#-------------------------------------------------------------------------------
# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
#
# This file is part of Jalview.
#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see .
#-------------------------------------------------------------------------------
What's new ?
What's new ?
Jalview 2.5.1 is a bug fix release for the 2.5 version of
Jalview. See the release
history for the bugs that this release resolves.
Highlights in Jalview Version 2.5
Linked viewing of nucleic acid sequences and structures
Automatic Scrolling option in View menu to display the currently
highlighted region of an alignment.
Order an alignment by sequence length, or using the average score or
total feature count for each sequence.
Shading features by score or associated description
Subdivide alignment and groups based on identity of selected
subsequence (Make Groups from Selection).
New hide/show options including Shift+Control+H to hide everything but
the currently selected region.
Jalview Desktop:
Fetch DB References capabilities and UI expanded to support retrieval
from DAS sequence sources
Enable or disable non-positional feature and database references in
sequence ID tooltip from View menu in application.
Group-associated consensus, sequence logos and conservation plots
Symbol distributions for each column can be exported and visualized as
sequence logos
Jalview Java Console
New webservice for submitting sequences and IDs to
Envision2
Workflows
Improved VAMSAS synchronization and sharing of selections.
JalviewLite:
Middle button resizes annotation row height
New Parameters - including default tree display settings.
Non-positional features displayed in ID tooltip
Issues Resolved (a select list)
Source field in GFF files parsed as feature source rather than
description
Non-positional features are now included in sequence feature and gff
files (controlled via non-positional feature visibility in tooltip).
URL links generated for all feature links (bugfix)
Codons containing ambiguous nucleotides translated as 'X' in peptide
product
Match case switch in find dialog box works for both sequence ID and
sequence string and query strings do not have to be in upper case to
match case-insensitively.
Jalview Annotation File generation/parsing consistent with
documentation (e.g. Stockholm annotation can be exported and
re-imported)
Find incrementally searches ID string matches as well as subsequence
matches, and correctly reports total number of both.
Desktop Issues
Better handling of exceptions during sequence retrieval
PDB files retrieved from URLs are cached properly
Sequence description lines properly shared via VAMSAS
Sequence fetcher fetches multiple records for all data sources
Ensured that command line das feature retrieval completes before
alignment figures are generated.
Reduced time taken when opening file browser for first time.
User defined group colours properly recovered from Jalview projects.
See the Release History page for
details of all new features and resolved issues.