website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html

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  79   SUMMARY:&nbsp;NESTED&nbsp;|&nbsp;<A HREF="#field_summary">FIELD</A>&nbsp;|&nbsp;<A HREF="#constructor_summary">CONSTR</A>&nbsp;|&nbsp;<A HREF="#method_summary">METHOD</A></FONT></TD>\r
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  91 compbio.data.sequence</FONT>\r
  92 <BR>\r
  93 Class ClustalAlignmentUtil</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.ClustalAlignmentUtil</B>\r
  97 </PRE>\r
  98 <HR>\r
  99 <DL>\r
 100 <DT><PRE>public final class <B>ClustalAlignmentUtil</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>\r
 101 </PRE>\r
 102 \r
 103 <P>\r
 104 Tools to read and write clustal formated files\r
 105 <P>\r
 106 \r
 107 <P>\r
 108 <DL>\r
 109 <DT><B>Version:</B></DT>\r
 110   <DD>1.0 September 2009</DD>\r
 111 <DT><B>Author:</B></DT>\r
 112   <DD>Petr Troshin based on jimp class</DD>\r
 113 </DL>\r
 114 <HR>\r
 115 \r
 116 <P>\r
 117 <!-- =========== FIELD SUMMARY =========== -->\r
 118 \r
 119 <A NAME="field_summary"><!-- --></A>\r
 120 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 121 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 122 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 123 <B>Field Summary</B></FONT></TH>\r
 124 </TR>\r
 125 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 126 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 127 <CODE>static&nbsp;char</CODE></FONT></TD>\r
 128 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></B></CODE>\r
 129 \r
 130 <BR>\r
 131 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Dash char to be used as gap char in the alignments</TD>\r
 132 </TR>\r
 133 </TABLE>\r
 134 &nbsp;\r
 135 <!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
 136 \r
 137 <A NAME="constructor_summary"><!-- --></A>\r
 138 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 139 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 140 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 141 <B>Constructor Summary</B></FONT></TH>\r
 142 </TR>\r
 143 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 144 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()">ClustalAlignmentUtil</A></B>()</CODE>\r
 145 \r
 146 <BR>\r
 147 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 148 </TR>\r
 149 </TABLE>\r
 150 &nbsp;\r
 151 <!-- ========== METHOD SUMMARY =========== -->\r
 152 \r
 153 <A NAME="method_summary"><!-- --></A>\r
 154 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 155 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 156 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 157 <B>Method Summary</B></FONT></TH>\r
 158 </TR>\r
 159 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 161 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
 162 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)">isValidClustalFile</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;input)</CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Please note this method closes the input stream provided as a parameter</TD>\r
 166 </TR>\r
 167 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 169 <CODE>static&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 170 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)">readClustalFile</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;file)</CODE>\r
 171 \r
 172 <BR>\r
 173 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 174 </TR>\r
 175 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 177 <CODE>static&nbsp;<A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 178 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)">readClustalFile</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;instream)</CODE>\r
 179 \r
 180 <BR>\r
 181 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read Clustal formatted alignment.</TD>\r
 182 </TR>\r
 183 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 184 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 185 <CODE>static&nbsp;void</CODE></FONT></TD>\r
 186 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outStream,\r
 187                       <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)</CODE>\r
 188 \r
 189 <BR>\r
 190 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Write Clustal formatted alignment Limitations: does not record the
 191  consensus.</TD>\r
 192 </TR>\r
 193 </TABLE>\r
 194 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
 195 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 196 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
 197 <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
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <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#finalize()" title="class or interface in java.lang">finalize</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
 201 </TR>\r
 202 </TABLE>\r
 203 &nbsp;\r
 204 <P>\r
 205 \r
 206 <!-- ============ FIELD DETAIL =========== -->\r
 207 \r
 208 <A NAME="field_detail"><!-- --></A>\r
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 210 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 211 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 212 <B>Field Detail</B></FONT></TH>\r
 213 </TR>\r
 214 </TABLE>\r
 215 \r
 216 <A NAME="gapchar"><!-- --></A><H3>\r
 217 gapchar</H3>\r
 218 <PRE>\r
 219 public static final char <B>gapchar</B></PRE>\r
 220 <DL>\r
 221 <DD>Dash char to be used as gap char in the alignments\r
 222 <P>\r
 223 <DL>\r
 224 <DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.data.sequence.ClustalAlignmentUtil.gapchar">Constant Field Values</A></DL>\r
 225 </DL>\r
 226 \r
 227 <!-- ========= CONSTRUCTOR DETAIL ======== -->\r
 228 \r
 229 <A NAME="constructor_detail"><!-- --></A>\r
 230 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 231 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 232 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 233 <B>Constructor Detail</B></FONT></TH>\r
 234 </TR>\r
 235 </TABLE>\r
 236 \r
 237 <A NAME="ClustalAlignmentUtil()"><!-- --></A><H3>\r
 238 ClustalAlignmentUtil</H3>\r
 239 <PRE>\r
 240 public <B>ClustalAlignmentUtil</B>()</PRE>\r
 241 <DL>\r
 242 </DL>\r
 243 \r
 244 <!-- ============ METHOD DETAIL ========== -->\r
 245 \r
 246 <A NAME="method_detail"><!-- --></A>\r
 247 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 248 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 249 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
 250 <B>Method Detail</B></FONT></TH>\r
 251 </TR>\r
 252 </TABLE>\r
 253 \r
 254 <A NAME="readClustalFile(java.io.InputStream)"><!-- --></A><H3>\r
 255 readClustalFile</H3>\r
 256 <PRE>\r
 257 public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</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;instream)\r
 258                                  throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
 259                                         <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></PRE>\r
 260 <DL>\r
 261 <DD>Read Clustal formatted alignment. Limitations: Does not read consensus
 262
 263  Sequence names as well as the sequences are not guaranteed to be unique!\r
 264 <P>\r
 265 <DD><DL>\r
 266 \r
 267 <DT><B>Throws:</B>\r
 268 <DD><CODE>{@link</CODE> - IOException}\r
 269 <DD><CODE>{@link</CODE> - UnknownFileFormatException}\r
 270 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
 271 <DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE></DL>\r
 272 </DD>\r
 273 </DL>\r
 274 <HR>\r
 275 \r
 276 <A NAME="isValidClustalFile(java.io.InputStream)"><!-- --></A><H3>\r
 277 isValidClustalFile</H3>\r
 278 <PRE>\r
 279 public static boolean <B>isValidClustalFile</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;input)</PRE>\r
 280 <DL>\r
 281 <DD>Please note this method closes the input stream provided as a parameter\r
 282 <P>\r
 283 <DD><DL>\r
 284 <DT><B>Parameters:</B><DD><CODE>input</CODE> - \r
 285 <DT><B>Returns:</B><DD>true if the file is recognised as Clustal formatted alignment,
 286          false otherwise</DL>\r
 287 </DD>\r
 288 </DL>\r
 289 <HR>\r
 290 \r
 291 <A NAME="writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><!-- --></A><H3>\r
 292 writeClustalAlignment</H3>\r
 293 <PRE>\r
 294 public static void <B>writeClustalAlignment</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outStream,\r
 295                                          <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)\r
 296                                   throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
 297 <DL>\r
 298 <DD>Write Clustal formatted alignment Limitations: does not record the
 299  consensus. Potential bug - records 60 chars length alignment where
 300  Clustal would have recorded 50 chars.\r
 301 <P>\r
 302 <DD><DL>\r
 303 <DT><B>Parameters:</B><DD><CODE>outStream</CODE> - <DD><CODE>alignment</CODE> - \r
 304 <DT><B>Throws:</B>\r
 305 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
 306 </DD>\r
 307 </DL>\r
 308 <HR>\r
 309 \r
 310 <A NAME="readClustalFile(java.io.File)"><!-- --></A><H3>\r
 311 readClustalFile</H3>\r
 312 <PRE>\r
 313 public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/File.html?is-external=true" title="class or interface in java.io">File</A>&nbsp;file)\r
 314                                  throws <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
 315                                         <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
 316 <DL>\r
 317 <DD><DL>\r
 318 \r
 319 <DT><B>Throws:</B>\r
 320 <DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
 321 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
 322 </DD>\r
 323 </DL>\r
 324 <!-- ========= END OF CLASS DATA ========= -->\r
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