website/full_javadoc/compbio/data/sequence/FastaReader.html

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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;FIELD&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  89 <H2>\r
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  91 compbio.data.sequence</FONT>\r
  92 <BR>\r
  93 Class FastaReader</H2>\r
  94 <PRE>\r
  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>\r
  96   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.FastaReader</B>\r
  97 </PRE>\r
  98 <DL>\r
  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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</DD>\r
 100 </DL>\r
 101 <HR>\r
 102 <DL>\r
 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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</DL>\r
 104 </PRE>\r
 105 \r
 106 <P>\r
 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.
 110
 111  Examples of the correct input:
 112
 113  <pre>
 114
 115  >zedpshvyzg
 116  GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD
 117
 118  >xovkactesa
 119  CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM
 120  FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG
 121  FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH
 122  DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC
 123
 124  >ntazzewyvv
 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
 131
 132     > 12 d t y wi               k       jbke
 133    KLSHHDCD
 134     N
 135      H
 136      HSKCTEPHCGNSHQMLHRDP
 137      CCDQCQSWEAENWCASMRKAILF
 138
 139  </pre>\r
 140 <P>\r
 141 \r
 142 <P>\r
 143 <DL>\r
 144 <DT><B>Version:</B></DT>\r
 145   <DD>1.0 April 2011</DD>\r
 146 <DT><B>Author:</B></DT>\r
 147   <DD>Peter Troshin</DD>\r
 148 </DL>\r
 149 <HR>\r
 150 \r
 151 <P>\r
 152 \r
 153 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 154 \r
 155 <A NAME="constructor_summary"><!-- --></A>\r
 156 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 157 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 158 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 159 <B>Constructor Summary</B></FONT></TH>\r
 160 </TR>\r
 161 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 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>&nbsp;inputStream)</CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This class will not close the incoming stream! So the client should do
 166  so.</TD>\r
 167 </TR>\r
 168 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 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>&nbsp;inputFile)</CODE>\r
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Header data can contain non-ASCII symbols and read in UTF8</TD>\r
 173 </TR>\r
 174 </TABLE>\r
 175 &nbsp;\r
 176 <!-- ========== METHOD SUMMARY =========== -->\r
 177 \r
 178 <A NAME="method_summary"><!-- --></A>\r
 179 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 180 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 181 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 182 <B>Method Summary</B></FONT></TH>\r
 183 </TR>\r
 184 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 185 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 186 <CODE>&nbsp;void</CODE></FONT></TD>\r
 187 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#close()">close</A></B>()</CODE>\r
 188 \r
 189 <BR>\r
 190 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Call this method to close the connection to the input file if you want to
 191  free up the resources.</TD>\r
 192 </TR>\r
 193 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 195 <CODE>&nbsp;boolean</CODE></FONT></TD>\r
 196 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#hasNext()">hasNext</A></B>()</CODE>\r
 197 \r
 198 <BR>\r
 199 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 200 </TR>\r
 201 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 202 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 203 <CODE>&nbsp;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></CODE></FONT></TD>\r
 204 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#next()">next</A></B>()</CODE>\r
 205 \r
 206 <BR>\r
 207 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads the next FastaSequence from the input</TD>\r
 208 </TR>\r
 209 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 211 <CODE>&nbsp;void</CODE></FONT></TD>\r
 212 <TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaReader.html#remove()">remove</A></B>()</CODE>\r
 213 \r
 214 <BR>\r
 215 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Not implemented</TD>\r
 216 </TR>\r
 217 </TABLE>\r
 218 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 219 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 220 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 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>\r
 222 </TR>\r
 223 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 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>\r
 225 </TR>\r
 226 </TABLE>\r
 227 &nbsp;\r
 228 <P>\r
 229 \r
 230 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 231 \r
 232 <A NAME="constructor_detail"><!-- --></A>\r
 233 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 234 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 235 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 236 <B>Constructor Detail</B></FONT></TH>\r
 237 </TR>\r
 238 </TABLE>\r
 239 \r
 240 <A NAME="FastaReader(java.lang.String)"><!-- --></A><H3>\r
 241 FastaReader</H3>\r
 242 <PRE>\r
 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>&nbsp;inputFile)\r
 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>\r
 245 <DL>\r
 246 <DD>Header data can contain non-ASCII symbols and read in UTF8\r
 247 <P>\r
 248 <DL>\r
 249 <DT><B>Parameters:</B><DD><CODE>inputFile</CODE> - the file containing the list of FASTA formatted sequences to
 250             read from\r
 251 <DT><B>Throws:</B>\r
 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\r
 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>\r
 254 </DL>\r
 255 <HR>\r
 256 \r
 257 <A NAME="FastaReader(java.io.InputStream)"><!-- --></A><H3>\r
 258 FastaReader</H3>\r
 259 <PRE>\r
 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>&nbsp;inputStream)\r
 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>\r
 262 <DL>\r
 263 <DD>This class will not close the incoming stream! So the client should do
 264  so.\r
 265 <P>\r
 266 <DL>\r
 267 <DT><B>Parameters:</B><DD><CODE>inputStream</CODE> - \r
 268 <DT><B>Throws:</B>\r
 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>\r
 270 </DL>\r
 271 \r
 272 <!-- ============ METHOD DETAIL ========== -->\r
 273 \r
 274 <A NAME="method_detail"><!-- --></A>\r
 275 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 276 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 277 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 278 <B>Method Detail</B></FONT></TH>\r
 279 </TR>\r
 280 </TABLE>\r
 281 \r
 282 <A NAME="hasNext()"><!-- --></A><H3>\r
 283 hasNext</H3>\r
 284 <PRE>\r
 285 public boolean <B>hasNext</B>()</PRE>\r
 286 <DL>\r
 287 <DD>\r
 288 <P>\r
 289 <DD><DL>\r
 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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></DL>\r
 291 </DD>\r
 292 <DD><DL>\r
 293 \r
 294 <DT><B>Throws:</B>\r
 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>\r
 296 </DD>\r
 297 </DL>\r
 298 <HR>\r
 299 \r
 300 <A NAME="next()"><!-- --></A><H3>\r
 301 next</H3>\r
 302 <PRE>\r
 303 public <A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A> <B>next</B>()</PRE>\r
 304 <DL>\r
 305 <DD>Reads the next FastaSequence from the input\r
 306 <P>\r
 307 <DD><DL>\r
 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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></DL>\r
 309 </DD>\r
 310 <DD><DL>\r
 311 \r
 312 <DT><B>Throws:</B>\r
 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\r
 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>\r
 315 </DD>\r
 316 </DL>\r
 317 <HR>\r
 318 \r
 319 <A NAME="remove()"><!-- --></A><H3>\r
 320 remove</H3>\r
 321 <PRE>\r
 322 public void <B>remove</B>()</PRE>\r
 323 <DL>\r
 324 <DD>Not implemented\r
 325 <P>\r
 326 <DD><DL>\r
 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>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></DL>\r
 328 </DD>\r
 329 <DD><DL>\r
 330 </DL>\r
 331 </DD>\r
 332 </DL>\r
 333 <HR>\r
 334 \r
 335 <A NAME="close()"><!-- --></A><H3>\r
 336 close</H3>\r
 337 <PRE>\r
 338 public void <B>close</B>()</PRE>\r
 339 <DL>\r
 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.\r
 344 <P>\r
 345 <DD><DL>\r
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