From 8ee7a0f79f6da26d5011c60a80226d6994733cab Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 26 May 2005 10:20:12 +0000
Subject: [PATCH] partially updated help. Added separate treeviewing item in
 the root menu.

---
 help/help.jhm                          |    4 +-
 help/helpTOC.xml                       |    5 ++-
 help/html/calculations/tree.html       |   51 ++++++---------------
 help/html/calculations/treeviewer.html |   77 ++++++++++++++++++++++++++++++++
 help/html/webServices/index.html       |   19 +++++---
 5 files changed, 109 insertions(+), 47 deletions(-)
 create mode 100755 help/html/calculations/treeviewer.html

diff --git a/help/help.jhm b/help/help.jhm
index 4081a57..9eda491 100755
--- a/help/help.jhm
+++ b/help/help.jhm
@@ -10,13 +10,15 @@
    <mapID target="seqfeatures" url="html/features/seqfeatures.html"/>
    
    <mapID target="webservice" url="html/webServices/index.html"/>
-   <mapID target="clustal" url="html/webServices/clustal.html"/>
+   <mapID target="clustal" url="html/webServices/msaws.html#clustal"/>
+   <mapID target="muscle" url="html/webServices/msaws.html#muscle"/>
    
    <mapID target="io" url="html/io/index.html"/>
    <mapID target="edit" url="html/editing/index.html"/>
 
    <mapID target="sorting" url="html/calculations/sorting.html"/>
    <mapID target="trees" url="html/calculations/tree.html"/>
+   <mapID target="treeview" url="html/calculations/treeviewer.html"/>
    <mapID target="pca" url="html/calculations/pca.html"/>
    <mapID target="pairwise" url="html/calculations/pairwise.html"/>
    <mapID target="redundancy" url="html/calculations/redundancy.html"/>
diff --git a/help/helpTOC.xml b/help/helpTOC.xml
index 0bcf3e6..160021c 100755
--- a/help/helpTOC.xml
+++ b/help/helpTOC.xml
@@ -9,10 +9,13 @@
 		<tocitem text="Sequence Features" target ="seqfeatures"/>
 	</tocitem>
 	<tocitem text="Web Services" target="webservice" expand="false">
-		<tocitem text="Clustal Alignment" target="clustal"/>
+                <tocitem text="Clustal Alignment" target="clustal"/>
+                <tocitem text="Muscle Alignment" target="muscle"/>
+                <tocitem text="JNet Secondary Structure Prediction" target="jnet"/>
 	</tocitem>
 	<tocitem text="Input /Output" target="io"/>
 	<tocitem text="Editing Alignment" target ="edit"/>
+  	<tocitem text="Viewing Trees" target ="treeview"/>
 	<tocitem text="Colour Schemes" target="colours" expand="false">
 		<tocitem text="ClustalX" target="colours.clustal"/>
 		<tocitem text="Zappo" target="colours.zappo"/>
diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html
index a8dbe59..c767bf2 100755
--- a/help/html/calculations/tree.html
+++ b/help/html/calculations/tree.html
@@ -38,48 +38,23 @@ phylogenetic tree construction, and may fail on very large alignments.
 </li>
 </ul>
 </p>
-<p></p>
-<p><strong>The Tree Viewing Window</strong></p>
-<p>
-  When the tree has been calculated a window is displayed showing the
-  tree, with the leaves labelled with sequence ids. 
-<p>Selecting the 'show distances' checkbox will put branch lengths on the branches.
-  These branch lengths are the percentage mismatch between two nodes. </p>
-  
-<p>
-  Selecting sequence ids at the leaves of the tree selects sequences
-  in the original alignment. These selections are reflected in any
-  other analysis windows open on the same alignment. </p>
-<p>
-  Clicking on an internal node of the tree will rearrange the tree
-  diagram, inverting the ordering of the branches at that node.
-</p>
-<p>
-  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 occured. Groups
-  are created containing sequences at the leaves of each connected
-  subtree. These groups are each given a different colour, which are
-  reflected in other windows in the same way as if the sequence ids
-  were selected, and can be edited in the same way as user defined
-  sequence groups.
-</p>
-<p>Tree partitions are useful for comparing clusterings produced by
-different methods and measures. They are also an effective way of
-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>A newly calculated tree will be displayed in a new <a
+href="../calculations/treeviewer.html">tree viewing window</a>. In
+addition, a new entry with the same treeviewer window name will be added in the <a href="../calculations/sort.html">Sort
+menu</a> so that the alignment can be reordered to reflect the ordering of
+the leafs of the tree.</p>
 
-
-<p><strong>External Sources for Phylogenetic Tree Construction</strong></p>
+<p><strong>External Sources for Phylogenetic Trees</strong></p>
   <p>A number of programs exist for the reliable construction of
   phylogenetic trees, which can cope with large numbers of sequences,
-  use better distance methods and can perform bootstrapping. See the
-  <a href="../webservices/phylogeny.html">Phylogenetic Web
-  Services</a> page for directly accessible methods. It will also be
-  possible to read trees into Jalview directly, in the near future.
+  use better distance methods and can perform bootstrapping. Jalview
+  can read <a
+  href="http://evolution.genetics.washington.edu/phylip/newick_doc.html">Newick</a>
+  format tree files using the 'Load Associated Tree' entry of the
+  alignment's File menu. Sequences in the alignment will be
+  automatically associated to nodes in the
   </p>
 
+
 </body>
 </html>
diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html
new file mode 100755
index 0000000..3f855ac
--- /dev/null
+++ b/help/html/calculations/treeviewer.html
@@ -0,0 +1,77 @@
+<html>
+<head>
+<title>The Tree Viewing Window</title>
+</head>
+<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>
+<p>
+  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>
+  Clicking on an internal node of the tree will rearrange the tree
+  diagram, inverting the ordering of the branches at that node.
+</p>
+<p>
+  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 occured. Groups
+  are created containing sequences at the leaves of each connected
+  subtree. These groups are each given a different colour, which are
+  reflected in other windows in the same way as if the sequence ids
+  were selected, and can be edited in the same way as user defined
+  sequence groups.
+</p>
+<p>Tree partitions are useful for comparing clusterings produced by
+different methods and measures. They are also an effective way of
+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>This menu allows the displayed tree to be saved as a Newick tree
+file (Save-&gt;Newick File), printed or exported as an image (PNG) or
+Postscript file.
+</p>
+<p><strong>View Menu</strong></p>
+<p>When the tree viewer is opened, it displays all the annotation
+associated with a tree. Trees calculated by Jalview have branch
+lengths, which correspond to the distance measure used to construct
+the tree. Tree imported from outside may also contain bootstrap information,
+or additional leaves from sequences not present in the associated
+alignment. 
+</p>
+<p>The view menu contains options controlling the way a tree is
+rendered and labelled:</p>
+<p><ul>
+<li><strong>Fit to Window</strong><p>
+The tree layout will be scaled to fit in the  display
+window. You may need to reduce the font size to minimise the leaf
+label overlap when this option is selected.
+</p></li>
+<li><strong>Font Size -</strong><em>n</em><p>
+Brings up a dialog box to set the font size for the leaf
+names. <em>n</em> is the current font size.
+</p></li>
+<li><strong>Show Distances</strong><p>
+Labels each branch or leaf with its associated branch length.
+</p></li>
+<li><strong>Show Bootstrap values</strong><p>
+Labels each branch or leaf with its associated bootstrap value.
+</p></li>
+<li><strong>Mark unlinked leaves</strong><p>
+Toggles the display of a '*' at the beginning of a leaf label to
+indicate that there is no sequence corresponding to that leaf in the associated alignment.
+</p></li>
+</ul>
+</p>
+</body>
+</html>
diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html
index 5d4025a..19fcd8f 100755
--- a/help/html/webServices/index.html
+++ b/help/html/webServices/index.html
@@ -1,15 +1,20 @@
 <html>
 <head><title>Web Services</title></head>
 <body>
-<p><strong>Web services </strong></p>
+<p><strong>Web services</strong></p>
 <p>Originally Jalview used SRS server to retrieve sequence features for a given
   alignment. In addition certain remote alignment programs could be called from
   the Jalview interface and the results displayed in a new alignment panel. </p>
-<p>The main emphasis of the current development of the Jalview Project is to implement
-  various sequence alignment programs, tree analysis, PCA algorithms on a large
-  cluster based witihin the Barton Group. Jalview will be able to call these remote
-  procedures without the user having to install any new software. <br>
-  The main advantage of using these remote web services is that the computing
-  power available is much greater than that of the users work station.</p>
+<p>Jalview's web based computations are now being developed further,
+  using SOAP based services to expose protein sequence alignment and
+  secondary structure prediction programs. These services actually run
+  on the cluster based in Dundee, and maintained by the Barton group.
+</p><p>In the future, Jalview will be able to discover services
+  dynamically, and the repertoire will include methods for repeat
+  analysis, sequence identification and remote homology
+  detection. The web service methodology will also allow potentially
+  expensive Jalview analysis functions like <a
+  href="../calculations/pca.html">PCA</a> to be distributed, if
+  necessary, when the user is dealing with very large numbers of sequences.</p>
 </body>
 </html>
-- 
1.7.10.2