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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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LocalAlignmentBlock (NeoBio API)
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<B><EM>NeoBio</EM> API</B></EM>
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neobio.alignment</FONT>
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Class LocalAlignmentBlock</H2>
<PRE>
java.lang.Object
|
+--<A HREF="../../neobio/alignment/AlignmentBlock.html">neobio.alignment.AlignmentBlock</A>
|
+--<B>neobio.alignment.LocalAlignmentBlock</B>
</PRE>
<HR>
<DL>
<DT>public class <A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.45"><B>LocalAlignmentBlock</B></A><DT>extends <A HREF="../../neobio/alignment/AlignmentBlock.html">AlignmentBlock</A></DL>
<P>
This class is used by the <A HREF="../../neobio/alignment/CrochemoreLandauZivUkelsonLocalAlignment.html">CrochemoreLandauZivUkelsonLocalAlignment</A>
algorithm to store the information of an alignment block. All fields are public (but
final) in order to simplify the access to the data.
<P>For more information on how this class is used, please refer to the specification
of the <CODE>CrochemoreLandauZivUkelsonLocalAlignment</CODE> class.</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/CrochemoreLandauZivUkelsonLocalAlignment.html"><CODE>CrochemoreLandauZivUkelsonLocalAlignment</CODE></A></DL>
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<CODE> int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/LocalAlignmentBlock.html#C">C</A></B></CODE>
<BR>
The value of the highest scoring path contained in this block, called C-path.</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> <A HREF="../../neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>[]</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/LocalAlignmentBlock.html#E_path_ancestor">E_path_ancestor</A></B></CODE>
<BR>
An array of pointers to blocks that are source of E-paths.</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> int[]</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/LocalAlignmentBlock.html#E_path_ancestor_index">E_path_ancestor_index</A></B></CODE>
<BR>
Indexes of of the entry in the ancestor block that is the source of the E-path.</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
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<CODE> int[]</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/LocalAlignmentBlock.html#E_path_score">E_path_score</A></B></CODE>
<BR>
The value of the highest scoring path which starts at the input border of this
block and ends inside it, called E-path.</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> byte[]</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/LocalAlignmentBlock.html#path_type">path_type</A></B></CODE>
<BR>
The type of the highest scoring path ending at a given position of the output
border of a block.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> byte</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/LocalAlignmentBlock.html#S_direction">S_direction</A></B></CODE>
<BR>
The direction to the source of the S-path of the new vertex of this block.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> int[]</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/LocalAlignmentBlock.html#S_path_score">S_path_score</A></B></CODE>
<BR>
The value of the highest scoring path which starts inside the block and ends at its
output border.</TD>
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<TD><B>Fields inherited from class neobio.alignment.<A HREF="../../neobio/alignment/AlignmentBlock.html">AlignmentBlock</A></B></TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><A HREF="../../neobio/alignment/AlignmentBlock.html#ancestor">ancestor</A>, <A HREF="../../neobio/alignment/AlignmentBlock.html#direction">direction</A>, <A HREF="../../neobio/alignment/AlignmentBlock.html#dist_column">dist_column</A>, <A HREF="../../neobio/alignment/AlignmentBlock.html#factor1">factor1</A>, <A HREF="../../neobio/alignment/AlignmentBlock.html#factor2">factor2</A>, <A HREF="../../neobio/alignment/AlignmentBlock.html#output_border">output_border</A>, <A HREF="../../neobio/alignment/AlignmentBlock.html#source_path">source_path</A></CODE></TD>
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<CODE>(package private)</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/LocalAlignmentBlock.html#LocalAlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor)">LocalAlignmentBlock</A></B>(<A HREF="../../neobio/alignment/Factor.html">Factor</A> factor1,
<A HREF="../../neobio/alignment/Factor.html">Factor</A> factor2)</CODE>
<BR>
Creates a new root block.</TD>
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<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>(package private)</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/LocalAlignmentBlock.html#LocalAlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)">LocalAlignmentBlock</A></B>(<A HREF="../../neobio/alignment/Factor.html">Factor</A> factor1,
<A HREF="../../neobio/alignment/Factor.html">Factor</A> factor2,
int size)</CODE>
<BR>
Creates a new alignment block, with all arrays created with the specified size.</TD>
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<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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<A NAME="E_path_score"><!-- --></A><H3>
E_path_score</H3>
<PRE>
public int[] <A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.51"><B>E_path_score</B></A></PRE>
<DL>
<DD>The value of the highest scoring path which starts at the input border of this
block and ends inside it, called E-path.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="E_path_ancestor"><!-- --></A><H3>
E_path_ancestor</H3>
<PRE>
public <A HREF="../../neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A>[] <A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.56"><B>E_path_ancestor</B></A></PRE>
<DL>
<DD>An array of pointers to blocks that are source of E-paths.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="E_path_ancestor_index"><!-- --></A><H3>
E_path_ancestor_index</H3>
<PRE>
public int[] <A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.61"><B>E_path_ancestor_index</B></A></PRE>
<DL>
<DD>Indexes of of the entry in the ancestor block that is the source of the E-path.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="S_path_score"><!-- --></A><H3>
S_path_score</H3>
<PRE>
public int[] <A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.67"><B>S_path_score</B></A></PRE>
<DL>
<DD>The value of the highest scoring path which starts inside the block and ends at its
output border.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="path_type"><!-- --></A><H3>
path_type</H3>
<PRE>
public byte[] <A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.73"><B>path_type</B></A></PRE>
<DL>
<DD>The type of the highest scoring path ending at a given position of the output
border of a block.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="S_direction"><!-- --></A><H3>
S_direction</H3>
<PRE>
public byte <A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.78"><B>S_direction</B></A></PRE>
<DL>
<DD>The direction to the source of the S-path of the new vertex of this block.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="C"><!-- --></A><H3>
C</H3>
<PRE>
public int <A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.83"><B>C</B></A></PRE>
<DL>
<DD>The value of the highest scoring path contained in this block, called C-path.
<P>
<DL>
</DL>
</DL>
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<A NAME="LocalAlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor)"><!-- --></A><H3>
LocalAlignmentBlock</H3>
<PRE>
<A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.91"><B>LocalAlignmentBlock</B></A>(<A HREF="../../neobio/alignment/Factor.html">Factor</A> factor1,
<A HREF="../../neobio/alignment/Factor.html">Factor</A> factor2)</PRE>
<DL>
<DD>Creates a new root block.
<P>
<DT><B>Parameters:</B><DD><CODE>factor1</CODE> - factor of the first sequence being aligned<DD><CODE>factor2</CODE> - factor of the second sequence being aligned</DL>
<HR>
<A NAME="LocalAlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><!-- --></A><H3>
LocalAlignmentBlock</H3>
<PRE>
<A HREF="../../src-html\neobio\alignment\LocalAlignmentBlock.html#line.107"><B>LocalAlignmentBlock</B></A>(<A HREF="../../neobio/alignment/Factor.html">Factor</A> factor1,
<A HREF="../../neobio/alignment/Factor.html">Factor</A> factor2,
int size)</PRE>
<DL>
<DD>Creates a new alignment block, with all arrays created with the specified size.
<P>
<DT><B>Parameters:</B><DD><CODE>factor1</CODE> - factor of the first sequence being aligned<DD><CODE>factor2</CODE> - factor of the second sequence being aligned<DD><CODE>size</CODE> - size of the arrays to be created</DL>
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