<!--NewPage-->\r
<HTML>\r
<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:42 GMT 2011 -->\r
<TITLE>\r
Uses of Class compbio.engine.client.SkeletalExecutable\r
</TITLE>\r
\r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
\r
<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../../stylesheet.css" TITLE="Style">\r
\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines. </TD>\r
+<TD> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
-<TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>\r
+<TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>\r
+<TD> </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><A HREF="#compbio.runner.psiblast"><B>compbio.runner.psiblast</B></A></TD>\r
+<TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>\r
<TD> </TD>\r
</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
+<TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>\r
+</TR>\r
</TABLE>\r
\r
<P>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<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>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A></B>(java.lang.String errFile)</CODE>\r
+<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>\r
\r
<BR>\r
</TD>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<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>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String inFile)</CODE>\r
+<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>\r
\r
<BR>\r
</TD>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<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>\r
-<TD><CODE><B>SkeletalExecutable.</B><B><A HREF="../../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String outFile)</CODE>\r
+<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>\r
\r
<BR>\r
</TD>\r
</TABLE>\r
\r
<P>\r
-<A NAME="compbio.runner.msa"><!-- --></A>\r
+<A NAME="compbio.runner.conservation"><!-- --></A>\r
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-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
+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
</TR>\r
</TABLE>\r
\r
\r
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<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
+<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
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></CODE>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A></B></CODE>\r
\r
<BR>\r
- </TD>\r
+ Command line
+
+ java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.runner.disorder"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+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
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
+<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
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A></B></CODE>\r
\r
<BR>\r
- </TD>\r
+ DisEMBL.py smooth_frame peak_frame join_frame fold_coils fold_hotloops
+ fold_rem465 sequence_file print
+
+ 'A default run would be: ./DisEMBL.py 8 8 4 1.2 1.4 1.2 fasta_file > out'
+
+ This version of DisEMBL is 1.4 (latest available for download in Feb 2011)
+ capable of outputting raw values
+
+ The values of the parameters are hard coded in DisEMBL.py script.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></CODE>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A></B></CODE>\r
\r
<BR>\r
- </TD>\r
+ ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame
+
+ FASTAfile' Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
+ Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
+
+ Hard-coded values are 10 15 74 4 5.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A></B></CODE>\r
\r
<BR>\r
- </TD>\r
+ iupred sequenceFile <short long glob >
+
+ Maximum sequence length is 40000 chars.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A></B></CODE>\r
\r
<BR>\r
- </TD>\r
+ Command line
+
+ java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</TD>\r
</TR>\r
</TABLE>\r
\r
<P>\r
-<A NAME="compbio.runner.psiblast"><!-- --></A>\r
+<A NAME="compbio.runner.msa"><!-- --></A>\r
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-Uses of <A HREF="../../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A> in <A HREF="../../../../compbio/runner/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
+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
</TR>\r
</TABLE>\r
\r
\r
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
-<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/psiblast/package-summary.html">compbio.runner.psiblast</A></FONT></TH>\r
+<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
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> class</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A></B></CODE>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> class</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></B></CODE>\r
\r
<BR>\r
</TD>\r