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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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AlignmentBlock (NeoBio API)
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neobio.alignment</FONT>
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Class AlignmentBlock</H2>
<PRE>
java.lang.Object
|
+--<B>neobio.alignment.AlignmentBlock</B>
</PRE>
<DL>
<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../neobio/alignment/LocalAlignmentBlock.html">LocalAlignmentBlock</A></DD>
</DL>
<HR>
<DL>
<DT>public class <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.45"><B>AlignmentBlock</B></A><DT>extends java.lang.Object</DL>
<P>
This class is used by the <A HREF="../../neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</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>CrochemoreLandauZivUkelson</CODE> class and it subclasses.</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/CrochemoreLandauZivUkelson.html"><CODE>CrochemoreLandauZivUkelson</CODE></A></DL>
<HR>
<P>
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<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> <A HREF="../../neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>[]</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/AlignmentBlock.html#ancestor">ancestor</A></B></CODE>
<BR>
An array of pointers to prefix blocks of this block.</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/AlignmentBlock.html#direction">direction</A></B></CODE>
<BR>
An array of directions that must be followed to reach the source of the highest
scoring path for each entry in the output border.</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/AlignmentBlock.html#dist_column">dist_column</A></B></CODE>
<BR>
The DIST column of this block.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> <A HREF="../../neobio/alignment/Factor.html">Factor</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/AlignmentBlock.html#factor1">factor1</A></B></CODE>
<BR>
A pointer to the factor of the first sequence being aligned.</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/Factor.html">Factor</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/AlignmentBlock.html#factor2">factor2</A></B></CODE>
<BR>
A pointer to the factor of the second sequence being aligned.</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/AlignmentBlock.html#output_border">output_border</A></B></CODE>
<BR>
This block's output border.</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/AlignmentBlock.html#source_path">source_path</A></B></CODE>
<BR>
An array of indexes to the source of the highest scoring path for each entry in
the output border.</TD>
</TR>
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<TD><CODE><B><A HREF="../../neobio/alignment/AlignmentBlock.html#AlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor)">AlignmentBlock</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>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD><CODE><B><A HREF="../../neobio/alignment/AlignmentBlock.html#AlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)">AlignmentBlock</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="factor1"><!-- --></A><H3>
factor1</H3>
<PRE>
public final <A HREF="../../neobio/alignment/Factor.html">Factor</A> <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.50"><B>factor1</B></A></PRE>
<DL>
<DD>A pointer to the factor of the first sequence being aligned.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="factor2"><!-- --></A><H3>
factor2</H3>
<PRE>
public final <A HREF="../../neobio/alignment/Factor.html">Factor</A> <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.55"><B>factor2</B></A></PRE>
<DL>
<DD>A pointer to the factor of the second sequence being aligned.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="dist_column"><!-- --></A><H3>
dist_column</H3>
<PRE>
public final int[] <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.60"><B>dist_column</B></A></PRE>
<DL>
<DD>The DIST column of this block.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="ancestor"><!-- --></A><H3>
ancestor</H3>
<PRE>
public final <A HREF="../../neobio/alignment/AlignmentBlock.html">AlignmentBlock</A>[] <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.65"><B>ancestor</B></A></PRE>
<DL>
<DD>An array of pointers to prefix blocks of this block.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="output_border"><!-- --></A><H3>
output_border</H3>
<PRE>
public final int[] <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.70"><B>output_border</B></A></PRE>
<DL>
<DD>This block's output border.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="source_path"><!-- --></A><H3>
source_path</H3>
<PRE>
public final int[] <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.76"><B>source_path</B></A></PRE>
<DL>
<DD>An array of indexes to the source of the highest scoring path for each entry in
the output border.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="direction"><!-- --></A><H3>
direction</H3>
<PRE>
public final byte[] <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.87"><B>direction</B></A></PRE>
<DL>
<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.
<P>
<DL>
<DT><B>See Also:</B><DD><A HREF="../../neobio/alignment/CrochemoreLandauZivUkelson.html#STOP_DIRECTION"><CODE>CrochemoreLandauZivUkelson.STOP_DIRECTION</CODE></A>,
<A HREF="../../neobio/alignment/CrochemoreLandauZivUkelson.html#LEFT_DIRECTION"><CODE>CrochemoreLandauZivUkelson.LEFT_DIRECTION</CODE></A>,
<A HREF="../../neobio/alignment/CrochemoreLandauZivUkelson.html#DIAGONAL_DIRECTION"><CODE>CrochemoreLandauZivUkelson.DIAGONAL_DIRECTION</CODE></A>,
<A HREF="../../neobio/alignment/CrochemoreLandauZivUkelson.html#TOP_DIRECTION"><CODE>CrochemoreLandauZivUkelson.TOP_DIRECTION</CODE></A></DL>
</DL>
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<A NAME="AlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor)"><!-- --></A><H3>
AlignmentBlock</H3>
<PRE>
public <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.98"><B>AlignmentBlock</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. A root block does not have <CODE>source_path</CODE> and
<CODE>ancestor</CODE> arrays. Moreover, its <CODE>dist_column</CODE> and
<CODE>output_border</CODE> arrays are set to zero, and the <CODE>direction</CODE>
array is set to contain an <CODE>STOP_DIRECTION</CODE>.
<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="AlignmentBlock(neobio.alignment.Factor, neobio.alignment.Factor, int)"><!-- --></A><H3>
AlignmentBlock</H3>
<PRE>
public <A HREF="../../src-html\neobio\alignment\AlignmentBlock.html#line.116"><B>AlignmentBlock</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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