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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.data.sequence</FONT>
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93 Class SequenceUtil</H2>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.SequenceUtil</B>
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100 <DT><PRE>public final class <B>SequenceUtil</B><DT>extends java.lang.Object</DL>
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104 Utility class for operations on sequences
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109 <DT><B>Author:</B></DT>
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112 Date September 2009</DD>
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117 <!-- =========== FIELD SUMMARY =========== -->
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119 <A NAME="field_summary"><!-- --></A>
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120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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121 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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122 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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123 <B>Field Summary</B></FONT></TH>
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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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127 <CODE>static java.util.regex.Pattern</CODE></FONT></TD>
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128 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AA">AA</A></B></CODE>
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131 Valid Amino acids</TD>
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133 <TR BGCOLOR="white" CLASS="TableRowColor">
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134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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135 <CODE>static java.util.regex.Pattern</CODE></FONT></TD>
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136 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA">AMBIGUOUS_AA</A></B></CODE>
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139 Same as AA pattern but with two additional letters - XU</TD>
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141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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143 <CODE>static java.util.regex.Pattern</CODE></FONT></TD>
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144 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE">AMBIGUOUS_NUCLEOTIDE</A></B></CODE>
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147 Ambiguous nucleotide</TD>
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149 <TR BGCOLOR="white" CLASS="TableRowColor">
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150 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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151 <CODE>static java.util.regex.Pattern</CODE></FONT></TD>
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152 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#DIGIT">DIGIT</A></B></CODE>
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155 A digit</TD>
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157 <TR BGCOLOR="white" CLASS="TableRowColor">
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158 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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159 <CODE>static java.util.regex.Pattern</CODE></FONT></TD>
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160 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_AA">NON_AA</A></B></CODE>
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163 inversion of AA pattern</TD>
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165 <TR BGCOLOR="white" CLASS="TableRowColor">
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166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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167 <CODE>static java.util.regex.Pattern</CODE></FONT></TD>
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168 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE">NON_NUCLEOTIDE</A></B></CODE>
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171 Non nucleotide</TD>
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173 <TR BGCOLOR="white" CLASS="TableRowColor">
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174 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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175 <CODE>static java.util.regex.Pattern</CODE></FONT></TD>
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176 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NONWORD">NONWORD</A></B></CODE>
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179 Non word</TD>
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181 <TR BGCOLOR="white" CLASS="TableRowColor">
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182 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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183 <CODE>static java.util.regex.Pattern</CODE></FONT></TD>
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184 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE">NUCLEOTIDE</A></B></CODE>
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187 Nucleotides a, t, g, c, u</TD>
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189 <TR BGCOLOR="white" CLASS="TableRowColor">
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190 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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191 <CODE>static java.util.regex.Pattern</CODE></FONT></TD>
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192 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE">WHITE_SPACE</A></B></CODE>
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195 A whitespace character: [\t\n\x0B\f\r]</TD>
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199 <!-- ========== METHOD SUMMARY =========== -->
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205 <B>Method Summary</B></FONT></TH>
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207 <TR BGCOLOR="white" CLASS="TableRowColor">
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208 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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209 <CODE>static java.lang.String</CODE></FONT></TD>
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210 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#cleanSequence(java.lang.String)">cleanSequence</A></B>(java.lang.String sequence)</CODE>
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213 Removes all whitespace chars in the sequence string</TD>
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215 <TR BGCOLOR="white" CLASS="TableRowColor">
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216 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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217 <CODE>static java.lang.String</CODE></FONT></TD>
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218 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#deepCleanSequence(java.lang.String)">deepCleanSequence</A></B>(java.lang.String sequence)</CODE>
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221 Removes all special characters and digits as well as whitespace chars
222 from the sequence</TD>
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224 <TR BGCOLOR="white" CLASS="TableRowColor">
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225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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226 <CODE>static boolean</CODE></FONT></TD>
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227 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)">isAmbiguosProtein</A></B>(java.lang.String sequence)</CODE>
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230 Check whether the sequence confirms to amboguous protein sequence</TD>
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232 <TR BGCOLOR="white" CLASS="TableRowColor">
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233 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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234 <CODE>static boolean</CODE></FONT></TD>
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235 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)">isNonAmbNucleotideSequence</A></B>(java.lang.String sequence)</CODE>
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238 Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
241 <TR BGCOLOR="white" CLASS="TableRowColor">
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242 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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243 <CODE>static boolean</CODE></FONT></TD>
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244 <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>
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247 </TD>
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249 <TR BGCOLOR="white" CLASS="TableRowColor">
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250 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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251 <CODE>static boolean</CODE></FONT></TD>
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252 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)">isProteinSequence</A></B>(java.lang.String sequence)</CODE>
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255 </TD>
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257 <TR BGCOLOR="white" CLASS="TableRowColor">
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258 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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259 <CODE>static java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></FONT></TD>
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260 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)">readFasta</A></B>(java.io.InputStream inStream)</CODE>
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263 Reads fasta sequences from inStream into the list of FastaSequence
266 <TR BGCOLOR="white" CLASS="TableRowColor">
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267 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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268 <CODE>static void</CODE></FONT></TD>
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269 <TD><CODE><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)">writeFasta</A></B>(java.io.OutputStream os,
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270 java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)</CODE>
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273 Writes FastaSequence in the file, each sequence will take one line only</TD>
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275 <TR BGCOLOR="white" CLASS="TableRowColor">
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276 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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277 <CODE>static void</CODE></FONT></TD>
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278 <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,
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279 java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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280 int width)</CODE>
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283 Writes list of FastaSequeces into the outstream formatting the sequence
284 so that it contains width chars on each line</TD>
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287 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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288 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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289 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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290 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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292 <TR BGCOLOR="white" CLASS="TableRowColor">
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293 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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299 <!-- ============ FIELD DETAIL =========== -->
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301 <A NAME="field_detail"><!-- --></A>
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304 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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305 <B>Field Detail</B></FONT></TH>
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309 <A NAME="WHITE_SPACE"><!-- --></A><H3>
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312 public static final java.util.regex.Pattern <B>WHITE_SPACE</B></PRE>
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314 <DD>A whitespace character: [\t\n\x0B\f\r]
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321 <A NAME="DIGIT"><!-- --></A><H3>
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324 public static final java.util.regex.Pattern <B>DIGIT</B></PRE>
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333 <A NAME="NONWORD"><!-- --></A><H3>
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336 public static final java.util.regex.Pattern <B>NONWORD</B></PRE>
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345 <A NAME="AA"><!-- --></A><H3>
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348 public static final java.util.regex.Pattern <B>AA</B></PRE>
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350 <DD>Valid Amino acids
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357 <A NAME="NON_AA"><!-- --></A><H3>
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360 public static final java.util.regex.Pattern <B>NON_AA</B></PRE>
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362 <DD>inversion of AA pattern
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369 <A NAME="AMBIGUOUS_AA"><!-- --></A><H3>
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372 public static final java.util.regex.Pattern <B>AMBIGUOUS_AA</B></PRE>
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374 <DD>Same as AA pattern but with two additional letters - XU
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381 <A NAME="NUCLEOTIDE"><!-- --></A><H3>
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384 public static final java.util.regex.Pattern <B>NUCLEOTIDE</B></PRE>
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386 <DD>Nucleotides a, t, g, c, u
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393 <A NAME="AMBIGUOUS_NUCLEOTIDE"><!-- --></A><H3>
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394 AMBIGUOUS_NUCLEOTIDE</H3>
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396 public static final java.util.regex.Pattern <B>AMBIGUOUS_NUCLEOTIDE</B></PRE>
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398 <DD>Ambiguous nucleotide
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405 <A NAME="NON_NUCLEOTIDE"><!-- --></A><H3>
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406 NON_NUCLEOTIDE</H3>
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408 public static final java.util.regex.Pattern <B>NON_NUCLEOTIDE</B></PRE>
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416 <!-- ============ METHOD DETAIL ========== -->
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418 <A NAME="method_detail"><!-- --></A>
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421 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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422 <B>Method Detail</B></FONT></TH>
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426 <A NAME="isNucleotideSequence(compbio.data.sequence.FastaSequence)"><!-- --></A><H3>
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427 isNucleotideSequence</H3>
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429 public static boolean <B>isNucleotideSequence</B>(<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> s)</PRE>
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433 <DT><B>Returns:</B><DD>true is the sequence contains only letters a,c, t, g, u</DL>
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438 <A NAME="isNonAmbNucleotideSequence(java.lang.String)"><!-- --></A><H3>
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439 isNonAmbNucleotideSequence</H3>
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441 public static boolean <B>isNonAmbNucleotideSequence</B>(java.lang.String sequence)</PRE>
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443 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
452 <A NAME="cleanSequence(java.lang.String)"><!-- --></A><H3>
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455 public static java.lang.String <B>cleanSequence</B>(java.lang.String sequence)</PRE>
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457 <DD>Removes all whitespace chars in the sequence string
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460 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> -
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461 <DT><B>Returns:</B><DD>cleaned up sequence</DL>
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466 <A NAME="deepCleanSequence(java.lang.String)"><!-- --></A><H3>
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467 deepCleanSequence</H3>
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469 public static java.lang.String <B>deepCleanSequence</B>(java.lang.String sequence)</PRE>
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471 <DD>Removes all special characters and digits as well as whitespace chars
475 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> -
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476 <DT><B>Returns:</B><DD>cleaned up sequence</DL>
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481 <A NAME="isProteinSequence(java.lang.String)"><!-- --></A><H3>
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482 isProteinSequence</H3>
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484 public static boolean <B>isProteinSequence</B>(java.lang.String sequence)</PRE>
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487 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> -
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488 <DT><B>Returns:</B><DD>true is the sequence is a protein sequence, false overwise</DL>
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493 <A NAME="isAmbiguosProtein(java.lang.String)"><!-- --></A><H3>
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494 isAmbiguosProtein</H3>
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496 public static boolean <B>isAmbiguosProtein</B>(java.lang.String sequence)</PRE>
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498 <DD>Check whether the sequence confirms to amboguous protein sequence
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501 <DT><B>Parameters:</B><DD><CODE>sequence</CODE> -
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502 <DT><B>Returns:</B><DD>return true only if the sequence if ambiguous protein sequence
503 Return false otherwise. e.g. if the sequence is non-ambiguous
504 protein or DNA</DL>
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509 <A NAME="writeFasta(java.io.OutputStream, java.util.List, int)"><!-- --></A><H3>
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512 public static void <B>writeFasta</B>(java.io.OutputStream outstream,
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513 java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,
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515 throws java.io.IOException</PRE>
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517 <DD>Writes list of FastaSequeces into the outstream formatting the sequence
518 so that it contains width chars on each line
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521 <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
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523 <DD><CODE>java.io.IOException</CODE></DL>
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528 <A NAME="readFasta(java.io.InputStream)"><!-- --></A><H3>
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531 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)
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532 throws java.io.IOException</PRE>
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534 <DD>Reads fasta sequences from inStream into the list of FastaSequence
538 <DT><B>Parameters:</B><DD><CODE>inStream</CODE> - from
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539 <DT><B>Returns:</B><DD>list of FastaSequence objects
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541 <DD><CODE>java.io.IOException</CODE></DL>
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546 <A NAME="writeFasta(java.io.OutputStream, java.util.List)"><!-- --></A><H3>
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549 public static void <B>writeFasta</B>(java.io.OutputStream os,
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550 java.util.List<<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences)
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551 throws java.io.IOException</PRE>
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553 <DD>Writes FastaSequence in the file, each sequence will take one line only
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556 <DT><B>Parameters:</B><DD><CODE>os</CODE> - <DD><CODE>sequences</CODE> -
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558 <DD><CODE>java.io.IOException</CODE></DL>
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615 DETAIL: <A HREF="#field_detail">FIELD</A> | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>
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