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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN""http://www.w3.org/TR/REC-html40/loose.dtd">
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NeedlemanWunsch (NeoBio API)
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neobio.alignment</FONT>
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Class  NeedlemanWunsch</H2>
<PRE>
java.lang.Object
  |
  +--<A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html">neobio.alignment.PairwiseAlignmentAlgorithm</A>
        |
        +--<B>neobio.alignment.NeedlemanWunsch</B>
</PRE>
<HR>
<DL>
<DT>public class <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.83"><B>NeedlemanWunsch</B></A><DT>extends <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A></DL>

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

 <P>It is based on a dynamic programming approach. The idea consists of, given two
 sequences A and B of sizes n and m, respectively, building an (n+1 x m+1) matrix M that
 contains the similarity of prefixes of A and B. Every position M[i,j] in the matrix
 holds the score between the subsequences A[1..i] and B[1..j]. The first row and column
 represent alignments with spaces.</P>

 <P>Starting from row 0, column 0, the algorithm computes each position M[i,j] with the
 following recurrence:</P>

 <CODE><BLOCKQUOTE><PRE>
 M[0,0] = 0
 M[i,j] = max { M[i,j-1]   + scoreInsertion (B[j]),
                M[i-1,j-1] + scoreSubstitution (A[i], B[j]),
                M[i-1,j]   + scoreDeletion(A[i])             }
 </PRE></BLOCKQUOTE></CODE>

 <P>In the end, the value at the last position (last row, last column) will contain
 the similarity between the two sequences. This part of the algorithm is accomplished
 by the <A HREF="../../neobio/alignment/NeedlemanWunsch.html#computeMatrix()"><CODE>computeMatrix</CODE></A> method. It has quadratic space complexity
 since it needs to keep an (n+1 x m+1) matrix in memory. And since the work of computing
 each cell is constant, it also has quadratic time complexity.</P>

 <P>After the matrix has been computed, the alignment can be retrieved by tracing a path
 back in the matrix from the last position to the first. This step is performed by
 the <A HREF="../../neobio/alignment/NeedlemanWunsch.html#buildOptimalAlignment()"><CODE>buildOptimalAlignment</CODE></A> method, and since the path can
 be roughly as long as (m + n), this method has O(n) time complexity.</P>

 <P>If the similarity value only is needed (and not the alignment itself), it is easy to
 reduce the space requirement to O(n) by keeping just the last row or column in memory.
 This is precisely what is done by the <A HREF="../../neobio/alignment/NeedlemanWunsch.html#computeScore()"><CODE>computeScore</CODE></A> method. Note
 that it still requires O(n<SUP>2</SUP>) time.</P>

 <P>For a more efficient approach to the global alignment problem, see the
 <A HREF="../../neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A> algorithm. For local alignment, see the
 <A HREF="../../neobio/alignment/SmithWaterman.html">SmithWaterman</A> algorithm.</P>
<P>

<P>
<DL>
<DT><B>Author:</B><DD>Sergio A. de Carvalho Jr.</DD>
</DD>
<DT><B>See Also:</B><DD><A HREF="../../neobio/alignment/SmithWaterman.html"><CODE>SmithWaterman</CODE></A>, 
<A HREF="../../neobio/alignment/CrochemoreLandauZivUkelson.html"><CODE>CrochemoreLandauZivUkelson</CODE></A>, 
<A HREF="../../neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html"><CODE>CrochemoreLandauZivUkelsonLocalAlignment</CODE></A>, 
<A HREF="../../neobio/alignment/CrochemoreLandauZivUkelsonGlobalAlignment.html"><CODE>CrochemoreLandauZivUkelsonGlobalAlignment</CODE></A></DL>
<HR>

<P>
<!-- ======== NESTED CLASS SUMMARY ======== -->


<!-- =========== FIELD SUMMARY =========== -->

<A NAME="field_summary"><!-- --></A>
<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TD COLSPAN=2><FONT SIZE="+2">
<B>Field Summary</B></FONT></TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected &nbsp;int[][]</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#matrix">matrix</A></B></CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The dynamic programming matrix. </TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected &nbsp;<A HREF="../../neobio/alignment/CharSequence.html">CharSequence</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#seq1">seq1</A></B></CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The first sequence of an alignment.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected &nbsp;<A HREF="../../neobio/alignment/CharSequence.html">CharSequence</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#seq2">seq2</A></B></CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The second sequence of an alignment.</TD>
</TR>
</TABLE>
&nbsp;<A NAME="fields_inherited_from_class_neobio.alignment.PairwiseAlignmentAlgorithm"><!-- --></A>
<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
<TD><B>Fields inherited from class neobio.alignment.<A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A></B></TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#alignment">alignment</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#APPROXIMATE_MATCH_TAG">APPROXIMATE_MATCH_TAG</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#GAP_CHARACTER">GAP_CHARACTER</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#GAP_TAG">GAP_TAG</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#MATCH_TAG">MATCH_TAG</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#MISMATCH_TAG">MISMATCH_TAG</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#score">score</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#score_computed">score_computed</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#scoring">scoring</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#sequences_loaded">sequences_loaded</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#use_match_tag">use_match_tag</A></CODE></TD>
</TR>
</TABLE>
&nbsp;
<!-- ======== CONSTRUCTOR SUMMARY ======== -->

<A NAME="constructor_summary"><!-- --></A>
<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TD COLSPAN=2><FONT SIZE="+2">
<B>Constructor Summary</B></FONT></TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#NeedlemanWunsch()">NeedlemanWunsch</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
</TR>
</TABLE>
&nbsp;
<!-- ========== METHOD SUMMARY =========== -->

<A NAME="method_summary"><!-- --></A>
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<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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<B>Method Summary</B></FONT></TD>
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<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected &nbsp;<A HREF="../../neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#buildOptimalAlignment()">buildOptimalAlignment</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Builds an optimal global alignment between the loaded sequences. </TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected &nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#computeMatrix()">computeMatrix</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Computes the dynamic programming matrix.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected &nbsp;<A HREF="../../neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#computePairwiseAlignment()">computePairwiseAlignment</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Builds an optimal global alignment between the loaded sequences after computing the
 dynamic programming matrix. </TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected &nbsp;int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#computeScore()">computeScore</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Computes the score of the best global alignment between the two sequences using the
 scoring scheme previously set. </TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected &nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#loadSequencesInternal(java.io.Reader, java.io.Reader)">loadSequencesInternal</A></B>(java.io.Reader&nbsp;input1,
                                           java.io.Reader&nbsp;input2)</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Loads sequences into <A HREF="../../neobio/alignment/CharSequence.html">CharSequence</A> instances. </TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected &nbsp;void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/NeedlemanWunsch.html#unloadSequencesInternal()">unloadSequencesInternal</A></B>()</CODE>

<BR>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Frees pointers to loaded sequences and the dynamic programming matrix so that their
 data can be garbage collected.</TD>
</TR>
</TABLE>
&nbsp;<A NAME="methods_inherited_from_class_neobio.alignment.PairwiseAlignmentAlgorithm"><!-- --></A>
<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
<TD><B>Methods inherited from class neobio.alignment.<A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A></B></TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#getPairwiseAlignment()">getPairwiseAlignment</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#getScore()">getScore</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#loadSequences(java.io.Reader, java.io.Reader)">loadSequences</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#max(int, int)">max</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#max(int, int, int)">max</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#max(int, int, int, int)">max</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#scoreDeletion(char)">scoreDeletion</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#scoreInsertion(char)">scoreInsertion</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#scoreSubstitution(char, char)">scoreSubstitution</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#setScoringScheme(neobio.alignment.ScoringScheme)">setScoringScheme</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#unloadSequences()">unloadSequences</A>, <A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#useMatchTag()">useMatchTag</A></CODE></TD>
</TR>
</TABLE>
&nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
<TD><B>Methods inherited from class java.lang.Object</B></TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
</TR>
</TABLE>
&nbsp;
<P>

<!-- ============ FIELD DETAIL =========== -->

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<B>Field Detail</B></FONT></TD>
</TR>
</TABLE>

<A NAME="seq1"><!-- --></A><H3>
seq1</H3>
<PRE>
protected <A HREF="../../neobio/alignment/CharSequence.html">CharSequence</A> <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.88"><B>seq1</B></A></PRE>
<DL>
<DD>The first sequence of an alignment.
<P>
<DL>
</DL>
</DL>
<HR>

<A NAME="seq2"><!-- --></A><H3>
seq2</H3>
<PRE>
protected <A HREF="../../neobio/alignment/CharSequence.html">CharSequence</A> <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.93"><B>seq2</B></A></PRE>
<DL>
<DD>The second sequence of an alignment.
<P>
<DL>
</DL>
</DL>
<HR>

<A NAME="matrix"><!-- --></A><H3>
matrix</H3>
<PRE>
protected int[][] <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.100"><B>matrix</B></A></PRE>
<DL>
<DD>The dynamic programming matrix. Each position (i, j) represents the best score
 between the firsts i characters of <CODE>seq1</CODE> and j characters of
 <CODE>seq2</CODE>.
<P>
<DL>
</DL>
</DL>

<!-- ========= CONSTRUCTOR DETAIL ======== -->

<A NAME="constructor_detail"><!-- --></A>
<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
<TD COLSPAN=1><FONT SIZE="+2">
<B>Constructor Detail</B></FONT></TD>
</TR>
</TABLE>

<A NAME="NeedlemanWunsch()"><!-- --></A><H3>
NeedlemanWunsch</H3>
<PRE>
public <B>NeedlemanWunsch</B>()</PRE>
<DL>
</DL>

<!-- ============ METHOD DETAIL ========== -->

<A NAME="method_detail"><!-- --></A>
<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" WIDTH="100%">
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<B>Method Detail</B></FONT></TD>
</TR>
</TABLE>

<A NAME="loadSequencesInternal(java.io.Reader, java.io.Reader)"><!-- --></A><H3>
loadSequencesInternal</H3>
<PRE>
protected void <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.113"><B>loadSequencesInternal</B></A>(java.io.Reader&nbsp;input1,
                                     java.io.Reader&nbsp;input2)
                              throws java.io.IOException,
                                     <A HREF="../../neobio/alignment/InvalidSequenceException.html">InvalidSequenceException</A></PRE>
<DL>
<DD>Loads sequences into <A HREF="../../neobio/alignment/CharSequence.html">CharSequence</A> instances. In case of any error,
 an exception is raised by the constructor of <CODE>CharSequence</CODE> (please
 check the specification of that class for specific requirements).
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#loadSequencesInternal(java.io.Reader, java.io.Reader)">loadSequencesInternal</A></CODE> in class <CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>Parameters:</B><DD><CODE>input1</CODE> - Input for first sequence<DD><CODE>input2</CODE> - Input for second sequence
<DT><B>Throws:</B>
<DD><CODE>java.io.IOException</CODE> - If an I/O error occurs when reading the sequences
<DD><CODE><A HREF="../../neobio/alignment/InvalidSequenceException.html">InvalidSequenceException</A></CODE> - If the sequences are not valid<DT><B>See Also:</B><DD><A HREF="../../neobio/alignment/CharSequence.html"><CODE>CharSequence</CODE></A></DL>
</DD>
</DL>
<HR>

<A NAME="unloadSequencesInternal()"><!-- --></A><H3>
unloadSequencesInternal</H3>
<PRE>
protected void <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.125"><B>unloadSequencesInternal</B></A>()</PRE>
<DL>
<DD>Frees pointers to loaded sequences and the dynamic programming matrix so that their
 data can be garbage collected.
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#unloadSequencesInternal()">unloadSequencesInternal</A></CODE> in class <CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A></CODE></DL>
</DD>
<DD><DL>
<DT><B>See Also:</B><DD><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#unloadSequences()"><CODE>PairwiseAlignmentAlgorithm.unloadSequences()</CODE></A></DL>
</DD>
</DL>
<HR>

<A NAME="computePairwiseAlignment()"><!-- --></A><H3>
computePairwiseAlignment</H3>
<PRE>
protected <A HREF="../../neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A> <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.144"><B>computePairwiseAlignment</B></A>()
                                              throws <A HREF="../../neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A></PRE>
<DL>
<DD>Builds an optimal global alignment between the loaded sequences after computing the
 dynamic programming matrix. It calls the <CODE>buildOptimalAlignment</CODE> method
 after the <CODE>computeMatrix</CODE> method computes the dynamic programming
 matrix.
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#computePairwiseAlignment()">computePairwiseAlignment</A></CODE> in class <CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A></CODE></DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>an optimal global alignment between the loaded sequences
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A></CODE> - If the scoring scheme is not compatible
 with the loaded sequences.<DT><B>See Also:</B><DD><A HREF="../../neobio/alignment/NeedlemanWunsch.html#computeMatrix()"><CODE>computeMatrix()</CODE></A>, 
<A HREF="../../neobio/alignment/NeedlemanWunsch.html#buildOptimalAlignment()"><CODE>buildOptimalAlignment()</CODE></A></DL>
</DD>
</DL>
<HR>

<A NAME="computeMatrix()"><!-- --></A><H3>
computeMatrix</H3>
<PRE>
protected void <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.165"><B>computeMatrix</B></A>()
                      throws <A HREF="../../neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A></PRE>
<DL>
<DD>Computes the dynamic programming matrix.
<P>
<DD><DL>

<DT><B>Throws:</B>
<DD><CODE><A HREF="../../neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A></CODE> - If the scoring scheme is not compatible
 with the loaded sequences.</DL>
</DD>
</DL>
<HR>

<A NAME="buildOptimalAlignment()"><!-- --></A><H3>
buildOptimalAlignment</H3>
<PRE>
protected <A HREF="../../neobio/alignment/PairwiseAlignment.html">PairwiseAlignment</A> <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.207"><B>buildOptimalAlignment</B></A>()
                                           throws <A HREF="../../neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A></PRE>
<DL>
<DD>Builds an optimal global alignment between the loaded sequences. Before it is
 executed, the dynamic programming matrix must already have been computed by
 the <CODE>computeMatrix</CODE> method.
<P>
<DD><DL>

<DT><B>Returns:</B><DD>an optimal global alignment between the loaded sequences
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A></CODE> - If the scoring scheme
 is not compatible with the loaded sequences.<DT><B>See Also:</B><DD><A HREF="../../neobio/alignment/NeedlemanWunsch.html#computeMatrix()"><CODE>computeMatrix()</CODE></A></DL>
</DD>
</DL>
<HR>

<A NAME="computeScore()"><!-- --></A><H3>
computeScore</H3>
<PRE>
protected int <A HREF="../../src-html\neobio\alignment\NeedlemanWunsch.html#line.283"><B>computeScore</B></A>()
                    throws <A HREF="../../neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A></PRE>
<DL>
<DD>Computes the score of the best global alignment between the two sequences using the
 scoring scheme previously set. This method calculates the similarity value only
 (doesn't build the whole matrix so the alignment cannot be recovered, however it
 has the advantage of requiring O(n) space only).
<P>
<DD><DL>
<DT><B>Specified by:</B><DD><CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#computeScore()">computeScore</A></CODE> in class <CODE><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html">PairwiseAlignmentAlgorithm</A></CODE></DL>
</DD>
<DD><DL>

<DT><B>Returns:</B><DD>score of the best global alignment between the loaded sequences
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../neobio/alignment/IncompatibleScoringSchemeException.html">IncompatibleScoringSchemeException</A></CODE> - If the scoring scheme is not compatible
 with the loaded sequences.<DT><B>See Also:</B><DD><A HREF="../../neobio/alignment/PairwiseAlignmentAlgorithm.html#getScore()"><CODE>PairwiseAlignmentAlgorithm.getScore()</CODE></A></DL>
</DD>
</DL>
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