From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 6 Sep 2012 14:53:52 +0000 (+0100)
Subject: PCA what's new and score matrix documentation page
X-Git-Tag: Jalview_2_9~323
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ea284df32dbcbbac847bcd251a070551d0f64061;p=jalview.git

PCA what's new and score matrix documentation page
---

diff --git a/help/help.jhm b/help/help.jhm
index e1bc443..732b6a6 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -106,6 +106,7 @@
    <mapID target="aminoAcids" url="html/misc/aminoAcids.html" />
    <mapID target="aaProperties" url="html/misc/aaproperties.html" />
    <mapID target="geneticCode" url="html/misc/geneticCode.html" />
+   <mapID target="subtMatrices" url="html/calculations/scorematrices.html" />
    
    <mapID target="backIcon" url="icons/back.png" />
    <mapID target="forwardIcon" url="icons/forward.png" />
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 75aa6d2..62bc222 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -29,6 +29,7 @@
 		<tocitem text="Per-sequence Annotation Colouring" target="colours.annotation"/>
 	  <tocitem text="Sequence Database Retrieval Dialog" target="seqfetch"/>
 	  <tocitem text="JABAWS Web Service Preferences" target="wsprefs"/>
+	  <tocitem text="DNA or Protein PCA calculation" target="pca"/>
 	</tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>	
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -142,5 +143,7 @@
 	<tocitem text="Amino Acid Table" target="aminoAcids"/>
 	<tocitem text="Amino Acid Properties" target="aaProperties"/>
 	<tocitem text="The Genetic Code" target="geneticCode"/>
+	<tocitem text="Sequence Substitution Matrices" target="subtMatrices"/>
+  
 </tocitem>
 </toc>