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updated javadoc for the system as well as new redirect address for download app
[jabaws.git] / website / full_javadoc / index-files / index-14.html
diff --git a/website/full_javadoc/index-files/index-14.html b/website/full_javadoc/index-files/index-14.html
new file mode 100644 (file)
index 0000000..0795b15
--- /dev/null
+++ b/website/full_javadoc/index-files/index-14.html
@@ -0,0 +1,191 @@
+<!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 12:30:43 GMT 2011 -->\r
+<TITLE>\r
+N-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="N-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-13.html"><B>PREV LETTER</B></A>&nbsp;\r
+&nbsp;<A HREF="index-15.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="../index.html?index-filesindex-14.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="index-14.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">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
+<A NAME="_N_"><!-- --></A><H2>\r
+<B>N</B></H2>\r
+<DL>\r
+<DT><A HREF="../compbio/data/msa/Category.html#name"><B>name</B></A> - \r
+Variable in class compbio.data.msa.<A HREF="../compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl"><B>NetNglyc</B></A> - Class in <A HREF="../compbio/runner/_impl/package-summary.html">compbio.runner._impl</A><DD>&nbsp;<DT><A HREF="../compbio/runner/_impl/NetNglyc.html#NetNglyc()"><B>NetNglyc()</B></A> - \r
+Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/NetNglyc.html" title="class in compbio.runner._impl">NetNglyc</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)"><B>newCommandBuilder(List&lt;? extends Option&lt;T&gt;&gt;, String)</B></A> - \r
+Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</A>\r
+<DD>This produces the same result as getCommands method.\r
+<DT><A HREF="../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)"><B>newConfExecutable(RunConfiguration)</B></A> - \r
+Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/FilePuller.html#newFilePuller(java.lang.String, int)"><B>newFilePuller(String, int)</B></A> - \r
+Static method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#newInstance(java.util.Map)"><B>newInstance(Map&lt;String, Set&lt;Score&gt;&gt;)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore(java.util.Map)"><B>newInstanceSingleScore(Map&lt;String, Score&gt;)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence(java.util.Set)"><B>newInstanceSingleSequence(Set&lt;Score&gt;)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/LimitExceededException.html#newLimitExceeded(compbio.metadata.Limit, java.util.List)"><B>newLimitExceeded(Limit&lt;?&gt;, List&lt;FastaSequence&gt;)</B></A> - \r
+Static method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/FilePuller.html#newProgressPuller(java.lang.String)"><B>newProgressPuller(String)</B></A> - \r
+Static method in class compbio.engine.<A HREF="../compbio/engine/FilePuller.html" title="class in compbio.engine">FilePuller</A>\r
+<DD>Progress Puller is designed to read 3 characters from the beginning of
+ the file, nothing more.\r
+<DT><A HREF="../compbio/stat/servlet/util/StatCollection.html#newStatCollecton(java.util.Date, java.util.Date)"><B>newStatCollecton(Date, Date)</B></A> - \r
+Static method in class compbio.stat.servlet.util.<A HREF="../compbio/stat/servlet/util/StatCollection.html" title="class in compbio.stat.servlet.util">StatCollection</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/FastaReader.html#next()"><B>next()</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>Reads the next FastaSequence from the input\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_AA"><B>NON_AA</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>inversion of AA pattern\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NON_NUCLEOTIDE"><B>NON_NUCLEOTIDE</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Non nucleotide\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NONWORD"><B>NONWORD</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Non word\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#NUCLEOTIDE"><B>NUCLEOTIDE</B></A> - \r
+Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>Nucleotides a, t, g, c, u\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="#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-13.html"><B>PREV LETTER</B></A>&nbsp;\r
+&nbsp;<A HREF="index-15.html"><B>NEXT LETTER</B></A></FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+  <A HREF="../index.html?index-filesindex-14.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
+&nbsp;<A HREF="index-14.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
+<A HREF="index-1.html">A</A> <A HREF="index-2.html">B</A> <A HREF="index-3.html">C</A> <A HREF="index-4.html">D</A> <A HREF="index-5.html">E</A> <A HREF="index-6.html">F</A> <A HREF="index-7.html">G</A> <A HREF="index-8.html">H</A> <A HREF="index-9.html">I</A> <A HREF="index-10.html">J</A> <A HREF="index-11.html">K</A> <A HREF="index-12.html">L</A> <A HREF="index-13.html">M</A> <A HREF="index-14.html">N</A> <A HREF="index-15.html">O</A> <A HREF="index-16.html">P</A> <A HREF="index-17.html">R</A> <A HREF="index-18.html">S</A> <A HREF="index-19.html">T</A> <A HREF="index-20.html">U</A> <A HREF="index-21.html">V</A> <A HREF="index-22.html">W</A> <A HREF="index-23.html">_</A> <HR>\r
+\r
+</BODY>\r
+</HTML>\r