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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / full_javadoc / compbio / data / _structure / package-summary.html
diff --git a/website/full_javadoc/compbio/data/_structure/package-summary.html b/website/full_javadoc/compbio/data/_structure/package-summary.html
new file mode 100644 (file)
index 0000000..39e4ddc
--- /dev/null
+++ b/website/full_javadoc/compbio/data/_structure/package-summary.html
@@ -0,0 +1,203 @@
+<!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 Wed Dec 07 12:30:42 GMT 2011 -->\r
+<TITLE>\r
+compbio.data._structure\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2011-12-07">\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.data._structure";\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>&nbsp;</TD>\r
+  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</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
+&nbsp;PREV PACKAGE&nbsp;\r
+&nbsp;<A HREF="../../../compbio/data/msa/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/data/_structure/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
+&nbsp;<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.data._structure\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/data/_structure/JpredResult.html" title="class in compbio.data._structure">JpredResult</A></B></TD>\r
+<TD>Jnet result
+ 
+ jnetpred:-,H,H,H,H,H,H,H,H,H,H,H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,
+ -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H
+ ,H,H,-,-,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,-,-,-,-,H,H,H,H,
+ -,-,-,-,-,-,-,-,-,-,-,-,H,H,H,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-
+ , JNETCONF:7,3,7,9,9,9,9,9,9,9,7,5,2,6,6,3,6,7,5,1,0,5,3,3,6,4,6,6,7,7,7,7,7,
+ 7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,7,6,3,6,8,9,9,9,9,9,9,9
+ 7,3,7,7,6,2,4,4,1,5,7,8,7,7,7,7,7,7,7,6,5,3,5,6,6,6,4,0,0,2,1,3,5,7,7,7,7,7,7
+ , JNETSOL25:B,B,-,-,-,B,-,B,-,B,B,B,-,-,-,B,-,B,-,-,-,-,-,B,-,B,-,-,-,-,-,-,
+ -,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,-,B,-,B,-
+ , B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,B,-,-,-,-,B,-,-,B,B,-,-
+ ,B,
+ JNETSOL5:-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,B,B,B,B,-,-,-,B,-,-,-,-,-,-,-,-,-
+ ,-,-
+ JNETSOL0:-,-,-,-,-,-,B,-,-,B,-,B,-,-,-,-,-,-,-,-,B,-,-,-,-,-,-,-,-,-,-,-,
+ -,-,- ,-,-,-,-,-,-,-,-,-,-,-,-,B,-,-,B,-,B,-,-,
+ JNETHMM:-,H,H,H,H,H,H,H,H,H,H,
+ H,-,-,-,-,-,-,-,-,E,E,E,-,-,-,-,-,-,-,-,-,-,-,-,
+ -,-,-,-,-,-,-,-,-,-,-,-,-,-,-
+ ,-,-,-,-,-,-,-,-,-,-,-,-,-,H,H,H,H,H,H,H,H,H,H,H,
+ JNETPROPH:0.0110,0.1125,0.8552,0.0107
+ ,0.6245,0.3614,0.0120,0.8702,0.1238,0.0120
+ ,0.0193,0.9284,0.0708,0.0278,0.8703,0.1244
+ ,0.1591,0.7399,0.1456,0.2488,0.5824,0.1017,
+ JNETPROPE:0.0107,0.6245,0.3614,0.0120
+ ,0.8702,0.1238,0.0120,0.9335,0.0656,0.0102
+ ,0.9586,0.0465,0.0094,0.9662,0.0433,
+ ,0.1525,0.7103,0.1088,0.1181,0.7425,0.1784,</TD>\r
+</TR>\r
+</TABLE>\r
+&nbsp;\r
+\r
+<P>\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>Enum Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/_structure/JnetAnnotation.html" title="enum in compbio.data._structure">JnetAnnotation</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/_structure/JpredAnnotation.html" title="enum in compbio.data._structure">JpredAnnotation</A></B></TD>\r
+<TD>&nbsp;</TD>\r
+</TR>\r
+</TABLE>\r
+&nbsp;\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>&nbsp;</TD>\r
+  <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Package</B></FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-use.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A>&nbsp;</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
+&nbsp;PREV PACKAGE&nbsp;\r
+&nbsp;<A HREF="../../../compbio/data/msa/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/data/_structure/package-summary.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="package-summary.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
+&nbsp;<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