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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / dm_javadoc / index-files / index-15.html
diff --git a/website/dm_javadoc/index-files/index-15.html b/website/dm_javadoc/index-files/index-15.html
new file mode 100644 (file)
index 0000000..fe911ae
--- /dev/null
+++ b/website/dm_javadoc/index-files/index-15.html
@@ -0,0 +1,231 @@
+<!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 12:08:25 GMT 2011 -->\r
+<TITLE>\r
+R-Index\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="R-Index";\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="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Index</B></FONT>&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;<A HREF="index-14.html"><B>PREV LETTER</B></A>&nbsp;\r
+&nbsp;<A HREF="index-16.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="../index.html?index-filesindex-15.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="index-15.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
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">C</A> <A HREF="index-3.html">D</A> <A HREF="index-4.html">E</A> <A HREF="index-5.html">F</A> <A HREF="index-6.html">G</A> <A HREF="index-7.html">H</A> <A HREF="index-8.html">I</A> <A HREF="index-9.html">J</A> <A HREF="index-10.html">L</A> <A HREF="index-11.html">M</A> <A HREF="index-12.html">N</A> <A HREF="index-13.html">O</A> <A HREF="index-14.html">P</A> <A HREF="index-15.html">R</A> <A HREF="index-16.html">S</A> <A HREF="index-17.html">T</A> <A HREF="index-18.html">U</A> <A HREF="index-19.html">V</A> <A HREF="index-20.html">W</A> <HR>\r
+<A NAME="_R_"><!-- --></A><H2>\r
+<B>R</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence"><B>Range</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>&nbsp;<DT><A HREF="../compbio/data/sequence/Range.html#Range(int, int)"><B>Range(int, int)</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/Range.html#Range(java.lang.String[])"><B>Range(String[])</B></A> - \r
+Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readAAConResults(java.io.InputStream)"><B>readAAConResults(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Read AACon result with no alignment files.\r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.InputStream)"><B>readClustalFile(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<DD>Read Clustal formatted alignment.\r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#readClustalFile(java.io.File)"><B>readClustalFile(File)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readDisembl(java.io.InputStream)"><B>readDisembl(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>> Foobar_dundeefriends
+ 
+ # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
+ 
+ # REM465 355-368
+ 
+ # HOTLOOPS 190-204
+ 
+ # RESIDUE COILS REM465 HOTLOOPS
+ 
+ M 0.86010 0.88512 0.37094
+ 
+ T 0.79983 0.85864 0.44331
+ 
+ >Next Sequence name\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readFasta(java.io.InputStream)"><B>readFasta(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Reads fasta sequences from inStream into the list of FastaSequence
+ objects\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readGlobPlot(java.io.InputStream)"><B>readGlobPlot(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>> Foobar_dundeefriends
+ 
+ # COILS 34-41, 50-58, 83-91, 118-127, 160-169, 191-220, 243-252, 287-343
+ 
+ # REM465 355-368
+ 
+ # HOTLOOPS 190-204
+ 
+ # RESIDUE COILS REM465 HOTLOOPS
+ 
+ M 0.86010 0.88512 0.37094
+ 
+ T 0.79983 0.85864 0.44331
+ 
+ >Next Sequence name\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readIUPred(java.io.File)"><B>readIUPred(File)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Read IUPred output\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.File)"><B>readJRonn(File)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#readJRonn(java.io.InputStream)"><B>readJRonn(InputStream)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Reader for JRonn horizontal file format\r
+<DT><A HREF="../compbio/data/msa/RegistryWS.html" title="interface in compbio.data.msa"><B>RegistryWS</B></A> - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>JABAWS services registry<DT><A HREF="../compbio/data/sequence/FastaReader.html#remove()"><B>remove()</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A>\r
+<DD>Not implemented\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)"><B>removeArgument(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Removes the argument <A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)"><B>removeArgumentByOptionName(String)</B></A> - \r
+Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>Removes the argument which can be a Parameter or an Option instance by
+ the value in <optionNames> element of the runner configuration
+ descriptor.\r
+<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>ResultNotAvailableException</B></A> - Exception in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>ResultNotAvailableException is thrown wherever the results of the calculation
+ cannot be obtained.<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String)"><B>ResultNotAvailableException(String)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.Throwable)"><B>ResultNotAvailableException(Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/ResultNotAvailableException.html#ResultNotAvailableException(java.lang.String, java.lang.Throwable)"><B>ResultNotAvailableException(String, Throwable)</B></A> - \r
+Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>ResultNotAvailableExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html#ResultNotAvailableExceptionBean()"><B>ResultNotAvailableExceptionBean()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.html" title="class in compbio.data.msa.jaxws">ResultNotAvailableExceptionBean</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata"><B>RunnerConfig</B></A>&lt;<A HREF="../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>The list of <A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.<DT><A HREF="../compbio/metadata/RunnerConfig.html#RunnerConfig()"><B>RunnerConfig()</B></A> - \r
+Constructor for class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
+<DD>&nbsp;\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
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+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
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+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <FONT CLASS="NavBarFont1">Use</FONT>&nbsp;</TD>\r
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+  <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
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+    document.writeln('<A HREF="../allclasses-noframe.html"><B>All Classes</B></A>');\r
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+\r
+</BODY>\r
+</HTML>\r