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5 <!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:42 GMT 2011 -->
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7 Uses of Class compbio.engine.client.SkeletalExecutable
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42 <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A> </TD>
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84 <B>Uses of Class<br>compbio.engine.client.SkeletalExecutable</B></H2>
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87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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90 Packages that use <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A></FONT></TH>
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92 <TR BGCOLOR="white" CLASS="TableRowColor">
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93 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>
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94 <TD> </TD>
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96 <TR BGCOLOR="white" CLASS="TableRowColor">
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97 <TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>
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98 <TD> </TD>
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100 <TR BGCOLOR="white" CLASS="TableRowColor">
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101 <TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>
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102 <TD> </TD>
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104 <TR BGCOLOR="white" CLASS="TableRowColor">
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105 <TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>
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106 <TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>
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111 <A NAME="compbio.engine.client"><!-- --></A>
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112 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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113 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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114 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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121 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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122 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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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>
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125 <TR BGCOLOR="white" CLASS="TableRowColor">
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126 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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127 <CODE> <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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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> errFile)</CODE>
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131 </TD>
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133 <TR BGCOLOR="white" CLASS="TableRowColor">
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134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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135 <CODE> <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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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> inFile)</CODE>
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139 </TD>
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141 <TR BGCOLOR="white" CLASS="TableRowColor">
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142 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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143 <CODE> <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>
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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> outFile)</CODE>
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147 </TD>
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152 <A NAME="compbio.runner.conservation"><!-- --></A>
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153 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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154 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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155 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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162 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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163 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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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>
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166 <TR BGCOLOR="white" CLASS="TableRowColor">
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167 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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168 <CODE> class</CODE></FONT></TD>
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169 <TD><CODE><B><A HREF="../../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A></B></CODE>
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172 Command line
174 java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</TD>
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179 <A NAME="compbio.runner.disorder"><!-- --></A>
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180 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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181 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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182 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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189 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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190 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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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>
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193 <TR BGCOLOR="white" CLASS="TableRowColor">
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194 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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195 <CODE> class</CODE></FONT></TD>
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196 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A></B></CODE>
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199 DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
200 fold_rem465 sequence_file print
202 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
204 This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
205 capable of outputting raw values
207 The values of the parameters are hard coded in DisEMBL.py script.</TD>
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209 <TR BGCOLOR="white" CLASS="TableRowColor">
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210 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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211 <CODE> class</CODE></FONT></TD>
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212 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A></B></CODE>
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215 ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
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'
220 Hard-coded values are 10 15 74 4 5.</TD>
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222 <TR BGCOLOR="white" CLASS="TableRowColor">
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223 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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224 <CODE> class</CODE></FONT></TD>
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225 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A></B></CODE>
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228 iupred sequenceFile <short long glob >
230 Maximum sequence length is 40000 chars.</TD>
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232 <TR BGCOLOR="white" CLASS="TableRowColor">
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233 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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234 <CODE> class</CODE></FONT></TD>
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235 <TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A></B></CODE>
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238 Command line
240 java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</TD>
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245 <A NAME="compbio.runner.msa"><!-- --></A>
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246 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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247 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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248 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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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>
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255 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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256 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
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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>
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259 <TR BGCOLOR="white" CLASS="TableRowColor">
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260 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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261 <CODE> class</CODE></FONT></TD>
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262 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A></B></CODE>
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265 </TD>
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267 <TR BGCOLOR="white" CLASS="TableRowColor">
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268 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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269 <CODE> class</CODE></FONT></TD>
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270 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></CODE>
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273 </TD>
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275 <TR BGCOLOR="white" CLASS="TableRowColor">
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276 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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277 <CODE> class</CODE></FONT></TD>
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278 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>
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281 </TD>
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283 <TR BGCOLOR="white" CLASS="TableRowColor">
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284 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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285 <CODE> class</CODE></FONT></TD>
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286 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></CODE>
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289 </TD>
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291 <TR BGCOLOR="white" CLASS="TableRowColor">
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292 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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293 <CODE> class</CODE></FONT></TD>
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294 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>
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297 </TD>
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299 <TR BGCOLOR="white" CLASS="TableRowColor">
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300 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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301 <CODE> class</CODE></FONT></TD>
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302 <TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>
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305 </TD>
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