+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
-<!--NewPage-->\r
-<HTML>\r
-<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
-<TITLE>\r
-compbio.pipeline._jpred\r
-</TITLE>\r
-\r
-<META NAME="date" CONTENT="2011-08-12">\r
-\r
-<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
-\r
-<SCRIPT type="text/javascript">\r
-function windowTitle()\r
-{\r
- if (location.href.indexOf('is-external=true') == -1) {\r
- parent.document.title="compbio.pipeline._jpred";\r
- }\r
-}\r
-</SCRIPT>\r
-<NOSCRIPT>\r
-</NOSCRIPT>\r
-\r
-</HEAD>\r
-\r
-<BODY BGCOLOR="white" onload="windowTitle();">\r
-<HR>\r
-\r
-\r
-<!-- ========= START OF TOP NAVBAR ======= -->\r
-<A NAME="navbar_top"><!-- --></A>\r
-<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_top_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
- <TR ALIGN="center" VALIGN="top">\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/metadata/package-summary.html"><B>PREV PACKAGE</B></A> \r
- <A HREF="../../../compbio/runner/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/pipeline/_jpred/package-summary.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
- //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_top"></A>\r
-<!-- ========= END OF TOP NAVBAR ========= -->\r
-\r
-<HR>\r
-<H2>\r
-Package compbio.pipeline._jpred\r
-</H2>\r
-\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
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastBlastComparator.html" title="class in compbio.pipeline._jpred">BlastBlastComparator</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastHmmerComparator.html" title="class in compbio.pipeline._jpred">BlastHmmerComparator</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/BlastParser.html" title="class in compbio.pipeline._jpred">BlastParser</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.html" title="class in compbio.pipeline._jpred">Hit</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.EvalueComporator.html" title="class in compbio.pipeline._jpred">Hit.EvalueComporator</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Hit.NumberComporator.html" title="class in compbio.pipeline._jpred">Hit.NumberComporator</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/JackHmmerHitParser.html" title="class in compbio.pipeline._jpred">JackHmmerHitParser</A></B></TD>\r
-<TD>Parser for the following files:</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Jpred4.html" title="class in compbio.pipeline._jpred">Jpred4</A></B></TD>\r
-<TD>jpred --sequence <fasta file> OR --alignment <clustalW alignment> [--db
- <database>] [--pred-nohits] [--logLevel=(ERROR|INFO|DEBUG)] [--help]
-
- jpred4 --sequence <fasta file> The path to the sequence (in FASTA format) you
- want to predict OR
-
- [--alignment <clustalW alignment>] The alignment which to use for prediction
-
- [--profile=<path to HMM profile>]
-
- [--db <database>] Database to use for PSI-BLAST querying.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/Pairwise.html" title="class in compbio.pipeline._jpred">Pairwise</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/pipeline/_jpred/PScore.html" title="class in compbio.pipeline._jpred">PScore</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-<DL>\r
-</DL>\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
- <TR ALIGN="center" VALIGN="top">\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <FONT CLASS="NavBarFont1">Class</FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
- </TR>\r
-</TABLE>\r
-</TD>\r
-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/metadata/package-summary.html"><B>PREV PACKAGE</B></A> \r
- <A HREF="../../../compbio/runner/package-summary.html"><B>NEXT PACKAGE</B></A></FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/pipeline/_jpred/package-summary.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
- //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
-\r
-</FONT></TD>\r
-</TR>\r
-</TABLE>\r
-<A NAME="skip-navbar_bottom"></A>\r
-<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
-\r
-<HR>\r
-\r
-</BODY>\r
-</HTML>\r
git://source.jalview.org / jabaws.git / blobdiff