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Index (NeoBio API)
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<A HREF="#_A_">A</A> <A HREF="#_B_">B</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_F_">F</A> <A HREF="#_G_">G</A> <A HREF="#_H_">H</A> <A HREF="#_I_">I</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_O_">O</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_V_">V</A> <A HREF="#_W_">W</A> <HR>
<A NAME="_A_"><!-- --></A><H2>
<B>A</B></H2>
<DL>
<DT><A HREF="neobio/gui/NeoBio.html#about_menuitem"><B>about_menuitem</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/AboutDialog.html"><B>AboutDialog</B></A> - class neobio.gui.<A HREF="neobio/gui/AboutDialog.html">AboutDialog</A>.<DD>About screen.<DT><A HREF="neobio/gui/AboutDialog.html#AboutDialog(java.awt.Frame)"><B>AboutDialog(Frame)</B></A> -
Constructor for class neobio.gui.<A HREF="neobio/gui/AboutDialog.html">AboutDialog</A>
<DD>Creates a new instance of the About screen.
<DT><A HREF="neobio/gui/NeoBio.html#aboutMenuItemActionPerformed(java.awt.event.ActionEvent)"><B>aboutMenuItemActionPerformed(ActionEvent)</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#add(javax.swing.JComponent, javax.swing.JComponent, java.awt.GridBagConstraints, int, int)"><B>add(JComponent, JComponent, GridBagConstraints, int, int)</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/Trie.html#add(java.lang.Object, char)"><B>add(Object, char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>Adds a new child to this node.
<DT><A HREF="neobio/alignment/Trie.html#addSibling(java.lang.Object, char)"><B>addSibling(Object, char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>Adds a sibling to this node.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#algorithm"><B>algorithm</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#algorithm_combo"><B>algorithm_combo</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#algorithm_name"><B>algorithm_name</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#algorithm_panel"><B>algorithm_panel</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#alignment"><B>alignment</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Stores the product of the last pairwise alignment performed.
<DT><A HREF="neobio/gui/NeoBio.html#alignment_button"><B>alignment_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/alignment/AlignmentBlock.html"><B>AlignmentBlock</B></A> - class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>.<DD>This class is used by the <A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A> algorithm to store
the information of an alignment block. <DT><A HREF="neobio/alignment/AlignmentBlock.html#AlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor)"><B>AlignmentBlock(Factor, Factor)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>
<DD>Creates a new root block.
<DT><A HREF="neobio/alignment/AlignmentBlock.html#AlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><B>AlignmentBlock(Factor, Factor, int)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>
<DD>Creates a new alignment block, with all arrays created with the specified size.
<DT><A HREF="neobio/alignment/AlignmentBlock.html#ancestor"><B>ancestor</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>
<DD>An array of pointers to prefix blocks of this block.
<DT><A HREF="neobio/alignment/Factor.html#ancestor"><B>ancestor</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>A pointer to this factor's ancestor, which represents a prefix of this factor's
text.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#APPROXIMATE_MATCH_TAG"><B>APPROXIMATE_MATCH_TAG</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Tag character that signals an approximate match in the score tag line of an
alignment.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#assembleDistMatrix(neobio.alignment.AlignmentBlock, int, int, int, int)"><B>assembleDistMatrix(AlignmentBlock, int, int, int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Assembles the DIST matrix of a block by retrieving the DIST columns of its prefix
blocks.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#assembleInputBorder(int, int, int, int)"><B>assembleInputBorder(int, int, int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Assembles the input border of a block by retrieving the values at the output
borders of the left and top blocks.
</DL>
<HR>
<A NAME="_B_"><!-- --></A><H2>
<B>B</B></H2>
<DL>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#basic_button"><B>basic_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#basic_scheme"><B>basic_scheme</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/BasicScoringScheme.html"><B>BasicScoringScheme</B></A> - class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>.<DD>This class implements a basic scoring scheme. <DT><A HREF="neobio/alignment/BasicScoringScheme.html#BasicScoringScheme(int, int, int)"><B>BasicScoringScheme(int, int, int)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>Creates a new instance of a basic scoring scheme with the specified values of
match reward, mismatch penalty and gap cost.
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#BasicScoringScheme(int, int, int, boolean)"><B>BasicScoringScheme(int, int, int, boolean)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>Creates a new instance of basic scoring scheme with the specified values of
match reward, mismatch penalty and gap cost.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#block_table"><B>block_table</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>The block table, which is a matrix of alignment blocks where each block represents
the alignment between one factor of each sequence.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#buildOptimalAlignment()"><B>buildOptimalAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Retrieves an optimal alignment between the loaded sequences.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#buildOptimalAlignment()"><B>buildOptimalAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>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.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html#buildOptimalAlignment()"><B>buildOptimalAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html">CrochemoreLandauZivUkelsonGlobalAlignment</A>
<DD>Builds an optimal global alignment between the loaded sequences after the block
table has been computed.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#buildOptimalAlignment()"><B>buildOptimalAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>Builds an optimal global alignment between the loaded sequences.
<DT><A HREF="neobio/alignment/SmithWaterman.html#buildOptimalAlignment()"><B>buildOptimalAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>Builds an optimal local alignment between the loaded sequences.
</DL>
<HR>
<A NAME="_C_"><!-- --></A><H2>
<B>C</B></H2>
<DL>
<DT><A HREF="neobio/alignment/LocalAlignmentBlock.html#C"><B>C</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>
<DD>The value of the highest scoring path contained in this block, called C-path.
<DT><A HREF="neobio/alignment/ScoringScheme.html#case_sensitive"><B>case_sensitive</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>
<DD>Determines whether this scoring scheme ignores the case of characters when
computing their score.
<DT><A HREF="neobio/alignment/CharSequence.html#charAt(int)"><B>charAt(int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CharSequence.html">CharSequence</A>
<DD>Returns the character at a given position.
<DT><A HREF="neobio/alignment/CharSequence.html"><B>CharSequence</B></A> - class neobio.alignment.<A HREF="neobio/alignment/CharSequence.html">CharSequence</A>.<DD>This class implements a sequence of characters stored as an array that provides random
access to any position in constant time.
<DT><A HREF="neobio/alignment/CharSequence.html#CharSequence(java.io.Reader)"><B>CharSequence(Reader)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/CharSequence.html">CharSequence</A>
<DD>Creates a new instance of a <CODE>CharSequence</CODE>, loading the sequence data
from the <CODE>Reader</CODE> input stream.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#checkRunButtonStatus()"><B>checkRunButtonStatus()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/AboutDialog.html#closeDialog(java.awt.event.WindowEvent)"><B>closeDialog(WindowEvent)</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/AboutDialog.html">AboutDialog</A>
<DD>
<DT><A HREF="neobio/alignment/Smawk.html#col"><B>col</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>An array of column indexes reflecting the current state of the matrix.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#col_codes"><B>col_codes</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Stores matrix column headers in the order they were found.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#COMMENT_CHAR"><B>COMMENT_CHAR</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>The character used to start a comment line in the scoring matrix file.
<DT><A HREF="neobio/alignment/FactorSequence.html#COMMENT_CHAR"><B>COMMENT_CHAR</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>The character used to start a comment line in a sequence file.
<DT><A HREF="neobio/alignment/CharSequence.html#COMMENT_CHAR"><B>COMMENT_CHAR</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/CharSequence.html">CharSequence</A>
<DD>The character used to start a comment line in a sequence file.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#computeBlockTable()"><B>computeBlockTable()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Computes the block table.
<DT><A HREF="neobio/alignment/Smawk.html#computeColumnMaxima(int[])"><B>computeColumnMaxima(int[])</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>This method implements the SMAWK algorithm to compute the column maxima of a given
matrix.
<DT><A HREF="neobio/alignment/Smawk.html#computeColumnMaxima(neobio.alignment.Matrix, int[])"><B>computeColumnMaxima(Matrix, int[])</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>Computes the column maxima of a given matrix.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#computeMatrix()"><B>computeMatrix()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>Computes the dynamic programming matrix.
<DT><A HREF="neobio/alignment/SmithWaterman.html#computeMatrix()"><B>computeMatrix()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>Computes the dynamic programming matrix.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html#computeOutputBorder(neobio.alignment.AlignmentBlock, int, int, int, int, int)"><B>computeOutputBorder(AlignmentBlock, int, int, int, int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html">CrochemoreLandauZivUkelsonGlobalAlignment</A>
<DD>Computes the output border of a block.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#computeOutputBorder(neobio.alignment.LocalAlignmentBlock, int, int, int, int, int)"><B>computeOutputBorder(LocalAlignmentBlock, int, int, int, int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>Computes the output border of a block.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#computePairwiseAlignment()"><B>computePairwiseAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Computes the block table (the result depends on subclasses, see
<CODE>computeBlockTable</CODE> for details) and requests subclasses to retrieve an
optimal alignment between the loaded sequences.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#computePairwiseAlignment()"><B>computePairwiseAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>Builds an optimal global alignment between the loaded sequences after computing the
dynamic programming matrix.
<DT><A HREF="neobio/alignment/SmithWaterman.html#computePairwiseAlignment()"><B>computePairwiseAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>Builds an optimal local alignment between the loaded sequences after computing the
dynamic programming matrix.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#computePairwiseAlignment()"><B>computePairwiseAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Subclasses must implement this method to compute an alignment between the loaded
sequences using the scoring scheme previously set.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#computeScore()"><B>computeScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Computes the block table (the result depends on subclasses, see
<CODE>computeBlockTable</CODE> for details) and requests subclasses to locate the
score of the highest scoring alignment between the two sequences in the block
table.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#computeScore()"><B>computeScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>Computes the score of the best global alignment between the two sequences using the
scoring scheme previously set.
<DT><A HREF="neobio/alignment/SmithWaterman.html#computeScore()"><B>computeScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>Computes the score of the best local alignment between the two sequences using the
scoring scheme previously set.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#computeScore()"><B>computeScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Subclasses must implement this method to compute the score of the alignment between
the loaded sequences using the scoring scheme previously set.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#createBlock(neobio.alignment.Factor, neobio.alignment.Factor, int, int)"><B>createBlock(Factor, Factor, int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>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.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#createBlock(neobio.alignment.Factor, neobio.alignment.Factor, int, int)"><B>createBlock(Factor, Factor, int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>Creates and computes all information of an alignment block.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html#createBlock(neobio.alignment.Factor, neobio.alignment.Factor, int, int)"><B>createBlock(Factor, Factor, int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html">CrochemoreLandauZivUkelsonGlobalAlignment</A>
<DD>Creates and computes all information of an alignment block.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#createFirstColumnBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><B>createFirstColumnBlock(Factor, Factor, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>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.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#createFirstColumnBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><B>createFirstColumnBlock(Factor, Factor, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>Creates and computes all information of an alignment block of the first column of
the block table.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html#createFirstColumnBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><B>createFirstColumnBlock(Factor, Factor, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html">CrochemoreLandauZivUkelsonGlobalAlignment</A>
<DD>Creates and computes all information of an alignment block of the first column of
the block table.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#createFirstRowBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><B>createFirstRowBlock(Factor, Factor, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>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.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#createFirstRowBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><B>createFirstRowBlock(Factor, Factor, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>Creates and computes all information of an alignment block of the first column of
the block table.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html#createFirstRowBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><B>createFirstRowBlock(Factor, Factor, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html">CrochemoreLandauZivUkelsonGlobalAlignment</A>
<DD>Creates and computes all information of an alignment block of the first row of the
block table.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#createRootBlock(neobio.alignment.Factor, neobio.alignment.Factor)"><B>createRootBlock(Factor, Factor)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Computes the root block of the block table.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#createRootBlock(neobio.alignment.Factor, neobio.alignment.Factor)"><B>createRootBlock(Factor, Factor)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>Creates the root block.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html#createRootBlock(neobio.alignment.Factor, neobio.alignment.Factor)"><B>createRootBlock(Factor, Factor)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html">CrochemoreLandauZivUkelsonGlobalAlignment</A>
<DD>Creates the root block.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html"><B>CrochemoreLandauZivUkelson</B></A> - class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>.<DD>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).
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#CrochemoreLandauZivUkelson()"><B>CrochemoreLandauZivUkelson()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html"><B>CrochemoreLandauZivUkelsonGlobalAlignment</B></A> - class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html">CrochemoreLandauZivUkelsonGlobalAlignment</A>.<DD>This class implements the <B>global</B> pairwise sequence alignment algorithm (with
linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal
Ziv-Ukelson (2002).
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html#CrochemoreLandauZivUkelsonGlobalAlignment()"><B>CrochemoreLandauZivUkelsonGlobalAlignment()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html">CrochemoreLandauZivUkelsonGlobalAlignment</A>
<DD>
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html"><B>CrochemoreLandauZivUkelsonLocalAlignment</B></A> - class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>.<DD>This class implements the <B>local</B> pairwise sequence alignment algorithm (with
linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal
Ziv-Ukelson (2002).
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#CrochemoreLandauZivUkelsonLocalAlignment()"><B>CrochemoreLandauZivUkelsonLocalAlignment()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>
</DL>
<HR>
<A NAME="_D_"><!-- --></A><H2>
<B>D</B></H2>
<DL>
<DT><A HREF="neobio/alignment/Trie.html#data"><B>data</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>This node's stored data.
<DT><A HREF="neobio/alignment/Smawk.html#deleteOddColumns()"><B>deleteOddColumns()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>This method simulates a deletion of odd rows by manipulating the <CODE>col</CODE>
array of indexes.
<DT><A HREF="neobio/alignment/Smawk.html#deleteRow(int, int)"><B>deleteRow(int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>This method simulates a deletion of a row in the matrix during the
<CODE>reduce</CODE> operation.
<DT><A HREF="neobio/gui/NeoBio.html#desktop_pane"><B>desktop_pane</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#DIAGONAL_DIRECTION"><B>DIAGONAL_DIRECTION</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>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.
<DT><A HREF="neobio/alignment/OutMatrix.html#dim"><B>dim</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>The dimension of the OUT matrix.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#dimension"><B>dimension</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Dimension of the (squared) matrix.
<DT><A HREF="neobio/alignment/AlignmentBlock.html#direction"><B>direction</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>
<DD>An array of directions that must be followed to reach the source of the highest
scoring path for each entry in the output border.
<DT><A HREF="neobio/alignment/OutMatrix.html#dist"><B>dist</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>The DIST matrix of a block.
<DT><A HREF="neobio/alignment/AlignmentBlock.html#dist_column"><B>dist_column</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>
<DD>The DIST column of this block.
<DT><A HREF="neobio/textui/RandomFactorSequenceGenerator.html#DNA_CHARS"><B>DNA_CHARS</B></A> -
Static variable in class neobio.textui.<A HREF="neobio/textui/RandomFactorSequenceGenerator.html">RandomFactorSequenceGenerator</A>
<DD>Character set for DNA sequences.
<DT><A HREF="neobio/textui/RandomSequenceGenerator.html#DNA_CHARS"><B>DNA_CHARS</B></A> -
Static variable in class neobio.textui.<A HREF="neobio/textui/RandomSequenceGenerator.html">RandomSequenceGenerator</A>
<DD>Character set for DNA sequences.
</DL>
<HR>
<A NAME="_E_"><!-- --></A><H2>
<B>E</B></H2>
<DL>
<DT><A HREF="neobio/alignment/LocalAlignmentBlock.html#E_path_ancestor"><B>E_path_ancestor</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>
<DD>An array of pointers to blocks that are source of E-paths.
<DT><A HREF="neobio/alignment/LocalAlignmentBlock.html#E_path_ancestor_index"><B>E_path_ancestor_index</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>
<DD>Indexes of of the entry in the ancestor block that is the source of the E-path.
<DT><A HREF="neobio/alignment/LocalAlignmentBlock.html#E_path_score"><B>E_path_score</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>
<DD>The value of the highest scoring path which starts at the input border of this
block and ends inside it, called E-path.
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#equals(java.lang.Object)"><B>equals(Object)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>Compares this object to the specified object.
<DT><A HREF="neobio/gui/NeoBio.html#exit_menuitem"><B>exit_menuitem</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/NeoBio.html#exitForm()"><B>exitForm()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/NeoBio.html#exitMenuItemActionPerformed(java.awt.event.ActionEvent)"><B>exitMenuItemActionPerformed(ActionEvent)</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
</DL>
<HR>
<A NAME="_F_"><!-- --></A><H2>
<B>F</B></H2>
<DL>
<DT><A HREF="neobio/alignment/Factor.html"><B>Factor</B></A> - class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>.<DD>This class is used by <A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A> to create a linked list of factors of
a text as induced by its Lempel-Ziv (LZ78) factorisation.
<DT><A HREF="neobio/alignment/Factor.html#Factor()"><B>Factor()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>Creates a new empty <CODE>Factor</CODE>.
<DT><A HREF="neobio/alignment/Factor.html#Factor(neobio.alignment.Factor, int, char)"><B>Factor(Factor, int, char)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>Creates a new <CODE>Factor</CODE> instance with the specified serial number and
new character, and pointing to the given ancestor.
<DT><A HREF="neobio/alignment/AlignmentBlock.html#factor1"><B>factor1</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>
<DD>A pointer to the factor of the first sequence being aligned.
<DT><A HREF="neobio/alignment/AlignmentBlock.html#factor2"><B>factor2</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>
<DD>A pointer to the factor of the second sequence being aligned.
<DT><A HREF="neobio/alignment/FactorSequence.html"><B>FactorSequence</B></A> - class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>.<DD>This class builds a list of factors of a character sequence as induced by its
Lempel-Ziv (LZ78) factorisation. <DT><A HREF="neobio/alignment/FactorSequence.html#FactorSequence(java.io.Reader)"><B>FactorSequence(Reader)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>Creates a new instance of a <CODE>FactorSequence</CODE>, loading the sequence data
from the <CODE>Reader</CODE> input stream.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#file_button"><B>file_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/NeoBio.html#file_menu"><B>file_menu</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/NeoBio.html#file_toolbar"><B>file_toolbar</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#find_dialog"><B>find_dialog</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#find_matrix_button"><B>find_matrix_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#find_output_button"><B>find_output_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#find_seq1_button"><B>find_seq1_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#find_seq2_button"><B>find_seq2_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#findMatrixButtonActionPerformed()"><B>findMatrixButtonActionPerformed()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#findOutputButtonActionPerformed()"><B>findOutputButtonActionPerformed()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#findSeq1ButtonActionPerformed()"><B>findSeq1ButtonActionPerformed()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#findSeq2ButtonActionPerformed()"><B>findSeq2ButtonActionPerformed()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
</DL>
<HR>
<A NAME="_G_"><!-- --></A><H2>
<B>G</B></H2>
<DL>
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#GAP_CHARACTER"><B>GAP_CHARACTER</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Character that signals a gap in sequence.
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#gap_cost"><B>gap_cost</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>The cost of a gap (an insertion or deletion of a character).
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#gap_field"><B>gap_field</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#gap_label"><B>gap_label</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#GAP_TAG"><B>GAP_TAG</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Character that signals a gap in the score tag line of an alignment.
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#gapped_seq1"><B>gapped_seq1</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>First gapped sequence.
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#gapped_seq2"><B>gapped_seq2</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>Second gapped sequence.
<DT><A HREF="neobio/alignment/Factor.html#getAncestor()"><B>getAncestor()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>Returns this factor's ancestor factor.
<DT><A HREF="neobio/alignment/Factor.html#getAncestorSerialNumber()"><B>getAncestorSerialNumber()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>This method is a shorthand to return the serial number of this factor's ancestor.
<DT><A HREF="neobio/alignment/Trie.html#getData()"><B>getData()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>Returns the data associated with this node.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#getDiagonalPrefix(neobio.alignment.AlignmentBlock)"><B>getDiagonalPrefix(AlignmentBlock)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>This method is a shorthand to retrieve the diagonal prefix of a block from the
block table.
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#getGappedSequence1()"><B>getGappedSequence1()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>Returns the first gapped sequence.
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#getGappedSequence2()"><B>getGappedSequence2()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>Returns the second gapped sequence.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#getLeftPrefix(neobio.alignment.AlignmentBlock)"><B>getLeftPrefix(AlignmentBlock)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>This method is a shorthand to retrieve the left prefix of a block from the block
table.
<DT><A HREF="neobio/alignment/Factor.html#getNewChar()"><B>getNewChar()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>Returns this factor's new character.
<DT><A HREF="neobio/alignment/Factor.html#getNext()"><B>getNext()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>Returns this factor's next factor.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#getPairwiseAlignment()"><B>getPairwiseAlignment()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Return the last pairwise alignment computed (if any) or request subclasses to
compute one and return the result by calling the
<CODE>computePairwiseAlignment</CODE> method.
<DT><A HREF="neobio/alignment/FactorSequence.html#getRootFactor()"><B>getRootFactor()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>Returns the root factor, the one that starts the list of factors.
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#getScore()"><B>getScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>Returns the score for this alignment.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#getScore()"><B>getScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Returns the score of the last alignment computed (if any) or request subclasses to
compute one and return the result by calling the <CODE>computeScore</CODE> method.
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#getScoreTagLine()"><B>getScoreTagLine()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>Returns the score tag line.
<DT><A HREF="neobio/alignment/Factor.html#getSerialNumber()"><B>getSerialNumber()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>Returns this factor's serial number.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#getTopPrefix(neobio.alignment.AlignmentBlock)"><B>getTopPrefix(AlignmentBlock)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>This method is a shorthand to retrieve the top prefix of a block from the block
table.
</DL>
<HR>
<A NAME="_H_"><!-- --></A><H2>
<B>H</B></H2>
<DL>
<DT><A HREF="neobio/gui/NeoBio.html#help_menu"><B>help_menu</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
</DL>
<HR>
<A NAME="_I_"><!-- --></A><H2>
<B>I</B></H2>
<DL>
<DT><A HREF="neobio/gui/AboutDialog.html#image_label"><B>image_label</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/AboutDialog.html">AboutDialog</A>
<DD>
<DT><A HREF="neobio/alignment/IncompatibleScoringSchemeException.html"><B>IncompatibleScoringSchemeException</B></A> - exception neobio.alignment.<A HREF="neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A>.<DD>Signals that an scoring scheme is not compatible with the sequences being aligned.<DT><A HREF="neobio/alignment/IncompatibleScoringSchemeException.html#IncompatibleScoringSchemeException()"><B>IncompatibleScoringSchemeException()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A>
<DD>Constructs an <CODE>IncompatibleScoringSchemeException</CODE> with null as its
error detail message.
<DT><A HREF="neobio/alignment/IncompatibleScoringSchemeException.html#IncompatibleScoringSchemeException(java.lang.String)"><B>IncompatibleScoringSchemeException(String)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A>
<DD>Constructs an <CODE>IncompatibleScoringSchemeException</CODE> with the specified
detail message.
<DT><A HREF="neobio/alignment/IncompatibleScoringSchemeException.html#IncompatibleScoringSchemeException(java.lang.String, java.lang.Throwable)"><B>IncompatibleScoringSchemeException(String, Throwable)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A>
<DD>Constructs an <CODE>IncompatibleScoringSchemeException</CODE> with the specified
detail message and cause.
<DT><A HREF="neobio/alignment/IncompatibleScoringSchemeException.html#IncompatibleScoringSchemeException(java.lang.Throwable)"><B>IncompatibleScoringSchemeException(Throwable)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A>
<DD>Constructs an <CODE>IncompatibleScoringSchemeException</CODE> with the specified
cause (and a detail message that typically contains the class and detail message
of cause).
<DT><A HREF="neobio/alignment/ScoringMatrix.html#INDEL_CHAR"><B>INDEL_CHAR</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>The character that indicates the row and column for insertion and deletion
penalties in the matrix.
<DT><A HREF="neobio/alignment/OutMatrix.html#init(int, int)"><B>init(int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>Initialised this OUT matrix interface.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#initComponents()"><B>initComponents()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/NeoBio.html#initComponents()"><B>initComponents()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/AboutDialog.html#initComponents()"><B>initComponents()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/AboutDialog.html">AboutDialog</A>
<DD>
<DT><A HREF="neobio/alignment/OutMatrix.html#input_border"><B>input_border</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>The input border of a block.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#input_panel"><B>input_panel</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/InvalidScoringMatrixException.html"><B>InvalidScoringMatrixException</B></A> - exception neobio.alignment.<A HREF="neobio/alignment/InvalidScoringMatrixException.html">InvalidScoringMatrixException</A>.<DD>Signals that the substitution matrix does not comply with the specification (see
<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A> for details).<DT><A HREF="neobio/alignment/InvalidScoringMatrixException.html#InvalidScoringMatrixException()"><B>InvalidScoringMatrixException()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/InvalidScoringMatrixException.html">InvalidScoringMatrixException</A>
<DD>Constructs an <CODE>InvalidScoringMatrixException</CODE> with null as its error
detail message.
<DT><A HREF="neobio/alignment/InvalidScoringMatrixException.html#InvalidScoringMatrixException(java.lang.String)"><B>InvalidScoringMatrixException(String)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/InvalidScoringMatrixException.html">InvalidScoringMatrixException</A>
<DD>Constructs an <CODE>InvalidScoringMatrixException</CODE> with the specified detail
message.
<DT><A HREF="neobio/alignment/InvalidScoringMatrixException.html#InvalidScoringMatrixException(java.lang.String, java.lang.Throwable)"><B>InvalidScoringMatrixException(String, Throwable)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/InvalidScoringMatrixException.html">InvalidScoringMatrixException</A>
<DD>Constructs an <CODE>InvalidScoringMatrixException</CODE> with the specified detail
message and cause.
<DT><A HREF="neobio/alignment/InvalidScoringMatrixException.html#InvalidScoringMatrixException(java.lang.Throwable)"><B>InvalidScoringMatrixException(Throwable)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/InvalidScoringMatrixException.html">InvalidScoringMatrixException</A>
<DD>Constructs an <CODE>InvalidScoringMatrixException</CODE> with the specified cause
(and a detail message that typically contains the class and detail message of
cause).
<DT><A HREF="neobio/alignment/InvalidSequenceException.html"><B>InvalidSequenceException</B></A> - exception neobio.alignment.<A HREF="neobio/alignment/InvalidSequenceException.html">InvalidSequenceException</A>.<DD>Signals that the sequence does not comply with the specification (see
<A HREF="neobio/alignment/CharSequence.html">CharSequence</A> or <A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A> for details).<DT><A HREF="neobio/alignment/InvalidSequenceException.html#InvalidSequenceException()"><B>InvalidSequenceException()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/InvalidSequenceException.html">InvalidSequenceException</A>
<DD>Constructs an <CODE>InvalidSequenceException</CODE> with null as its
error detail message.
<DT><A HREF="neobio/alignment/InvalidSequenceException.html#InvalidSequenceException(java.lang.String)"><B>InvalidSequenceException(String)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/InvalidSequenceException.html">InvalidSequenceException</A>
<DD>Constructs an <CODE>InvalidSequenceException</CODE> with the specified
detail message.
<DT><A HREF="neobio/alignment/InvalidSequenceException.html#InvalidSequenceException(java.lang.String, java.lang.Throwable)"><B>InvalidSequenceException(String, Throwable)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/InvalidSequenceException.html">InvalidSequenceException</A>
<DD>Constructs an <CODE>InvalidSequenceException</CODE> with the specified
detail message and cause.
<DT><A HREF="neobio/alignment/InvalidSequenceException.html#InvalidSequenceException(java.lang.Throwable)"><B>InvalidSequenceException(Throwable)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/InvalidSequenceException.html">InvalidSequenceException</A>
<DD>Constructs an <CODE>InvalidSequenceException</CODE> with the specified
cause (and a detail message that typically contains the class and detail message
of cause).
<DT><A HREF="neobio/alignment/ScoringScheme.html#isCaseSensitive()"><B>isCaseSensitive()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>
<DD>Tells whether this scoring scheme ignores the case of characters when computing
their score.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#isPartialMatchSupported()"><B>isPartialMatchSupported()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Tells whether this scoring scheme supports partial matches, which it does, although
a particular scoring matrix loaded by this instace might not.
<DT><A HREF="neobio/alignment/ScoringScheme.html#isPartialMatchSupported()"><B>isPartialMatchSupported()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>
<DD>Returns <CODE>true</CODE> if this scoring scheme supports partial matches,
<CODE>false</CODE> otherwise.
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#isPartialMatchSupported()"><B>isPartialMatchSupported()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>Tells whether this scoring scheme supports partial matches, which it does not.
</DL>
<HR>
<A NAME="_L_"><!-- --></A><H2>
<B>L</B></H2>
<DL>
<DT><A HREF="neobio/alignment/OutMatrix.html#lc"><B>lc</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>The number of columns of the block.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#LEFT_DIRECTION"><B>LEFT_DIRECTION</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>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.
<DT><A HREF="neobio/alignment/Factor.html#length"><B>length</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>The number of characters of the text represented by this factor.
<DT><A HREF="neobio/alignment/Factor.html#length()"><B>length()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>Returns this factor's length.
<DT><A HREF="neobio/alignment/CharSequence.html#length()"><B>length()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CharSequence.html">CharSequence</A>
<DD>Returns the number of characters of this sequence.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#loadSequences(java.io.Reader, java.io.Reader)"><B>loadSequences(Reader, Reader)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Request subclasses to load the sequences according to their own needs.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#loadSequencesInternal(java.io.Reader, java.io.Reader)"><B>loadSequencesInternal(Reader, Reader)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Loads sequences into <CODE>FactorSequence</CODE> instances.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#loadSequencesInternal(java.io.Reader, java.io.Reader)"><B>loadSequencesInternal(Reader, Reader)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>Loads sequences into <A HREF="neobio/alignment/CharSequence.html">CharSequence</A> instances.
<DT><A HREF="neobio/alignment/SmithWaterman.html#loadSequencesInternal(java.io.Reader, java.io.Reader)"><B>loadSequencesInternal(Reader, Reader)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>Loads sequences into <A HREF="neobio/alignment/CharSequence.html">CharSequence</A> instances.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#loadSequencesInternal(java.io.Reader, java.io.Reader)"><B>loadSequencesInternal(Reader, Reader)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Subclasses must implement this method to load sequences according to their own
needs and throw an exception in case of any failure.
<DT><A HREF="neobio/alignment/LocalAlignmentBlock.html"><B>LocalAlignmentBlock</B></A> - class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>.<DD>This class is used by the <A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
algorithm to store the information of an alignment block. <DT><A HREF="neobio/alignment/LocalAlignmentBlock.html#LocalAlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor)"><B>LocalAlignmentBlock(Factor, Factor)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>
<DD>Creates a new root block.
<DT><A HREF="neobio/alignment/LocalAlignmentBlock.html#LocalAlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><B>LocalAlignmentBlock(Factor, Factor, int)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>
<DD>Creates a new alignment block, with all arrays created with the specified size.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#locateScore()"><B>locateScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Locates the score of the highest scoring alignment between the two sequences in the
block table after is thas been computed.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#locateScore()"><B>locateScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>Returns the score of the high scoring local alignment in the block table.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html#locateScore()"><B>locateScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html">CrochemoreLandauZivUkelsonGlobalAlignment</A>
<DD>Locate the score of the highest scoring global alignment in the block table.
</DL>
<HR>
<A NAME="_M_"><!-- --></A><H2>
<B>M</B></H2>
<DL>
<DT><A HREF="neobio/textui/RandomFactorSequenceGenerator.html#main(java.lang.String[])"><B>main(String[])</B></A> -
Static method in class neobio.textui.<A HREF="neobio/textui/RandomFactorSequenceGenerator.html">RandomFactorSequenceGenerator</A>
<DD>The main method takes three parameters from the command line to generate a
sequence.
<DT><A HREF="neobio/textui/RandomSequenceGenerator.html#main(java.lang.String[])"><B>main(String[])</B></A> -
Static method in class neobio.textui.<A HREF="neobio/textui/RandomSequenceGenerator.html">RandomSequenceGenerator</A>
<DD>The main method takes three parameters from the command line to generate a
sequence.
<DT><A HREF="neobio/textui/NeoBio.html#main(java.lang.String[])"><B>main(String[])</B></A> -
Static method in class neobio.textui.<A HREF="neobio/textui/NeoBio.html">NeoBio</A>
<DD>The main method takes parameters from the command line to compute a pairwise
sequence alignment.
<DT><A HREF="neobio/gui/NeoBio.html#main(java.lang.String[])"><B>main(String[])</B></A> -
Static method in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>Create and run a new interface.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#match_field"><B>match_field</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#match_label"><B>match_label</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#match_reward"><B>match_reward</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>The reward for a match (a substitution of equal characters).
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#MATCH_TAG"><B>MATCH_TAG</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Tag character that signals a match in the score tag line of an alignment.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#matrix"><B>matrix</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Stores values for each operation (substitution, insertion or deletion) defined by
this matrix.
<DT><A HREF="neobio/alignment/Smawk.html#matrix"><B>matrix</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>A pointer to the matrix that is being manipulated.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#matrix"><B>matrix</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>The dynamic programming matrix.
<DT><A HREF="neobio/alignment/SmithWaterman.html#matrix"><B>matrix</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>The dynamic programming matrix.
<DT><A HREF="neobio/alignment/Matrix.html"><B>Matrix</B></A> - interface neobio.alignment.<A HREF="neobio/alignment/Matrix.html">Matrix</A>.<DD>This interface defines a minimal set of operations that a matrix must implement. <DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#matrix_button"><B>matrix_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#matrix_field"><B>matrix_field</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/ScoringMatrix.html#max_absolute_score"><B>max_absolute_score</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>The maximum absolute score that this matrix can return for any substitution,
deletion or insertion.
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#max_absolute_score"><B>max_absolute_score</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>The maximum absolute score that this scoring scheme can return, which is the
maximum absolute value among <CODE>match_reward</CODE>,
<CODE>mismatch_penalty</CODE> and <CODE>gap_cost</CODE>.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#max_col"><B>max_col</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>The column index of a block (in the block table) where the high scoring local
alignment ends.
<DT><A HREF="neobio/alignment/SmithWaterman.html#max_col"><B>max_col</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>Indicate the column of where an optimal local alignment can be found in the matrix.
<DT><A HREF="neobio/alignment/OutMatrix.html#max_length"><B>max_length</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>The length of the longest sequence (number of characters) being aligned.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#max_path_type"><B>max_path_type</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>The type of the high scoring local alignment found.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#max_row"><B>max_row</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>The row index of a block (in the block table) where the high scoring local
alignment ends.
<DT><A HREF="neobio/alignment/SmithWaterman.html#max_row"><B>max_row</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>Indicate the row of where an optimal local alignment can be found in the matrix..
<DT><A HREF="neobio/alignment/OutMatrix.html#max_score"><B>max_score</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>The maximum absolute score that the current scoring scheme can return.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#max_score"><B>max_score</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>The score of the high scoring local alignment found.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#max_source_index"><B>max_source_index</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>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.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#max(int, int)"><B>max(int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Helper method to compute the the greater of two values.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#max(int, int, int)"><B>max(int, int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Helper method to compute the the greater of three values.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#max(int, int, int, int)"><B>max(int, int, int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Helper method to compute the the greater of four values.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#maxAbsoluteScore()"><B>maxAbsoluteScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Returns the maximum absolute score that this scoring scheme can return for any
substitution, deletion or insertion.
<DT><A HREF="neobio/alignment/ScoringScheme.html#maxAbsoluteScore()"><B>maxAbsoluteScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>
<DD>Returns the maximum absolute score that this scoring scheme can return for any
substitution, deletion or insertion.
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#maxAbsoluteScore()"><B>maxAbsoluteScore()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>Returns the maximum absolute score that this scoring scheme can return for any
substitution, deletion or insertion, which is the maximum absolute value among
<CODE>match_reward</CODE>, <CODE>mismatch_penalty</CODE> and
<CODE>gap_cost</CODE>.
<DT><A HREF="neobio/gui/NeoBio.html#menu_bar"><B>menu_bar</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/NeoBio.html#mid_separator"><B>mid_separator</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#mismatch_field"><B>mismatch_field</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#mismatch_label"><B>mismatch_label</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#mismatch_penalty"><B>mismatch_penalty</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>The penalty for a mismatch (a substitution of different characters).
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#MISMATCH_TAG"><B>MISMATCH_TAG</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Character that signals a mismatch in the score tag line of an alignment.
</DL>
<HR>
<A NAME="_N_"><!-- --></A><H2>
<B>N</B></H2>
<DL>
<DT><A HREF="neobio/alignment/Smawk.html#naiveComputeColumnMaxima(neobio.alignment.Matrix, int[])"><B>naiveComputeColumnMaxima(Matrix, int[])</B></A> -
Static method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>This is a simpler method for calculating column maxima.
<DT><A HREF="neobio/alignment/Smawk.html#naiveComputeRowMaxima(neobio.alignment.Matrix, int[])"><B>naiveComputeRowMaxima(Matrix, int[])</B></A> -
Static method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>This is a simpler method for calculating row maxima.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html"><B>NeedlemanWunsch</B></A> - class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>.<DD>This class implements the classic global alignment algorithm (with linear gap penalty
function) due to S.B.Needleman and C.D.Wunsch (1970).
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#NeedlemanWunsch()"><B>NeedlemanWunsch()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>
<DT><A HREF="neobio/textui/NeoBio.html"><B>NeoBio</B></A> - class neobio.textui.<A HREF="neobio/textui/NeoBio.html">NeoBio</A>.<DD>This class is a simple command line based utility for computing pairwise sequence
alignments using one of the the algorithms provided in the <A HREF="neobio/alignment/package-summary.html">neobio.alignment</A>
package.
<DT><A HREF="neobio/gui/NeoBio.html"><B>NeoBio</B></A> - class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>.<DD>This class is a simple GUI utility for computing pairwise sequence alignments using one
of the the algorithms provided in the <A HREF="neobio/alignment/package-summary.html">neobio.alignment</A> package.<DT><A HREF="neobio/alignment/package-summary.html"><B>neobio.alignment</B></A> - package neobio.alignment<DD>Provides implementation of sequence alignment algorithms.<DT><A HREF="neobio/gui/package-summary.html"><B>neobio.gui</B></A> - package neobio.gui<DD>Graphical user interface tools to run the algorithms provided by other packages.<DT><A HREF="neobio/textui/package-summary.html"><B>neobio.textui</B></A> - package neobio.textui<DD>Command line based tools to run the algorithms provided by other packages.<DT><A HREF="neobio/textui/NeoBio.html#NeoBio()"><B>NeoBio()</B></A> -
Constructor for class neobio.textui.<A HREF="neobio/textui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/gui/NeoBio.html#NeoBio()"><B>NeoBio()</B></A> -
Constructor for class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>Creates a new instance of a graphical interface.
<DT><A HREF="neobio/gui/NeoBio.html#new_alignment_item"><B>new_alignment_item</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/alignment/Factor.html#new_char"><B>new_char</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>The new character of this factor.
<DT><A HREF="neobio/gui/NeoBio.html#newAlignmentActionPerformed(java.awt.event.ActionEvent)"><B>newAlignmentActionPerformed(ActionEvent)</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/alignment/Factor.html#next"><B>next</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>A pointer to the next factor.
<DT><A HREF="neobio/alignment/FactorSequence.html#num_chars"><B>num_chars</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>The numbers of character represented by this sequence.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#num_cols"><B>num_cols</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Number of columns of the block table.
<DT><A HREF="neobio/alignment/FactorSequence.html#num_factors"><B>num_factors</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>The numbers of factors generated by the LZ78 parsing of the sequence.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#num_rows"><B>num_rows</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Number of rows of the block table.
<DT><A HREF="neobio/alignment/FactorSequence.html#numChars()"><B>numChars()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>Returns the number of characters of the original sequence.
<DT><A HREF="neobio/alignment/Smawk.html#numcols"><B>numcols</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>The matrix's current number of columns.
<DT><A HREF="neobio/alignment/OutMatrix.html#numColumns()"><B>numColumns()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>Returns the number of columns of this OUT matrix.
<DT><A HREF="neobio/alignment/Matrix.html#numColumns()"><B>numColumns()</B></A> -
Method in interface neobio.alignment.<A HREF="neobio/alignment/Matrix.html">Matrix</A>
<DD>Returns the number of columns that this matrix has.
<DT><A HREF="neobio/alignment/FactorSequence.html#numFactors()"><B>numFactors()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>Returns the number of factors produced by the LZ78 parsing of the text.
<DT><A HREF="neobio/alignment/Smawk.html#numrows"><B>numrows</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>The matrix's current number of rows.
<DT><A HREF="neobio/alignment/OutMatrix.html#numRows()"><B>numRows()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>Returns the number of rows of this OUT matrix.
<DT><A HREF="neobio/alignment/Matrix.html#numRows()"><B>numRows()</B></A> -
Method in interface neobio.alignment.<A HREF="neobio/alignment/Matrix.html">Matrix</A>
<DD>Returns the number of rows that this matrix has.
</DL>
<HR>
<A NAME="_O_"><!-- --></A><H2>
<B>O</B></H2>
<DL>
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#out_matrix"><B>out_matrix</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>An instance of the <CODE>OutMatrix</CODE> class that encodes the OUT matrix of a
block when supplied with the DIST matrix and the input border array of a block.
<DT><A HREF="neobio/alignment/OutMatrix.html"><B>OutMatrix</B></A> - class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>.<DD>Implements an interface to the OUT matrix of a block. <DT><A HREF="neobio/alignment/OutMatrix.html#OutMatrix()"><B>OutMatrix()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#output_area"><B>output_area</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/AlignmentBlock.html#output_border"><B>output_border</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>
<DD>This block's output border.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#output_field"><B>output_field</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#output_group"><B>output_group</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#output_panel"><B>output_panel</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#output_tab"><B>output_tab</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#output_tab_panel"><B>output_tab_panel</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#output_to_file"><B>output_to_file</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#outputOptionStateChanged()"><B>outputOptionStateChanged()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
</DL>
<HR>
<A NAME="_P_"><!-- --></A><H2>
<B>P</B></H2>
<DL>
<DT><A HREF="neobio/alignment/PairwiseAlignment.html"><B>PairwiseAlignment</B></A> - class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>.<DD>This class is the product of a pairwise alignment, generated by one subclasses of
<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>. <DT><A HREF="neobio/gui/NeoBio.html#pairwiseAlignment()"><B>pairwiseAlignment()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#PairwiseAlignment(java.lang.String, java.lang.String, java.lang.String, int)"><B>PairwiseAlignment(String, String, String, int)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>Creates a <CODE>PairwiseAlignment</CODE> instance with the specified gapped
sequences, score tag line and score value.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html"><B>PairwiseAlignmentAlgorithm</B></A> - class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>.<DD>This abstract class is the superclass of all classes implementing pairwise sequence
alignment algorithms. <DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#PairwiseAlignmentAlgorithm()"><B>PairwiseAlignmentAlgorithm()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html"><B>PairwiseAlignmentFrame</B></A> - class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>.<DD>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 <A HREF="neobio/alignment/package-summary.html">neobio.alignment</A> package.<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#PairwiseAlignmentFrame(java.awt.Frame)"><B>PairwiseAlignmentFrame(Frame)</B></A> -
Constructor for class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>Creates a new instance of the internal frame.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#parent_frame"><B>parent_frame</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/LocalAlignmentBlock.html#path_type"><B>path_type</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>
<DD>The type of the highest scoring path ending at a given position of the output
border of a block.
<DT><A HREF="neobio/alignment/FactorSequence.html#printFactors()"><B>printFactors()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>Returns a string representation of the actual list of factors produced by the LZ78
parsing of the text.
<DT><A HREF="neobio/alignment/Smawk.html#printMatrix()"><B>printMatrix()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>Prints the current state of the matrix (reflecting deleted rows and columns) in the
standard output.
<DT><A HREF="neobio/alignment/Smawk.html#printMatrix(neobio.alignment.Matrix)"><B>printMatrix(Matrix)</B></A> -
Static method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>Prints the contents of an object implementing the matrix interface in the standard
output.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#progress_area"><B>progress_area</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#progress_tab_panel"><B>progress_tab_panel</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/textui/RandomFactorSequenceGenerator.html#PROT_CHARS"><B>PROT_CHARS</B></A> -
Static variable in class neobio.textui.<A HREF="neobio/textui/RandomFactorSequenceGenerator.html">RandomFactorSequenceGenerator</A>
<DD>Character set for protein sequences.
<DT><A HREF="neobio/textui/RandomSequenceGenerator.html#PROT_CHARS"><B>PROT_CHARS</B></A> -
Static variable in class neobio.textui.<A HREF="neobio/textui/RandomSequenceGenerator.html">RandomSequenceGenerator</A>
<DD>Character set for protein sequences.
</DL>
<HR>
<A NAME="_R_"><!-- --></A><H2>
<B>R</B></H2>
<DL>
<DT><A HREF="neobio/textui/RandomFactorSequenceGenerator.html"><B>RandomFactorSequenceGenerator</B></A> - class neobio.textui.<A HREF="neobio/textui/RandomFactorSequenceGenerator.html">RandomFactorSequenceGenerator</A>.<DD>This class is a simple command line based utility for generating random sequences with
optimal LZ78 factorisation.
<DT><A HREF="neobio/textui/RandomFactorSequenceGenerator.html#RandomFactorSequenceGenerator()"><B>RandomFactorSequenceGenerator()</B></A> -
Constructor for class neobio.textui.<A HREF="neobio/textui/RandomFactorSequenceGenerator.html">RandomFactorSequenceGenerator</A>
<DD>
<DT><A HREF="neobio/textui/RandomSequenceGenerator.html"><B>RandomSequenceGenerator</B></A> - class neobio.textui.<A HREF="neobio/textui/RandomSequenceGenerator.html">RandomSequenceGenerator</A>.<DD>This class is a simple command line based utility for generating random sequences.
<DT><A HREF="neobio/textui/RandomSequenceGenerator.html#RandomSequenceGenerator()"><B>RandomSequenceGenerator()</B></A> -
Constructor for class neobio.textui.<A HREF="neobio/textui/RandomSequenceGenerator.html">RandomSequenceGenerator</A>
<DD>
<DT><A HREF="neobio/alignment/Smawk.html#reduce()"><B>reduce()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>This method is the key component of the SMAWK algorithm.
<DT><A HREF="neobio/alignment/Smawk.html#restoreOddColumns(int)"><B>restoreOddColumns(int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>Restores the <CODE>col</CODE> array of indexes to the state it was before the
<CODE>deleteOddColumns</CODE> method was called.
<DT><A HREF="neobio/alignment/Smawk.html#restoreRows(int)"><B>restoreRows(int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>Restores the <CODE>row</CODE> array of indexes to the state it was before the
<CODE>reduce</CODE> method was called.
<DT><A HREF="neobio/alignment/FactorSequence.html#root_factor"><B>root_factor</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>A pointer to the root factor, the one that starts the list of factors.
<DT><A HREF="neobio/alignment/Smawk.html#row"><B>row</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>An array of row indexes reflecting the current state of the matrix.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#row_codes"><B>row_codes</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Stores matrix row headers in the order they were found.
<DT><A HREF="neobio/alignment/Smawk.html#row_position"><B>row_position</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>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 <CODE>row</CODE> array.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#run_button"><B>run_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#runButtonActionPerformed()"><B>runButtonActionPerformed()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
</DL>
<HR>
<A NAME="_S_"><!-- --></A><H2>
<B>S</B></H2>
<DL>
<DT><A HREF="neobio/alignment/LocalAlignmentBlock.html#S_direction"><B>S_direction</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>
<DD>The direction to the source of the S-path of the new vertex of this block.
<DT><A HREF="neobio/alignment/LocalAlignmentBlock.html#S_path_score"><B>S_path_score</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>
<DD>The value of the highest scoring path which starts inside the block and ends at its
output border.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#schemeOptionStateChanged()"><B>schemeOptionStateChanged()</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#score"><B>score</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>The overall score value for this alignment.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#score"><B>score</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>This field stores just the score of the last pairwise alignment performed (if the
<CODE>score_computed flag</CODE> is set to true).
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#score_computed"><B>score_computed</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Flags whether the score of the alignment between the last two loaded sequences has
already been computed.
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#score_tag_line"><B>score_tag_line</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>The score tag line.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#scoreDeletion(char)"><B>scoreDeletion(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Returns the score of a deletion of character <CODE>a</CODE> according to this
scoring matrix.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#scoreDeletion(char)"><B>scoreDeletion(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Helper method to invoke the <CODE>scoreDeletion</CODE> method of the scoring scheme
set to this algorithm.
<DT><A HREF="neobio/alignment/ScoringScheme.html#scoreDeletion(char)"><B>scoreDeletion(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>
<DD>Returns the score of a deletion of character <CODE>a</CODE> according to this
scoring scheme.
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#scoreDeletion(char)"><B>scoreDeletion(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>Always returns <CODE>gap_cost</CODE> for the deletion of any character.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#scoreInsertion(char)"><B>scoreInsertion(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Returns the score of an insertion of character <CODE>a</CODE> according to this
scoring matrix.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#scoreInsertion(char)"><B>scoreInsertion(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Helper method to invoke the <CODE>scoreInsertion</CODE> method of the scoring
scheme set to this algorithm.
<DT><A HREF="neobio/alignment/ScoringScheme.html#scoreInsertion(char)"><B>scoreInsertion(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>
<DD>Returns the score of an insertion of character <CODE>a</CODE> according to this
scoring scheme.
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#scoreInsertion(char)"><B>scoreInsertion(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>Always returns <CODE>gap_cost</CODE> for the insertion of any character.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#scoreSubstitution(char, char)"><B>scoreSubstitution(char, char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Returns the score of a substitution of character <CODE>a</CODE> for character
<CODE>b</CODE> according to this scoring matrix.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#scoreSubstitution(char, char)"><B>scoreSubstitution(char, char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Helper method to invoke the <CODE>scoreSubstitution</CODE> method of the scoring
scheme set to this algorithm.
<DT><A HREF="neobio/alignment/ScoringScheme.html#scoreSubstitution(char, char)"><B>scoreSubstitution(char, char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>
<DD>Returns the score of a substitution of character <CODE>a</CODE> for character
<CODE>b</CODE> according to this scoring scheme.
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#scoreSubstitution(char, char)"><B>scoreSubstitution(char, char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>Returns the score of a substitution of character <CODE>a</CODE> for character
<CODE>b</CODE> according to this scoring scheme.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#scoring"><B>scoring</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>The scoring scheme used to compute a pairwise sequence alignment.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#scoring_group"><B>scoring_group</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#scoring_panel"><B>scoring_panel</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/ScoringMatrix.html"><B>ScoringMatrix</B></A> - class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>.<DD>This class implements a scoring scheme based on a substitution matrix. <DT><A HREF="neobio/alignment/ScoringMatrix.html#ScoringMatrix(java.io.Reader)"><B>ScoringMatrix(Reader)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Creates a new instance of a substitution matrix loaded from the character stream.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#ScoringMatrix(java.io.Reader, boolean)"><B>ScoringMatrix(Reader, boolean)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Creates a new instance of a substitution matrix loaded from the character stream.
<DT><A HREF="neobio/alignment/ScoringScheme.html"><B>ScoringScheme</B></A> - class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>.<DD>This abstract class is the superclass of all scoring schemes. <DT><A HREF="neobio/alignment/ScoringScheme.html#ScoringScheme()"><B>ScoringScheme()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>
<DD>Creates a new instance of an scoring scheme.
<DT><A HREF="neobio/alignment/ScoringScheme.html#ScoringScheme(boolean)"><B>ScoringScheme(boolean)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/ScoringScheme.html">ScoringScheme</A>
<DD>Creates a new instance of an scoring scheme.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#screen_button"><B>screen_button</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#seq1"><B>seq1</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>The first factorised sequence being aligned.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#seq1"><B>seq1</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>The first sequence of an alignment.
<DT><A HREF="neobio/alignment/SmithWaterman.html#seq1"><B>seq1</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>The first sequence of an alignment.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#seq1_field"><B>seq1_field</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#seq1_label"><B>seq1_label</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#seq2"><B>seq2</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>The second factorised sequence being aligned.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#seq2"><B>seq2</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>The second sequence of an alignment.
<DT><A HREF="neobio/alignment/SmithWaterman.html#seq2"><B>seq2</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>The second sequence of an alignment.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#seq2_field"><B>seq2_field</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#seq2_label"><B>seq2_label</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/CharSequence.html#sequence"><B>sequence</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CharSequence.html">CharSequence</A>
<DD>Stores the sequence as an array of characters.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#sequences_loaded"><B>sequences_loaded</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Flags whether sequences have been loaded.
<DT><A HREF="neobio/alignment/Factor.html#serial_number"><B>serial_number</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>This factor's serial number, which indicates the order of this factor inside the
linked list of factors of a text.
<DT><A HREF="neobio/alignment/OutMatrix.html#setData(int[][], int[], int, int)"><B>setData(int[][], int[], int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>Sets this interface's data to represent an OUT matrix for a block.
<DT><A HREF="neobio/alignment/Factor.html#setNext(neobio.alignment.Factor)"><B>setNext(Factor)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>Sets this factor's <CODE>next</CODE> pointer to point to the specified factor.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#setScoringScheme(neobio.alignment.ScoringScheme)"><B>setScoringScheme(ScoringScheme)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Sets the scoring scheme to be used for the next alignments.
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#showError(java.lang.String)"><B>showError(String)</B></A> -
Method in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
<DT><A HREF="neobio/alignment/Trie.html#sibling"><B>sibling</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>A pointer to this node's next sibling.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#smawk"><B>smawk</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>An instance of the <CODE>Smawk</CODE> class that implements the SMAWK algorithm to
compute the column maxima of a totally monotone matrix.
<DT><A HREF="neobio/alignment/Smawk.html"><B>Smawk</B></A> - class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>.<DD>This class implement the SMAWK algorithm to compute column maxima on a totally monotone
matrix as described.
<DT><A HREF="neobio/alignment/Smawk.html#Smawk()"><B>Smawk()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>
<DT><A HREF="neobio/alignment/SmithWaterman.html"><B>SmithWaterman</B></A> - class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>.<DD>This class implement the classic local alignment algorithm (with linear gap penalty
function) due to T.F.Smith and M.S.Waterman (1981).
<DT><A HREF="neobio/alignment/SmithWaterman.html#SmithWaterman()"><B>SmithWaterman()</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>
<DT><A HREF="neobio/alignment/Trie.html#son"><B>son</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>A pointer to the first of this node's children.
<DT><A HREF="neobio/alignment/AlignmentBlock.html#source_path"><B>source_path</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>
<DD>An array of indexes to the source of the highest scoring path for each entry in
the output border.
<DT><A HREF="neobio/alignment/Trie.html#spellDown(char)"><B>spellDown(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>Follows a path from this node to one of its children by spelling the character
supplied as an argument.
<DT><A HREF="neobio/alignment/Trie.html#spellRight(char)"><B>spellRight(char)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>Follows a path from this node to one of its sibling by spelling the character
supplied as an argument.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#STOP_DIRECTION"><B>STOP_DIRECTION</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>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.
</DL>
<HR>
<A NAME="_T_"><!-- --></A><H2>
<B>T</B></H2>
<DL>
<DT><A HREF="neobio/alignment/Trie.html#to_sibling"><B>to_sibling</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>The character that labels the edge from this node to the sibling pointer by
<CODE>sibling</CODE>.
<DT><A HREF="neobio/alignment/Trie.html#to_son"><B>to_son</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>The character that labels the edge from this node to the child node pointer by
<CODE>son</CODE>.
<DT><A HREF="neobio/gui/NeoBio.html#toolbar_panel"><B>toolbar_panel</B></A> -
Variable in class neobio.gui.<A HREF="neobio/gui/NeoBio.html">NeoBio</A>
<DD>
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#TOP_DIRECTION"><B>TOP_DIRECTION</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>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.
<DT><A HREF="neobio/alignment/ScoringMatrix.html#toString()"><B>toString()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/ScoringMatrix.html">ScoringMatrix</A>
<DD>Returns a String representation of this scoring matrix.
<DT><A HREF="neobio/alignment/Factor.html#toString()"><B>toString()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Factor.html">Factor</A>
<DD>Returns a string representation of the text represented by this factor.
<DT><A HREF="neobio/alignment/PairwiseAlignment.html#toString()"><B>toString()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A>
<DD>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.
<DT><A HREF="neobio/alignment/FactorSequence.html#toString()"><B>toString()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/FactorSequence.html">FactorSequence</A>
<DD>Reconstructs the sequence from the list of factors induced by the LZ78 parsing of
the text.
<DT><A HREF="neobio/alignment/CharSequence.html#toString()"><B>toString()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CharSequence.html">CharSequence</A>
<DD>Returns a string representation of the sequence.
<DT><A HREF="neobio/alignment/BasicScoringScheme.html#toString()"><B>toString()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/BasicScoringScheme.html">BasicScoringScheme</A>
<DD>Returns a String representation of this scoring scheme.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#traverseBlock(neobio.alignment.AlignmentBlock, int, java.lang.StringBuffer, java.lang.StringBuffer, java.lang.StringBuffer)"><B>traverseBlock(AlignmentBlock, int, StringBuffer, StringBuffer, StringBuffer)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>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.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#traverseBlockCrossingPath(neobio.alignment.LocalAlignmentBlock, java.lang.StringBuffer, java.lang.StringBuffer, java.lang.StringBuffer)"><B>traverseBlockCrossingPath(LocalAlignmentBlock, StringBuffer, StringBuffer, StringBuffer)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>Traverses a series of block crossing paths to retrieve an optimal alignment.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#traverseS_Path(neobio.alignment.LocalAlignmentBlock, java.lang.StringBuffer, java.lang.StringBuffer, java.lang.StringBuffer)"><B>traverseS_Path(LocalAlignmentBlock, StringBuffer, StringBuffer, StringBuffer)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>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.
<DT><A HREF="neobio/alignment/Trie.html"><B>Trie</B></A> - class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>.<DD>This class implements a trie, or a digital search tree. <DT><A HREF="neobio/alignment/Trie.html#Trie(java.lang.Object)"><B>Trie(Object)</B></A> -
Constructor for class neobio.alignment.<A HREF="neobio/alignment/Trie.html">Trie</A>
<DD>Creates a new trie node with the specified data.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#TYPE_C_PATH"><B>TYPE_C_PATH</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>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.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#TYPE_CROSSING_PATH"><B>TYPE_CROSSING_PATH</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>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).
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#TYPE_E_PATH"><B>TYPE_E_PATH</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>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.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html#TYPE_S_PATH"><B>TYPE_S_PATH</B></A> -
Static variable in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
<DD>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).
</DL>
<HR>
<A NAME="_U_"><!-- --></A><H2>
<B>U</B></H2>
<DL>
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#unloadSequences()"><B>unloadSequences()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Frees pointer to loaded sequences and computed alignments (if any) so that their
data can be garbage collected.
<DT><A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html#unloadSequencesInternal()"><B>unloadSequencesInternal()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A>
<DD>Frees pointers to loaded sequences and the the block table so that their data can
be garbage collected.
<DT><A HREF="neobio/alignment/NeedlemanWunsch.html#unloadSequencesInternal()"><B>unloadSequencesInternal()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/NeedlemanWunsch.html">NeedlemanWunsch</A>
<DD>Frees pointers to loaded sequences and the dynamic programming matrix so that their
data can be garbage collected.
<DT><A HREF="neobio/alignment/SmithWaterman.html#unloadSequencesInternal()"><B>unloadSequencesInternal()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/SmithWaterman.html">SmithWaterman</A>
<DD>Frees pointers to loaded sequences and the dynamic programming matrix so that their
data can be garbage collected.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#unloadSequencesInternal()"><B>unloadSequencesInternal()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>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.
<DT><A HREF="neobio/textui/RandomFactorSequenceGenerator.html#usage()"><B>usage()</B></A> -
Static method in class neobio.textui.<A HREF="neobio/textui/RandomFactorSequenceGenerator.html">RandomFactorSequenceGenerator</A>
<DD>Prints command line usage.
<DT><A HREF="neobio/textui/RandomSequenceGenerator.html#usage()"><B>usage()</B></A> -
Static method in class neobio.textui.<A HREF="neobio/textui/RandomSequenceGenerator.html">RandomSequenceGenerator</A>
<DD>Prints command line usage.
<DT><A HREF="neobio/textui/NeoBio.html#usage()"><B>usage()</B></A> -
Static method in class neobio.textui.<A HREF="neobio/textui/NeoBio.html">NeoBio</A>
<DD>Prints command line usage.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#use_match_tag"><B>use_match_tag</B></A> -
Variable in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Indicates if the <CODE>MATCH_TAG</CODE> tag should be used or not.
<DT><A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html#useMatchTag()"><B>useMatchTag()</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A>
<DD>Tells wether the <CODE>MATCH_TAG</CODE> tag should be used or not.
</DL>
<HR>
<A NAME="_V_"><!-- --></A><H2>
<B>V</B></H2>
<DL>
<DT><A HREF="neobio/alignment/OutMatrix.html#valueAt(int, int)"><B>valueAt(int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/OutMatrix.html">OutMatrix</A>
<DD>Returns the value at a given position of the matrix.
<DT><A HREF="neobio/alignment/Smawk.html#valueAt(int, int)"><B>valueAt(int, int)</B></A> -
Method in class neobio.alignment.<A HREF="neobio/alignment/Smawk.html">Smawk</A>
<DD>This is a helper method to simplify the call to the <CODE>valueAt</CODE> method
of the matrix.
<DT><A HREF="neobio/alignment/Matrix.html#valueAt(int, int)"><B>valueAt(int, int)</B></A> -
Method in interface neobio.alignment.<A HREF="neobio/alignment/Matrix.html">Matrix</A>
<DD>Returns the value at an specified row and column.
</DL>
<HR>
<A NAME="_W_"><!-- --></A><H2>
<B>W</B></H2>
<DL>
<DT><A HREF="neobio/gui/PairwiseAlignmentFrame.html#window_number"><B>window_number</B></A> -
Static variable in class neobio.gui.<A HREF="neobio/gui/PairwiseAlignmentFrame.html">PairwiseAlignmentFrame</A>
<DD>
</DL>
<HR>
<A HREF="#_A_">A</A> <A HREF="#_B_">B</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_F_">F</A> <A HREF="#_G_">G</A> <A HREF="#_H_">H</A> <A HREF="#_I_">I</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_O_">O</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_V_">V</A> <A HREF="#_W_">W</A>
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