preliminary EMBL and mapping documentation

diff --git a/help/help.jhm b/help/help.jhm
index 056a813..bb3b49f 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -17,6 +17,8 @@
    <mapID target="mafft" url="html/webServices/mafft.html"/>
    <mapID target="jnet" url="html/webServices/jnet.html"/>
    <mapID target="seqfetch" url="html/features/seqfetch.html"/>
+   <mapID target="seqmappings" url="html/features/seqmappings.html"/>
+   <mapID target="cdnafeatures" url="html/features/codingfeatures.html"/>
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
    <mapID target="seqfeatedit" url="html/features/editingFeatures.html"/>
    <mapID target="seqfeatcreat" url="html/features/creatinFeatures.html"/>

diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 7d9e595..04bfc7e 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -2,10 +2,13 @@
 <!DOCTYPE toc PUBLIC "-//Sun Microsystems Inc.//DTD JavaHelp TOC Version 1.0//EN" "http://java.sun.com/products/javahelp/toc_1_0.dtd">
 <toc version="1.0">
 <tocitem text="Jalview Documentation" target="home" expand="true" >
-       <tocitem text="What's new" target="new" expand="true"/>
-        <tocitem text="Release History" target="release"/>
-        <tocitem text="Editing Alignments" target ="edit"/>    
-        <tocitem text="Cursor Mode" target="cursor"/>
+       <tocitem text="What's new" target="new" expand="true">
+      <tocitem text="Release History" target="release"/>
+         <tocitem text="Mapping between Sequences" target="seqmappings"/>
+         <tocitem text="Coding Region Sequence Features" target="cdnafeatures"/>
+    </tocitem>
+    <tocitem text="Editing Alignments" target ="edit"/>        
+    <tocitem text="Cursor Mode" target="cursor"/>
        <tocitem text="Key Strokes" target="keys"/>
        <tocitem text="Input / Output" target="io"/>
        <tocitem text="Making figures" target="export"/>