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88 <!-- ======== START OF CLASS DATA ======== -->
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91 compbio.data.sequence</FONT>
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93 Class FastaReader</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.FastaReader</B>
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99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="http://java.sun.com/javase/6/docs/api/java/util/Iterator.html?is-external=true" title="class or interface in java.util">Iterator</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></DD>
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103 <DT><PRE>public class <B>FastaReader</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><DT>implements <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Iterator.html?is-external=true" title="class or interface in java.util">Iterator</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></DL>
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107 Reads files with FASTA formatted sequences. All the information in the FASTA
108 header is preserved including trailing white spaces. All the white spaces are
109 removed from the sequence.
111 Examples of the correct input:
116 GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
119 CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
120 FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
121 FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
122 DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
125 CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD
126 EASINM AQQWRSLPPSRIMKLNG HGCDCMHSHMEAD DTKQSGIKGTFWNG HDAQWLCRWG
127 EFITEA WWGRWGAITFFHAH ENKNEIQECSDQNLKE SRTTCEIID TCHLFTRHLDGW
128 RCEKCQANATHMTW ACTKSCAEQW FCAKELMMN
129 W KQMGWRCKIFRKLFRDNCWID FELPWWPICFCCKGLSTKSHSAHDGDQCRRW WPDCARDWLGPGIRGEF
130 FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI
137 CCDQCQSWEAENWCASMRKAILF
144 <DT><B>Version:</B></DT>
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145 <DD>1.0 April 2011</DD>
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146 <DT><B>Author:</B></DT>
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147 <DD>Peter Troshin</DD>
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153 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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159 <B>Constructor Summary</B></FONT></TH>
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161 <TR BGCOLOR="white" CLASS="TableRowColor">
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162 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#FastaReader(java.io.InputStream)">FastaReader</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inputStream)</CODE>
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165 This class will not close the incoming stream! So the client should do
168 <TR BGCOLOR="white" CLASS="TableRowColor">
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169 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#FastaReader(java.lang.String)">FastaReader</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> inputFile)</CODE>
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172 Header data can contain non-ASCII symbols and read in UTF8</TD>
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184 <TR BGCOLOR="white" CLASS="TableRowColor">
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185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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186 <CODE> void</CODE></FONT></TD>
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187 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#close()">close</A></B>()</CODE>
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190 Call this method to close the connection to the input file if you want to
191 free up the resources.</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> boolean</CODE></FONT></TD>
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196 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#hasNext()">hasNext</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="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></FONT></TD>
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204 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#next()">next</A></B>()</CODE>
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207 Reads the next FastaSequence from the input</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> void</CODE></FONT></TD>
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212 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#remove()">remove</A></B>()</CODE>
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215 Not implemented</TD>
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218 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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221 <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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224 <TD><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>, <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#hashCode()" title="class or interface in java.lang">hashCode</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#toString()" title="class or interface in java.lang">toString</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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230 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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236 <B>Constructor Detail</B></FONT></TH>
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240 <A NAME="FastaReader(java.lang.String)"><!-- --></A><H3>
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243 public <B>FastaReader</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> inputFile)
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244 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></PRE>
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246 <DD>Header data can contain non-ASCII symbols and read in UTF8
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249 <DT><B>Parameters:</B><DD><CODE>inputFile</CODE> - the file containing the list of FASTA formatted sequences to
252 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE> - if the input file is not found
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253 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalStateException.html?is-external=true" title="class or interface in java.lang">IllegalStateException</A></CODE> - if the close method was called on this instance</DL>
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257 <A NAME="FastaReader(java.io.InputStream)"><!-- --></A><H3>
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260 public <B>FastaReader</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A> inputStream)
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261 throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></PRE>
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263 <DD>This class will not close the incoming stream! So the client should do
267 <DT><B>Parameters:</B><DD><CODE>inputStream</CODE> -
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269 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE></DL>
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282 <A NAME="hasNext()"><!-- --></A><H3>
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285 public boolean <B>hasNext</B>()</PRE>
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290 <DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/util/Iterator.html?is-external=true#hasNext()" title="class or interface in java.util">hasNext</A></CODE> in interface <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/util/Iterator.html?is-external=true" title="class or interface in java.util">Iterator</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></DL>
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295 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalStateException.html?is-external=true" title="class or interface in java.lang">IllegalStateException</A></CODE> - if the close method was called on this instance</DL>
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300 <A NAME="next()"><!-- --></A><H3>
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303 public <A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> <B>next</B>()</PRE>
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305 <DD>Reads the next FastaSequence from the input
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308 <DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/util/Iterator.html?is-external=true#next()" title="class or interface in java.util">next</A></CODE> in interface <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/util/Iterator.html?is-external=true" title="class or interface in java.util">Iterator</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></DL>
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313 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/AssertionError.html?is-external=true" title="class or interface in java.lang">AssertionError</A></CODE> - if the header or the sequence is missing
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314 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/IllegalStateException.html?is-external=true" title="class or interface in java.lang">IllegalStateException</A></CODE> - if the close method was called on this instance</DL>
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319 <A NAME="remove()"><!-- --></A><H3>
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322 public void <B>remove</B>()</PRE>
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324 <DD>Not implemented
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327 <DT><B>Specified by:</B><DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/util/Iterator.html?is-external=true#remove()" title="class or interface in java.util">remove</A></CODE> in interface <CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/util/Iterator.html?is-external=true" title="class or interface in java.util">Iterator</A><<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>></CODE></DL>
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335 <A NAME="close()"><!-- --></A><H3>
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338 public void <B>close</B>()</PRE>
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340 <DD>Call this method to close the connection to the input file if you want to
341 free up the resources. The connection will be closed on the JVM shutdown
342 if this method was not called explicitly. No further reading on this
343 instance of the FastaReader will be possible after calling this method.
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