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

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   7 Uses of Interface compbio.engine.client.PipedExecutable\r
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  83 <H2>\r
  84 <B>Uses of Interface<br>compbio.engine.client.PipedExecutable</B></H2>\r
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  86 \r
  87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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  89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  90 Packages that use <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</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.disorder"><B>compbio.runner.disorder</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.msa"><B>compbio.runner.msa</B></A></TD>\r
 102 <TD>Wrappers for native executables for multiple sequence alignment (msa)&nbsp;</TD>\r
 103 </TR>\r
 104 </TABLE>\r
 105 &nbsp;\r
 106 <P>\r
 107 <A NAME="compbio.engine.client"><!-- --></A>\r
 108 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 109 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 110 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 111 Uses of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
 112 </TR>\r
 113 </TABLE>\r
 114 &nbsp;\r
 115 <P>\r
 116 \r
 117 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 118 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 119 <TH ALIGN="left" COLSPAN="2">Subinterfaces of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
 120 </TR>\r
 121 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 122 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 123 <CODE>&nbsp;interface</CODE></FONT></TD>\r
 124 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable&lt;T&gt;</A></B></CODE>\r
 125 \r
 126 <BR>\r
 127 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 128 </TR>\r
 129 </TABLE>\r
 130 &nbsp;\r
 131 <P>\r
 132 \r
 133 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 134 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 135 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that implement <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>\r
 136 </TR>\r
 137 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 138 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 139 <CODE>&nbsp;class</CODE></FONT></TD>\r
 140 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable&lt;T&gt;</A></B></CODE>\r
 141 \r
 142 <BR>\r
 143 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 144 </TR>\r
 145 </TABLE>\r
 146 &nbsp;\r
 147 <P>\r
 148 <A NAME="compbio.runner.disorder"><!-- --></A>\r
 149 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 150 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 151 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 152 Uses of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>\r
 153 </TR>\r
 154 </TABLE>\r
 155 &nbsp;\r
 156 <P>\r
 157 \r
 158 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 159 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 160 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A> that implement <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>\r
 161 </TR>\r
 162 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 163 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 164 <CODE>&nbsp;class</CODE></FONT></TD>\r
 165 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A></B></CODE>\r
 166 \r
 167 <BR>\r
 168 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
 169  fold_rem465 sequence_file print
 170
 171  'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
 172
 173  This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
 174  capable of outputting raw values
 175
 176  The values of the parameters are hard coded in DisEMBL.py script.</TD>\r
 177 </TR>\r
 178 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 179 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 180 <CODE>&nbsp;class</CODE></FONT></TD>\r
 181 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A></B></CODE>\r
 182 \r
 183 <BR>\r
 184 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
 185
 186  FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
 187  Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
 188
 189  Hard-coded values are 10 15 74 4 5.</TD>\r
 190 </TR>\r
 191 </TABLE>\r
 192 &nbsp;\r
 193 <P>\r
 194 <A NAME="compbio.runner.msa"><!-- --></A>\r
 195 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 196 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 197 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 198 Uses of <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A> in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A></FONT></TH>\r
 199 </TR>\r
 200 </TABLE>\r
 201 &nbsp;\r
 202 <P>\r
 203 \r
 204 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 205 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
 206 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</A> that implement <A HREF="../../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</A></FONT></TH>\r
 207 </TR>\r
 208 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 210 <CODE>&nbsp;class</CODE></FONT></TD>\r
 211 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>\r
 212 \r
 213 <BR>\r
 214 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 215 </TR>\r
 216 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 217 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 218 <CODE>&nbsp;class</CODE></FONT></TD>\r
 219 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>\r
 220 \r
 221 <BR>\r
 222 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 223 </TR>\r
 224 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 225 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 226 <CODE>&nbsp;class</CODE></FONT></TD>\r
 227 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>\r
 228 \r
 229 <BR>\r
 230 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 231 </TR>\r
 232 </TABLE>\r
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