website/full_javadoc/compbio/engine/client/class-use/SkeletalExecutable.html

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   7 Uses of Class compbio.engine.client.SkeletalExecutable\r
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  84 <B>Uses of Class<br>compbio.engine.client.SkeletalExecutable</B></H2>\r
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  86 \r
  87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
  88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
  89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  90 Packages that use <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></FONT></TH>\r
  91 </TR>\r
  92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  93 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
  94 <TD>&nbsp;&nbsp;</TD>\r
  95 </TR>\r
  96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  97 <TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>\r
  98 <TD>&nbsp;&nbsp;</TD>\r
  99 </TR>\r
 100 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 101 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>\r
 102 <TD>&nbsp;&nbsp;</TD>\r
 103 </TR>\r
 104 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 105 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
 106 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
 107 </TR>\r
 108 </TABLE>\r
 109 &nbsp;\r
 110 <P>\r
 111 <A NAME="compbio.engine.client"><!-- --></A>\r
 112 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 113 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 114 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 115 Uses of <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
 116 </TR>\r
 117 </TABLE>\r
 118 &nbsp;\r
 119 <P>\r
 120 \r
 121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 122 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 123 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></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>&nbsp;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 128 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</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;errFile)</CODE>\r
 129 \r
 130 <BR>\r
 131 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 132 </TR>\r
 133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 135 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 136 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</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;inFile)</CODE>\r
 137 \r
 138 <BR>\r
 139 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 140 </TR>\r
 141 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 143 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>&lt;<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>&gt;</CODE></FONT></TD>\r
 144 <TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</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;outFile)</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 <P>\r
 152 <A NAME="compbio.runner.conservation"><!-- --></A>\r
 153 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 154 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 155 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 156 Uses of <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A> in <A HREF="../../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>\r
 157 </TR>\r
 158 </TABLE>\r
 159 &nbsp;\r
 160 <P>\r
 161 \r
 162 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 163 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 164 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A> in <A HREF="../../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>\r
 165 </TR>\r
 166 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 168 <CODE>&nbsp;class</CODE></FONT></TD>\r
 169 <TD><CODE><B><A HREF="../../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A></B></CODE>\r
 170 \r
 171 <BR>\r
 172 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line
 173
 174  java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</TD>\r
 175 </TR>\r
 176 </TABLE>\r
 177 &nbsp;\r
 178 <P>\r
 179 <A NAME="compbio.runner.disorder"><!-- --></A>\r
 180 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 181 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 182 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 183 Uses of <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A> in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>\r
 184 </TR>\r
 185 </TABLE>\r
 186 &nbsp;\r
 187 <P>\r
 188 \r
 189 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 190 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 191 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A> in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>\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;class</CODE></FONT></TD>\r
 196 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A></B></CODE>\r
 197 \r
 198 <BR>\r
 199 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
 200  fold_rem465 sequence_file print
 201
 202  'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
 203
 204  This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
 205  capable of outputting raw values
 206
 207  The values of the parameters are hard coded in DisEMBL.py script.</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;class</CODE></FONT></TD>\r
 212 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A></B></CODE>\r
 213 \r
 214 <BR>\r
 215 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
 216
 217  FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
 218  Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
 219
 220  Hard-coded values are 10 15 74 4 5.</TD>\r
 221 </TR>\r
 222 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 223 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 224 <CODE>&nbsp;class</CODE></FONT></TD>\r
 225 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A></B></CODE>\r
 226 \r
 227 <BR>\r
 228 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;iupred sequenceFile <short long glob >
 229
 230  Maximum sequence length is 40000 chars.</TD>\r
 231 </TR>\r
 232 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 233 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 234 <CODE>&nbsp;class</CODE></FONT></TD>\r
 235 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A></B></CODE>\r
 236 \r
 237 <BR>\r
 238 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Command line
 239
 240  java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</TD>\r
 241 </TR>\r
 242 </TABLE>\r
 243 &nbsp;\r
 244 <P>\r
 245 <A NAME="compbio.runner.msa"><!-- --></A>\r
 246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 247 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 248 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 249 Uses of <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
 250 </TR>\r
 251 </TABLE>\r
 252 &nbsp;\r
 253 <P>\r
 254 \r
 255 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 256 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 257 <TH ALIGN="left" COLSPAN="2">Subclasses of <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
 258 </TR>\r
 259 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 261 <CODE>&nbsp;class</CODE></FONT></TD>\r
 262 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A></B></CODE>\r
 263 \r
 264 <BR>\r
 265 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 266 </TR>\r
 267 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 268 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 269 <CODE>&nbsp;class</CODE></FONT></TD>\r
 270 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></CODE>\r
 271 \r
 272 <BR>\r
 273 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 274 </TR>\r
 275 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 276 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 277 <CODE>&nbsp;class</CODE></FONT></TD>\r
 278 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>\r
 279 \r
 280 <BR>\r
 281 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 282 </TR>\r
 283 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 284 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 285 <CODE>&nbsp;class</CODE></FONT></TD>\r
 286 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></CODE>\r
 287 \r
 288 <BR>\r
 289 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 290 </TR>\r
 291 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 292 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 293 <CODE>&nbsp;class</CODE></FONT></TD>\r
 294 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>\r
 295 \r
 296 <BR>\r
 297 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 298 </TR>\r
 299 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 300 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 301 <CODE>&nbsp;class</CODE></FONT></TD>\r
 302 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>\r
 303 \r
 304 <BR>\r
 305 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 306 </TR>\r
 307 </TABLE>\r
 308 &nbsp;\r
 309 <P>\r
 310 <HR>\r
 311 \r
 312 \r
 313 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
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