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

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   7 ClustalAlignmentUtil\r
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  91 compbio.data.sequence</FONT>\r
  92 <BR>\r
  93 Class ClustalAlignmentUtil</H2>\r
  94 <PRE>\r
  95 java.lang.Object\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 java.lang.Object</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>Author:</B></DT>\r
 110   <DD>Petr Troshin based on jimp class
 111
 112          Date September 2009</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>(java.io.InputStream&nbsp;input)</CODE>\r
 163 \r
 164 <BR>\r
 165 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</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>(java.io.File&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>(java.io.InputStream&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>(java.io.OutputStream&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
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 197 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 198 </TR>\r
 199 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 200 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
 201 </TR>\r
 202 </TABLE>\r
 203 &nbsp;\r
 204 <P>\r
 205 \r
 206 <!-- ============ FIELD DETAIL =========== -->\r
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 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
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 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
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 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>(java.io.InputStream&nbsp;instream)\r
 258                                  throws java.io.IOException,\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>java.io.IOException</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>(java.io.InputStream&nbsp;input)</PRE>\r
 280 <DL>\r
 281 <DD><DL>\r
 282 <DT><B>Parameters:</B><DD><CODE>input</CODE> - \r
 283 <DT><B>Returns:</B><DD>true if the file is recognised as Clustal formatted alignment,
 284          false otherwise</DL>\r
 285 </DD>\r
 286 </DL>\r
 287 <HR>\r
 288 \r
 289 <A NAME="writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><!-- --></A><H3>\r
 290 writeClustalAlignment</H3>\r
 291 <PRE>\r
 292 public static void <B>writeClustalAlignment</B>(java.io.OutputStream&nbsp;outStream,\r
 293                                          <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)\r
 294                                   throws java.io.IOException</PRE>\r
 295 <DL>\r
 296 <DD>Write Clustal formatted alignment Limitations: does not record the
 297  consensus. Potential bug - records 60 chars length alignment where
 298  Clustal would have recorded 50 chars.\r
 299 <P>\r
 300 <DD><DL>\r
 301 <DT><B>Parameters:</B><DD><CODE>outStream</CODE> - <DD><CODE>alignment</CODE> - \r
 302 <DT><B>Throws:</B>\r
 303 <DD><CODE>java.io.IOException</CODE></DL>\r
 304 </DD>\r
 305 </DL>\r
 306 <HR>\r
 307 \r
 308 <A NAME="readClustalFile(java.io.File)"><!-- --></A><H3>\r
 309 readClustalFile</H3>\r
 310 <PRE>\r
 311 public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</B>(java.io.File&nbsp;file)\r
 312                                  throws <A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
 313                                         java.io.IOException</PRE>\r
 314 <DL>\r
 315 <DD><DL>\r
 316 \r
 317 <DT><B>Throws:</B>\r
 318 <DD><CODE><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
 319 <DD><CODE>java.io.IOException</CODE></DL>\r
 320 </DD>\r
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