Index (NeoBio API)

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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

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