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-SequenceUtil\r
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-<H2>\r
-<FONT SIZE="-1">\r
-compbio.data.sequence</FONT>\r
-<BR>\r
-Class SequenceUtil</H2>\r
-<PRE>\r
-java.lang.Object\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.SequenceUtil</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>SequenceUtil</B><DT>extends java.lang.Object</DL>\r
-</PRE>\r
-\r
-<P>\r
-Utility class for operations on sequences\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin
-
- Date September 2009</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
-\r
-<A NAME="field_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Field Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AA">AA</A></B></CODE>\r
-\r
-<BR>\r
- Valid Amino acids</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA">AMBIGUOUS_AA</A></B></CODE>\r
-\r
-<BR>\r
- Same as AA pattern but with two additional letters - XU</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE">AMBIGUOUS_NUCLEOTIDE</A></B></CODE>\r
-\r
-<BR>\r
- Ambiguous nucleotide</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#DIGIT">DIGIT</A></B></CODE>\r
-\r
-<BR>\r
- A digit</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_AA">NON_AA</A></B></CODE>\r
-\r
-<BR>\r
- inversion of AA pattern</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE">NON_NUCLEOTIDE</A></B></CODE>\r
-\r
-<BR>\r
- Non nucleotide</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NONWORD">NONWORD</A></B></CODE>\r
-\r
-<BR>\r
- Non word</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE">NUCLEOTIDE</A></B></CODE>\r
-\r
-<BR>\r
- Nucleotides a, t, g, c, u</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.regex.Pattern</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE">WHITE_SPACE</A></B></CODE>\r
-\r
-<BR>\r
- A whitespace character: [\t\n\x0B\f\r]</TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<!-- ========== METHOD SUMMARY =========== -->\r
-\r
-<A NAME="method_summary"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Method Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)">cleanSequence</A></B>(java.lang.String sequence)</CODE>\r
-\r
-<BR>\r
- Removes all whitespace chars in the sequence string</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)">deepCleanSequence</A></B>(java.lang.String sequence)</CODE>\r
-\r
-<BR>\r
- Removes all special characters and digits as well as whitespace chars
- from the sequence</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)">isAmbiguosProtein</A></B>(java.lang.String sequence)</CODE>\r
-\r
-<BR>\r
- Check whether the sequence confirms to amboguous protein sequence</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)">isNonAmbNucleotideSequence</A></B>(java.lang.String sequence)</CODE>\r
-\r
-<BR>\r
- Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
- (!) - B char</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNucleotideSequence(compbio.data.sequence.FastaSequence)">isNucleotideSequence</A></B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)">isProteinSequence</A></B>(java.lang.String sequence)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(java.io.InputStream inStream)</CODE>\r
-\r
-<BR>\r
- Reads fasta sequences from inStream into the list of FastaSequence
- objects</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(java.io.OutputStream os,\r
- java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>\r
-\r
-<BR>\r
- Writes FastaSequence in the file, each sequence will take one line only</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List, int)">writeFasta</A></B>(java.io.OutputStream outstream,\r
- java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
- int width)</CODE>\r
-\r
-<BR>\r
- Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line</TD>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="WHITE_SPACE"><!-- --></A><H3>\r
-WHITE_SPACE</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>WHITE_SPACE</B></PRE>\r
-<DL>\r
-<DD>A whitespace character: [\t\n\x0B\f\r]\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="DIGIT"><!-- --></A><H3>\r
-DIGIT</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>DIGIT</B></PRE>\r
-<DL>\r
-<DD>A digit\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NONWORD"><!-- --></A><H3>\r
-NONWORD</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>NONWORD</B></PRE>\r
-<DL>\r
-<DD>Non word\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="AA"><!-- --></A><H3>\r
-AA</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>AA</B></PRE>\r
-<DL>\r
-<DD>Valid Amino acids\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NON_AA"><!-- --></A><H3>\r
-NON_AA</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>NON_AA</B></PRE>\r
-<DL>\r
-<DD>inversion of AA pattern\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="AMBIGUOUS_AA"><!-- --></A><H3>\r
-AMBIGUOUS_AA</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>AMBIGUOUS_AA</B></PRE>\r
-<DL>\r
-<DD>Same as AA pattern but with two additional letters - XU\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NUCLEOTIDE"><!-- --></A><H3>\r
-NUCLEOTIDE</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>NUCLEOTIDE</B></PRE>\r
-<DL>\r
-<DD>Nucleotides a, t, g, c, u\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="AMBIGUOUS_NUCLEOTIDE"><!-- --></A><H3>\r
-AMBIGUOUS_NUCLEOTIDE</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>AMBIGUOUS_NUCLEOTIDE</B></PRE>\r
-<DL>\r
-<DD>Ambiguous nucleotide\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="NON_NUCLEOTIDE"><!-- --></A><H3>\r
-NON_NUCLEOTIDE</H3>\r
-<PRE>\r
-public static final java.util.regex.Pattern <B>NON_NUCLEOTIDE</B></PRE>\r
-<DL>\r
-<DD>Non nucleotide\r
-<P>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="isNucleotideSequence(compbio.data.sequence.FastaSequence)"><!-- --></A><H3>\r
-isNucleotideSequence</H3>\r
-<PRE>\r
-public static boolean <B>isNucleotideSequence</B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>true is the sequence contains only letters a,c, t, g, u</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isNonAmbNucleotideSequence(java.lang.String)"><!-- --></A><H3>\r
-isNonAmbNucleotideSequence</H3>\r
-<PRE>\r
-public static boolean <B>isNonAmbNucleotideSequence</B>(java.lang.String sequence)</PRE>\r
-<DL>\r
-<DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
- (!) - B char\r
-<P>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="cleanSequence(java.lang.String)"><!-- --></A><H3>\r
-cleanSequence</H3>\r
-<PRE>\r
-public static java.lang.String <B>cleanSequence</B>(java.lang.String sequence)</PRE>\r
-<DL>\r
-<DD>Removes all whitespace chars in the sequence string\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="deepCleanSequence(java.lang.String)"><!-- --></A><H3>\r
-deepCleanSequence</H3>\r
-<PRE>\r
-public static java.lang.String <B>deepCleanSequence</B>(java.lang.String sequence)</PRE>\r
-<DL>\r
-<DD>Removes all special characters and digits as well as whitespace chars
- from the sequence\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>cleaned up sequence</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isProteinSequence(java.lang.String)"><!-- --></A><H3>\r
-isProteinSequence</H3>\r
-<PRE>\r
-public static boolean <B>isProteinSequence</B>(java.lang.String sequence)</PRE>\r
-<DL>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>true is the sequence is a protein sequence, false overwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isAmbiguosProtein(java.lang.String)"><!-- --></A><H3>\r
-isAmbiguosProtein</H3>\r
-<PRE>\r
-public static boolean <B>isAmbiguosProtein</B>(java.lang.String sequence)</PRE>\r
-<DL>\r
-<DD>Check whether the sequence confirms to amboguous protein sequence\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>sequence</CODE> - \r
-<DT><B>Returns:</B><DD>return true only if the sequence if ambiguous protein sequence
- Return false otherwise. e.g. if the sequence is non-ambiguous
- protein or DNA</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeFasta(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>\r
-writeFasta</H3>\r
-<PRE>\r
-public static void <B>writeFasta</B>(java.io.OutputStream outstream,\r
- java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
- int width)\r
- throws java.io.IOException</PRE>\r
-<DL>\r
-<DD>Writes list of FastaSequeces into the outstream formatting the sequence
- so that it contains width chars on each line\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>outstream</CODE> - <DD><CODE>sequences</CODE> - <DD><CODE>width</CODE> - - the maximum number of characters to write in one line\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="readFasta(java.io.InputStream)"><!-- --></A><H3>\r
-readFasta</H3>\r
-<PRE>\r
-public static java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> <B>readFasta</B>(java.io.InputStream inStream)\r
- throws java.io.IOException</PRE>\r
-<DL>\r
-<DD>Reads fasta sequences from inStream into the list of FastaSequence
- objects\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>inStream</CODE> - from\r
-<DT><B>Returns:</B><DD>list of FastaSequence objects\r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeFasta(java.io.OutputStream, java.util.List)"><!-- --></A><H3>\r
-writeFasta</H3>\r
-<PRE>\r
-public static void <B>writeFasta</B>(java.io.OutputStream os,\r
- java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)\r
- throws java.io.IOException</PRE>\r
-<DL>\r
-<DD>Writes FastaSequence in the file, each sequence will take one line only\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>os</CODE> - <DD><CODE>sequences</CODE> - \r
-<DT><B>Throws:</B>\r
-<DD><CODE>java.io.IOException</CODE></DL>\r
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