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91 compbio.data.sequence</FONT>
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93 Class FastaSequence</H2>
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96 <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.FastaSequence</B>
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100 <DT><PRE><FONT SIZE="-1">@Immutable
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101 </FONT>public class <B>FastaSequence</B><DT>extends java.lang.Object</DL>
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105 A FASTA formatted sequence. Please note that this class does not make any
106 assumptions as to what sequence it stores e.g. it could be nucleotide,
107 protein or even gapped alignment sequence! The only guarantee it makes is
108 that the sequence does not contain white space characters e.g. spaces, new
114 <DT><B>Version:</B></DT>
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115 <DD>1.0 September 2009</DD>
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116 <DT><B>Author:</B></DT>
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123 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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125 <A NAME="constructor_summary"><!-- --></A>
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126 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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128 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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129 <B>Constructor Summary</B></FONT></TH>
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131 <TR BGCOLOR="white" CLASS="TableRowColor">
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132 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)">FastaSequence</A></B>(java.lang.String id,
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133 java.lang.String sequence)</CODE>
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136 Upon construction the any whitespace characters are removed from the
141 <!-- ========== METHOD SUMMARY =========== -->
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143 <A NAME="method_summary"><!-- --></A>
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147 <B>Method Summary</B></FONT></TH>
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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 int</CODE></FONT></TD>
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152 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</A></B>(java.lang.String theString,
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153 java.lang.String theRegExp)</CODE>
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156 </TD>
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158 <TR BGCOLOR="white" CLASS="TableRowColor">
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159 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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160 <CODE> boolean</CODE></FONT></TD>
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161 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object obj)</CODE>
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164 </TD>
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166 <TR BGCOLOR="white" CLASS="TableRowColor">
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167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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168 <CODE> java.lang.String</CODE></FONT></TD>
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169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A></B>(int width)</CODE>
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172 Format sequence per width letter in one string.</TD>
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174 <TR BGCOLOR="white" CLASS="TableRowColor">
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175 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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176 <CODE> java.lang.String</CODE></FONT></TD>
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177 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A></B>()</CODE>
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180 </TD>
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182 <TR BGCOLOR="white" CLASS="TableRowColor">
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183 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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184 <CODE> java.lang.String</CODE></FONT></TD>
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185 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getId()">getId</A></B>()</CODE>
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188 Gets the value of id</TD>
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190 <TR BGCOLOR="white" CLASS="TableRowColor">
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191 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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192 <CODE> int</CODE></FONT></TD>
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193 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getLength()">getLength</A></B>()</CODE>
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196 </TD>
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198 <TR BGCOLOR="white" CLASS="TableRowColor">
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199 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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200 <CODE> java.lang.String</CODE></FONT></TD>
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201 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A></B>()</CODE>
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204 </TD>
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206 <TR BGCOLOR="white" CLASS="TableRowColor">
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207 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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208 <CODE> java.lang.String</CODE></FONT></TD>
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209 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#getSequence()">getSequence</A></B>()</CODE>
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212 Gets the value of sequence</TD>
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214 <TR BGCOLOR="white" CLASS="TableRowColor">
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215 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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216 <CODE> int</CODE></FONT></TD>
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217 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#hashCode()">hashCode</A></B>()</CODE>
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220 </TD>
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222 <TR BGCOLOR="white" CLASS="TableRowColor">
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223 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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224 <CODE> java.lang.String</CODE></FONT></TD>
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225 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#toString()">toString</A></B>()</CODE>
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228 Same as oneLineFasta</TD>
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231 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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232 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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233 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
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234 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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236 <TR BGCOLOR="white" CLASS="TableRowColor">
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237 <TD><CODE>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</CODE></TD>
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243 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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248 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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249 <B>Constructor Detail</B></FONT></TH>
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253 <A NAME="FastaSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>
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256 public <B>FastaSequence</B>(java.lang.String id,
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257 java.lang.String sequence)</PRE>
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259 <DD>Upon construction the any whitespace characters are removed from the
263 <DT><B>Parameters:</B><DD><CODE>id</CODE> - <DD><CODE>sequence</CODE> - </DL>
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272 <B>Method Detail</B></FONT></TH>
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276 <A NAME="getId()"><!-- --></A><H3>
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279 public java.lang.String <B>getId</B>()</PRE>
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281 <DD>Gets the value of id
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285 <DT><B>Returns:</B><DD>the value of id</DL>
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290 <A NAME="getSequence()"><!-- --></A><H3>
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293 public java.lang.String <B>getSequence</B>()</PRE>
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295 <DD>Gets the value of sequence
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299 <DT><B>Returns:</B><DD>the value of sequence</DL>
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304 <A NAME="countMatchesInSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>
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305 countMatchesInSequence</H3>
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307 public static int <B>countMatchesInSequence</B>(java.lang.String theString,
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308 java.lang.String theRegExp)</PRE>
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316 <A NAME="getFormattedFasta()"><!-- --></A><H3>
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317 getFormattedFasta</H3>
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319 public java.lang.String <B>getFormattedFasta</B>()</PRE>
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327 <A NAME="getOnelineFasta()"><!-- --></A><H3>
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328 getOnelineFasta</H3>
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330 public java.lang.String <B>getOnelineFasta</B>()</PRE>
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334 <DT><B>Returns:</B><DD>one line name, next line sequence, no matter what the sequence
340 <A NAME="getFormatedSequence(int)"><!-- --></A><H3>
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341 getFormatedSequence</H3>
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343 public java.lang.String <B>getFormatedSequence</B>(int width)</PRE>
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345 <DD>Format sequence per width letter in one string. Without spaces.
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349 <DT><B>Returns:</B><DD>multiple line formated sequence, one line width letters length</DL>
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354 <A NAME="getLength()"><!-- --></A><H3>
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357 public int <B>getLength</B>()</PRE>
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361 <DT><B>Returns:</B><DD>sequence length</DL>
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366 <A NAME="toString()"><!-- --></A><H3>
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369 public java.lang.String <B>toString</B>()</PRE>
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371 <DD>Same as oneLineFasta
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374 <DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>
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382 <A NAME="hashCode()"><!-- --></A><H3>
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385 public int <B>hashCode</B>()</PRE>
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388 <DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>
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396 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
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399 public boolean <B>equals</B>(java.lang.Object obj)</PRE>
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402 <DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>
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