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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / dm_javadoc / constant-values.html
diff --git a/website/dm_javadoc/constant-values.html b/website/dm_javadoc/constant-values.html
new file mode 100644 (file)
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--- /dev/null
+++ b/website/dm_javadoc/constant-values.html
@@ -0,0 +1,332 @@
+<!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 12:08:24 GMT 2011 -->\r
+<TITLE>\r
+Constant Field Values\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="Constant Field Values";\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="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-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&nbsp;\r
+&nbsp;NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="index.html?constant-values.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="constant-values.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
+<CENTER>\r
+<H1>\r
+Constant Field Values</H1>\r
+</CENTER>\r
+<HR SIZE="4" NOSHADE>\r
+<B>Contents</B><UL>\r
+<LI><A HREF="#compbio.data">compbio.data.*</A>\r
+<LI><A HREF="#compbio.metadata">compbio.metadata.*</A>\r
+<LI><A HREF="#compbio.ws">compbio.ws.*</A>\r
+</UL>\r
+\r
+<A NAME="compbio.data"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left"><FONT SIZE="+2">\r
+compbio.data.*</FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="3">compbio.data.msa.<A HREF="compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.msa.Category.CATEGORY_ALIGNMENT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_ALIGNMENT">CATEGORY_ALIGNMENT</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"Alignment"</CODE></TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.msa.Category.CATEGORY_CONSERVATION"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_CONSERVATION">CATEGORY_CONSERVATION</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"Conservation"</CODE></TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.msa.Category.CATEGORY_DISORDER"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_DISORDER">CATEGORY_DISORDER</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"Protein Disorder"</CODE></TD>\r
+</TR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="3">compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.msa.JABAService.SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"http://msa.data.compbio/01/01/2010/"</CODE></TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.msa.JABAService.V2_SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"http://msa.data.compbio/01/12/2010/"</CODE></TD>\r
+</TR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.sequence.ClustalAlignmentUtil.gapchar"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;char</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>45</CODE></TD>\r
+</TR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"Alignment"</CODE></TD>\r
+</TR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;double</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>0.1</CODE></TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;int</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>7</CODE></TD>\r
+</TR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<P>\r
+<A NAME="compbio.metadata"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left"><FONT SIZE="+2">\r
+compbio.metadata.*</FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="3">compbio.metadata.<A HREF="compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A>&lt;<A HREF="compbio/metadata/PresetManager.html" title="type parameter in PresetManager">T</A>&gt;</TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"# LocalEngineExecutionLimit #"</CODE></TD>\r
+</TR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<P>\r
+<A NAME="compbio.ws"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left"><FONT SIZE="+2">\r
+compbio.ws.*</FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left" COLSPAN="3">compbio.ws.client.<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.ws.client.WSTester.fastaAlignment"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/ws/client/WSTester.html#fastaAlignment">fastaAlignment</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n&gt;Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<A NAME="compbio.ws.client.WSTester.fastaInput"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">\r
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>\r
+<TD ALIGN="left"><CODE><A HREF="compbio/ws/client/WSTester.html#fastaInput">fastaInput</A></CODE></TD>\r
+<TD ALIGN="right"><CODE>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n&gt;Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>\r
+</TR>\r
+</FONT></TD>\r
+</TR>\r
+</TABLE>\r
+\r
+<P>\r
+\r
+<P>\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="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Package</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Class</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="overview-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&nbsp;\r
+&nbsp;NEXT</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="index.html?constant-values.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="constant-values.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