From ee9e7bf2289ef0161307b23658ade7a908d80f14 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 6 Sep 2012 22:59:52 +0100
Subject: [PATCH] JAL-1065 whats new entry for tcoffee scores

---
 help/help.jhm    |    1 +
 help/helpTOC.xml |    3 +++
 2 files changed, 4 insertions(+)

diff --git a/help/help.jhm b/help/help.jhm
index 732b6a6..095196f 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -38,6 +38,7 @@
    <mapID target="io" url="html/io/index.html"/>
    <mapID target="io.modellerpir" url="html/io/modellerpir.html"/>
    <mapID target="io.seqreport" url="html/io/exportseqreport.html"/>
+   <mapID target="io.tcoffeescores" url="html/io/tcoffeescores.html"/>
    <mapID target="export" url="html/io/export.html"/>
    <mapID target="alformats" url="html/io/fileformats.html"/>
    <mapID target="annotations.fileformat" url="html/features/annotationsFormat.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 62bc222..f59dd70 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -26,10 +26,12 @@
 		<tocitem text="RNA Structure Consensus" target="calcs.alstrconsensus"/>
 		<tocitem text="RNA Helices coloring" target="colours.rnahelices"/>
 		<tocitem text="HTML annotation report" target="io.seqreport"/>
+		<tocitem text="T-COFFEE Alignment Score display" target="io.tcoffeescores"/>
 		<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 text="Normalised sequence logo display" target="calcs.consensus"/>
 	</tocitem>
     <tocitem text="Editing Alignments" target ="edit"/>	
     <tocitem text="Cursor Mode" target="cursor"/>
@@ -87,6 +89,7 @@
 		<tocitem text="User Defined" target="colours.user"/>
 		<tocitem text="Above Percentage Identity" target="colours.abovepid"/>
 		<tocitem text="By conservation" target="colours.conservation"/>
+    <tocitem text="T-COFFEE Scores" target="io.tcoffeescores"/>
 		<tocitem text="By Annotation" target="colours.annotation"/>
 		<tocitem text="By RNA Helices" target="colours.rnahelices"/>
 	</tocitem>
-- 
1.7.10.2