Additions to the Dendrogram display
(by Richard Bruskiewich)
- Phylogenetic tree "bootstrap" values have been added to the model and the display. The display
of these values is controlled by new ?Tree and ?TreeNode tags. The "New Hampshire" format may
also be used to input bootstrap values. These features are documented in an updated Dendrogram.html.
- Picking the message box permits copying of its contents to the ACEDB post buffer (for cut and paste)
without changing the currently selected node.
- The active node is now highlighted with green (B 'n W mode labels in blue... Colour mode ?Taxon coloured
nodes are reverse complemented).
- Parts of taxonomic trees may be read in and integrated into an existing taxonomic tree. If the root node
of the new subtree is already present in the specified tree, then the tree is properly hooked up to the
existing tree. If a Label is seen in the phylogenetic tree (.ph) file before any parenthesized tree list
description, then it is taken as being both the name of the ?Tree and the label for the Root ?TreeNode,
and the user is not prompted for the tree name.
- The ?Taxon (actually, ?Species) of a given ?Sequence or ?Protein ?TreeNode leaf may be indirectly
specified in the associated ?Sequence or ?Protein object itself via a Species ?Species tag-value pair,
rather than directly in the ?TreeNode .. Taxon ?Taxon.
- The ?Species model now has a "Taxonomy UNIQUE ?TreeNode" tag-value pair which points to the (one) taxonomy
tree in the system to which which it belongs, and which is displayed when _VSpecies -D DtDendrogram is
set in options.wrm.
- The "Export" (pop-up menu command)functionality has been extended in two ways. First, if a given
?TreeNode is selected, then the export is done relative to that node, i.e. on the subtree, otherwise,
the if no node is selected, the whole tree is exported. Second, one can either export a ".ace" file of
the ?Tree, ?TreeNode and "Contained" objects, or one can dump Fasta-formatted sequences (of the given
expected type) from DNA or Protein phylogenetic (sub)trees.
- Added explicit "Pick_me_to_call" functionality to dendrogram.
New type of homol column in fmap display. This displays each sequnces homology
in a seperate line so that clustering information can be displayed
easily. It does however insist that the method name is EMBOSS. It uses
this to decide that to use the new column. - (by il)
EMBL dumping now uses methods for subsequence dumping (EMBL_feature field) - (by rd)
changed behaviour of crash and error messages. Introduced more graceful error/exit messages for harmless errors.
Crash messages now give developers information on program/filename and line number of where the error occured. - (by edgrif)
Fixed bug that caused crash when clicking on grey timestamp boxes in
tree display (when 'toggle timestamp' option is on) - (by fw)
dna fasta dumping from tace/aceclient supports new -mismatch option - (by rd)
empty longtext or DNA objects are now allowed - (by rd)
