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Re-formatting the file
[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
index 7db8e89..0795b15 100644 (file)
--- a/website/full_javadoc/index-files/index-14.html
+++ b/website/full_javadoc/index-files/index-14.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\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="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -82,6 +82,9 @@ function windowTitle()
 <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
@@ -94,6 +97,15 @@ Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/C
 <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
@@ -101,6 +113,12 @@ Static method in exception compbio.metadata.<A HREF="../compbio/metadata/LimitEx
 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