website/full_javadoc/compbio/data/sequence/class-use/UnknownFileFormatException.html

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   7 Uses of Class compbio.data.sequence.UnknownFileFormatException\r
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  84 <B>Uses of Class<br>compbio.data.sequence.UnknownFileFormatException</B></H2>\r
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  89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  90 Packages that use <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
  94 <TD>A data model for multiple sequence alignment web services and utility methods
  95  that work on the objects of this model.&nbsp;</TD>\r
  96 </TR>\r
  97 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  98 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
  99 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
 100 </TR>\r
 101 </TABLE>\r
 102 &nbsp;\r
 103 <P>\r
 104 <A NAME="compbio.data.sequence"><!-- --></A>\r
 105 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 106 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 107 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 108 Uses of <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A> in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A></FONT></TH>\r
 109 </TR>\r
 110 </TABLE>\r
 111 &nbsp;\r
 112 <P>\r
 113 \r
 114 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 115 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 116 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> that throw <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
 117 </TR>\r
 118 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 119 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 120 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>\r
 121 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#openInputStream(java.lang.String)">openInputStream</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;inFilePath)</CODE>\r
 122 \r
 123 <BR>\r
 124 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reads and parses Fasta or Clustal formatted file into a list of
 125  FastaSequence objects</TD>\r
 126 </TR>\r
 127 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 128 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 129 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 130 <TD><CODE><B>ClustalAlignmentUtil.</B><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
 131 \r
 132 <BR>\r
 133 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 134 </TR>\r
 135 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 136 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 137 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 138 <TD><CODE><B>ClustalAlignmentUtil.</B><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
 139 \r
 140 <BR>\r
 141 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read Clustal formatted alignment.</TD>\r
 142 </TR>\r
 143 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 145 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashMap.html?is-external=true" title="class or interface in java.util">HashMap</A>&lt;<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>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
 146 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readDisembl(java.io.InputStream)">readDisembl</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
 147 \r
 148 <BR>\r
 149 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;> Foobar_dundeefriends
 150
 151  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 152
 153  # REM465 355-368
 154
 155  # HOTLOOPS 190-204
 156
 157  # RESIDUE COILS REM465 HOTLOOPS
 158
 159  M 0.86010 0.88512 0.37094
 160
 161  T 0.79983 0.85864 0.44331
 162
 163  >Next Sequence name</TD>\r
 164 </TR>\r
 165 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 166 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 167 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/HashMap.html?is-external=true" title="class or interface in java.util">HashMap</A>&lt;<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>,<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</A>&lt;<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;&gt;</CODE></FONT></TD>\r
 168 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readGlobPlot(java.io.InputStream)">readGlobPlot</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
 169 \r
 170 <BR>\r
 171 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;> Foobar_dundeefriends
 172
 173  # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
 174
 175  # REM465 355-368
 176
 177  # HOTLOOPS 190-204
 178
 179  # RESIDUE COILS REM465 HOTLOOPS
 180
 181  M 0.86010 0.88512 0.37094
 182
 183  T 0.79983 0.85864 0.44331
 184
 185  >Next Sequence name</TD>\r
 186 </TR>\r
 187 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 188 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 189 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
 190 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readIUPred(java.io.File)">readIUPred</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;result)</CODE>\r
 191 \r
 192 <BR>\r
 193 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Read IUPred output</TD>\r
 194 </TR>\r
 195 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 196 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 197 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
 198 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)">readJRonn</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;result)</CODE>\r
 199 \r
 200 <BR>\r
 201 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 202 </TR>\r
 203 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 204 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 205 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
 206 <TD><CODE><B>SequenceUtil.</B><B><A HREF="../../../../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)">readJRonn</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
 207 \r
 208 <BR>\r
 209 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Reader for JRonn horizontal file format</TD>\r
 210 </TR>\r
 211 </TABLE>\r
 212 &nbsp;\r
 213 <P>\r
 214 <A NAME="compbio.runner"><!-- --></A>\r
 215 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 216 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 217 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 218 Uses of <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
 219 </TR>\r
 220 </TABLE>\r
 221 &nbsp;\r
 222 <P>\r
 223 \r
 224 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 225 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 226 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> that throw <A HREF="../../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></FONT></TH>\r
 227 </TR>\r
 228 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 229 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 230 <CODE>static&nbsp;<A HREF="../../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
 231 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</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;workDirectory,\r
 232                 <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;clustFile)</CODE>\r
 233 \r
 234 <BR>\r
 235 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 236 </TR>\r
 237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 239 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A>&lt;<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>,<A HREF="../../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>&gt;</CODE></FONT></TD>\r
 240 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#readJronnFile(java.lang.String, java.lang.String)">readJronnFile</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;workDirectory,\r
 241               <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;clustFile)</CODE>\r
 242 \r
 243 <BR>\r
 244 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 245 </TR>\r
 246 </TABLE>\r
 247 &nbsp;\r
 248 <P>\r
 249 <HR>\r
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 285   <!--\r
 286   if(window==top) {\r
 287     document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
 288   }\r
 289   //-->\r
 290 </SCRIPT>\r
 291 <NOSCRIPT>\r
 292   <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
 293 </NOSCRIPT>\r
 294 \r
 295 \r
 296 </FONT></TD>\r
 297 </TR>\r
 298 </TABLE>\r
 299 <A NAME="skip-navbar_bottom"></A>\r
 300 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
 301 \r
 302 <HR>\r
 303 \r
 304 </BODY>\r
 305 </HTML>\r