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FactorSequence (NeoBio API)
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neobio.alignment</FONT>
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Class FactorSequence</H2>
<PRE>
java.lang.Object
|
+--<B>neobio.alignment.FactorSequence</B>
</PRE>
<HR>
<DL>
<DT>public class <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.101"><B>FactorSequence</B></A><DT>extends java.lang.Object</DL>
<P>
This class builds a list of factors of a character sequence as induced by its
Lempel-Ziv (LZ78) factorisation. Each factor is enconded as the longest factor
previously seen plus one character.
<P>The input can come from any source, provided it is encapsulated in a proper
<CODE>Reader</CODE> instance. The stream is expected to be ready (i.e. the next
<CODE>read</CODE> operation must return the first character of the sequence) and it is
not closed when its end is reached, so the client is allowed to reset it and maybe use
it for another purpose.</P>
<P>Sequences can contain letters only although lines started with the
<CODE>COMMENT_CHAR</CODE> character ('>') are regarded as comments and are completely
skipped. White spaces (including tabs, line feeds and carriage returns) are also
ignored throughout.</P>
<P>This class uses a <A HREF="../../neobio/alignment/Trie.html">Trie</A> to keep track of a list of factors. Each node of
the trie contains a <A HREF="../../neobio/alignment/Factor.html">Factor</A> of the text. As the sequence is read from the
input, the trie is traversed as far as possible. When a leaf node is reached (which
means that the longest prefix of the input has been found), two tasks are
accomplished:</P>
<UL>
<LI>a new <CODE>Factor</CODE> is created with the character at the current position of
the input and the leaf node's factor;
<LI>a new node is added to the trie with the character at the current position of the
input;
</UL>
<P>Each factor also receives a serial number according to the order they are found and
a pointer to the next factor (in that order) for fast access. This pointer, together
with the factor's ancestor pointer forms a doubly-linked list of factors. The original
text can then be reconstructed simply by following the linked list and writing out its
factors.</P>
<P>As an example, the sequence <CODE>ACTAAACCGCATTAATAATAAAA</CODE> is parsed into the
following 12 factors:</P>
<CODE><BLOCKQUOTE><PRE>
0 ( , ) = empty
1 (0,A) = A
2 (0,C) = C
3 (0,T) = T
4 (1,A) = AA
5 (1,C) = AC
6 (2,G) = CG
7 (2,A) = CA
8 (3,T) = TT
9 (4,T) = AAT
10 (9,A) = AATA
11 (4,A) = AAA
serial # (prefix, new char) = factor text
</PRE></BLOCKQUOTE></CODE>
<P>This class is used by <A HREF="../../neobio/alignment/CrochemoreLandauZivUkelson.html">CrochemoreLandauZivUkelson</A> algorithm to speed up
the classic dynamic programming approach to sequence alignment.</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/Factor.html"><CODE>Factor</CODE></A>,
<A HREF="../../neobio/alignment/Trie.html"><CODE>Trie</CODE></A>,
<A HREF="../../neobio/alignment/CrochemoreLandauZivUkelson.html"><CODE>CrochemoreLandauZivUkelson</CODE></A></DL>
<HR>
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<CODE>protected static char</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/FactorSequence.html#COMMENT_CHAR">COMMENT_CHAR</A></B></CODE>
<BR>
The character used to start a comment line in a sequence file. </TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/FactorSequence.html#num_chars">num_chars</A></B></CODE>
<BR>
The numbers of character represented by this sequence.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected int</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/FactorSequence.html#num_factors">num_factors</A></B></CODE>
<BR>
The numbers of factors generated by the LZ78 parsing of the sequence.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>protected <A HREF="../../neobio/alignment/Factor.html">Factor</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/FactorSequence.html#root_factor">root_factor</A></B></CODE>
<BR>
A pointer to the root factor, the one that starts the list of factors.</TD>
</TR>
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<TD><CODE><B><A HREF="../../neobio/alignment/FactorSequence.html#FactorSequence(java.io.Reader)">FactorSequence</A></B>(java.io.Reader reader)</CODE>
<BR>
Creates a new instance of a <CODE>FactorSequence</CODE>, loading the sequence data
from the <CODE>Reader</CODE> input stream. </TD>
</TR>
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<CODE> <A HREF="../../neobio/alignment/Factor.html">Factor</A></CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/FactorSequence.html#getRootFactor()">getRootFactor</A></B>()</CODE>
<BR>
Returns the root factor, the one that starts the list of factors.</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/FactorSequence.html#numChars()">numChars</A></B>()</CODE>
<BR>
Returns the number of characters of the original sequence.</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/FactorSequence.html#numFactors()">numFactors</A></B>()</CODE>
<BR>
Returns the number of factors produced by the LZ78 parsing of the text.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/FactorSequence.html#printFactors()">printFactors</A></B>()</CODE>
<BR>
Returns a string representation of the actual list of factors produced by the LZ78
parsing of the text. </TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../neobio/alignment/FactorSequence.html#toString()">toString</A></B>()</CODE>
<BR>
Reconstructs the sequence from the list of factors induced by the LZ78 parsing of
the text.</TD>
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<TD><B>Methods inherited from class java.lang.Object</B></TD>
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<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait</CODE></TD>
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<P>
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<A NAME="COMMENT_CHAR"><!-- --></A><H3>
COMMENT_CHAR</H3>
<PRE>
protected static final char <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.107"><B>COMMENT_CHAR</B></A></PRE>
<DL>
<DD>The character used to start a comment line in a sequence file. When this character
is found, the rest of the line is ignored.
<P>
<DL>
<DT><B>See Also:</B><DD><A HREF="../../constant-values.html#neobio.alignment.FactorSequence.COMMENT_CHAR">Constant Field Values</A></DL>
</DL>
<HR>
<A NAME="root_factor"><!-- --></A><H3>
root_factor</H3>
<PRE>
protected <A HREF="../../neobio/alignment/Factor.html">Factor</A> <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.112"><B>root_factor</B></A></PRE>
<DL>
<DD>A pointer to the root factor, the one that starts the list of factors.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="num_chars"><!-- --></A><H3>
num_chars</H3>
<PRE>
protected int <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.117"><B>num_chars</B></A></PRE>
<DL>
<DD>The numbers of character represented by this sequence.
<P>
<DL>
</DL>
</DL>
<HR>
<A NAME="num_factors"><!-- --></A><H3>
num_factors</H3>
<PRE>
protected int <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.122"><B>num_factors</B></A></PRE>
<DL>
<DD>The numbers of factors generated by the LZ78 parsing of the sequence.
<P>
<DL>
</DL>
</DL>
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<A NAME="FactorSequence(java.io.Reader)"><!-- --></A><H3>
FactorSequence</H3>
<PRE>
public <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.133"><B>FactorSequence</B></A>(java.io.Reader reader)
throws java.io.IOException,
<A HREF="../../neobio/alignment/InvalidSequenceException.html">InvalidSequenceException</A></PRE>
<DL>
<DD>Creates a new instance of a <CODE>FactorSequence</CODE>, loading the sequence data
from the <CODE>Reader</CODE> input stream. A doubly-linked list of factors is built
according to its LZ78 factorisation.
<P>
<DT><B>Parameters:</B><DD><CODE>reader</CODE> - source of characters for this sequence
<DT><B>Throws:</B>
<DD><CODE>java.io.IOException</CODE> - if an I/O exception occurs when reading the input
<DD><CODE><A HREF="../../neobio/alignment/InvalidSequenceException.html">InvalidSequenceException</A></CODE> - if the input does not contain a valid sequence</DL>
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<A NAME="getRootFactor()"><!-- --></A><H3>
getRootFactor</H3>
<PRE>
public <A HREF="../../neobio/alignment/Factor.html">Factor</A> <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.220"><B>getRootFactor</B></A>()</PRE>
<DL>
<DD>Returns the root factor, the one that starts the list of factors.
<P>
<DD><DL>
<DT><B>Returns:</B><DD>root factor</DL>
</DD>
</DL>
<HR>
<A NAME="numFactors()"><!-- --></A><H3>
numFactors</H3>
<PRE>
public int <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.230"><B>numFactors</B></A>()</PRE>
<DL>
<DD>Returns the number of factors produced by the LZ78 parsing of the text.
<P>
<DD><DL>
<DT><B>Returns:</B><DD>number of factors</DL>
</DD>
</DL>
<HR>
<A NAME="numChars()"><!-- --></A><H3>
numChars</H3>
<PRE>
public int <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.240"><B>numChars</B></A>()</PRE>
<DL>
<DD>Returns the number of characters of the original sequence.
<P>
<DD><DL>
<DT><B>Returns:</B><DD>number of characters of the original sequence</DL>
</DD>
</DL>
<HR>
<A NAME="toString()"><!-- --></A><H3>
toString</H3>
<PRE>
public java.lang.String <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.251"><B>toString</B></A>()</PRE>
<DL>
<DD>Reconstructs the sequence from the list of factors induced by the LZ78 parsing of
the text.
<P>
<DD><DL>
<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>
</DD>
<DD><DL>
<DT><B>Returns:</B><DD>the original sequence</DL>
</DD>
</DL>
<HR>
<A NAME="printFactors()"><!-- --></A><H3>
printFactors</H3>
<PRE>
public java.lang.String <A HREF="../../src-html\neobio\alignment\FactorSequence.html#line.276"><B>printFactors</B></A>()</PRE>
<DL>
<DD>Returns a string representation of the actual list of factors produced by the LZ78
parsing of the text. Each factor is printed out in a separate line, in the order
they appear in the text, with its serial number, its ancestor's serial number, its
new character, length and a string representation of the factor itself.
<P>
<DD><DL>
<DT><B>Returns:</B><DD>a string representation of the list of factors</DL>
</DD>
</DL>
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