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give treeviewer description its own contents entry and link it in better.
authorjprocter <Jim Procter>
Wed, 8 Aug 2007 11:59:20 +0000 (11:59 +0000)
committerjprocter <Jim Procter>
Wed, 8 Aug 2007 11:59:20 +0000 (11:59 +0000)
help/help.jhm patch | blob | history
help/helpTOC.xml patch | blob | history
help/html/calculations/tree.html patch | blob | history
help/html/calculations/treeviewer.html patch | blob | history

diff --git a/help/help.jhm b/help/help.jhm
index c0a9d68..2eba565 100755 (executable)
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -41,6 +41,7 @@
    <mapID target="jalarchive" url="html/features/jalarchive.html"/>
    <mapID target="multipleviews" url="html/features/multipleViews.html"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
+   <mapID target="treeviewer" url="html/calculations/treeviewer.html"/>
    <mapID target="sorting" url="html/calculations/sorting.html"/>
    <mapID target="pca" url="html/calculations/pca.html"/>
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 59d30e4..b2f82ae 100755 (executable)
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -14,6 +14,7 @@
        <tocitem text="Making figures" target="export"/>
        <tocitem text="Hidden Regions" target="hiddenRegions"/>
        <tocitem text="Multiple Views" target="multipleviews"/>
+       <tocitem text="Viewing Trees" target="treeviewer" expand="false"/>
        <tocitem text="Sequence Features" target="seqfeatures" expand="false">
           <tocitem text="Sequence Feature Settings" target="seqfeatures.settings"/>
           <tocitem text="Sequence Features File" target="features.fileformat"/>
@@ -57,7 +58,7 @@
                <tocitem text="Pairwise Alignments" target="pairwise"/>
                <tocitem text="Remove Redundancy" target="redundancy"/>
        </tocitem>
-       <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
+       <tocitem text="Alignment Annotations" target ="alannotation" expand="false">
           <tocitem text="Conservation" target="calcs.alconserv"/>
           <tocitem text="Quality" target="calcs.alquality"/>
           <tocitem text="Consensus" target="calcs.consensus"/>
diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index 1e2e0d0..c425a83 100755 (executable)
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -4,7 +4,9 @@
 <p><strong>Calculation of trees from alignments</strong></p>
 <p>Trees are calculated on either the complete alignment, or just the
 currently selected group of sequences, using the functions in the
-<strong>Calculate&#8594;Calculate tree</strong> submenu. There are
+<strong>Calculate&#8594;Calculate tree</strong> submenu. 
+Once calculated, trees are displayed in a new <a 
+href="../calculations/treeviewer.html">tree viewing window</a>. There are
 four different calculations, using one of two distance measures and
 constructing the tree from one of two algorithms :
 </p>
diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
index f2c7d3d..f98ea5d 100755 (executable)
--- a/help/html/calculations/treeviewer.html
+++ b/help/html/calculations/treeviewer.html
@@ -5,28 +5,18 @@
 <body>
 <p><strong>The Tree Viewing Window</strong></p>
 <p>
-  When a tree has been calculated from an alignment, or imported via a
-  file or web service it is displayed by Jalview's tree viewing
-  window. Trees can be rearranged, used to select sequences and groups
-  in the associated alignment, saved in Newick format or exported as an
-  image or postscript file.</p>
+  The tree viewing window is opened when a tree has been <a href="tree.html">calculated 
+  from an alignment</a>, or imported via a file or web service. It includes <a href="#menus">menus</a> for 
+  controlling layout and file and figure creation, and enables 
+  various selection and colouring operations on the 
+  associated sequences in the alignment.</p>
 <p>
+<strong><em>Selecting Sequence Leaf Nodes</em></strong><br>
   Selecting sequence ids at the leaves of the tree selects the
   corresponding sequences in the original alignment. These selections
   are also reflected in any other analysis windows associated with the
   alignment, such as another tree viewer.</p>
-
-<p>Moving the mouse over an internal node of the tree will highlight
-  it. You can then : <ul>
-  <li>Click the highlighted node to select all the sequences in that branch.
-  <li>Double-click the highlighted node to rearrange the tree
-  diagram by inverting the branch ordering at that
-  node.
-  <li>Right-click to open the 'Select Sub-Tree Colour' dialog box, to
-  pick a new colour for the sub-tree and associated sequences.
-  </ul>
-</p>
-<p>
+<p><strong><em>Grouping sequences by partitioning the tree at a particular distanec</em></strong><br>
   Clicking anywhere along the extent of the tree (but not on a leaf or
   internal node) defines a tree 'partition', by cutting every branch
   of the tree spanning the depth where the mouse-click occurred. Groups
@@ -42,7 +32,20 @@ identifying specific patterns of conservation and mutation
 corresponding to the overall phylogenetic structure, when combined
 with the <a href="../colourSchemes/conservation.html">conservation
 based colour scheme</a>.</p>
-<p><strong>File Menu</strong></p>
+<p>
+<strong><em>Selecting Subtrees and changing the branch order and subtree group colour</em></strong><br>
+Moving the mouse over an internal node of the tree will highlight
+  it. You can then : <ul>
+  <li>Click the highlighted node to select all the sequences in that branch.
+  <li>Double-click the highlighted node to rearrange the tree
+  diagram by inverting the branch ordering at that
+  node.
+  <li>Right-click to open the 'Select Sub-Tree Colour' dialog box, to
+  pick a new colour for the sub-tree and associated sequences.
+  </ul>
+</p>
+<p><strong><a name="menus">
+File Menu</a></strong></p>
 <p>This menu allows the displayed tree to be saved as a Newick tree
 file (Save&#8594;Newick File), printed or exported as an image (PNG) or
 Postscript file. Finally, data used to calculate the tree can be