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adding clustalO documentation
[jabaws.git] / website / full_javadoc / index-files / index-15.html
diff --git a/website/full_javadoc/index-files/index-15.html b/website/full_javadoc/index-files/index-15.html
index 20d4d09..58a97ca 100644 (file)
--- a/website/full_javadoc/index-files/index-15.html
+++ b/website/full_javadoc/index-files/index-15.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 Fri Aug 12 14:32:36 BST 2011 -->\r
 <TITLE>\r
 O-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-08-12">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -88,6 +88,10 @@ Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.h
 <DT><A HREF="../compbio/runner/_impl/OB.html#OB(java.lang.String)"><B>OB(String)</B></A> - \r
 Constructor for class compbio.runner._impl.<A HREF="../compbio/runner/_impl/OB.html" title="class in compbio.runner._impl">OB</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#openInputStream(java.lang.String)"><B>openInputStream(String)</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 and parses Fasta or Clustal formatted file into a list of
+ FastaSequence objects\r
 <DT><A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata"><B>Option</B></A>&lt;<A HREF="../compbio/metadata/Option.html" title="type parameter in Option">T</A>&gt; - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Command line option/flag or multiple exclusive options with no value.<DT><A HREF="../compbio/metadata/Option.html#Option(java.lang.String, java.lang.String)"><B>Option(String, String)</B></A> - \r
 Constructor for class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 <DD>&nbsp;\r
@@ -97,6 +101,9 @@ Constructor for class compbio.runner.<A HREF="../compbio/runner/OptionCombinator
 <DT><A HREF="../compbio/runner/OptionCombinator.html#optionsToCommandString(java.util.List)"><B>optionsToCommandString(List&lt;Option&lt;?&gt;&gt;)</B></A> - \r
 Method in class compbio.runner.<A HREF="../compbio/runner/OptionCombinator.html" title="class in compbio.runner">OptionCombinator</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/engine/client/SkeletalExecutable.html#OUTPUT"><B>OUTPUT</B></A> - \r
+Static variable in class compbio.engine.client.<A HREF="../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A>\r
+<DD>&nbsp;\r
 </DL>\r
 <HR>\r
 \r