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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.data.sequence</FONT>
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93 Class FastaSequence</H2>
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95 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.FastaSequence</B>
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99 <DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A></DD>
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103 <DT><PRE><FONT SIZE="-1">@Immutable
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104 </FONT>public class <B>FastaSequence</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>
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108 A FASTA formatted sequence. Please note that this class does not make any
109 assumptions as to what sequence it stores e.g. it could be nucleotide,
110 protein or even gapped alignment sequence! The only guarantee it makes is
111 that the sequence does not contain white space characters e.g. spaces, new
117 <DT><B>Version:</B></DT>
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118 <DD>1.0 September 2009</DD>
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119 <DT><B>Author:</B></DT>
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126 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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128 <A NAME="constructor_summary"><!-- --></A>
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129 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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130 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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131 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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132 <B>Constructor Summary</B></FONT></TH>
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134 <TR BGCOLOR="white" CLASS="TableRowColor">
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135 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)">FastaSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> id,
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136 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</CODE>
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139 Upon construction the any whitespace characters are removed from the
144 <!-- ========== METHOD SUMMARY =========== -->
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147 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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149 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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150 <B>Method Summary</B></FONT></TH>
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152 <TR BGCOLOR="white" CLASS="TableRowColor">
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153 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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154 <CODE>static int</CODE></FONT></TD>
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155 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> theString,
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156 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> theRegExp)</CODE>
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159 </TD>
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161 <TR BGCOLOR="white" CLASS="TableRowColor">
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162 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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163 <CODE> boolean</CODE></FONT></TD>
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164 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)">equals</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</CODE>
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167 </TD>
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169 <TR BGCOLOR="white" CLASS="TableRowColor">
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170 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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171 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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172 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A></B>(int width)</CODE>
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175 Format sequence per width letter in one string.</TD>
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177 <TR BGCOLOR="white" CLASS="TableRowColor">
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178 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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179 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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180 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A></B>()</CODE>
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183 </TD>
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185 <TR BGCOLOR="white" CLASS="TableRowColor">
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186 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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187 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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188 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getId()">getId</A></B>()</CODE>
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191 Gets the value of id</TD>
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193 <TR BGCOLOR="white" CLASS="TableRowColor">
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194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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195 <CODE> int</CODE></FONT></TD>
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196 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getLength()">getLength</A></B>()</CODE>
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199 </TD>
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201 <TR BGCOLOR="white" CLASS="TableRowColor">
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202 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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203 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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204 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A></B>()</CODE>
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207 </TD>
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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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211 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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212 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getSequence()">getSequence</A></B>()</CODE>
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215 Gets the value of sequence</TD>
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217 <TR BGCOLOR="white" CLASS="TableRowColor">
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218 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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219 <CODE> int</CODE></FONT></TD>
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220 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#hashCode()">hashCode</A></B>()</CODE>
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223 </TD>
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225 <TR BGCOLOR="white" CLASS="TableRowColor">
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226 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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227 <CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
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228 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">toString</A></B>()</CODE>
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231 Same as oneLineFasta</TD>
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234 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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235 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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236 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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237 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>
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239 <TR BGCOLOR="white" CLASS="TableRowColor">
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240 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>
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246 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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250 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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251 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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252 <B>Constructor Detail</B></FONT></TH>
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256 <A NAME="FastaSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>
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259 public <B>FastaSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> id,
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260 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> sequence)</PRE>
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262 <DD>Upon construction the any whitespace characters are removed from the
266 <DT><B>Parameters:</B><DD><CODE>id</CODE> - <DD><CODE>sequence</CODE> - </DL>
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269 <!-- ============ METHOD DETAIL ========== -->
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271 <A NAME="method_detail"><!-- --></A>
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274 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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275 <B>Method Detail</B></FONT></TH>
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279 <A NAME="getId()"><!-- --></A><H3>
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282 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getId</B>()</PRE>
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284 <DD>Gets the value of id
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288 <DT><B>Returns:</B><DD>the value of id</DL>
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293 <A NAME="getSequence()"><!-- --></A><H3>
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296 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getSequence</B>()</PRE>
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298 <DD>Gets the value of sequence
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302 <DT><B>Returns:</B><DD>the value of sequence</DL>
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307 <A NAME="countMatchesInSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>
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308 countMatchesInSequence</H3>
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310 public static int <B>countMatchesInSequence</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> theString,
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311 <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> theRegExp)</PRE>
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319 <A NAME="getFormattedFasta()"><!-- --></A><H3>
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320 getFormattedFasta</H3>
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322 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getFormattedFasta</B>()</PRE>
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330 <A NAME="getOnelineFasta()"><!-- --></A><H3>
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331 getOnelineFasta</H3>
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333 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getOnelineFasta</B>()</PRE>
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337 <DT><B>Returns:</B><DD>one line name, next line sequence, no matter what the sequence
343 <A NAME="getFormatedSequence(int)"><!-- --></A><H3>
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344 getFormatedSequence</H3>
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346 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>getFormatedSequence</B>(int width)</PRE>
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348 <DD>Format sequence per width letter in one string. Without spaces.
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352 <DT><B>Returns:</B><DD>multiple line formated sequence, one line width letters length</DL>
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357 <A NAME="getLength()"><!-- --></A><H3>
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360 public int <B>getLength</B>()</PRE>
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364 <DT><B>Returns:</B><DD>sequence length</DL>
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369 <A NAME="toString()"><!-- --></A><H3>
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372 public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>
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374 <DD>Same as oneLineFasta
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377 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
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385 <A NAME="hashCode()"><!-- --></A><H3>
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388 public int <B>hashCode</B>()</PRE>
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391 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
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399 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
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402 public boolean <B>equals</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A> obj)</PRE>
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405 <DT><B>Overrides:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A></CODE> in class <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></CODE></DL>
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