - class neobio.alignment.AlignmentBlock.

This class is used by the CrochemoreLandauZivUkelson algorithm to store the information of an alignment block.

AlignmentBlock(Factor, Factor) - Constructor for class neobio.alignment.AlignmentBlock

Creates a new root block.

AlignmentBlock(Factor, Factor, int) - Constructor for class neobio.alignment.AlignmentBlock

Creates a new alignment block, with all arrays created with the specified size.

ancestor - Variable in class neobio.alignment.AlignmentBlock

An array of pointers to prefix blocks of this block.

ancestor - Variable in class neobio.alignment.Factor

A pointer to this factor's ancestor, which represents a prefix of this factor's text.

APPROXIMATE_MATCH_TAG - Static variable in class neobio.alignment.PairwiseAlignmentAlgorithm

Tag character that signals an approximate match in the score tag line of an alignment.

assembleDistMatrix(AlignmentBlock, int, int, int, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Assembles the DIST matrix of a block by retrieving the DIST columns of its prefix blocks.

assembleInputBorder(int, int, int, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Assembles the input border of a block by retrieving the values at the output borders of the left and top blocks.

B

basic_button - Variable in class neobio.gui.PairwiseAlignmentFrame

basic_scheme - Variable in class neobio.gui.PairwiseAlignmentFrame

BasicScoringScheme - class neobio.alignment.BasicScoringScheme.

This class implements a basic scoring scheme.

BasicScoringScheme(int, int, int) - Constructor for class neobio.alignment.BasicScoringScheme

Creates a new instance of a basic scoring scheme with the specified values of match reward, mismatch penalty and gap cost.

BasicScoringScheme(int, int, int, boolean) - Constructor for class neobio.alignment.BasicScoringScheme

Creates a new instance of basic scoring scheme with the specified values of match reward, mismatch penalty and gap cost.

block_table - Variable in class neobio.alignment.CrochemoreLandauZivUkelson

The block table, which is a matrix of alignment blocks where each block represents the alignment between one factor of each sequence.

buildOptimalAlignment() - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Retrieves an optimal alignment between the loaded sequences.

buildOptimalAlignment() - Method in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

Builds an optimal local alignment between the loaded sequences after the block table has been computed by tracing a path back in the block table.

buildOptimalAlignment() - Method in class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment

Builds an optimal global alignment between the loaded sequences after the block table has been computed.

buildOptimalAlignment() - Method in class neobio.alignment.NeedlemanWunsch

Builds an optimal global alignment between the loaded sequences.

buildOptimalAlignment() - Method in class neobio.alignment.SmithWaterman

Builds an optimal local alignment between the loaded sequences.

C

C - Variable in class neobio.alignment.LocalAlignmentBlock

The value of the highest scoring path contained in this block, called C-path.

case_sensitive - Variable in class neobio.alignment.ScoringScheme

Determines whether this scoring scheme ignores the case of characters when computing their score.

charAt(int) - Method in class neobio.alignment.CharSequence

Returns the character at a given position.

CharSequence - class neobio.alignment.CharSequence.

This class implements a sequence of characters stored as an array that provides random access to any position in constant time.

CharSequence(Reader) - Constructor for class neobio.alignment.CharSequence

Creates a new instance of a CharSequence, loading the sequence data from the Reader input stream.

checkRunButtonStatus() - Method in class neobio.gui.PairwiseAlignmentFrame

closeDialog(WindowEvent) - Method in class neobio.gui.AboutDialog

col - Variable in class neobio.alignment.Smawk

An array of column indexes reflecting the current state of the matrix.

col_codes - Variable in class neobio.alignment.ScoringMatrix

Stores matrix column headers in the order they were found.

COMMENT_CHAR - Static variable in class neobio.alignment.ScoringMatrix

The character used to start a comment line in the scoring matrix file.

COMMENT_CHAR - Static variable in class neobio.alignment.FactorSequence

The character used to start a comment line in a sequence file.

COMMENT_CHAR - Static variable in class neobio.alignment.CharSequence

The character used to start a comment line in a sequence file.

computeBlockTable() - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Computes the block table.

computeColumnMaxima(int[]) - Method in class neobio.alignment.Smawk

This method implements the SMAWK algorithm to compute the column maxima of a given matrix.

computeColumnMaxima(Matrix, int[]) - Method in class neobio.alignment.Smawk

Computes the column maxima of a given matrix.

computeMatrix() - Method in class neobio.alignment.NeedlemanWunsch

Computes the dynamic programming matrix.

computeMatrix() - Method in class neobio.alignment.SmithWaterman

Computes the dynamic programming matrix.

computeOutputBorder(AlignmentBlock, int, int, int, int, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment

Computes the output border of a block.

computeOutputBorder(LocalAlignmentBlock, int, int, int, int, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

Computes the output border of a block.

computePairwiseAlignment() - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Computes the block table (the result depends on subclasses, see computeBlockTable for details) and requests subclasses to retrieve an optimal alignment between the loaded sequences.

computePairwiseAlignment() - Method in class neobio.alignment.NeedlemanWunsch

Builds an optimal global alignment between the loaded sequences after computing the dynamic programming matrix.

computePairwiseAlignment() - Method in class neobio.alignment.SmithWaterman

Builds an optimal local alignment between the loaded sequences after computing the dynamic programming matrix.

computePairwiseAlignment() - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Subclasses must implement this method to compute an alignment between the loaded sequences using the scoring scheme previously set.

computeScore() - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Computes the block table (the result depends on subclasses, see computeBlockTable for details) and requests subclasses to locate the score of the highest scoring alignment between the two sequences in the block table.

computeScore() - Method in class neobio.alignment.NeedlemanWunsch

Computes the score of the best global alignment between the two sequences using the scoring scheme previously set.

computeScore() - Method in class neobio.alignment.SmithWaterman

Computes the score of the best local alignment between the two sequences using the scoring scheme previously set.

computeScore() - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Subclasses must implement this method to compute the score of the alignment between the loaded sequences using the scoring scheme previously set.

createBlock(Factor, Factor, int, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Computes a block of the block table, which corresponds to an alignment block between one factor of sequence 1 and one factor of sequence 2.

createBlock(Factor, Factor, int, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

Creates and computes all information of an alignment block.

createBlock(Factor, Factor, int, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment

Creates and computes all information of an alignment block.

createFirstColumnBlock(Factor, Factor, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Computes a block at the first column (column zero) of the block table, which corresponds to an alignment block between one factor of sequence 1 and an empty string.

createFirstColumnBlock(Factor, Factor, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

Creates and computes all information of an alignment block of the first column of the block table.

createFirstColumnBlock(Factor, Factor, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment

Creates and computes all information of an alignment block of the first column of the block table.

createFirstRowBlock(Factor, Factor, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Computes a block at the first row (row zero) of the block table, which corresponds to an alignment block between one factor of sequence 2 and an empty string.

createFirstRowBlock(Factor, Factor, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

Creates and computes all information of an alignment block of the first column of the block table.

createFirstRowBlock(Factor, Factor, int) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment

Creates and computes all information of an alignment block of the first row of the block table.

createRootBlock(Factor, Factor) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Computes the root block of the block table.

createRootBlock(Factor, Factor) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

Creates the root block.

createRootBlock(Factor, Factor) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment

Creates the root block.

CrochemoreLandauZivUkelson - class neobio.alignment.CrochemoreLandauZivUkelson.

This abstract class is the superclass of both global and local sequence alignment algorithms (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).

CrochemoreLandauZivUkelson() - Constructor for class neobio.alignment.CrochemoreLandauZivUkelson

CrochemoreLandauZivUkelsonGlobalAlignment - class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment.

This class implements the global pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).

CrochemoreLandauZivUkelsonGlobalAlignment() - Constructor for class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment

CrochemoreLandauZivUkelsonLocalAlignment - class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment.

This class implements the local pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).

CrochemoreLandauZivUkelsonLocalAlignment() - Constructor for class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

D

data - Variable in class neobio.alignment.Trie

This node's stored data.

deleteOddColumns() - Method in class neobio.alignment.Smawk

This method simulates a deletion of odd rows by manipulating the col array of indexes.

deleteRow(int, int) - Method in class neobio.alignment.Smawk

This method simulates a deletion of a row in the matrix during the reduce operation.

desktop_pane - Variable in class neobio.gui.NeoBio

DIAGONAL_DIRECTION - Static variable in class neobio.alignment.CrochemoreLandauZivUkelson

A constant that indicates that the diagonal direction must be followed to reach the source of an optimal path in a block during the trace back procedure to retrieve a high scoring alignment.

dim - Variable in class neobio.alignment.OutMatrix

The dimension of the OUT matrix.

dimension - Variable in class neobio.alignment.ScoringMatrix

Dimension of the (squared) matrix.

direction - Variable in class neobio.alignment.AlignmentBlock

An array of directions that must be followed to reach the source of the highest scoring path for each entry in the output border.

dist - Variable in class neobio.alignment.OutMatrix

The DIST matrix of a block.

dist_column - Variable in class neobio.alignment.AlignmentBlock

The DIST column of this block.

DNA_CHARS - Static variable in class neobio.textui.RandomFactorSequenceGenerator

Character set for DNA sequences.

DNA_CHARS - Static variable in class neobio.textui.RandomSequenceGenerator

Character set for DNA sequences.

E

E_path_ancestor - Variable in class neobio.alignment.LocalAlignmentBlock

An array of pointers to blocks that are source of E-paths.

E_path_ancestor_index - Variable in class neobio.alignment.LocalAlignmentBlock

Indexes of of the entry in the ancestor block that is the source of the E-path.

E_path_score - Variable in class neobio.alignment.LocalAlignmentBlock

The value of the highest scoring path which starts at the input border of this block and ends inside it, called E-path.

equals(Object) - Method in class neobio.alignment.PairwiseAlignment

Compares this object to the specified object.

exit_menuitem - Variable in class neobio.gui.NeoBio

exitForm() - Method in class neobio.gui.NeoBio

exitMenuItemActionPerformed(ActionEvent) - Method in class neobio.gui.NeoBio

F

Factor - class neobio.alignment.Factor.

This class is used by FactorSequence to create a linked list of factors of a text as induced by its Lempel-Ziv (LZ78) factorisation.

Factor() - Constructor for class neobio.alignment.Factor

Creates a new empty Factor.

Factor(Factor, int, char) - Constructor for class neobio.alignment.Factor

Creates a new Factor instance with the specified serial number and new character, and pointing to the given ancestor.

factor1 - Variable in class neobio.alignment.AlignmentBlock

A pointer to the factor of the first sequence being aligned.

factor2 - Variable in class neobio.alignment.AlignmentBlock

A pointer to the factor of the second sequence being aligned.

FactorSequence - class neobio.alignment.FactorSequence.

This class builds a list of factors of a character sequence as induced by its Lempel-Ziv (LZ78) factorisation.

FactorSequence(Reader) - Constructor for class neobio.alignment.FactorSequence

Creates a new instance of a FactorSequence, loading the sequence data from the Reader input stream.

file_button - Variable in class neobio.gui.PairwiseAlignmentFrame

file_menu - Variable in class neobio.gui.NeoBio

file_toolbar - Variable in class neobio.gui.NeoBio

find_dialog - Variable in class neobio.gui.PairwiseAlignmentFrame

find_matrix_button - Variable in class neobio.gui.PairwiseAlignmentFrame

find_output_button - Variable in class neobio.gui.PairwiseAlignmentFrame

find_seq1_button - Variable in class neobio.gui.PairwiseAlignmentFrame

find_seq2_button - Variable in class neobio.gui.PairwiseAlignmentFrame

findMatrixButtonActionPerformed() - Method in class neobio.gui.PairwiseAlignmentFrame

findOutputButtonActionPerformed() - Method in class neobio.gui.PairwiseAlignmentFrame

findSeq1ButtonActionPerformed() - Method in class neobio.gui.PairwiseAlignmentFrame

findSeq2ButtonActionPerformed() - Method in class neobio.gui.PairwiseAlignmentFrame

G

GAP_CHARACTER - Static variable in class neobio.alignment.PairwiseAlignmentAlgorithm

Character that signals a gap in sequence.

gap_cost - Variable in class neobio.alignment.BasicScoringScheme

The cost of a gap (an insertion or deletion of a character).

gap_field - Variable in class neobio.gui.PairwiseAlignmentFrame

gap_label - Variable in class neobio.gui.PairwiseAlignmentFrame

GAP_TAG - Static variable in class neobio.alignment.PairwiseAlignmentAlgorithm

Character that signals a gap in the score tag line of an alignment.

gapped_seq1 - Variable in class neobio.alignment.PairwiseAlignment

First gapped sequence.

gapped_seq2 - Variable in class neobio.alignment.PairwiseAlignment

Second gapped sequence.

getAncestor() - Method in class neobio.alignment.Factor

Returns this factor's ancestor factor.

getAncestorSerialNumber() - Method in class neobio.alignment.Factor

This method is a shorthand to return the serial number of this factor's ancestor.

getData() - Method in class neobio.alignment.Trie

Returns the data associated with this node.

getDiagonalPrefix(AlignmentBlock) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

This method is a shorthand to retrieve the diagonal prefix of a block from the block table.

getGappedSequence1() - Method in class neobio.alignment.PairwiseAlignment

Returns the first gapped sequence.

getGappedSequence2() - Method in class neobio.alignment.PairwiseAlignment

Returns the second gapped sequence.

getLeftPrefix(AlignmentBlock) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

This method is a shorthand to retrieve the left prefix of a block from the block table.

getNewChar() - Method in class neobio.alignment.Factor

Returns this factor's new character.

getNext() - Method in class neobio.alignment.Factor

Returns this factor's next factor.

getPairwiseAlignment() - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Return the last pairwise alignment computed (if any) or request subclasses to compute one and return the result by calling the computePairwiseAlignment method.

getRootFactor() - Method in class neobio.alignment.FactorSequence

Returns the root factor, the one that starts the list of factors.

getScore() - Method in class neobio.alignment.PairwiseAlignment

Returns the score for this alignment.

getScore() - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Returns the score of the last alignment computed (if any) or request subclasses to compute one and return the result by calling the computeScore method.

getScoreTagLine() - Method in class neobio.alignment.PairwiseAlignment

Returns the score tag line.

getSerialNumber() - Method in class neobio.alignment.Factor

Returns this factor's serial number.

getTopPrefix(AlignmentBlock) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

This method is a shorthand to retrieve the top prefix of a block from the block table.

H

help_menu - Variable in class neobio.gui.NeoBio

I

image_label - Variable in class neobio.gui.AboutDialog

IncompatibleScoringSchemeException - exception neobio.alignment.IncompatibleScoringSchemeException.

Signals that an scoring scheme is not compatible with the sequences being aligned.

IncompatibleScoringSchemeException() - Constructor for class neobio.alignment.IncompatibleScoringSchemeException

Constructs an IncompatibleScoringSchemeException with null as its error detail message.

IncompatibleScoringSchemeException(String) - Constructor for class neobio.alignment.IncompatibleScoringSchemeException

Constructs an IncompatibleScoringSchemeException with the specified detail message.

IncompatibleScoringSchemeException(String, Throwable) - Constructor for class neobio.alignment.IncompatibleScoringSchemeException

Constructs an IncompatibleScoringSchemeException with the specified detail message and cause.

IncompatibleScoringSchemeException(Throwable) - Constructor for class neobio.alignment.IncompatibleScoringSchemeException

Constructs an IncompatibleScoringSchemeException with the specified cause (and a detail message that typically contains the class and detail message of cause).

INDEL_CHAR - Static variable in class neobio.alignment.ScoringMatrix

The character that indicates the row and column for insertion and deletion penalties in the matrix.

init(int, int) - Method in class neobio.alignment.OutMatrix

Initialised this OUT matrix interface.

initComponents() - Method in class neobio.gui.PairwiseAlignmentFrame

initComponents() - Method in class neobio.gui.NeoBio

initComponents() - Method in class neobio.gui.AboutDialog

input_border - Variable in class neobio.alignment.OutMatrix

The input border of a block.

input_panel - Variable in class neobio.gui.PairwiseAlignmentFrame

InvalidScoringMatrixException - exception neobio.alignment.InvalidScoringMatrixException.

Signals that the substitution matrix does not comply with the specification (see ScoringMatrix for details).

InvalidScoringMatrixException() - Constructor for class neobio.alignment.InvalidScoringMatrixException

Constructs an InvalidScoringMatrixException with null as its error detail message.

InvalidScoringMatrixException(String) - Constructor for class neobio.alignment.InvalidScoringMatrixException

Constructs an InvalidScoringMatrixException with the specified detail message.

InvalidScoringMatrixException(String, Throwable) - Constructor for class neobio.alignment.InvalidScoringMatrixException

Constructs an InvalidScoringMatrixException with the specified detail message and cause.

InvalidScoringMatrixException(Throwable) - Constructor for class neobio.alignment.InvalidScoringMatrixException

Constructs an InvalidScoringMatrixException with the specified cause (and a detail message that typically contains the class and detail message of cause).

InvalidSequenceException - exception neobio.alignment.InvalidSequenceException.

Signals that the sequence does not comply with the specification (see CharSequence or FactorSequence for details).

InvalidSequenceException() - Constructor for class neobio.alignment.InvalidSequenceException

Constructs an InvalidSequenceException with null as its error detail message.

InvalidSequenceException(String) - Constructor for class neobio.alignment.InvalidSequenceException

Constructs an InvalidSequenceException with the specified detail message.

InvalidSequenceException(String, Throwable) - Constructor for class neobio.alignment.InvalidSequenceException

Constructs an InvalidSequenceException with the specified detail message and cause.

InvalidSequenceException(Throwable) - Constructor for class neobio.alignment.InvalidSequenceException

Constructs an InvalidSequenceException with the specified cause (and a detail message that typically contains the class and detail message of cause).

isCaseSensitive() - Method in class neobio.alignment.ScoringScheme

Tells whether this scoring scheme ignores the case of characters when computing their score.

isPartialMatchSupported() - Method in class neobio.alignment.ScoringMatrix

Tells whether this scoring scheme supports partial matches, which it does, although a particular scoring matrix loaded by this instace might not.

isPartialMatchSupported() - Method in class neobio.alignment.ScoringScheme

Returns true if this scoring scheme supports partial matches, false otherwise.

isPartialMatchSupported() - Method in class neobio.alignment.BasicScoringScheme

Tells whether this scoring scheme supports partial matches, which it does not.

L

lc - Variable in class neobio.alignment.OutMatrix

The number of columns of the block.

LEFT_DIRECTION - Static variable in class neobio.alignment.CrochemoreLandauZivUkelson

A constant that indicates that the left direction must be followed to reach the source of an optimal path in a block during the trace back procedure to retrieve a high scoring alignment.

length - Variable in class neobio.alignment.Factor

The number of characters of the text represented by this factor.

length() - Method in class neobio.alignment.Factor

Returns this factor's length.

length() - Method in class neobio.alignment.CharSequence

Returns the number of characters of this sequence.

loadSequences(Reader, Reader) - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Request subclasses to load the sequences according to their own needs.

loadSequencesInternal(Reader, Reader) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Loads sequences into FactorSequence instances.

loadSequencesInternal(Reader, Reader) - Method in class neobio.alignment.NeedlemanWunsch

Loads sequences into CharSequence instances.

loadSequencesInternal(Reader, Reader) - Method in class neobio.alignment.SmithWaterman

Loads sequences into CharSequence instances.

loadSequencesInternal(Reader, Reader) - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Subclasses must implement this method to load sequences according to their own needs and throw an exception in case of any failure.

LocalAlignmentBlock - class neobio.alignment.LocalAlignmentBlock.

This class is used by the CrochemoreLandauZivUkelsonLocalAlignment algorithm to store the information of an alignment block.

LocalAlignmentBlock(Factor, Factor) - Constructor for class neobio.alignment.LocalAlignmentBlock

Creates a new root block.

LocalAlignmentBlock(Factor, Factor, int) - Constructor for class neobio.alignment.LocalAlignmentBlock

Creates a new alignment block, with all arrays created with the specified size.

locateScore() - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Locates the score of the highest scoring alignment between the two sequences in the block table after is thas been computed.

locateScore() - Method in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

Returns the score of the high scoring local alignment in the block table.

locateScore() - Method in class neobio.alignment.CrochemoreLandauZivUkelsonGlobalAlignment

Locate the score of the highest scoring global alignment in the block table.

M

main(String[]) - Static method in class neobio.textui.RandomFactorSequenceGenerator

The main method takes three parameters from the command line to generate a sequence.

main(String[]) - Static method in class neobio.textui.RandomSequenceGenerator

The main method takes three parameters from the command line to generate a sequence.

main(String[]) - Static method in class neobio.textui.NeoBio

The main method takes parameters from the command line to compute a pairwise sequence alignment.

main(String[]) - Static method in class neobio.gui.NeoBio

Create and run a new interface.

match_field - Variable in class neobio.gui.PairwiseAlignmentFrame

match_label - Variable in class neobio.gui.PairwiseAlignmentFrame

match_reward - Variable in class neobio.alignment.BasicScoringScheme

The reward for a match (a substitution of equal characters).

MATCH_TAG - Static variable in class neobio.alignment.PairwiseAlignmentAlgorithm

Tag character that signals a match in the score tag line of an alignment.

matrix - Variable in class neobio.alignment.ScoringMatrix

Stores values for each operation (substitution, insertion or deletion) defined by this matrix.

matrix - Variable in class neobio.alignment.Smawk

A pointer to the matrix that is being manipulated.

matrix - Variable in class neobio.alignment.NeedlemanWunsch

The dynamic programming matrix.

matrix - Variable in class neobio.alignment.SmithWaterman

The dynamic programming matrix.

Matrix - interface neobio.alignment.Matrix.

This interface defines a minimal set of operations that a matrix must implement.

matrix_button - Variable in class neobio.gui.PairwiseAlignmentFrame

matrix_field - Variable in class neobio.gui.PairwiseAlignmentFrame

max_absolute_score - Variable in class neobio.alignment.ScoringMatrix

The maximum absolute score that this matrix can return for any substitution, deletion or insertion.

max_absolute_score - Variable in class neobio.alignment.BasicScoringScheme

The maximum absolute score that this scoring scheme can return, which is the maximum absolute value among match_reward, mismatch_penalty and gap_cost.

max_col - Variable in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

The column index of a block (in the block table) where the high scoring local alignment ends.

max_col - Variable in class neobio.alignment.SmithWaterman

Indicate the column of where an optimal local alignment can be found in the matrix.

max_length - Variable in class neobio.alignment.OutMatrix

The length of the longest sequence (number of characters) being aligned.

max_path_type - Variable in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

The type of the high scoring local alignment found.

max_row - Variable in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

The row index of a block (in the block table) where the high scoring local alignment ends.

max_row - Variable in class neobio.alignment.SmithWaterman

Indicate the row of where an optimal local alignment can be found in the matrix..

max_score - Variable in class neobio.alignment.OutMatrix

The maximum absolute score that the current scoring scheme can return.

max_score - Variable in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

The score of the high scoring local alignment found.

max_source_index - Variable in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

If the high scoring local alignment ends in an E-path at a block B, this field contains the index of the entry in the input border of B that where the E-path starts.

max(int, int) - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Helper method to compute the the greater of two values.

max(int, int, int) - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Helper method to compute the the greater of three values.

max(int, int, int, int) - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Helper method to compute the the greater of four values.

maxAbsoluteScore() - Method in class neobio.alignment.ScoringMatrix

Returns the maximum absolute score that this scoring scheme can return for any substitution, deletion or insertion.

maxAbsoluteScore() - Method in class neobio.alignment.ScoringScheme

Returns the maximum absolute score that this scoring scheme can return for any substitution, deletion or insertion.

maxAbsoluteScore() - Method in class neobio.alignment.BasicScoringScheme

Returns the maximum absolute score that this scoring scheme can return for any substitution, deletion or insertion, which is the maximum absolute value among match_reward, mismatch_penalty and gap_cost.

menu_bar - Variable in class neobio.gui.NeoBio

mid_separator - Variable in class neobio.gui.NeoBio

mismatch_field - Variable in class neobio.gui.PairwiseAlignmentFrame

mismatch_label - Variable in class neobio.gui.PairwiseAlignmentFrame

mismatch_penalty - Variable in class neobio.alignment.BasicScoringScheme

The penalty for a mismatch (a substitution of different characters).

MISMATCH_TAG - Static variable in class neobio.alignment.PairwiseAlignmentAlgorithm

Character that signals a mismatch in the score tag line of an alignment.

N

naiveComputeColumnMaxima(Matrix, int[]) - Static method in class neobio.alignment.Smawk

This is a simpler method for calculating column maxima.

naiveComputeRowMaxima(Matrix, int[]) - Static method in class neobio.alignment.Smawk

This is a simpler method for calculating row maxima.

NeedlemanWunsch - class neobio.alignment.NeedlemanWunsch.

This class implements the classic global alignment algorithm (with linear gap penalty function) due to S.B.Needleman and C.D.Wunsch (1970).

NeedlemanWunsch() - Constructor for class neobio.alignment.NeedlemanWunsch

NeoBio - class neobio.textui.NeoBio.

This class is a simple command line based utility for computing pairwise sequence alignments using one of the the algorithms provided in the neobio.alignment package.

NeoBio - class neobio.gui.NeoBio.

This class is a simple GUI utility for computing pairwise sequence alignments using one of the the algorithms provided in the neobio.alignment package.

neobio.alignment - package neobio.alignment

Provides implementation of sequence alignment algorithms.

neobio.gui - package neobio.gui

Graphical user interface tools to run the algorithms provided by other packages.

neobio.textui - package neobio.textui

Command line based tools to run the algorithms provided by other packages.

NeoBio() - Constructor for class neobio.textui.NeoBio

NeoBio() - Constructor for class neobio.gui.NeoBio

Creates a new instance of a graphical interface.

new_alignment_item - Variable in class neobio.gui.NeoBio

new_char - Variable in class neobio.alignment.Factor

The new character of this factor.

newAlignmentActionPerformed(ActionEvent) - Method in class neobio.gui.NeoBio

next - Variable in class neobio.alignment.Factor

A pointer to the next factor.

num_chars - Variable in class neobio.alignment.FactorSequence

The numbers of character represented by this sequence.

num_cols - Variable in class neobio.alignment.CrochemoreLandauZivUkelson

Number of columns of the block table.

num_factors - Variable in class neobio.alignment.FactorSequence

The numbers of factors generated by the LZ78 parsing of the sequence.

num_rows - Variable in class neobio.alignment.CrochemoreLandauZivUkelson

Number of rows of the block table.

numChars() - Method in class neobio.alignment.FactorSequence

Returns the number of characters of the original sequence.

numcols - Variable in class neobio.alignment.Smawk

The matrix's current number of columns.

numColumns() - Method in class neobio.alignment.OutMatrix

Returns the number of columns of this OUT matrix.

numColumns() - Method in interface neobio.alignment.Matrix

Returns the number of columns that this matrix has.

numFactors() - Method in class neobio.alignment.FactorSequence

Returns the number of factors produced by the LZ78 parsing of the text.

numrows - Variable in class neobio.alignment.Smawk

The matrix's current number of rows.

numRows() - Method in class neobio.alignment.OutMatrix

Returns the number of rows of this OUT matrix.

numRows() - Method in interface neobio.alignment.Matrix

Returns the number of rows that this matrix has.

O

out_matrix - Variable in class neobio.alignment.CrochemoreLandauZivUkelson

An instance of the OutMatrix class that encodes the OUT matrix of a block when supplied with the DIST matrix and the input border array of a block.

OutMatrix - class neobio.alignment.OutMatrix.

Implements an interface to the OUT matrix of a block.

OutMatrix() - Constructor for class neobio.alignment.OutMatrix

output_area - Variable in class neobio.gui.PairwiseAlignmentFrame

output_border - Variable in class neobio.alignment.AlignmentBlock

This block's output border.

output_field - Variable in class neobio.gui.PairwiseAlignmentFrame

output_group - Variable in class neobio.gui.PairwiseAlignmentFrame

output_panel - Variable in class neobio.gui.PairwiseAlignmentFrame

output_tab - Variable in class neobio.gui.PairwiseAlignmentFrame

output_tab_panel - Variable in class neobio.gui.PairwiseAlignmentFrame

output_to_file - Variable in class neobio.gui.PairwiseAlignmentFrame

outputOptionStateChanged() - Method in class neobio.gui.PairwiseAlignmentFrame

P

PairwiseAlignment - class neobio.alignment.PairwiseAlignment.

This class is the product of a pairwise alignment, generated by one subclasses of PairwiseAlignmentAlgorithm.

pairwiseAlignment() - Method in class neobio.gui.NeoBio

PairwiseAlignment(String, String, String, int) - Constructor for class neobio.alignment.PairwiseAlignment

Creates a PairwiseAlignment instance with the specified gapped sequences, score tag line and score value.

PairwiseAlignmentAlgorithm - class neobio.alignment.PairwiseAlignmentAlgorithm.

This abstract class is the superclass of all classes implementing pairwise sequence alignment algorithms.

PairwiseAlignmentAlgorithm() - Constructor for class neobio.alignment.PairwiseAlignmentAlgorithm

PairwiseAlignmentFrame - class neobio.gui.PairwiseAlignmentFrame.

This class is the internal frame of NeoBio's graphical interface for computing pairwise sequence alignments using one of the the algorithms provided in the neobio.alignment package.

PairwiseAlignmentFrame(Frame) - Constructor for class neobio.gui.PairwiseAlignmentFrame

Creates a new instance of the internal frame.

parent_frame - Variable in class neobio.gui.PairwiseAlignmentFrame

path_type - Variable in class neobio.alignment.LocalAlignmentBlock

The type of the highest scoring path ending at a given position of the output border of a block.

printFactors() - Method in class neobio.alignment.FactorSequence

Returns a string representation of the actual list of factors produced by the LZ78 parsing of the text.

printMatrix() - Method in class neobio.alignment.Smawk

Prints the current state of the matrix (reflecting deleted rows and columns) in the standard output.

printMatrix(Matrix) - Static method in class neobio.alignment.Smawk

Prints the contents of an object implementing the matrix interface in the standard output.

progress_area - Variable in class neobio.gui.PairwiseAlignmentFrame

progress_tab_panel - Variable in class neobio.gui.PairwiseAlignmentFrame

PROT_CHARS - Static variable in class neobio.textui.RandomFactorSequenceGenerator

Character set for protein sequences.

PROT_CHARS - Static variable in class neobio.textui.RandomSequenceGenerator

Character set for protein sequences.

R

RandomFactorSequenceGenerator - class neobio.textui.RandomFactorSequenceGenerator.

This class is a simple command line based utility for generating random sequences with optimal LZ78 factorisation.

RandomFactorSequenceGenerator() - Constructor for class neobio.textui.RandomFactorSequenceGenerator

RandomSequenceGenerator - class neobio.textui.RandomSequenceGenerator.

This class is a simple command line based utility for generating random sequences.

RandomSequenceGenerator() - Constructor for class neobio.textui.RandomSequenceGenerator

reduce() - Method in class neobio.alignment.Smawk

This method is the key component of the SMAWK algorithm.

restoreOddColumns(int) - Method in class neobio.alignment.Smawk

Restores the col array of indexes to the state it was before the deleteOddColumns method was called.

restoreRows(int) - Method in class neobio.alignment.Smawk

Restores the row array of indexes to the state it was before the reduce method was called.

root_factor - Variable in class neobio.alignment.FactorSequence

A pointer to the root factor, the one that starts the list of factors.

row - Variable in class neobio.alignment.Smawk

An array of row indexes reflecting the current state of the matrix.

row_codes - Variable in class neobio.alignment.ScoringMatrix

Stores matrix row headers in the order they were found.

row_position - Variable in class neobio.alignment.Smawk

This array is used to store for each row of the original matrix, its index in the current state of the matrix, i.e. its index in the row array.

run_button - Variable in class neobio.gui.PairwiseAlignmentFrame

runButtonActionPerformed() - Method in class neobio.gui.PairwiseAlignmentFrame

S

S_direction - Variable in class neobio.alignment.LocalAlignmentBlock

The direction to the source of the S-path of the new vertex of this block.

S_path_score - Variable in class neobio.alignment.LocalAlignmentBlock

The value of the highest scoring path which starts inside the block and ends at its output border.

schemeOptionStateChanged() - Method in class neobio.gui.PairwiseAlignmentFrame

score - Variable in class neobio.alignment.PairwiseAlignment

The overall score value for this alignment.

score - Variable in class neobio.alignment.PairwiseAlignmentAlgorithm

This field stores just the score of the last pairwise alignment performed (if the score_computed flag is set to true).

score_computed - Variable in class neobio.alignment.PairwiseAlignmentAlgorithm

Flags whether the score of the alignment between the last two loaded sequences has already been computed.

score_tag_line - Variable in class neobio.alignment.PairwiseAlignment

The score tag line.

scoreDeletion(char) - Method in class neobio.alignment.ScoringMatrix

Returns the score of a deletion of character a according to this scoring matrix.

scoreDeletion(char) - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Helper method to invoke the scoreDeletion method of the scoring scheme set to this algorithm.

scoreDeletion(char) - Method in class neobio.alignment.ScoringScheme

Returns the score of a deletion of character a according to this scoring scheme.

scoreDeletion(char) - Method in class neobio.alignment.BasicScoringScheme

Always returns gap_cost for the deletion of any character.

scoreInsertion(char) - Method in class neobio.alignment.ScoringMatrix

Returns the score of an insertion of character a according to this scoring matrix.

scoreInsertion(char) - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Helper method to invoke the scoreInsertion method of the scoring scheme set to this algorithm.

scoreInsertion(char) - Method in class neobio.alignment.ScoringScheme

Returns the score of an insertion of character a according to this scoring scheme.

scoreInsertion(char) - Method in class neobio.alignment.BasicScoringScheme

Always returns gap_cost for the insertion of any character.

scoreSubstitution(char, char) - Method in class neobio.alignment.ScoringMatrix

Returns the score of a substitution of character a for character b according to this scoring matrix.

scoreSubstitution(char, char) - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Helper method to invoke the scoreSubstitution method of the scoring scheme set to this algorithm.

scoreSubstitution(char, char) - Method in class neobio.alignment.ScoringScheme

Returns the score of a substitution of character a for character b according to this scoring scheme.

scoreSubstitution(char, char) - Method in class neobio.alignment.BasicScoringScheme

Returns the score of a substitution of character a for character b according to this scoring scheme.

scoring - Variable in class neobio.alignment.PairwiseAlignmentAlgorithm

The scoring scheme used to compute a pairwise sequence alignment.

scoring_group - Variable in class neobio.gui.PairwiseAlignmentFrame

scoring_panel - Variable in class neobio.gui.PairwiseAlignmentFrame

ScoringMatrix - class neobio.alignment.ScoringMatrix.

This class implements a scoring scheme based on a substitution matrix.

ScoringMatrix(Reader) - Constructor for class neobio.alignment.ScoringMatrix

Creates a new instance of a substitution matrix loaded from the character stream.

ScoringMatrix(Reader, boolean) - Constructor for class neobio.alignment.ScoringMatrix

Creates a new instance of a substitution matrix loaded from the character stream.

ScoringScheme - class neobio.alignment.ScoringScheme.

This abstract class is the superclass of all scoring schemes.

ScoringScheme() - Constructor for class neobio.alignment.ScoringScheme

Creates a new instance of an scoring scheme.

ScoringScheme(boolean) - Constructor for class neobio.alignment.ScoringScheme

Creates a new instance of an scoring scheme.

screen_button - Variable in class neobio.gui.PairwiseAlignmentFrame

seq1 - Variable in class neobio.alignment.CrochemoreLandauZivUkelson

The first factorised sequence being aligned.

seq1 - Variable in class neobio.alignment.NeedlemanWunsch

The first sequence of an alignment.

seq1 - Variable in class neobio.alignment.SmithWaterman

The first sequence of an alignment.

seq1_field - Variable in class neobio.gui.PairwiseAlignmentFrame

seq1_label - Variable in class neobio.gui.PairwiseAlignmentFrame

seq2 - Variable in class neobio.alignment.CrochemoreLandauZivUkelson

The second factorised sequence being aligned.

seq2 - Variable in class neobio.alignment.NeedlemanWunsch

The second sequence of an alignment.

seq2 - Variable in class neobio.alignment.SmithWaterman

The second sequence of an alignment.

seq2_field - Variable in class neobio.gui.PairwiseAlignmentFrame

seq2_label - Variable in class neobio.gui.PairwiseAlignmentFrame

sequence - Variable in class neobio.alignment.CharSequence

Stores the sequence as an array of characters.

sequences_loaded - Variable in class neobio.alignment.PairwiseAlignmentAlgorithm

Flags whether sequences have been loaded.

serial_number - Variable in class neobio.alignment.Factor

This factor's serial number, which indicates the order of this factor inside the linked list of factors of a text.

setData(int[][], int[], int, int) - Method in class neobio.alignment.OutMatrix

Sets this interface's data to represent an OUT matrix for a block.

setNext(Factor) - Method in class neobio.alignment.Factor

Sets this factor's next pointer to point to the specified factor.

setScoringScheme(ScoringScheme) - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Sets the scoring scheme to be used for the next alignments.

showError(String) - Method in class neobio.gui.PairwiseAlignmentFrame

sibling - Variable in class neobio.alignment.Trie

A pointer to this node's next sibling.

smawk - Variable in class neobio.alignment.CrochemoreLandauZivUkelson

An instance of the Smawk class that implements the SMAWK algorithm to compute the column maxima of a totally monotone matrix.

Smawk - class neobio.alignment.Smawk.

This class implement the SMAWK algorithm to compute column maxima on a totally monotone matrix as described.

Smawk() - Constructor for class neobio.alignment.Smawk

SmithWaterman - class neobio.alignment.SmithWaterman.

This class implement the classic local alignment algorithm (with linear gap penalty function) due to T.F.Smith and M.S.Waterman (1981).

SmithWaterman() - Constructor for class neobio.alignment.SmithWaterman

son - Variable in class neobio.alignment.Trie

A pointer to the first of this node's children.

source_path - Variable in class neobio.alignment.AlignmentBlock

An array of indexes to the source of the highest scoring path for each entry in the output border.

spellDown(char) - Method in class neobio.alignment.Trie

Follows a path from this node to one of its children by spelling the character supplied as an argument.

spellRight(char) - Method in class neobio.alignment.Trie

Follows a path from this node to one of its sibling by spelling the character supplied as an argument.

STOP_DIRECTION - Static variable in class neobio.alignment.CrochemoreLandauZivUkelson

A constant that indicates that the source of an optimal path has been reached in a block and that the trace back procedure to retrieve a high scoring alignment can stop.

T

to_sibling - Variable in class neobio.alignment.Trie

The character that labels the edge from this node to the sibling pointer by sibling.

to_son - Variable in class neobio.alignment.Trie

The character that labels the edge from this node to the child node pointer by son.

toolbar_panel - Variable in class neobio.gui.NeoBio

TOP_DIRECTION - Static variable in class neobio.alignment.CrochemoreLandauZivUkelson

A constant that indicates that the top direction must be followed to reach the source of an optimal path in a block during the trace back procedure to retrieve a high scoring alignment.

toString() - Method in class neobio.alignment.ScoringMatrix

Returns a String representation of this scoring matrix.

toString() - Method in class neobio.alignment.Factor

Returns a string representation of the text represented by this factor.

toString() - Method in class neobio.alignment.PairwiseAlignment

Returns a four-line String representation of this alignment in the following order: first gapped sequence, score tag line, second gapped sequence and the score value.

toString() - Method in class neobio.alignment.FactorSequence

Reconstructs the sequence from the list of factors induced by the LZ78 parsing of the text.

toString() - Method in class neobio.alignment.CharSequence

Returns a string representation of the sequence.

toString() - Method in class neobio.alignment.BasicScoringScheme

Returns a String representation of this scoring scheme.

traverseBlock(AlignmentBlock, int, StringBuffer, StringBuffer, StringBuffer) - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Traverses a block to retrieve a part of an optimal alignment from the specified source in the output border to an entry in the input border.

traverseBlockCrossingPath(LocalAlignmentBlock, StringBuffer, StringBuffer, StringBuffer) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

Traverses a series of block crossing paths to retrieve an optimal alignment.

traverseS_Path(LocalAlignmentBlock, StringBuffer, StringBuffer, StringBuffer) - Method in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

Traverses an S-path of a block to retrieve a part of an optimal alignment from the new vertex of a block to entry in its input border.

Trie - class neobio.alignment.Trie.

This class implements a trie, or a digital search tree.

Trie(Object) - Constructor for class neobio.alignment.Trie

Creates a new trie node with the specified data.

TYPE_C_PATH - Static variable in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

A constant that indicates that the high scoring path ending in a given block is a C-path, i.e. one that starts inside the block.

TYPE_CROSSING_PATH - Static variable in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

A constant that indicates that the best path ending at a given entry of the output border is a block-crossing path (one that starts outside the block).

TYPE_E_PATH - Static variable in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

A constant that indicates that the high scoring path ending in a given block is an E-path, i.e. one that starts at its input border.

TYPE_S_PATH - Static variable in class neobio.alignment.CrochemoreLandauZivUkelsonLocalAlignment

A constant that indicates that the best path ending at a given entry of the output border is a S-path (one that starts inside the block).

U

unloadSequences() - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Frees pointer to loaded sequences and computed alignments (if any) so that their data can be garbage collected.

unloadSequencesInternal() - Method in class neobio.alignment.CrochemoreLandauZivUkelson

Frees pointers to loaded sequences and the the block table so that their data can be garbage collected.

unloadSequencesInternal() - Method in class neobio.alignment.NeedlemanWunsch

Frees pointers to loaded sequences and the dynamic programming matrix so that their data can be garbage collected.

unloadSequencesInternal() - Method in class neobio.alignment.SmithWaterman

Frees pointers to loaded sequences and the dynamic programming matrix so that their data can be garbage collected.

unloadSequencesInternal() - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Subclasses must implement this method to unload sequences according to their own storage, freeing pointers to sequences and any intermediate data so that they can be garbage collected.

usage() - Static method in class neobio.textui.RandomFactorSequenceGenerator

Prints command line usage.

usage() - Static method in class neobio.textui.RandomSequenceGenerator

Prints command line usage.

usage() - Static method in class neobio.textui.NeoBio

Prints command line usage.

use_match_tag - Variable in class neobio.alignment.PairwiseAlignmentAlgorithm

Indicates if the MATCH_TAG tag should be used or not.

useMatchTag() - Method in class neobio.alignment.PairwiseAlignmentAlgorithm

Tells wether the MATCH_TAG tag should be used or not.

V

valueAt(int, int) - Method in class neobio.alignment.OutMatrix

Returns the value at a given position of the matrix.

valueAt(int, int) - Method in class neobio.alignment.Smawk

This is a helper method to simplify the call to the valueAt method of the matrix.

valueAt(int, int) - Method in interface neobio.alignment.Matrix

Returns the value at an specified row and column.

W

window_number - Static variable in class neobio.gui.PairwiseAlignmentFrame

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