X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fconstant-values.html;h=bc3aff02c7cc5ff06ea58cf6cf4e1484a91bcc0b;hb=56a5e5629fda01d8db22bb62aae1f0b7fc29a57d;hp=44abb42cf2552ac711c5c17aac6ddd164f339e5e;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/website/dm_javadoc/constant-values.html b/website/dm_javadoc/constant-values.html
index 44abb42..bc3aff0 100644
--- a/website/dm_javadoc/constant-values.html
+++ b/website/dm_javadoc/constant-values.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:28 GMT 2010 -->
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:08:24 GMT 2011 -->
 <TITLE>
 Constant Field Values
 </TITLE>
 
-<META NAME="date" CONTENT="2010-02-17">
+<META NAME="date" CONTENT="2011-12-07">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="stylesheet.css" TITLE="Style">
 
@@ -87,6 +87,7 @@ Constant Field Values</H1>
 <B>Contents</B><UL>
 <LI><A HREF="#compbio.data">compbio.data.*</A>
 <LI><A HREF="#compbio.metadata">compbio.metadata.*</A>
+<LI><A HREF="#compbio.ws">compbio.ws.*</A>
 </UL>
 
 <A NAME="compbio.data"><!-- --></A>
@@ -101,6 +102,60 @@ compbio.data.*</FONT></TH>
 
 <TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TH ALIGN="left" COLSPAN="3">compbio.data.msa.<A HREF="compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A></TH>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.data.msa.Category.CATEGORY_ALIGNMENT"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_ALIGNMENT">CATEGORY_ALIGNMENT</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Alignment"</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.data.msa.Category.CATEGORY_CONSERVATION"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_CONSERVATION">CATEGORY_CONSERVATION</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Conservation"</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.data.msa.Category.CATEGORY_DISORDER"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/Category.html#CATEGORY_DISORDER">CATEGORY_DISORDER</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Protein Disorder"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TH ALIGN="left" COLSPAN="3">compbio.data.msa.<A HREF="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</A></TH>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.data.msa.JABAService.SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</A></CODE></TD>
+<TD ALIGN="right"><CODE>"http://msa.data.compbio/01/01/2010/"</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.data.msa.JABAService.V2_SERVICE_NAMESPACE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</A></CODE></TD>
+<TD ALIGN="right"><CODE>"http://msa.data.compbio/01/12/2010/"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
 <TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></TH>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
@@ -116,6 +171,48 @@ compbio.data.*</FONT></TH>
 <P>
 
 <P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></TH>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</A></CODE></TD>
+<TD ALIGN="right"><CODE>"Alignment"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TH ALIGN="left" COLSPAN="3">compbio.data.sequence.<A HREF="compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></TH>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;double</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</A></CODE></TD>
+<TD ALIGN="right"><CODE>0.1</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;int</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</A></CODE></TD>
+<TD ALIGN="right"><CODE>7</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
 <A NAME="compbio.metadata"><!-- --></A>
 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
@@ -143,6 +240,39 @@ compbio.metadata.*</FONT></TH>
 <P>
 
 <P>
+<A NAME="compbio.ws"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TH ALIGN="left"><FONT SIZE="+2">
+compbio.ws.*</FONT></TH>
+</TR>
+</TABLE>
+
+<P>
+
+<TABLE BORDER="1" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
+<TH ALIGN="left" COLSPAN="3">compbio.ws.client.<A HREF="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A></TH>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.ws.client.WSTester.fastaAlignment"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/ws/client/WSTester.html#fastaAlignment">fastaAlignment</A></CODE></TD>
+<TD ALIGN="right"><CODE>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n&gt;Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<A NAME="compbio.ws.client.WSTester.fastaInput"><!-- --></A><TD ALIGN="right"><FONT SIZE="-1">
+<CODE>public&nbsp;static&nbsp;final&nbsp;java.lang.String</CODE></FONT></TD>
+<TD ALIGN="left"><CODE><A HREF="compbio/ws/client/WSTester.html#fastaInput">fastaInput</A></CODE></TD>
+<TD ALIGN="right"><CODE>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n&gt;Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"</CODE></TD>
+</TR>
+</FONT></TD>
+</TR>
+</TABLE>
+
+<P>
+
+<P>
 <HR>
 
 

compbio.data.msa.Category
+`public static final java.lang.String`	`CATEGORY_ALIGNMENT`	`"Alignment"`
+`public static final java.lang.String`	`CATEGORY_CONSERVATION`	`"Conservation"`
+`public static final java.lang.String`	`CATEGORY_DISORDER`	`"Protein Disorder"`
compbio.data.msa.JABAService
+`public static final java.lang.String`	`SERVICE_NAMESPACE`	`"http://msa.data.compbio/01/01/2010/"`
+`public static final java.lang.String`	`V2_SERVICE_NAMESPACE`	`"http://msa.data.compbio/01/12/2010/"`
compbio.data.sequence.SMERFSConstraints
+`public static final double`	`DEFAULT_GAP_THRESHOLD`	`0.1`
+`public static final int`	`DEFAULT_WINDOW_SIZE`	`7`
compbio.ws.client.WSTester
+`public static final java.lang.String`	`fastaAlignment`	`">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n>Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"`
+`public static final java.lang.String`	`fastaInput`	`">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n>Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"`