From 5db78fd966c7a3586986be6c608a06ca18b7c341 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 8 Aug 2007 11:59:20 +0000 Subject: [PATCH] give treeviewer description its own contents entry and link it in better. --- help/help.jhm | 1 + help/helpTOC.xml | 3 ++- help/html/calculations/tree.html | 4 +++- help/html/calculations/treeviewer.html | 39 +++++++++++++++++--------------- 4 files changed, 27 insertions(+), 20 deletions(-) diff --git a/help/help.jhm b/help/help.jhm index c0a9d68..2eba565 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -41,6 +41,7 @@ + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 59d30e4..b2f82ae 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -14,6 +14,7 @@ + @@ -57,7 +58,7 @@ - + diff --git a/help/html/calculations/tree.html b/help/html/calculations/tree.html index 1e2e0d0..c425a83 100755 --- a/help/html/calculations/tree.html +++ b/help/html/calculations/tree.html @@ -4,7 +4,9 @@

Calculation of trees from alignments

Trees are calculated on either the complete alignment, or just the currently selected group of sequences, using the functions in the -Calculate→Calculate tree submenu. There are +Calculate→Calculate tree submenu. +Once calculated, trees are displayed in a new tree viewing window. There are four different calculations, using one of two distance measures and constructing the tree from one of two algorithms :

diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index f2c7d3d..f98ea5d 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -5,28 +5,18 @@

The Tree Viewing Window

- 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.

+ The tree viewing window is opened when a tree has been calculated + from an alignment, or imported via a file or web service. It includes menus for + controlling layout and file and figure creation, and enables + various selection and colouring operations on the + associated sequences in the alignment.

+Selecting Sequence Leaf Nodes
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.

- -

Moving the mouse over an internal node of the tree will highlight - it. You can then :

Click the highlighted node to select all the sequences in that branch. -
Double-click the highlighted node to rearrange the tree - diagram by inverting the branch ordering at that - node. -
Right-click to open the 'Select Sub-Tree Colour' dialog box, to - pick a new colour for the sub-tree and associated sequences. -

Grouping sequences by partitioning the tree at a particular distanec
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 conservation based colour scheme.

File Menu

+Selecting Subtrees and changing the branch order and subtree group colour
+Moving the mouse over an internal node of the tree will highlight + it. You can then :

Click the highlighted node to select all the sequences in that branch. +
Double-click the highlighted node to rearrange the tree + diagram by inverting the branch ordering at that + node. +
Right-click to open the 'Select Sub-Tree Colour' dialog box, to + pick a new colour for the sub-tree and associated sequences. +

+File Menu

This menu allows the displayed tree to be saved as a Newick tree file (Save→Newick File), printed or exported as an image (PNG) or Postscript file. Finally, data used to calculate the tree can be -- 1.7.10.2