-->
<head>
<title>Release History</title>
+<!--
+this tip works for the browser and the Java help browser:
+http://stackoverflow.com/questions/13626531/swing-html-rendering-shows-very-large-bullet-point
+this tip works for the browser but not in the Java help browser:
+http://stackoverflow.com/questions/17158253/indenting-the-2nd-line-of-a-paragraph-with-css
+-->
+<style>
+ul {
+ list-style-type: none;
+ margin-left: 10px
+}
+li {
+ margin-left: 1em;
+ text-indent: -1em;
+ }
+</style>
</head>
<body>
<p>
<td><div align="left">
<em>General</em>
<ul>
- <li>
+ <li>•
<!-- JAL-98 -->Improved memory usage: sparse arrays used
for all consensus calculations
</li>
- <li>
+ <li>•
<!-- JAL-2177 -->Jmol updated to version 14.6.4 (released 3rd Oct 2016)
</li>
- <li>Updated Jalview's Certum code signing certificate
+ <li>• Updated Jalview's Certum code signing certificate
for 2016-2017</li>
</ul>
<em>Application</em>
<ul>
- <li>
+ <li>•
<!-- JAL-1723 -->Sequence ID tool tip presents abridged
set of database cross-references, sorted alphabetically
</li>
- <li>
+ <li>•
<!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
from database cross references. Users with custom links
will receive a <a href="webServices/urllinks.html#warning">warning
dialog</a> asking them to update their preferences.
</li>
- <li>
+ <li>•
<!-- JAL-2287-->Cancel button and escape listener on
dialog warning user about disconnecting Jalview from a
Chimera session
</li>
- <li>
+ <li>•
<!-- JAL-2320-->Jalview's Chimera control window closes if
the Chimera it is connected to is shut down
</li>
- <li>
+ <li>•
<!-- JAL-1738-->New keystroke (B) and Select highlighted
columns menu item to mark columns containing
highlighted regions (e.g. from structure selections or results
of a Find operation)
</li>
- <li>
+ <li>•
<!-- JAL-2284-->Command line option for batch-generation
of HTML pages rendering alignment data with the BioJS
MSAviewer
<div align="left">
<em>General</em>
<ul>
- <li>
+ <li>•
<!-- JAL-2286 -->Columns with more than one modal residue
are not coloured or thresholded according to percent
identity (first observed in Jalview 2.8.2)
</li>
- <li>
+ <li>•
<!-- JAL-2301 -->Threonine incorrectly reported as not
hydrophobic
</li>
- <li>
+ <li>•
<!-- JAL-2318 -->Updates to documentation pages (above PID
threshold, amino acid properties)
</li>
- <li>
+ <li>•
<!-- JAL-2292 -->Lower case residues in sequences are not
reported as mapped to residues in a structure file in the
View Mapping report
</li>
- <li>
+ <li>•
<!--JAL-2324 -->Identical features with non-numeric scores
could be added multiple times to a sequence
</li>
- <li>
+ <li>•
<!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
bond features shown as two highlighted residues rather
than a range in linked structure views, and treated
correctly when selecting and computing trees from features
</li>
- <li>
+ <li>•
<!-- JAL-2281-->Custom URL links for database
cross-references are matched to database name regardless
of case
</ul>
<em>Application</em>
<ul>
- <li>
+ <li>•
<!-- JAL-2282-->Custom URL links for specific database
names without regular expressions also offer links from
Sequence ID
</li>
- <li>
+ <li>•
<!-- JAL-2315-->Removing a single configured link in the
URL links pane in Connections preferences doesn't actually
update Jalview configuration
</li>
- <li>
+ <li>•
<!-- JAL-2272-->CTRL-Click on a selected region to open
the alignment area popup menu doesn't work on El-Capitan
</li>
- <li>
+ <li>•
<!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
files with similarly named sequences if dropped onto the
alignment
</li>
- <li>
+ <li>•
<!-- JAL-2312 -->Additional mappings are shown for PDB
entries where more chains exist in the PDB accession than
are reported in the SIFTS file
</li>
- <li>
+ <li>•
<!-- JAL-2317-->Certain structures do not get mapped to
the structure view when displayed with Chimera
</li>
- <li>
+ <li>•
<!-- JAL-2317-->No chains shown in the Chimera view
panel's View->Show Chains submenu
</li>
- <li>
+ <li>•
<!--JAL-2277 -->Export as HTML with embedded SVG doesn't
work for wrapped alignment views
</li>
- <li>
+ <li>•
<!--JAL-2197 -->Rename UI components for running JPred
predictions from 'JNet' to 'JPred'
</li>
- <li>
+ <li>•
<!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
corrupted when annotation panel vertical scroll is not at
first annotation row
</li>
- <li>
+ <li>•
<!--JAL-2332 -->Attempting to view structure for Hen
lysozyme results in a PDB Client error dialog box
</li>
</ul>
<!-- <em>New Known Issues</em>
<ul>
- <li></li>
+ <li>• </li>
</ul> -->
</div>
</td>
</td>
<td><em>Application</em>
<ul>
- <li>3D Structure chooser opens with 'Cached structures'
+ <li>• 3D Structure chooser opens with 'Cached structures'
view if structures already loaded</li>
- <li>Progress bar reports models as they are loaded to
+ <li>• Progress bar reports models as they are loaded to
structure views</li>
</ul></td>
<td>
<div align="left">
<em>General</em>
<ul>
- <li>Colour by conservation always enabled and no tick
+ <li>• Colour by conservation always enabled and no tick
shown in menu when BLOSUM or PID shading applied</li>
- <li>FER1_ARATH and FER2_ARATH labels were switched in
+ <li>• FER1_ARATH and FER2_ARATH labels were switched in
example sequences/projects/trees</li>
</ul>
<em>Application</em>
<ul>
- <li>Jalview projects with views of local PDB structure
+ <li>• Jalview projects with views of local PDB structure
files saved on Windows cannot be opened on OSX</li>
- <li>Multiple structure views can be opened and
+ <li>• Multiple structure views can be opened and
superposed without timeout for structures with multiple
models or multiple sequences in alignment</li>
- <li>Cannot import or associated local PDB files without
+ <li>• Cannot import or associated local PDB files without
a PDB ID HEADER line</li>
- <li>RMSD is not output in Jmol console when
+ <li>• RMSD is not output in Jmol console when
superposition is performed</li>
- <li>Drag and drop of URL from Browser fails for Linux
+ <li>• Drag and drop of URL from Browser fails for Linux
and OSX versions earlier than El Capitan</li>
- <li>ENA client ignores invalid content from ENA server</li>
- <li>Exceptions are not raised in console when ENA
+ <li>• ENA client ignores invalid content from ENA server</li>
+ <li>• Exceptions are not raised in console when ENA
client attempts to fetch non-existent IDs via Fetch DB
Refs UI option</li>
- <li>Exceptions are not raised in console when a new
+ <li>• Exceptions are not raised in console when a new
view is created on the alignment</li>
- <li>OSX right-click fixed for group selections:
+ <li>• OSX right-click fixed for group selections:
CMD-click to insert/remove gaps in groups and CTRL-click
to open group pop-up menu</li>
</ul>
<em>Build and deployment</em>
<ul>
- <li>URL link checker now copes with multi-line anchor
+ <li>• URL link checker now copes with multi-line anchor
tags</li>
</ul>
<em>New Known Issues</em>
<ul>
- <li>Drag and drop from URL links in browsers do not
+ <li>• Drag and drop from URL links in browsers do not
work on Windows</li>
</ul>
</div>
</td>
<td><em>General</em>
<ul>
- <li>
+ <li>•
<!-- JAL-2124 -->Updated Spanish translations.
</li>
- <li>
+ <li>•
<!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
for importing structure data to Jalview. Enables mmCIF and
better PDB parsing.
</li>
- <li>
+ <li>•
<!-- JAL-192 --->Alignment ruler shows positions relative to
reference sequence
</li>
- <li>
+ <li>•
<!-- JAL-2202 -->Position/residue shown in status bar when
mousing over sequence associated annotation
</li>
- <li>
+ <li>•
<!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
for manual entry
</li>
- <li>
+ <li>•
<!-- JAL-2214 -->RNA Structure consensus indicates wc-only
'()', canonical '[]' and invalid '{}' base pair populations
for each column
</li>
- <li>
+ <li>•
<!-- JAL-2092 -->Feature settings popup menu options for
showing or hiding columns containing a feature
</li>
- <li>
+ <li>•
<!-- JAL-1557 -->Edit selected group by double clicking on
group and sequence associated annotation labels
</li>
- <li>
+ <li>•
<!-- JAL-2236 -->Sequence name added to annotation label in
select/hide columns by annotation and colour by annotation
dialogs
</ul> <em>Application</em>
<ul>
- <li>
+ <li>•
<!-- JAL-2050-->Automatically hide introns when opening a
gene/transcript view
</li>
- <li>
+ <li>•
<!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
dialog
</li>
- <li>
+ <li>•
<!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
structure mappings with the EMBL-EBI PDBe SIFTS database
</li>
- <li>
+ <li>•
<!-- JAL-2079 -->Updated download sites used for Rfam and
Pfam sources to xfam.org
</li>
- <li>
+ <li>•
<!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
</li>
- <li>
+ <li>•
<!-- JAL-2123 -->Show residue labels in Chimera when mousing
over sequences in Jalview
</li>
- <li>
+ <li>•
<!-- JAL-2027-->Support for reverse-complement coding
regions in ENA and EMBL
</li>
- <li>
+ <li>•
<!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
for record retrieval via ENA rest API
</li>
- <li>
+ <li>•
<!-- JAL-2027 -->Support for ENA CDS records with reverse
complement operator
</li>
- <li>
+ <li>•
<!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
groovy script execution
</li>
- <li>
+ <li>•
<!-- JAL-1812 -->New 'execute Groovy script' option in an
alignment window's Calculate menu
</li>
- <li>
+ <li>•
<!-- JAL-1812 -->Allow groovy scripts that call
Jalview.getAlignFrames() to run in headless mode
</li>
- <li>
+ <li>•
<!-- JAL-2068 -->Support for creating new alignment
calculation workers from groovy scripts
</li>
- <li>
+ <li>•
<!-- JAL-1369 --->Store/restore reference sequence in
Jalview projects
</li>
- <li>
+ <li>•
<!-- JAL-1803 -->Chain codes for a sequence's PDB
associations are now saved/restored from project
</li>
- <li>
+ <li>•
<!-- JAL-1993 -->Database selection dialog always shown
before sequence fetcher is opened
</li>
- <li>
+ <li>•
<!-- JAL-2183 -->Double click on an entry in Jalview's
database chooser opens a sequence fetcher
</li>
- <li>
+ <li>•
<!-- JAL-1563 -->Free-text search client for UniProt using
the UniProt REST API
</li>
- <li>
+ <li>•
<!-- JAL-2168 -->-nonews command line parameter to prevent
the news reader opening
</li>
- <li>
+ <li>•
<!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
querying stored in preferences
</li>
- <li>
+ <li>•
<!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
search results
</li>
- <li>
+ <li>•
<!-- JAL-1977-->Tooltips shown on database chooser
</li>
- <li>
+ <li>•
<!-- JAL-391 -->Reverse complement function in calculate
menu for nucleotide sequences
</li>
- <li>
+ <li>•
<!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
and feature counts preserves alignment ordering (and
debugged for complex feature sets).
</li>
- <li>
+ <li>•
<!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
viewing structures with Jalview 2.10
</li>
- <li>
+ <li>•
<!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
genome, transcript CCDS and gene ids via the Ensembl and
Ensembl Genomes REST API
</li>
- <li>
+ <li>•
<!-- JAL-2049 -->Protein sequence variant annotation
computed for 'sequence_variant' annotation on CDS regions
(Ensembl)
</li>
- <li>
+ <li>•
<!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
sequences
</li>
- <li>
+ <li>•
<!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
Ref Fetcher fails to match, or otherwise updates sequence
data from external database records.
</li>
- <li>
+ <li>•
<!-- JAL-2154 -->Revised Jalview Project format for
efficient recovery of sequence coding and alignment
annotation relationships.
</li>
</ul> <!-- <em>Applet</em>
<ul>
- <li>
+ <li>•
-- JAL---
</li>
</ul> --></td>
<div align="left">
<em>General</em>
<ul>
- <li>
+ <li>•
<!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
menu on OSX
</li>
- <li>
+ <li>•
<!-- JAL-2018-->Export features in Jalview format (again)
includes graduated colourschemes
</li>
- <li>
+ <li>•
<!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
working with big alignments and lots of hidden columns
</li>
- <li>
+ <li>•
<!-- JAL-2053-->Hidden column markers not always rendered
at right of alignment window
</li>
- <li>
+ <li>•
<!-- JAL-2067 -->Tidied up links in help file table of
contents
</li>
- <li>
+ <li>•
<!-- JAL-2072 -->Feature based tree calculation not shown
for DNA alignments
</li>
- <li>
+ <li>•
<!-- JAL-2075 -->Hidden columns ignored during feature
based tree calculation
</li>
- <li>
+ <li>•
<!-- JAL-2065 -->Alignment view stops updating when show
unconserved enabled for group on alignment
</li>
- <li>
+ <li>•
<!-- JAL-2086 -->Cannot insert gaps into sequence when
set as reference
</li>
- <li>
+ <li>•
<!-- JAL-2146 -->Alignment column in status incorrectly
shown as "Sequence position" when mousing over
annotation
</li>
- <li>
+ <li>•
<!-- JAL-2099 -->Incorrect column numbers in ruler when
hidden columns present
</li>
- <li>
+ <li>•
<!-- JAL-1577 -->Colour by RNA Helices not enabled when
user created annotation added to alignment
</li>
- <li>
+ <li>•
<!-- JAL-1841 -->RNA Structure consensus only computed for
'()' base pair annotation
</li>
- <li>
+ <li>•
<!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
in zero scores for all base pairs in RNA Structure
Consensus
</li>
- <li>
+ <li>•
<!-- JAL-2174-->Extend selection with columns containing
feature not working
</li>
- <li>
+ <li>•
<!-- JAL-2275 -->Pfam format writer puts extra space at
beginning of sequence
</li>
- <li>
+ <li>•
<!-- JAL-1827 -->Incomplete sequence extracted from pdb
entry 3a6s
</li>
- <li>
+ <li>•
<!-- JAL-2238 -->Cannot create groups on an alignment from
from a tree when t-coffee scores are shown
</li>
- <li>
+ <li>•
<!-- JAL-1836,1967 -->Cannot import and view PDB
structures with chains containing negative resnums (4q4h)
</li>
- <li>
+ <li>•
<!-- JAL-1998 -->ArithmeticExceptions raised when parsing
some structures
</li>
- <li>
+ <li>•
<!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
to Clustal, PIR and PileUp output
</li>
- <li>
+ <li>•
<!-- JAL-2008 -->Reordering sequence features that are
not visible causes alignment window to repaint
</li>
- <li>
+ <li>•
<!-- JAL-2006 -->Threshold sliders don't work in
graduated colour and colour by annotation row for e-value
scores associated with features and annotation rows
</li>
- <li>
+ <li>•
<!-- JAL-1797 -->amino acid physicochemical conservation
calculation should be case independent
</li>
- <li>
+ <li>•
<!-- JAL-2173 -->Remove annotation also updates hidden
columns
</li>
- <li>
+ <li>•
<!-- JAL-2234 -->FER1_ARATH and FER2_ARATH mislabelled in
example file (uniref50.fa, feredoxin.fa, unaligned.fa,
exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar)
</li>
- <li>
+ <li>•
<!-- JAL-2065 -->Null pointer exceptions and redraw
problems when reference sequence defined and 'show
non-conserved' enabled
</li>
- <li>
+ <li>•
<!-- JAL-1306 -->Quality and Conservation are now shown on
load even when Consensus calculation is disabled
</li>
- <li>
+ <li>•
<!-- JAL-1932 -->Remove right on penultimate column of
alignment does nothing
</li>
</ul>
<em>Application</em>
<ul>
- <li>
+ <li>•
<!-- JAL-1552-->URLs and links can't be imported by
drag'n'drop on OSX when launched via webstart (note - not
yet fixed for El Capitan)
</li>
- <li>
+ <li>•
<!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
output when running on non-gb/us i18n platforms
</li>
- <li>
+ <li>•
<!-- JAL-1944 -->Error thrown when exporting a view with
hidden sequences as flat-file alignment
</li>
- <li>
+ <li>•
<!-- JAL-2030-->InstallAnywhere distribution fails when
launching Chimera
</li>
- <li>
+ <li>•
<!-- JAL-2080-->Jalview very slow to launch via webstart
(also hotfix for 2.9.0b2)
</li>
- <li>
+ <li>•
<!-- JAL-2085 -->Cannot save project when view has a
reference sequence defined
</li>
- <li>
+ <li>•
<!-- JAL-1011 -->Columns are suddenly selected in other
alignments and views when revealing hidden columns
</li>
- <li>
+ <li>•
<!-- JAL-1989 -->Hide columns not mirrored in complement
view in a cDNA/Protein splitframe
</li>
- <li>
+ <li>•
<!-- JAL-1369 -->Cannot save/restore representative
sequence from project when only one sequence is
represented
</li>
- <li>
+ <li>•
<!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
in Structure Chooser
</li>
- <li>
+ <li>•
<!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
structure consensus didn't refresh annotation panel
</li>
- <li>
+ <li>•
<!-- JAL-1962 -->View mapping in structure view shows
mappings between sequence and all chains in a PDB file
</li>
- <li>
+ <li>•
<!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
dialogs format columns correctly, don't display array
data, sort columns according to type
</li>
- <li>
+ <li>•
<!-- JAL-1975 -->Export complete shown after destination
file chooser is cancelled during an image export
</li>
- <li>
+ <li>•
<!-- JAL-2025 -->Error when querying PDB Service with
sequence name containing special characters
</li>
- <li>
+ <li>•
<!-- JAL-2024 -->Manual PDB structure querying should be
case insensitive
</li>
- <li>
+ <li>•
<!-- JAL-2104 -->Large tooltips with broken HTML
formatting don't wrap
</li>
- <li>
+ <li>•
<!-- JAL-1128 -->Figures exported from wrapped view are
truncated so L looks like I in consensus annotation
</li>
- <li>
+ <li>•
<!-- JAL-2003 -->Export features should only export the
currently displayed features for the current selection or
view
</li>
- <li>
+ <li>•
<!-- JAL-2036 -->Enable 'Get Cross-References' in menu
after fetching cross-references, and restoring from project
</li>
- <li>
+ <li>•
<!-- JAL-2032 -->Mouseover of a copy of a sequence is not
followed in the structure viewer
</li>
- <li>
+ <li>•
<!-- JAL-2163 -->Titles for individual alignments in
splitframe not restored from project
</li>
- <li>
+ <li>•
<!-- JAL-2145 -->missing autocalculated annotation at
trailing end of protein alignment in transcript/product
splitview when pad-gaps not enabled by default
</li>
- <li>
+ <li>•
<!-- JAL-1797 -->amino acid physicochemical conservation
is case dependent
</li>
- <li>
+ <li>•
<!-- JAL-1448 -->RSS reader doesn't stay hidden after last
article has been read (reopened issue due to
internationalisation problems)
</li>
- <li>
+ <li>•
<!-- JAL-1960 -->Only offer PDB structures in structure
viewer based on sequence name, PDB and UniProt
cross-references
</li>
- <li>
+ <li>•
<!-- JAL-1976 -->No progress bar shown during export of
alignment as HTML
</li>
- <li>
+ <li>•
<!-- JAL-2213 -->Structures not always superimposed after
multiple structures are shown for one or more sequences.
</li>
- <li>
+ <li>•
<!-- JAL-1370 -->Reference sequence characters should not
be replaced with '.' when 'Show unconserved' format option
is enabled.
</li>
- <li>
+ <li>•
<!-- JAL-1823 -->Cannot specify chain code when entering
specific PDB id for sequence
</li>
- <li>
+ <li>•
<!-- JAL-1944 -->File->Export->.. as doesn't work when
'Export hidden sequences' is enabled, but 'export hidden
columns' is disabled.
</li>
- <li>
+ <li>•
<!--JAL-2026-->Best Quality option in structure chooser
selects lowest rather than highest resolution structures
for each sequence
</li>
- <li>
+ <li>•
<!-- JAL-1887 -->Incorrect start and end reported for PDB
to sequence mapping in 'View Mappings' report
</li>
- <li>
+ <li>•
<!-- JAL-2284 -->Unable to read old Jalview projects that
contain non-XML data added after Jalvew wrote project.
</li>
- <li><!-- JAL-2118 -->Newly created annotation row reorders
+ <li>• <!-- JAL-2118 -->Newly created annotation row reorders
after clicking on it to create new annotation for a
column.
</li>
</ul>
<em>Applet</em>
<ul>
- <li>
+ <li>•
<!-- JAL-2151 -->Incorrect columns are selected when
hidden columns present before start of sequence
</li>
- <li>
+ <li>•
<!-- JAL-1986 -->Missing dependencies on applet pages
(JSON jars)
</li>
- <li>
+ <li>•
<!-- JAL-1947 -->Overview pixel size changes when
sequences are hidden in applet
</li>
- <li>
+ <li>•
<!-- JAL-1996 -->Updated instructions for applet
deployment on examples pages.
</li>
</td>
<td><em>General</em>
<ul>
- <li>Time stamps for signed Jalview application and applet
+ <li>• Time stamps for signed Jalview application and applet
jars</li>
</ul></td>
<td>
<div align="left">
<em>Application</em>
<ul>
- <li>Duplicate group consensus and conservation rows
+ <li>• Duplicate group consensus and conservation rows
shown when tree is partitioned</li>
- <li>Erratic behaviour when tree partitions made with
+ <li>• Erratic behaviour when tree partitions made with
multiple cDNA/Protein split views</li>
</ul>
</div>
</td>
<td><em>General</em>
<ul>
- <li>Updated Spanish translations of localized text for
+ <li>• Updated Spanish translations of localized text for
2.9</li>
</ul> <em>Application</em>
<ul>
- <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
- <li>Signed OSX InstallAnywhere installer<br></li>
- <li>Support for per-sequence based annotations in BioJSON</li>
+ <!-- <li>• cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
+ <li>• Signed OSX InstallAnywhere installer<br></li>
+ <li>• Support for per-sequence based annotations in BioJSON</li>
</ul> <em>Applet</em>
<ul>
- <li>Split frame example added to applet examples page</li>
+ <li>• Split frame example added to applet examples page</li>
</ul><em>Build and Deployment</em>
<ul>
- <li><!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
+ <li>• <!-- JAL-1888 -->New ant target for running Jalview's test suite</li>
</ul></td>
<td>
<div align="left">
<em>General</em>
<ul>
- <li>Mapping of cDNA to protein in split frames
+ <li>• Mapping of cDNA to protein in split frames
incorrect when sequence start > 1</li>
- <li>Broken images in filter column by annotation dialog
+ <li>• Broken images in filter column by annotation dialog
documentation</li>
- <li>Feature colours not parsed from features file</li>
- <li>Exceptions and incomplete link URLs recovered when
+ <li>• Feature colours not parsed from features file</li>
+ <li>• Exceptions and incomplete link URLs recovered when
loading a features file containing HTML tags in feature
description</li>
</ul>
<em>Application</em>
<ul>
- <li>Annotations corrupted after BioJS export and
+ <li>• Annotations corrupted after BioJS export and
reimport</li>
- <li>Incorrect sequence limits after Fetch DB References
+ <li>• Incorrect sequence limits after Fetch DB References
with 'trim retrieved sequences'</li>
- <li>Incorrect warning about deleting all data when
+ <li>• Incorrect warning about deleting all data when
deleting selected columns</li>
- <li>Patch to build system for shipping properly signed
+ <li>• Patch to build system for shipping properly signed
JNLP templates for webstart launch</li>
- <li>EMBL-PDBe fetcher/viewer dialogs do not offer
+ <li>• EMBL-PDBe fetcher/viewer dialogs do not offer
unreleased structures for download or viewing</li>
- <li>Tab/space/return keystroke operation of EMBL-PDBe
+ <li>• Tab/space/return keystroke operation of EMBL-PDBe
fetcher/viewer dialogs works correctly</li>
- <li>Disabled 'minimise' button on Jalview windows
+ <li>• Disabled 'minimise' button on Jalview windows
running on OSX to workaround redraw hang bug</li>
- <li>Split cDNA/Protein view position and geometry not
+ <li>• Split cDNA/Protein view position and geometry not
recovered from jalview project</li>
- <li>Initial enabled/disabled state of annotation menu
+ <li>• Initial enabled/disabled state of annotation menu
sorter 'show autocalculated first/last' corresponds to
alignment view</li>
- <li>Restoring of Clustal, RNA Helices and T-Coffee
+ <li>• Restoring of Clustal, RNA Helices and T-Coffee
color schemes from BioJSON</li>
</ul>
<em>Applet</em>
<ul>
- <li>Reorder sequences mirrored in cDNA/Protein split
+ <li>• Reorder sequences mirrored in cDNA/Protein split
frame</li>
- <li>Applet with Jmol examples not loading correctly</li>
+ <li>• Applet with Jmol examples not loading correctly</li>
</ul>
</div>
</td>
</div></td>
<td><em>General</em>
<ul>
- <li>Linked visualisation and analysis of DNA and Protein
+ <li>• Linked visualisation and analysis of DNA and Protein
alignments:
<ul>
- <li>Translated cDNA alignments shown as split protein
+ <li>• Translated cDNA alignments shown as split protein
and DNA alignment views</li>
- <li>Codon consensus annotation for linked protein and
+ <li>• Codon consensus annotation for linked protein and
cDNA alignment views</li>
- <li>Link cDNA or Protein product sequences by loading
+ <li>• Link cDNA or Protein product sequences by loading
them onto Protein or cDNA alignments</li>
- <li>Reconstruct linked cDNA alignment from aligned
+ <li>• Reconstruct linked cDNA alignment from aligned
protein sequences</li>
</ul>
</li>
- <li>Jmol integration updated to Jmol v14.2.14</li>
- <li>Import and export of Jalview alignment views as <a
+ <li>• Jmol integration updated to Jmol v14.2.14</li>
+ <li>• Import and export of Jalview alignment views as <a
href="features/bioJsonFormat.html">BioJSON</a></li>
- <li>New alignment annotation file statements for
+ <li>• New alignment annotation file statements for
reference sequences and marking hidden columns</li>
- <li>Reference sequence based alignment shading to
+ <li>• Reference sequence based alignment shading to
highlight variation</li>
- <li>Select or hide columns according to alignment
+ <li>• Select or hide columns according to alignment
annotation</li>
- <li>Find option for locating sequences by description</li>
- <li>Conserved physicochemical properties shown in amino
+ <li>• Find option for locating sequences by description</li>
+ <li>• Conserved physicochemical properties shown in amino
acid conservation row</li>
- <li>Alignments can be sorted by number of RNA helices</li>
+ <li>• Alignments can be sorted by number of RNA helices</li>
</ul> <em>Application</em>
<ul>
- <li>New cDNA/Protein analysis capabilities
+ <li>• New cDNA/Protein analysis capabilities
<ul>
- <li>Get Cross-References should open a Split Frame
+ <li>• Get Cross-References should open a Split Frame
view with cDNA/Protein</li>
- <li>Detect when nucleotide sequences and protein
+ <li>• Detect when nucleotide sequences and protein
sequences are placed in the same alignment</li>
- <li>Split cDNA/Protein views are saved in Jalview
+ <li>• Split cDNA/Protein views are saved in Jalview
projects</li>
</ul>
</li>
- <li>Use REST API to talk to Chimera</li>
- <li>Selected regions in Chimera are highlighted in linked
+ <li>• Use REST API to talk to Chimera</li>
+ <li>• Selected regions in Chimera are highlighted in linked
Jalview windows</li>
- <li>VARNA RNA viewer updated to v3.93</li>
- <li>VARNA views are saved in Jalview Projects</li>
- <li>Pseudoknots displayed as Jalview RNA annotation can
+ <li>• VARNA RNA viewer updated to v3.93</li>
+ <li>• VARNA views are saved in Jalview Projects</li>
+ <li>• Pseudoknots displayed as Jalview RNA annotation can
be shown in VARNA</li>
- <li>Make groups for selection uses marked columns as well
+ <li>• Make groups for selection uses marked columns as well
as the active selected region</li>
- <li>Calculate UPGMA and NJ trees using sequence feature
+ <li>• Calculate UPGMA and NJ trees using sequence feature
similarity</li>
- <li>New Export options
+ <li>• New Export options
<ul>
- <li>New Export Settings dialog to control hidden
+ <li>• New Export Settings dialog to control hidden
region export in flat file generation</li>
- <li>Export alignment views for display with the <a
+ <li>• Export alignment views for display with the <a
href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
- <li>Export scrollable SVG in HTML page</li>
- <li>Optional embedding of BioJSON data when exporting
+ <li>• Export scrollable SVG in HTML page</li>
+ <li>• Optional embedding of BioJSON data when exporting
alignment figures to HTML</li>
</li>
- <li>3D structure retrieval and display
+ <li>• 3D structure retrieval and display
<ul>
- <li>Free text and structured queries with the PDBe
+ <li>• Free text and structured queries with the PDBe
Search API</li>
- <li>PDBe Search API based discovery and selection of
+ <li>• PDBe Search API based discovery and selection of
PDB structures for a sequence set</li>
</ul>
</li>
- <li>JPred4 employed for protein secondary structure
+ <li>• JPred4 employed for protein secondary structure
predictions</li>
- <li>Hide Insertions menu option to hide unaligned columns
+ <li>• Hide Insertions menu option to hide unaligned columns
for one or a group of sequences</li>
- <li>Automatically hide insertions in alignments imported
+ <li>• Automatically hide insertions in alignments imported
from the JPred4 web server</li>
- <li>(Nearly) Native 'Quaqua' dialogs for browsing file
+ <li>• (Nearly) Native 'Quaqua' dialogs for browsing file
system on OSX<br />LGPL libraries courtesy of <a
href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
</li>
- <li>changed 'View nucleotide structure' submenu to 'View
+ <li>• changed 'View nucleotide structure' submenu to 'View
VARNA 2D Structure'</li>
- <li>change "View protein structure" menu option to "3D
+ <li>• change "View protein structure" menu option to "3D
Structure ..."</li>
</ul> <em>Applet</em>
<ul>
- <li>New layout for applet example pages</li>
- <li>New parameters to enable SplitFrame view
+ <li>• New layout for applet example pages</li>
+ <li>• New parameters to enable SplitFrame view
(file2,enableSplitFrame, scaleProteinAsCdna)</li>
- <li>New example demonstrating linked viewing of cDNA and
+ <li>• New example demonstrating linked viewing of cDNA and
Protein alignments</li>
</ul> <em>Development and deployment</em>
<ul>
- <li>Java 1.7 minimum requirement for Jalview 2.9</li>
- <li>Include installation type and git revision in build
+ <li>• Java 1.7 minimum requirement for Jalview 2.9</li>
+ <li>• Include installation type and git revision in build
properties and console log output</li>
- <li>Jalview Github organisation, and new github site for
+ <li>• Jalview Github organisation, and new github site for
storing BioJsMSA Templates</li>
- <li>Jalview's unit tests now managed with TestNG</li>
+ <li>• Jalview's unit tests now managed with TestNG</li>
</ul></td>
<td>
<!-- <em>General</em>
<ul>
</ul> --> <!-- issues resolved --> <em>Application</em>
<ul>
- <li>Escape should close any open find dialogs</li>
- <li>Typo in select-by-features status report</li>
- <li>Consensus RNA secondary secondary structure
+ <li>• Escape should close any open find dialogs</li>
+ <li>• Typo in select-by-features status report</li>
+ <li>• Consensus RNA secondary secondary structure
predictions are not highlighted in amber</li>
- <li>Missing gap character in v2.7 example file means
+ <li>• Missing gap character in v2.7 example file means
alignment appears unaligned when pad-gaps is not enabled</li>
- <li>First switch to RNA Helices colouring doesn't colour
+ <li>• First switch to RNA Helices colouring doesn't colour
associated structure views</li>
- <li>ID width preference option is greyed out when auto
+ <li>• ID width preference option is greyed out when auto
width checkbox not enabled</li>
- <li>Stopped a warning dialog from being shown when
+ <li>• Stopped a warning dialog from being shown when
creating user defined colours</li>
- <li>'View Mapping' in structure viewer shows sequence
+ <li>• 'View Mapping' in structure viewer shows sequence
mappings for just that viewer's sequences</li>
- <li>Workaround for superposing PDB files containing
+ <li>• Workaround for superposing PDB files containing
multiple models in Chimera</li>
- <li>Report sequence position in status bar when hovering
+ <li>• Report sequence position in status bar when hovering
over Jmol structure</li>
- <li>Cannot output gaps as '.' symbols with Selection ->
+ <li>• Cannot output gaps as '.' symbols with Selection ->
output to text box</li>
- <li>Flat file exports of alignments with hidden columns
+ <li>• Flat file exports of alignments with hidden columns
have incorrect sequence start/end</li>
- <li>'Aligning' a second chain to a Chimera structure from
+ <li>• 'Aligning' a second chain to a Chimera structure from
Jalview fails</li>
- <li>Colour schemes applied to structure viewers don't
+ <li>• Colour schemes applied to structure viewers don't
work for nucleotide</li>
- <li>Loading/cut'n'pasting an empty or invalid file leads
+ <li>• Loading/cut'n'pasting an empty or invalid file leads
to a grey/invisible alignment window</li>
- <li>Exported Jpred annotation from a sequence region
+ <li>• Exported Jpred annotation from a sequence region
imports to different position</li>
- <li>Space at beginning of sequence feature tooltips shown
+ <li>• Space at beginning of sequence feature tooltips shown
on some platforms</li>
- <li>Chimera viewer 'View | Show Chain' menu is not
+ <li>• Chimera viewer 'View | Show Chain' menu is not
populated</li>
- <li>'New View' fails with a Null Pointer Exception in
+ <li>• 'New View' fails with a Null Pointer Exception in
console if Chimera has been opened</li>
- <li>Mouseover to Chimera not working</li>
- <li>Miscellaneous ENA XML feature qualifiers not
+ <li>• Mouseover to Chimera not working</li>
+ <li>• Miscellaneous ENA XML feature qualifiers not
retrieved</li>
- <li>NPE in annotation renderer after 'Extract Scores'</li>
- <li>If two structures in one Chimera window, mouseover of
+ <li>• NPE in annotation renderer after 'Extract Scores'</li>
+ <li>• If two structures in one Chimera window, mouseover of
either sequence shows on first structure</li>
- <li>'Show annotations' options should not make
+ <li>• 'Show annotations' options should not make
non-positional annotations visible</li>
- <li>Subsequence secondary structure annotation not shown
+ <li>• Subsequence secondary structure annotation not shown
in right place after 'view flanking regions'</li>
- <li>File Save As type unset when current file format is
+ <li>• File Save As type unset when current file format is
unknown</li>
- <li>Save as '.jar' option removed for saving Jalview
+ <li>• Save as '.jar' option removed for saving Jalview
projects</li>
- <li>Colour by Sequence colouring in Chimera more
+ <li>• Colour by Sequence colouring in Chimera more
responsive</li>
- <li>Cannot 'add reference annotation' for a sequence in
+ <li>• Cannot 'add reference annotation' for a sequence in
several views on same alignment</li>
- <li>Cannot show linked products for EMBL / ENA records</li>
- <li>Jalview's tooltip wraps long texts containing no
+ <li>• Cannot show linked products for EMBL / ENA records</li>
+ <li>• Jalview's tooltip wraps long texts containing no
spaces</li>
</ul> <em>Applet</em>
<ul>
- <li>Jmol to JalviewLite mouseover/link not working</li>
- <li>JalviewLite can't import sequences with ID
+ <li>• Jmol to JalviewLite mouseover/link not working</li>
+ <li>• JalviewLite can't import sequences with ID
descriptions containing angle brackets</li>
</ul> <em>General</em>
<ul>
- <li>Cannot export and reimport RNA secondary structure
+ <li>• Cannot export and reimport RNA secondary structure
via jalview annotation file</li>
- <li>Random helix colour palette for colour by annotation
+ <li>• Random helix colour palette for colour by annotation
with RNA secondary structure</li>
- <li>Mouseover to cDNA from STOP residue in protein
+ <li>• Mouseover to cDNA from STOP residue in protein
translation doesn't work.</li>
- <li>hints when using the select by annotation dialog box</li>
- <li>Jmol alignment incorrect if PDB file has alternate CA
+ <li>• hints when using the select by annotation dialog box</li>
+ <li>• Jmol alignment incorrect if PDB file has alternate CA
positions</li>
- <li>FontChooser message dialog appears to hang after
+ <li>• FontChooser message dialog appears to hang after
choosing 1pt font</li>
- <li>Peptide secondary structure incorrectly imported from
+ <li>• Peptide secondary structure incorrectly imported from
annotation file when annotation display text includes 'e' or
'h'</li>
- <li>Cannot set colour of new feature type whilst creating
+ <li>• Cannot set colour of new feature type whilst creating
new feature</li>
- <li>cDNA translation alignment should not be sequence
+ <li>• cDNA translation alignment should not be sequence
order dependent</li>
- <li>'Show unconserved' doesn't work for lower case
+ <li>• 'Show unconserved' doesn't work for lower case
sequences</li>
- <li>Nucleotide ambiguity codes involving R not recognised</li>
+ <li>• Nucleotide ambiguity codes involving R not recognised</li>
</ul> <em>Deployment and Documentation</em>
<ul>
- <li>Applet example pages appear different to the rest of
+ <li>• Applet example pages appear different to the rest of
www.jalview.org</li>
</ul> <em>Application Known issues</em>
<ul>
- <li>Incomplete sequence extracted from PDB entry 3a6s</li>
- <li>Misleading message appears after trying to delete
+ <li>• Incomplete sequence extracted from PDB entry 3a6s</li>
+ <li>• Misleading message appears after trying to delete
solid column.</li>
- <li>Jalview icon not shown in dock after InstallAnywhere
+ <li>• Jalview icon not shown in dock after InstallAnywhere
version launches</li>
- <li>Fetching EMBL reference for an RNA sequence results
+ <li>• Fetching EMBL reference for an RNA sequence results
fails with a sequence mismatch</li>
- <li>Corrupted or unreadable alignment display when
+ <li>• Corrupted or unreadable alignment display when
scrolling alignment to right</li>
- <li>ArrayIndexOutOfBoundsException thrown when remove
+ <li>• ArrayIndexOutOfBoundsException thrown when remove
empty columns called on alignment with ragged gapped ends</li>
- <li>auto calculated alignment annotation rows do not get
+ <li>• auto calculated alignment annotation rows do not get
placed above or below non-autocalculated rows</li>
- <li>Jalview dekstop becomes sluggish at full screen in
+ <li>• Jalview dekstop becomes sluggish at full screen in
ultra-high resolution</li>
- <li>Cannot disable consensus calculation independently of
+ <li>• Cannot disable consensus calculation independently of
quality and conservation</li>
- <li>Mouseover highlighting between cDNA and protein can
+ <li>• Mouseover highlighting between cDNA and protein can
become sluggish with more than one splitframe shown</li>
</ul> <em>Applet Known Issues</em>
<ul>
- <li>Core PDB parsing code requires Jmol</li>
- <li>Sequence canvas panel goes white when alignment
+ <li>• Core PDB parsing code requires Jmol</li>
+ <li>• Sequence canvas panel goes white when alignment
window is being resized</li>
</ul>
</div></td>
<td><em>General</em>
<ul>
- <li>Updated Java code signing certificate donated by
+ <li>• Updated Java code signing certificate donated by
Certum.PL.</li>
- <li>Features and annotation preserved when performing
+ <li>• Features and annotation preserved when performing
pairwise alignment</li>
- <li>RNA pseudoknot annotation can be
+ <li>• RNA pseudoknot annotation can be
imported/exported/displayed</li>
- <li>'colour by annotation' can colour by RNA and
+ <li>• 'colour by annotation' can colour by RNA and
protein secondary structure</li>
- <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
+ <li>• Warn user if 'Find' regular expression is invalid (<em>mentioned
post-hoc with 2.9 release</em>)
</li>
</ul> <em>Application</em>
<ul>
- <li>Extract and display secondary structure for sequences
+ <li>• Extract and display secondary structure for sequences
with 3D structures</li>
- <li>Support for parsing RNAML</li>
- <li>Annotations menu for layout
+ <li>• Support for parsing RNAML</li>
+ <li>• Annotations menu for layout
<ul>
- <li>sort sequence annotation rows by alignment</li>
- <li>place sequence annotation above/below alignment
+ <li>• sort sequence annotation rows by alignment</li>
+ <li>• place sequence annotation above/below alignment
annotation</li>
</ul>
- <li>Output in Stockholm format</li>
- <li>Internationalisation: improved Spanish (es)
+ <li>• Output in Stockholm format</li>
+ <li>• Internationalisation: improved Spanish (es)
translation</li>
- <li>Structure viewer preferences tab</li>
- <li>Disorder and Secondary Structure annotation tracks
+ <li>• Structure viewer preferences tab</li>
+ <li>• Disorder and Secondary Structure annotation tracks
shared between alignments</li>
- <li>UCSF Chimera launch and linked highlighting from
+ <li>• UCSF Chimera launch and linked highlighting from
Jalview</li>
- <li>Show/hide all sequence associated annotation rows for
+ <li>• Show/hide all sequence associated annotation rows for
all or current selection</li>
- <li>disorder and secondary structure predictions
+ <li>• disorder and secondary structure predictions
available as dataset annotation</li>
- <li>Per-sequence rna helices colouring</li>
+ <li>• Per-sequence rna helices colouring</li>
- <li>Sequence database accessions imported when fetching
+ <li>• Sequence database accessions imported when fetching
alignments from Rfam</li>
- <li>update VARNA version to 3.91</li>
+ <li>• update VARNA version to 3.91</li>
- <li>New groovy scripts for exporting aligned positions,
+ <li>• New groovy scripts for exporting aligned positions,
conservation values, and calculating sum of pairs scores.</li>
- <li>Command line argument to set default JABAWS server</li>
- <li>include installation type in build properties and
+ <li>• Command line argument to set default JABAWS server</li>
+ <li>• include installation type in build properties and
console log output</li>
- <li>Updated Jalview project format to preserve dataset
+ <li>• Updated Jalview project format to preserve dataset
annotation</li>
</ul></td>
<td>
<!-- issues resolved --> <em>Application</em>
<ul>
- <li>Distinguish alignment and sequence associated RNA
+ <li>• Distinguish alignment and sequence associated RNA
structure in structure->view->VARNA</li>
- <li>Raise dialog box if user deletes all sequences in an
+ <li>• Raise dialog box if user deletes all sequences in an
alignment</li>
- <li>Pressing F1 results in documentation opening twice</li>
- <li>Sequence feature tooltip is wrapped</li>
- <li>Double click on sequence associated annotation
+ <li>• Pressing F1 results in documentation opening twice</li>
+ <li>• Sequence feature tooltip is wrapped</li>
+ <li>• Double click on sequence associated annotation
selects only first column</li>
- <li>Redundancy removal doesn't result in unlinked
+ <li>• Redundancy removal doesn't result in unlinked
leaves shown in tree</li>
- <li>Undos after several redundancy removals don't undo
+ <li>• Undos after several redundancy removals don't undo
properly</li>
- <li>Hide sequence doesn't hide associated annotation</li>
- <li>User defined colours dialog box too big to fit on
+ <li>• Hide sequence doesn't hide associated annotation</li>
+ <li>• User defined colours dialog box too big to fit on
screen and buttons not visible</li>
- <li>author list isn't updated if already written to
+ <li>• author list isn't updated if already written to
Jalview properties</li>
- <li>Popup menu won't open after retrieving sequence
+ <li>• Popup menu won't open after retrieving sequence
from database</li>
- <li>File open window for associate PDB doesn't open</li>
- <li>Left-then-right click on a sequence id opens a
+ <li>• File open window for associate PDB doesn't open</li>
+ <li>• Left-then-right click on a sequence id opens a
browser search window</li>
- <li>Cannot open sequence feature shading/sort popup menu
+ <li>• Cannot open sequence feature shading/sort popup menu
in feature settings dialog</li>
- <li>better tooltip placement for some areas of Jalview
+ <li>• better tooltip placement for some areas of Jalview
desktop</li>
- <li>Allow addition of JABAWS Server which doesn't
+ <li>• Allow addition of JABAWS Server which doesn't
pass validation</li>
- <li>Web services parameters dialog box is too large to
+ <li>• Web services parameters dialog box is too large to
fit on screen</li>
- <li>Muscle nucleotide alignment preset obscured by
+ <li>• Muscle nucleotide alignment preset obscured by
tooltip</li>
- <li>JABAWS preset submenus don't contain newly
+ <li>• JABAWS preset submenus don't contain newly
defined user preset</li>
- <li>MSA web services warns user if they were launched
+ <li>• MSA web services warns user if they were launched
with invalid input</li>
- <li>Jalview cannot contact DAS Registy when running on
+ <li>• Jalview cannot contact DAS Registy when running on
Java 8</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
'Superpose with' submenu not shown when new view
created
<ul>
</ul>--> <em>Deployment and Documentation</em>
<ul>
- <li>2G and 1G options in launchApp have no effect on
+ <li>• 2G and 1G options in launchApp have no effect on
memory allocation</li>
- <li>launchApp service doesn't automatically open
+ <li>• launchApp service doesn't automatically open
www.jalview.org/examples/exampleFile.jar if no file is given</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
InstallAnywhere reports cannot find valid JVM when Java
1.7_055 is available
</li>
</ul> <em>Application Known issues</em>
<ul>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
corrupted or unreadable alignment display when scrolling
alignment to right
</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
retrieval fails but progress bar continues for DAS retrieval
with large number of ID
</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
flatfile output of visible region has incorrect sequence
start/end
</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
rna structure consensus doesn't update when secondary
structure tracks are rearranged
</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
invalid rna structure positional highlighting does not
highlight position of invalid base pairs
</li>
- <li>
+ <li>•
<!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
out of memory errors are not raised when saving Jalview
project from alignment window file menu
</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
Switching to RNA Helices colouring doesn't propagate to
structures
</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
colour by RNA Helices not enabled when user created
annotation added to alignment
</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
Jalview icon not shown on dock in Mountain Lion/Webstart
</li>
</ul> <em>Applet Known Issues</em>
<ul>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
</li>
- <li>
+ <li>•
<!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
Jalview and Jmol example not compatible with IE9
</li>
- <li>Sort by annotation score doesn't reverse order
+ <li>• Sort by annotation score doesn't reverse order
when selected</li>
</ul>
</td>
<!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
<em>General</em>
<ul>
- <li>Internationalisation of user interface (usually
+ <li>• Internationalisation of user interface (usually
called i18n support) and translation for Spanish locale</li>
- <li>Define/Undefine group on current selection with
+ <li>• Define/Undefine group on current selection with
Ctrl-G/Shift Ctrl-G</li>
- <li>Improved group creation/removal options in
+ <li>• Improved group creation/removal options in
alignment/sequence Popup menu</li>
- <li>Sensible precision for symbol distribution
+ <li>• Sensible precision for symbol distribution
percentages shown in logo tooltip.</li>
- <li>Annotation panel height set according to amount of
+ <li>• Annotation panel height set according to amount of
annotation when alignment first opened</li>
</ul> <em>Application</em>
<ul>
- <li>Interactive consensus RNA secondary structure
+ <li>• Interactive consensus RNA secondary structure
prediction VIENNA RNAAliFold JABA 2.1 service</li>
- <li>Select columns containing particular features from
+ <li>• Select columns containing particular features from
Feature Settings dialog</li>
- <li>View all 'representative' PDB structures for selected
+ <li>• View all 'representative' PDB structures for selected
sequences</li>
- <li>Update Jalview project format:
+ <li>• Update Jalview project format:
<ul>
- <li>New file extension for Jalview projects '.jvp'</li>
- <li>Preserve sequence and annotation dataset (to
+ <li>• New file extension for Jalview projects '.jvp'</li>
+ <li>• Preserve sequence and annotation dataset (to
store secondary structure annotation,etc)</li>
- <li>Per group and alignment annotation and RNA helix
+ <li>• Per group and alignment annotation and RNA helix
colouring</li>
</ul>
</li>
- <li>New similarity measures for PCA and Tree calculation
+ <li>• New similarity measures for PCA and Tree calculation
(PAM250)</li>
- <li>Experimental support for retrieval and viewing of
+ <li>• Experimental support for retrieval and viewing of
flanking regions for an alignment</li>
</ul>
</td>
<td>
<!-- issues resolved --> <em>Application</em>
<ul>
- <li>logo keeps spinning and status remains at queued or
+ <li>• logo keeps spinning and status remains at queued or
running after job is cancelled</li>
- <li>cannot export features from alignments imported from
+ <li>• cannot export features from alignments imported from
Jalview/VAMSAS projects</li>
- <li>Buggy slider for web service parameters that take
+ <li>• Buggy slider for web service parameters that take
float values</li>
- <li>Newly created RNA secondary structure line doesn't
+ <li>• Newly created RNA secondary structure line doesn't
have 'display all symbols' flag set</li>
- <li>T-COFFEE alignment score shading scheme and other
+ <li>• T-COFFEE alignment score shading scheme and other
annotation shading not saved in Jalview project</li>
- <li>Local file cannot be loaded in freshly downloaded
+ <li>• Local file cannot be loaded in freshly downloaded
Jalview</li>
- <li>Jalview icon not shown on dock in Mountain
+ <li>• Jalview icon not shown on dock in Mountain
Lion/Webstart</li>
- <li>Load file from desktop file browser fails</li>
- <li>Occasional NPE thrown when calculating large trees</li>
- <li>Cannot reorder or slide sequences after dragging an
+ <li>• Load file from desktop file browser fails</li>
+ <li>• Occasional NPE thrown when calculating large trees</li>
+ <li>• Cannot reorder or slide sequences after dragging an
alignment onto desktop</li>
- <li>Colour by annotation dialog throws NPE after using
+ <li>• Colour by annotation dialog throws NPE after using
'extract scores' function</li>
- <li>Loading/cut'n'pasting an empty file leads to a grey
+ <li>• Loading/cut'n'pasting an empty file leads to a grey
alignment window</li>
- <li>Disorder thresholds rendered incorrectly after
+ <li>• Disorder thresholds rendered incorrectly after
performing IUPred disorder prediction</li>
- <li>Multiple group annotated consensus rows shown when
+ <li>• Multiple group annotated consensus rows shown when
changing 'normalise logo' display setting</li>
- <li>Find shows blank dialog after 'finished searching' if
+ <li>• Find shows blank dialog after 'finished searching' if
nothing matches query</li>
- <li>Null Pointer Exceptions raised when sorting by
+ <li>• Null Pointer Exceptions raised when sorting by
feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
</li>
- <li>Errors in Jmol console when structures in alignment
+ <li>• Errors in Jmol console when structures in alignment
don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
</li>
- <li>Not all working JABAWS services are shown in
+ <li>• Not all working JABAWS services are shown in
Jalview's menu</li>
- <li>JAVAWS version of Jalview fails to launch with
+ <li>• JAVAWS version of Jalview fails to launch with
'invalid literal/length code'</li>
- <li>Annotation/RNA Helix colourschemes cannot be applied
+ <li>• Annotation/RNA Helix colourschemes cannot be applied
to alignment with groups (actually fixed in 2.8.0b1)</li>
- <li>RNA Helices and T-Coffee Scores available as default
+ <li>• RNA Helices and T-Coffee Scores available as default
colourscheme</li>
</ul> <em>Applet</em>
<ul>
- <li>Remove group option is shown even when selection is
+ <li>• Remove group option is shown even when selection is
not a group</li>
- <li>Apply to all groups ticked but colourscheme changes
+ <li>• Apply to all groups ticked but colourscheme changes
don't affect groups</li>
- <li>Documented RNA Helices and T-Coffee Scores as valid
+ <li>• Documented RNA Helices and T-Coffee Scores as valid
colourscheme name</li>
- <li>Annotation labels drawn on sequence IDs when
+ <li>• Annotation labels drawn on sequence IDs when
Annotation panel is not displayed</li>
- <li>Increased font size for dropdown menus on OSX and
+ <li>• Increased font size for dropdown menus on OSX and
embedded windows</li>
</ul> <em>Other</em>
<ul>
- <li>Consensus sequence for alignments/groups with a
+ <li>• Consensus sequence for alignments/groups with a
single sequence were not calculated</li>
- <li>annotation files that contain only groups imported as
+ <li>• annotation files that contain only groups imported as
annotation and junk sequences</li>
- <li>Fasta files with sequences containing '*' incorrectly
+ <li>• Fasta files with sequences containing '*' incorrectly
recognised as PFAM or BLC</li>
- <li>conservation/PID slider apply all groups option
+ <li>• conservation/PID slider apply all groups option
doesn't affect background (2.8.0b1)
- <li></li>
- <li>redundancy highlighting is erratic at 0% and 100%</li>
- <li>Remove gapped columns fails for sequences with ragged
+ <li>• </li>
+ <li>• redundancy highlighting is erratic at 0% and 100%</li>
+ <li>• Remove gapped columns fails for sequences with ragged
trailing gaps</li>
- <li>AMSA annotation row with leading spaces is not
+ <li>• AMSA annotation row with leading spaces is not
registered correctly on import</li>
- <li>Jalview crashes when selecting PCA analysis for
+ <li>• Jalview crashes when selecting PCA analysis for
certain alignments</li>
- <li>Opening the colour by annotation dialog for an
+ <li>• Opening the colour by annotation dialog for an
existing annotation based 'use original colours'
colourscheme loses original colours setting</li>
</ul>
</div></td>
<td>
<ul>
- <li>Trusted certificates for JalviewLite applet and
+ <li>• Trusted certificates for JalviewLite applet and
Jalview Desktop application<br />Certificate was donated by
<a href="https://www.certum.eu">Certum</a> to the Jalview
open source project).
</li>
- <li>Jalview SRS links replaced by UniProt and EBI-search
+ <li>• Jalview SRS links replaced by UniProt and EBI-search
</li>
- <li>Output in Stockholm format</li>
- <li>Allow import of data from gzipped files</li>
- <li>Export/import group and sequence associated line
+ <li>• Output in Stockholm format</li>
+ <li>• Allow import of data from gzipped files</li>
+ <li>• Export/import group and sequence associated line
graph thresholds</li>
- <li>Nucleotide substitution matrix that supports RNA and
+ <li>• Nucleotide substitution matrix that supports RNA and
ambiguity codes</li>
- <li>Allow disorder predictions to be made on the current
+ <li>• Allow disorder predictions to be made on the current
selection (or visible selection) in the same way that JPred
works</li>
- <li>Groovy scripting for headless Jalview operation</li>
+ <li>• Groovy scripting for headless Jalview operation</li>
</ul> <em>Other improvements</em>
<ul>
- <li>Upgrade desktop installer to InstallAnywhere 2013</li>
- <li>COMBINE statement uses current SEQUENCE_REF and
+ <li>• Upgrade desktop installer to InstallAnywhere 2013</li>
+ <li>• COMBINE statement uses current SEQUENCE_REF and
GROUP_REF scope to group annotation rows</li>
- <li>Support '' style escaping of quotes in Newick
+ <li>• Support '' style escaping of quotes in Newick
files</li>
- <li>Group options for JABAWS service by command line name</li>
- <li>Empty tooltip shown for JABA service options with a
+ <li>• Group options for JABAWS service by command line name</li>
+ <li>• Empty tooltip shown for JABA service options with a
link but no description</li>
- <li>Select primary source when selecting authority in
+ <li>• Select primary source when selecting authority in
database fetcher GUI</li>
- <li>Add .mfa to FASTA file extensions recognised by
+ <li>• Add .mfa to FASTA file extensions recognised by
Jalview</li>
- <li>Annotation label tooltip text wrap</li>
+ <li>• Annotation label tooltip text wrap</li>
</ul>
</td>
<td>
<ul>
- <li>Slow scrolling when lots of annotation rows are
+ <li>• Slow scrolling when lots of annotation rows are
displayed</li>
- <li>Lots of NPE (and slowness) after creating RNA
+ <li>• Lots of NPE (and slowness) after creating RNA
secondary structure annotation line</li>
- <li>Sequence database accessions not imported when
+ <li>• Sequence database accessions not imported when
fetching alignments from Rfam</li>
- <li>Incorrect SHMR submission for sequences with
+ <li>• Incorrect SHMR submission for sequences with
identical IDs</li>
- <li>View all structures does not always superpose
+ <li>• View all structures does not always superpose
structures</li>
- <li>Option widgets in service parameters not updated to
+ <li>• Option widgets in service parameters not updated to
reflect user or preset settings</li>
- <li>Null pointer exceptions for some services without
+ <li>• Null pointer exceptions for some services without
presets or adjustable parameters</li>
- <li>Discover PDB IDs entry in structure menu doesn't
+ <li>• Discover PDB IDs entry in structure menu doesn't
discover PDB xRefs</li>
- <li>Exception encountered while trying to retrieve
+ <li>• Exception encountered while trying to retrieve
features with DAS</li>
- <li>Lowest value in annotation row isn't coloured
+ <li>• Lowest value in annotation row isn't coloured
when colour by annotation (per sequence) is coloured</li>
- <li>Keyboard mode P jumps to start of gapped region when
+ <li>• Keyboard mode P jumps to start of gapped region when
residue follows a gap</li>
- <li>Jalview appears to hang importing an alignment with
+ <li>• Jalview appears to hang importing an alignment with
Wrap as default or after enabling Wrap</li>
- <li>'Right click to add annotations' message
+ <li>• 'Right click to add annotations' message
shown in wrap mode when no annotations present</li>
- <li>Disorder predictions fail with NPE if no automatic
+ <li>• Disorder predictions fail with NPE if no automatic
annotation already exists on alignment</li>
- <li>oninit javascript function should be called after
+ <li>• oninit javascript function should be called after
initialisation completes</li>
- <li>Remove redundancy after disorder prediction corrupts
+ <li>• Remove redundancy after disorder prediction corrupts
alignment window display</li>
- <li>Example annotation file in documentation is invalid</li>
- <li>Grouped line graph annotation rows are not exported
+ <li>• Example annotation file in documentation is invalid</li>
+ <li>• Grouped line graph annotation rows are not exported
to annotation file</li>
- <li>Multi-harmony analysis cannot be run when only two
+ <li>• Multi-harmony analysis cannot be run when only two
groups created</li>
- <li>Cannot create multiple groups of line graphs with
+ <li>• Cannot create multiple groups of line graphs with
several 'combine' statements in annotation file</li>
- <li>Pressing return several times causes Number Format
+ <li>• Pressing return several times causes Number Format
exceptions in keyboard mode</li>
- <li>Multi-harmony (SHMMR) method doesn't submit
+ <li>• Multi-harmony (SHMMR) method doesn't submit
correct partitions for input data</li>
- <li>Translation from DNA to Amino Acids fails</li>
- <li>Jalview fail to load newick tree with quoted label</li>
- <li>--headless flag isn't understood</li>
- <li>ClassCastException when generating EPS in headless
+ <li>• Translation from DNA to Amino Acids fails</li>
+ <li>• Jalview fail to load newick tree with quoted label</li>
+ <li>• --headless flag isn't understood</li>
+ <li>• ClassCastException when generating EPS in headless
mode</li>
- <li>Adjusting sequence-associated shading threshold only
+ <li>• Adjusting sequence-associated shading threshold only
changes one row's threshold</li>
- <li>Preferences and Feature settings panel panel
+ <li>• Preferences and Feature settings panel panel
doesn't open</li>
- <li>hide consensus histogram also hides conservation and
+ <li>• hide consensus histogram also hides conservation and
quality histograms</li>
</ul>
</td>
</div></td>
<td><em>Application</em>
<ul>
- <li>Support for JABAWS 2.0 Services (AACon alignment
+ <li>• Support for JABAWS 2.0 Services (AACon alignment
conservation, protein disorder and Clustal Omega)</li>
- <li>JABAWS server status indicator in Web Services
+ <li>• JABAWS server status indicator in Web Services
preferences</li>
- <li>VARNA (http://varna.lri.fr) viewer for RNA structures
+ <li>• VARNA (http://varna.lri.fr) viewer for RNA structures
in Jalview alignment window</li>
- <li>Updated Jalview build and deploy framework for OSX
+ <li>• Updated Jalview build and deploy framework for OSX
mountain lion, windows 7, and 8</li>
- <li>Nucleotide substitution matrix for PCA that supports
+ <li>• Nucleotide substitution matrix for PCA that supports
RNA and ambiguity codes</li>
- <li>Improved sequence database retrieval GUI</li>
- <li>Support fetching and database reference look up
+ <li>• Improved sequence database retrieval GUI</li>
+ <li>• Support fetching and database reference look up
against multiple DAS sources (Fetch all from in 'fetch db
refs')</li>
- <li>Jalview project improvements
+ <li>• Jalview project improvements
<ul>
- <li>Store and retrieve the 'belowAlignment'
+ <li>• Store and retrieve the 'belowAlignment'
flag for annotation</li>
- <li>calcId attribute to group annotation rows on the
+ <li>• calcId attribute to group annotation rows on the
alignment</li>
- <li>Store AACon calculation settings for a view in
+ <li>• Store AACon calculation settings for a view in
Jalview project</li>
</ul>
</li>
- <li>horizontal scrolling gesture support</li>
- <li>Visual progress indicator when PCA calculation is
+ <li>• horizontal scrolling gesture support</li>
+ <li>• Visual progress indicator when PCA calculation is
running</li>
- <li>Simpler JABA web services menus</li>
- <li>visual indication that web service results are still
+ <li>• Simpler JABA web services menus</li>
+ <li>• visual indication that web service results are still
being retrieved from server</li>
- <li>Serialise the dialogs that are shown when Jalview
+ <li>• Serialise the dialogs that are shown when Jalview
starts up for first time</li>
- <li>Jalview user agent string for interacting with HTTP
+ <li>• Jalview user agent string for interacting with HTTP
services</li>
- <li>DAS 1.6 and DAS 2.0 source support using new JDAS
+ <li>• DAS 1.6 and DAS 2.0 source support using new JDAS
client library</li>
- <li>Examples directory and Groovy library included in
+ <li>• Examples directory and Groovy library included in
InstallAnywhere distribution</li>
</ul> <em>Applet</em>
<ul>
- <li>RNA alignment and secondary structure annotation
+ <li>• RNA alignment and secondary structure annotation
visualization applet example</li>
</ul> <em>General</em>
<ul>
- <li>Normalise option for consensus sequence logo</li>
- <li>Reset button in PCA window to return dimensions to
+ <li>• Normalise option for consensus sequence logo</li>
+ <li>• Reset button in PCA window to return dimensions to
defaults</li>
- <li>Allow seqspace or Jalview variant of alignment PCA
+ <li>• Allow seqspace or Jalview variant of alignment PCA
calculation</li>
- <li>PCA with either nucleic acid and protein substitution
+ <li>• PCA with either nucleic acid and protein substitution
matrices
- <li>Allow windows containing HTML reports to be exported
+ <li>• Allow windows containing HTML reports to be exported
in HTML</li>
- <li>Interactive display and editing of RNA secondary
+ <li>• Interactive display and editing of RNA secondary
structure contacts</li>
- <li>RNA Helix Alignment Colouring</li>
- <li>RNA base pair logo consensus</li>
- <li>Parse sequence associated secondary structure
+ <li>• RNA Helix Alignment Colouring</li>
+ <li>• RNA base pair logo consensus</li>
+ <li>• Parse sequence associated secondary structure
information in Stockholm files</li>
- <li>HTML Export database accessions and annotation
+ <li>• HTML Export database accessions and annotation
information presented in tooltip for sequences</li>
- <li>Import secondary structure from LOCARNA clustalw
+ <li>• Import secondary structure from LOCARNA clustalw
style RNA alignment files</li>
- <li>import and visualise T-COFFEE quality scores for an
+ <li>• import and visualise T-COFFEE quality scores for an
alignment</li>
- <li>'colour by annotation' per sequence option to
+ <li>• 'colour by annotation' per sequence option to
shade each sequence according to its associated alignment
annotation</li>
- <li>New Jalview Logo</li>
+ <li>• New Jalview Logo</li>
</ul> <em>Documentation and Development</em>
<ul>
- <li>documentation for score matrices used in Jalview</li>
- <li>New Website!</li>
+ <li>• documentation for score matrices used in Jalview</li>
+ <li>• New Website!</li>
</ul></td>
<td><em>Application</em>
<ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via
+ <li>• PDB, Unprot and EMBL (ENA) databases retrieved via
wsdbfetch REST service</li>
- <li>Stop windows being moved outside desktop on OSX</li>
- <li>Filetype associations not installed for webstart
+ <li>• Stop windows being moved outside desktop on OSX</li>
+ <li>• Filetype associations not installed for webstart
launch</li>
- <li>Jalview does not always retrieve progress of a JABAWS
+ <li>• Jalview does not always retrieve progress of a JABAWS
job execution in full once it is complete</li>
- <li>revise SHMR RSBS definition to ensure alignment is
+ <li>• revise SHMR RSBS definition to ensure alignment is
uploaded via ali_file parameter</li>
- <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
- <li>View all structures superposed fails with exception</li>
- <li>Jnet job queues forever if a very short sequence is
+ <li>• Jalview 2.7 is incompatible with Jmol-12.2.2</li>
+ <li>• View all structures superposed fails with exception</li>
+ <li>• Jnet job queues forever if a very short sequence is
submitted for prediction</li>
- <li>Cut and paste menu not opened when mouse clicked on
+ <li>• Cut and paste menu not opened when mouse clicked on
desktop window</li>
- <li>Putting fractional value into integer text box in
+ <li>• Putting fractional value into integer text box in
alignment parameter dialog causes Jalview to hang</li>
- <li>Structure view highlighting doesn't work on
+ <li>• Structure view highlighting doesn't work on
windows 7</li>
- <li>View all structures fails with exception shown in
+ <li>• View all structures fails with exception shown in
structure view</li>
- <li>Characters in filename associated with PDBEntry not
+ <li>• Characters in filename associated with PDBEntry not
escaped in a platform independent way</li>
- <li>Jalview desktop fails to launch with exception when
+ <li>• Jalview desktop fails to launch with exception when
using proxy</li>
- <li>Tree calculation reports 'you must have 2 or more
+ <li>• Tree calculation reports 'you must have 2 or more
sequences selected' when selection is empty</li>
- <li>Jalview desktop fails to launch with jar signature
+ <li>• Jalview desktop fails to launch with jar signature
failure when java web start temporary file caching is
disabled</li>
- <li>DAS Sequence retrieval with range qualification
+ <li>• DAS Sequence retrieval with range qualification
results in sequence xref which includes range qualification</li>
- <li>Errors during processing of command line arguments
+ <li>• Errors during processing of command line arguments
cause progress bar (JAL-898) to be removed</li>
- <li>Replace comma for semi-colon option not disabled for
+ <li>• Replace comma for semi-colon option not disabled for
DAS sources in sequence fetcher</li>
- <li>Cannot close news reader when JABAWS server warning
+ <li>• Cannot close news reader when JABAWS server warning
dialog is shown</li>
- <li>Option widgets not updated to reflect user settings</li>
- <li>Edited sequence not submitted to web service</li>
- <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
- <li>InstallAnywhere installer doesn't unpack and run
+ <li>• Option widgets not updated to reflect user settings</li>
+ <li>• Edited sequence not submitted to web service</li>
+ <li>• Jalview 2.7 Webstart does not launch on mountain lion</li>
+ <li>• InstallAnywhere installer doesn't unpack and run
on OSX Mountain Lion</li>
- <li>Annotation panel not given a scroll bar when
+ <li>• Annotation panel not given a scroll bar when
sequences with alignment annotation are pasted into the
alignment</li>
- <li>Sequence associated annotation rows not associated
+ <li>• Sequence associated annotation rows not associated
when loaded from Jalview project</li>
- <li>Browser launch fails with NPE on java 1.7</li>
- <li>JABAWS alignment marked as finished when job was
+ <li>• Browser launch fails with NPE on java 1.7</li>
+ <li>• JABAWS alignment marked as finished when job was
cancelled or job failed due to invalid input</li>
- <li>NPE with v2.7 example when clicking on Tree
+ <li>• NPE with v2.7 example when clicking on Tree
associated with all views</li>
- <li>Exceptions when copy/paste sequences with grouped
+ <li>• Exceptions when copy/paste sequences with grouped
annotation rows to new window</li>
</ul> <em>Applet</em>
<ul>
- <li>Sequence features are momentarily displayed before
+ <li>• Sequence features are momentarily displayed before
they are hidden using hidefeaturegroups applet parameter</li>
- <li>loading features via javascript API automatically
+ <li>• loading features via javascript API automatically
enables feature display</li>
- <li>scrollToColumnIn javascript API method doesn't
+ <li>• scrollToColumnIn javascript API method doesn't
work</li>
</ul> <em>General</em>
<ul>
- <li>Redundancy removal fails for rna alignment</li>
- <li>PCA calculation fails when sequence has been selected
+ <li>• Redundancy removal fails for rna alignment</li>
+ <li>• PCA calculation fails when sequence has been selected
and then deselected</li>
- <li>PCA window shows grey box when first opened on OSX</li>
- <li>Letters coloured pink in sequence logo when alignment
+ <li>• PCA window shows grey box when first opened on OSX</li>
+ <li>• Letters coloured pink in sequence logo when alignment
coloured with clustalx</li>
- <li>Choosing fonts without letter symbols defined causes
+ <li>• Choosing fonts without letter symbols defined causes
exceptions and redraw errors</li>
- <li>Initial PCA plot view is not same as manually
+ <li>• Initial PCA plot view is not same as manually
reconfigured view</li>
- <li>Grouped annotation graph label has incorrect line
+ <li>• Grouped annotation graph label has incorrect line
colour</li>
- <li>Grouped annotation graph label display is corrupted
+ <li>• Grouped annotation graph label display is corrupted
for lots of labels</li>
</ul>
</tr>
</td>
<td><em>Application</em>
<ul>
- <li>Jalview Desktop News Reader</li>
- <li>Tweaked default layout of web services menu</li>
- <li>View/alignment association menu to enable user to
+ <li>• Jalview Desktop News Reader</li>
+ <li>• Tweaked default layout of web services menu</li>
+ <li>• View/alignment association menu to enable user to
easily specify which alignment a multi-structure view takes
its colours/correspondences from</li>
- <li>Allow properties file location to be specified as URL</li>
- <li>Extend Jalview project to preserve associations
+ <li>• Allow properties file location to be specified as URL</li>
+ <li>• Extend Jalview project to preserve associations
between many alignment views and a single Jmol display</li>
- <li>Store annotation row height in Jalview project file</li>
- <li>Annotation row column label formatting attributes
+ <li>• Store annotation row height in Jalview project file</li>
+ <li>• Annotation row column label formatting attributes
stored in project file</li>
- <li>Annotation row order for auto-calculated annotation
+ <li>• Annotation row order for auto-calculated annotation
rows preserved in Jalview project file</li>
- <li>Visual progress indication when Jalview state is
+ <li>• Visual progress indication when Jalview state is
saved using Desktop window menu</li>
- <li>Visual indication that command line arguments are
+ <li>• Visual indication that command line arguments are
still being processed</li>
- <li>Groovy script execution from URL</li>
- <li>Colour by annotation default min and max colours in
+ <li>• Groovy script execution from URL</li>
+ <li>• Colour by annotation default min and max colours in
preferences</li>
- <li>Automatically associate PDB files dragged onto an
+ <li>• Automatically associate PDB files dragged onto an
alignment with sequences that have high similarity and
matching IDs</li>
- <li>Update JGoogleAnalytics to latest release (0.3)</li>
- <li>'view structures' option to open many
+ <li>• Update JGoogleAnalytics to latest release (0.3)</li>
+ <li>• 'view structures' option to open many
structures in same window</li>
- <li>Sort associated views menu option for tree panel</li>
- <li>Group all JABA and non-JABA services for a particular
+ <li>• Sort associated views menu option for tree panel</li>
+ <li>• Group all JABA and non-JABA services for a particular
analysis function in its own submenu</li>
</ul> <em>Applet</em>
<ul>
- <li>Userdefined and autogenerated annotation rows for
+ <li>• Userdefined and autogenerated annotation rows for
groups</li>
- <li>Adjustment of alignment annotation pane height</li>
- <li>Annotation scrollbar for annotation panel</li>
- <li>Drag to reorder annotation rows in annotation panel</li>
- <li>'automaticScrolling' parameter</li>
- <li>Allow sequences with partial ID string matches to be
+ <li>• Adjustment of alignment annotation pane height</li>
+ <li>• Annotation scrollbar for annotation panel</li>
+ <li>• Drag to reorder annotation rows in annotation panel</li>
+ <li>• 'automaticScrolling' parameter</li>
+ <li>• Allow sequences with partial ID string matches to be
annotated from GFF/Jalview features files</li>
- <li>Sequence logo annotation row in applet</li>
- <li>Absolute paths relative to host server in applet
+ <li>• Sequence logo annotation row in applet</li>
+ <li>• Absolute paths relative to host server in applet
parameters are treated as such</li>
- <li>New in the JalviewLite javascript API:
+ <li>• New in the JalviewLite javascript API:
<ul>
- <li>JalviewLite.js javascript library</li>
- <li>Javascript callbacks for
+ <li>• JalviewLite.js javascript library</li>
+ <li>• Javascript callbacks for
<ul>
- <li>Applet initialisation</li>
- <li>Sequence/alignment mouse-overs and selections</li>
+ <li>• Applet initialisation</li>
+ <li>• Sequence/alignment mouse-overs and selections</li>
</ul>
</li>
- <li>scrollTo row and column alignment scrolling
+ <li>• scrollTo row and column alignment scrolling
functions</li>
- <li>Select sequence/alignment regions from javascript</li>
- <li>javascript structure viewer harness to pass
+ <li>• Select sequence/alignment regions from javascript</li>
+ <li>• javascript structure viewer harness to pass
messages between Jmol and Jalview when running as
distinct applets</li>
- <li>sortBy method</li>
- <li>Set of applet and application examples shipped
+ <li>• sortBy method</li>
+ <li>• Set of applet and application examples shipped
with documentation</li>
- <li>New example to demonstrate JalviewLite and Jmol
+ <li>• New example to demonstrate JalviewLite and Jmol
javascript message exchange</li>
</ul>
</ul> <em>General</em>
<ul>
- <li>Enable Jmol displays to be associated with multiple
+ <li>• Enable Jmol displays to be associated with multiple
multiple alignments</li>
- <li>Option to automatically sort alignment with new tree</li>
- <li>User configurable link to enable redirects to a
+ <li>• Option to automatically sort alignment with new tree</li>
+ <li>• User configurable link to enable redirects to a
www.Jalview.org mirror</li>
- <li>Jmol colours option for Jmol displays</li>
- <li>Configurable newline string when writing alignment
+ <li>• Jmol colours option for Jmol displays</li>
+ <li>• Configurable newline string when writing alignment
and other flat files</li>
- <li>Allow alignment annotation description lines to
+ <li>• Allow alignment annotation description lines to
contain html tags</li>
</ul> <em>Documentation and Development</em>
<ul>
- <li>Add groovy test harness for bulk load testing to
+ <li>• Add groovy test harness for bulk load testing to
examples</li>
- <li>Groovy script to load and align a set of sequences
+ <li>• Groovy script to load and align a set of sequences
using a web service before displaying the result in the
Jalview desktop</li>
- <li>Restructured javascript and applet api documentation</li>
- <li>Ant target to publish example html files with applet
+ <li>• Restructured javascript and applet api documentation</li>
+ <li>• Ant target to publish example html files with applet
archive</li>
- <li>Netbeans project for building Jalview from source</li>
- <li>ant task to create online javadoc for Jalview source</li>
+ <li>• Netbeans project for building Jalview from source</li>
+ <li>• ant task to create online javadoc for Jalview source</li>
</ul></td>
<td><em>Application</em>
<ul>
- <li>User defined colourscheme throws exception when
+ <li>• User defined colourscheme throws exception when
current built in colourscheme is saved as new scheme</li>
- <li>AlignFrame->Save in application pops up save
+ <li>• AlignFrame->Save in application pops up save
dialog for valid filename/format</li>
- <li>Cannot view associated structure for UniProt sequence</li>
- <li>PDB file association breaks for UniProt sequence
+ <li>• Cannot view associated structure for UniProt sequence</li>
+ <li>• PDB file association breaks for UniProt sequence
P37173</li>
- <li>Associate PDB from file dialog does not tell you
+ <li>• Associate PDB from file dialog does not tell you
which sequence is to be associated with the file</li>
- <li>Find All raises null pointer exception when query
+ <li>• Find All raises null pointer exception when query
only matches sequence IDs</li>
- <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
- <li>Jalview project with Jmol views created with Jalview
+ <li>• Pre 2.6 Jalview project cannot be loaded into v2.6</li>
+ <li>• Jalview project with Jmol views created with Jalview
2.4 cannot be loaded</li>
- <li>Filetype associations not installed for webstart
+ <li>• Filetype associations not installed for webstart
launch</li>
- <li>Two or more chains in a single PDB file associated
+ <li>• Two or more chains in a single PDB file associated
with sequences in different alignments do not get coloured
by their associated sequence</li>
- <li>Visibility status of autocalculated annotation row
+ <li>• Visibility status of autocalculated annotation row
not preserved when project is loaded</li>
- <li>Annotation row height and visibility attributes not
+ <li>• Annotation row height and visibility attributes not
stored in Jalview project</li>
- <li>Tree bootstraps are not preserved when saved as a
+ <li>• Tree bootstraps are not preserved when saved as a
Jalview project</li>
- <li>Envision2 workflow tooltips are corrupted</li>
- <li>Enabling show group conservation also enables colour
+ <li>• Envision2 workflow tooltips are corrupted</li>
+ <li>• Enabling show group conservation also enables colour
by conservation</li>
- <li>Duplicate group associated conservation or consensus
+ <li>• Duplicate group associated conservation or consensus
created on new view</li>
- <li>Annotation scrollbar not displayed after 'show
+ <li>• Annotation scrollbar not displayed after 'show
all hidden annotation rows' option selected</li>
- <li>Alignment quality not updated after alignment
+ <li>• Alignment quality not updated after alignment
annotation row is hidden then shown</li>
- <li>Preserve colouring of structures coloured by
+ <li>• Preserve colouring of structures coloured by
sequences in pre Jalview 2.7 projects</li>
- <li>Web service job parameter dialog is not laid out
+ <li>• Web service job parameter dialog is not laid out
properly</li>
- <li>Web services menu not refreshed after 'reset
+ <li>• Web services menu not refreshed after 'reset
services' button is pressed in preferences</li>
- <li>Annotation off by one in Jalview v2_3 example project</li>
- <li>Structures imported from file and saved in project
+ <li>• Annotation off by one in Jalview v2_3 example project</li>
+ <li>• Structures imported from file and saved in project
get name like jalview_pdb1234.txt when reloaded</li>
- <li>Jalview does not always retrieve progress of a JABAWS
+ <li>• Jalview does not always retrieve progress of a JABAWS
job execution in full once it is complete</li>
</ul> <em>Applet</em>
<ul>
- <li>Alignment height set incorrectly when lots of
+ <li>• Alignment height set incorrectly when lots of
annotation rows are displayed</li>
- <li>Relative URLs in feature HTML text not resolved to
+ <li>• Relative URLs in feature HTML text not resolved to
codebase</li>
- <li>View follows highlighting does not work for positions
+ <li>• View follows highlighting does not work for positions
in sequences</li>
- <li><= shown as = in tooltip</li>
- <li>Export features raises exception when no features
+ <li>• <= shown as = in tooltip</li>
+ <li>• Export features raises exception when no features
exist</li>
- <li>Separator string used for serialising lists of IDs
+ <li>• Separator string used for serialising lists of IDs
for javascript api is modified when separator string
provided as parameter</li>
- <li>Null pointer exception when selecting tree leaves for
+ <li>• Null pointer exception when selecting tree leaves for
alignment with no existing selection</li>
- <li>Relative URLs for datasources assumed to be relative
+ <li>• Relative URLs for datasources assumed to be relative
to applet's codebase</li>
- <li>Status bar not updated after finished searching and
+ <li>• Status bar not updated after finished searching and
search wraps around to first result</li>
- <li>StructureSelectionManager instance shared between
+ <li>• StructureSelectionManager instance shared between
several Jalview applets causes race conditions and memory
leaks</li>
- <li>Hover tooltip and mouseover of position on structure
+ <li>• Hover tooltip and mouseover of position on structure
not sent from Jmol in applet</li>
- <li>Certain sequences of javascript method calls to
+ <li>• Certain sequences of javascript method calls to
applet API fatally hang browser</li>
</ul> <em>General</em>
<ul>
- <li>View follows structure mouseover scrolls beyond
+ <li>• View follows structure mouseover scrolls beyond
position with wrapped view and hidden regions</li>
- <li>Find sequence position moves to wrong residue
+ <li>• Find sequence position moves to wrong residue
with/without hidden columns</li>
- <li>Sequence length given in alignment properties window
+ <li>• Sequence length given in alignment properties window
is off by 1</li>
- <li>InvalidNumberFormat exceptions thrown when trying to
+ <li>• InvalidNumberFormat exceptions thrown when trying to
import PDB like structure files</li>
- <li>Positional search results are only highlighted
+ <li>• Positional search results are only highlighted
between user-supplied sequence start/end bounds</li>
- <li>End attribute of sequence is not validated</li>
- <li>Find dialog only finds first sequence containing a
+ <li>• End attribute of sequence is not validated</li>
+ <li>• Find dialog only finds first sequence containing a
given sequence position</li>
- <li>Sequence numbering not preserved in MSF alignment
+ <li>• Sequence numbering not preserved in MSF alignment
output</li>
- <li>Jalview PDB file reader does not extract sequence
+ <li>• Jalview PDB file reader does not extract sequence
from nucleotide chains correctly</li>
- <li>Structure colours not updated when tree partition
+ <li>• Structure colours not updated when tree partition
changed in alignment</li>
- <li>Sequence associated secondary structure not correctly
+ <li>• Sequence associated secondary structure not correctly
parsed in interleaved stockholm</li>
- <li>Colour by annotation dialog does not restore current
+ <li>• Colour by annotation dialog does not restore current
state</li>
- <li>Hiding (nearly) all sequences doesn't work
+ <li>• Hiding (nearly) all sequences doesn't work
properly</li>
- <li>Sequences containing lowercase letters are not
+ <li>• Sequences containing lowercase letters are not
properly associated with their pdb files</li>
</ul> <em>Documentation and Development</em>
<ul>
- <li>schemas/JalviewWsParamSet.xsd corrupted by
+ <li>• schemas/JalviewWsParamSet.xsd corrupted by
ApplyCopyright tool</li>
</ul></td>
</tr>
</td>
<td><em>Application</em>
<ul>
- <li>New warning dialog when the Jalview Desktop cannot
+ <li>• New warning dialog when the Jalview Desktop cannot
contact web services</li>
- <li>JABA service parameters for a preset are shown in
+ <li>• JABA service parameters for a preset are shown in
service job window</li>
- <li>JABA Service menu entries reworded</li>
+ <li>• JABA Service menu entries reworded</li>
</ul></td>
<td>
<ul>
- <li>Modeller PIR IO broken - cannot correctly import a
+ <li>• Modeller PIR IO broken - cannot correctly import a
pir file emitted by Jalview</li>
- <li>Existing feature settings transferred to new
+ <li>• Existing feature settings transferred to new
alignment view created from cut'n'paste</li>
- <li>Improved test for mixed amino/nucleotide chains when
+ <li>• Improved test for mixed amino/nucleotide chains when
parsing PDB files</li>
- <li>Consensus and conservation annotation rows
+ <li>• Consensus and conservation annotation rows
occasionally become blank for all new windows</li>
- <li>Exception raised when right clicking above sequences
+ <li>• Exception raised when right clicking above sequences
in wrapped view mode</li>
</ul> <em>Application</em>
<ul>
- <li>multiple multiply aligned structure views cause cpu
+ <li>• multiple multiply aligned structure views cause cpu
usage to hit 100% and computer to hang</li>
- <li>Web Service parameter layout breaks for long user
+ <li>• Web Service parameter layout breaks for long user
parameter names</li>
- <li>Jaba service discovery hangs desktop if Jaba server
+ <li>• Jaba service discovery hangs desktop if Jaba server
is down</li>
</ul>
</td>
</td>
<td><em>Application</em>
<ul>
- <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
+ <li>• Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
<strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices
(JABAWS)
</li>
- <li>Web Services preference tab</li>
- <li>Analysis parameters dialog box and user defined
+ <li>• Web Services preference tab</li>
+ <li>• Analysis parameters dialog box and user defined
preferences</li>
- <li>Improved speed and layout of Envision2 service menu</li>
- <li>Superpose structures using associated sequence
+ <li>• Improved speed and layout of Envision2 service menu</li>
+ <li>• Superpose structures using associated sequence
alignment</li>
- <li>Export coordinates and projection as CSV from PCA
+ <li>• Export coordinates and projection as CSV from PCA
viewer</li>
</ul> <em>Applet</em>
<ul>
- <li>enable javascript: execution by the applet via the
+ <li>• enable javascript: execution by the applet via the
link out mechanism</li>
</ul> <em>Other</em>
<ul>
- <li>Updated the Jmol Jalview interface to work with Jmol
+ <li>• Updated the Jmol Jalview interface to work with Jmol
series 12</li>
- <li>The Jalview Desktop and JalviewLite applet now
+ <li>• The Jalview Desktop and JalviewLite applet now
require Java 1.5</li>
- <li>Allow Jalview feature colour specification for GFF
+ <li>• Allow Jalview feature colour specification for GFF
sequence annotation files</li>
- <li>New 'colour by label' keword in Jalview feature file
+ <li>• New 'colour by label' keword in Jalview feature file
type colour specification</li>
- <li>New Jalview Desktop Groovy API method that allows a
+ <li>• New Jalview Desktop Groovy API method that allows a
script to check if it being run in an interactive session or
in a batch operation from the Jalview command line</li>
</ul></td>
<td>
<ul>
- <li>clustalx colourscheme colours Ds preferentially when
+ <li>• clustalx colourscheme colours Ds preferentially when
both D+E are present in over 50% of the column</li>
</ul> <em>Application</em>
<ul>
- <li>typo in AlignmentFrame->View->Hide->all but
+ <li>• typo in AlignmentFrame->View->Hide->all but
selected Regions menu item</li>
- <li>sequence fetcher replaces ',' for ';' when the ',' is
+ <li>• sequence fetcher replaces ',' for ';' when the ',' is
part of a valid accession ID</li>
- <li>fatal OOM if object retrieved by sequence fetcher
+ <li>• fatal OOM if object retrieved by sequence fetcher
runs out of memory</li>
- <li>unhandled Out of Memory Error when viewing pca
+ <li>• unhandled Out of Memory Error when viewing pca
analysis results</li>
- <li>InstallAnywhere builds fail to launch on OS X java
+ <li>• InstallAnywhere builds fail to launch on OS X java
10.5 update 4 (due to apple Java 1.6 update)</li>
- <li>Installanywhere Jalview silently fails to launch</li>
+ <li>• Installanywhere Jalview silently fails to launch</li>
</ul> <em>Applet</em>
<ul>
- <li>Jalview.getFeatureGroups() raises an
+ <li>• Jalview.getFeatureGroups() raises an
ArrayIndexOutOfBoundsException if no feature groups are
defined.</li>
</ul>
<td></td>
<td>
<ul>
- <li>Alignment prettyprinter doesn't cope with long
+ <li>• Alignment prettyprinter doesn't cope with long
sequence IDs</li>
- <li>clustalx colourscheme colours Ds preferentially when
+ <li>• clustalx colourscheme colours Ds preferentially when
both D+E are present in over 50% of the column</li>
- <li>nucleic acid structures retrieved from PDB do not
+ <li>• nucleic acid structures retrieved from PDB do not
import correctly</li>
- <li>More columns get selected than were clicked on when a
+ <li>• More columns get selected than were clicked on when a
number of columns are hidden</li>
- <li>annotation label popup menu not providing correct
+ <li>• annotation label popup menu not providing correct
add/hide/show options when rows are hidden or none are
present</li>
- <li>Stockholm format shown in list of readable formats,
+ <li>• Stockholm format shown in list of readable formats,
and parser copes better with alignments from RFAM.</li>
- <li>CSV output of consensus only includes the percentage
+ <li>• CSV output of consensus only includes the percentage
of all symbols if sequence logo display is enabled</li>
</ul> <em>Applet</em>
<ul>
- <li>annotation panel disappears when annotation is
+ <li>• annotation panel disappears when annotation is
hidden/removed</li>
</ul> <em>Application</em>
<ul>
- <li>Alignment view not redrawn properly when new
+ <li>• Alignment view not redrawn properly when new
alignment opened where annotation panel is visible but no
annotations are present on alignment</li>
- <li>pasted region containing hidden columns is
+ <li>• pasted region containing hidden columns is
incorrectly displayed in new alignment window</li>
- <li>Jalview slow to complete operations when stdout is
+ <li>• Jalview slow to complete operations when stdout is
flooded (fix is to close the Jalview console)</li>
- <li>typo in AlignmentFrame->View->Hide->all but
+ <li>• typo in AlignmentFrame->View->Hide->all but
selected Rregions menu item.</li>
- <li>inconsistent group submenu and Format submenu entry
+ <li>• inconsistent group submenu and Format submenu entry
'Un' or 'Non'conserved</li>
- <li>Sequence feature settings are being shared by
+ <li>• Sequence feature settings are being shared by
multiple distinct alignments</li>
- <li>group annotation not recreated when tree partition is
+ <li>• group annotation not recreated when tree partition is
changed</li>
- <li>double click on group annotation to select sequences
+ <li>• double click on group annotation to select sequences
does not propagate to associated trees</li>
- <li>Mac OSX specific issues:
+ <li>• Mac OSX specific issues:
<ul>
- <li>exception raised when mouse clicked on desktop
+ <li>• exception raised when mouse clicked on desktop
window background</li>
- <li>Desktop menu placed on menu bar and application
+ <li>• Desktop menu placed on menu bar and application
name set correctly</li>
- <li>sequence feature settings not wide enough for the
+ <li>• sequence feature settings not wide enough for the
save feature colourscheme button</li>
</ul>
</li>
</td>
<td><em>New Capabilities</em>
<ul>
- <li>URL links generated from description line for
+ <li>• URL links generated from description line for
regular-expression based URL links (applet and application)
- <li>Non-positional feature URL links are shown in link
+ <li>• Non-positional feature URL links are shown in link
menu</li>
- <li>Linked viewing of nucleic acid sequences and
+ <li>• Linked viewing of nucleic acid sequences and
structures</li>
- <li>Automatic Scrolling option in View menu to display
+ <li>• Automatic Scrolling option in View menu to display
the currently highlighted region of an alignment.</li>
- <li>Order an alignment by sequence length, or using the
+ <li>• Order an alignment by sequence length, or using the
average score or total feature count for each sequence.</li>
- <li>Shading features by score or associated description</li>
- <li>Subdivide alignment and groups based on identity of
+ <li>• Shading features by score or associated description</li>
+ <li>• Subdivide alignment and groups based on identity of
selected subsequence (Make Groups from Selection).</li>
- <li>New hide/show options including Shift+Control+H to
+ <li>• New hide/show options including Shift+Control+H to
hide everything but the currently selected region.</li>
- <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
+ <!-- introduced but not yet documented <li>• Experimental blast report parser</li> -->
</ul> <em>Application</em>
<ul>
- <li>Fetch DB References capabilities and UI expanded to
+ <li>• Fetch DB References capabilities and UI expanded to
support retrieval from DAS sequence sources</li>
- <li>Local DAS Sequence sources can be added via the
+ <li>• Local DAS Sequence sources can be added via the
command line or via the Add local source dialog box.</li>
- <li>DAS Dbref and DbxRef feature types are parsed as
+ <li>• DAS Dbref and DbxRef feature types are parsed as
database references and protein_name is parsed as
description line (BioSapiens terms).</li>
- <li>Enable or disable non-positional feature and database
+ <li>• Enable or disable non-positional feature and database
references in sequence ID tooltip from View menu in
application.</li>
- <!-- <li>New hidden columns and rows and representatives capabilities
+ <!-- <li>• New hidden columns and rows and representatives capabilities
in annotations file (in progress - not yet fully implemented)</li> -->
- <li>Group-associated consensus, sequence logos and
+ <li>• Group-associated consensus, sequence logos and
conservation plots</li>
- <li>Symbol distributions for each column can be exported
+ <li>• Symbol distributions for each column can be exported
and visualized as sequence logos</li>
- <li>Optionally scale multi-character column labels to fit
+ <li>• Optionally scale multi-character column labels to fit
within each column of annotation row<!-- todo for applet -->
</li>
- <li>Optional automatic sort of associated alignment view
+ <li>• Optional automatic sort of associated alignment view
when a new tree is opened.</li>
- <li>Jalview Java Console</li>
- <li>Better placement of desktop window when moving
+ <li>• Jalview Java Console</li>
+ <li>• Better placement of desktop window when moving
between different screens.</li>
- <li>New preference items for sequence ID tooltip and
+ <li>• New preference items for sequence ID tooltip and
consensus annotation</li>
- <li>Client to submit sequences and IDs to Envision2
+ <li>• Client to submit sequences and IDs to Envision2
Workflows</li>
- <li><em>Vamsas Capabilities</em>
+ <li>• <em>Vamsas Capabilities</em>
<ul>
- <li>Improved VAMSAS synchronization (Jalview archive
+ <li>• Improved VAMSAS synchronization (Jalview archive
used to preserve views, structures, and tree display
settings)</li>
- <li>Import of vamsas documents from disk or URL via
+ <li>• Import of vamsas documents from disk or URL via
command line</li>
- <li>Sharing of selected regions between views and
+ <li>• Sharing of selected regions between views and
with other VAMSAS applications (Experimental feature!)</li>
- <li>Updated API to VAMSAS version 0.2</li>
+ <li>• Updated API to VAMSAS version 0.2</li>
</ul></li>
</ul> <em>Applet</em>
<ul>
- <li>Middle button resizes annotation row height</li>
- <li>New Parameters
+ <li>• Middle button resizes annotation row height</li>
+ <li>• New Parameters
<ul>
- <li>sortByTree (true/false) - automatically sort the
+ <li>• sortByTree (true/false) - automatically sort the
associated alignment view by the tree when a new tree is
opened.</li>
- <li>showTreeBootstraps (true/false) - show or hide
+ <li>• showTreeBootstraps (true/false) - show or hide
branch bootstraps (default is to show them if available)</li>
- <li>showTreeDistances (true/false) - show or hide
+ <li>• showTreeDistances (true/false) - show or hide
branch lengths (default is to show them if available)</li>
- <li>showUnlinkedTreeNodes (true/false) - indicate if
+ <li>• showUnlinkedTreeNodes (true/false) - indicate if
unassociated nodes should be highlighted in the tree
view</li>
- <li>heightScale and widthScale (1.0 or more) -
+ <li>• heightScale and widthScale (1.0 or more) -
increase the height or width of a cell in the alignment
grid relative to the current font size.</li>
</ul>
</li>
- <li>Non-positional features displayed in sequence ID
+ <li>• Non-positional features displayed in sequence ID
tooltip</li>
</ul> <em>Other</em>
<ul>
- <li>Features format: graduated colour definitions and
+ <li>• Features format: graduated colour definitions and
specification of feature scores</li>
- <li>Alignment Annotations format: new keywords for group
+ <li>• Alignment Annotations format: new keywords for group
associated annotation (GROUP_REF) and annotation row display
properties (ROW_PROPERTIES)</li>
- <li>XML formats extended to support graduated feature
+ <li>• XML formats extended to support graduated feature
colourschemes, group associated annotation, and profile
visualization settings.</li></td>
<td>
<ul>
- <li>Source field in GFF files parsed as feature source
+ <li>• Source field in GFF files parsed as feature source
rather than description</li>
- <li>Non-positional features are now included in sequence
+ <li>• Non-positional features are now included in sequence
feature and gff files (controlled via non-positional feature
visibility in tooltip).</li>
- <li>URL links generated for all feature links (bugfix)</li>
- <li>Added URL embedding instructions to features file
+ <li>• URL links generated for all feature links (bugfix)</li>
+ <li>• Added URL embedding instructions to features file
documentation.</li>
- <li>Codons containing ambiguous nucleotides translated as
+ <li>• Codons containing ambiguous nucleotides translated as
'X' in peptide product</li>
- <li>Match case switch in find dialog box works for both
+ <li>• 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.</li>
- <li>AMSA files only contain first column of
+ <li>• AMSA files only contain first column of
multi-character column annotation labels</li>
- <li>Jalview Annotation File generation/parsing consistent
+ <li>• Jalview Annotation File generation/parsing consistent
with documentation (e.g. Stockholm annotation can be
exported and re-imported)</li>
- <li>PDB files without embedded PDB IDs given a friendly
+ <li>• PDB files without embedded PDB IDs given a friendly
name</li>
- <li>Find incrementally searches ID string matches as well
+ <li>• Find incrementally searches ID string matches as well
as subsequence matches, and correctly reports total number
of both.</li>
- <li>Application:
+ <li>• Application:
<ul>
- <li>Better handling of exceptions during sequence
+ <li>• Better handling of exceptions during sequence
retrieval</li>
- <li>Dasobert generated non-positional feature URL
+ <li>• Dasobert generated non-positional feature URL
link text excludes the start_end suffix</li>
- <li>DAS feature and source retrieval buttons disabled
+ <li>• DAS feature and source retrieval buttons disabled
when fetch or registry operations in progress.</li>
- <li>PDB files retrieved from URLs are cached properly</li>
- <li>Sequence description lines properly shared via
+ <li>• PDB files retrieved from URLs are cached properly</li>
+ <li>• Sequence description lines properly shared via
VAMSAS</li>
- <li>Sequence fetcher fetches multiple records for all
+ <li>• Sequence fetcher fetches multiple records for all
data sources</li>
- <li>Ensured that command line das feature retrieval
+ <li>• Ensured that command line das feature retrieval
completes before alignment figures are generated.</li>
- <li>Reduced time taken when opening file browser for
+ <li>• Reduced time taken when opening file browser for
first time.</li>
- <li>isAligned check prior to calculating tree, PCA or
+ <li>• isAligned check prior to calculating tree, PCA or
submitting an MSA to JNet now excludes hidden sequences.</li>
- <li>User defined group colours properly recovered
+ <li>• User defined group colours properly recovered
from Jalview projects.</li>
</ul>
</li>
</td>
<td>
<ul>
- <li>Experimental support for google analytics usage
+ <li>• Experimental support for google analytics usage
tracking.</li>
- <li>Jalview privacy settings (user preferences and docs).</li>
+ <li>• Jalview privacy settings (user preferences and docs).</li>
</ul>
</td>
<td>
<ul>
- <li>Race condition in applet preventing startup in
+ <li>• Race condition in applet preventing startup in
jre1.6.0u12+.</li>
- <li>Exception when feature created from selection beyond
+ <li>• Exception when feature created from selection beyond
length of sequence.</li>
- <li>Allow synthetic PDB files to be imported gracefully</li>
- <li>Sequence associated annotation rows associate with
+ <li>• Allow synthetic PDB files to be imported gracefully</li>
+ <li>• Sequence associated annotation rows associate with
all sequences with a given id</li>
- <li>Find function matches case-insensitively for sequence
+ <li>• Find function matches case-insensitively for sequence
ID string searches</li>
- <li>Non-standard characters do not cause pairwise
+ <li>• Non-standard characters do not cause pairwise
alignment to fail with exception</li>
</ul> <em>Application Issues</em>
<ul>
- <li>Sequences are now validated against EMBL database</li>
- <li>Sequence fetcher fetches multiple records for all
+ <li>• Sequences are now validated against EMBL database</li>
+ <li>• Sequence fetcher fetches multiple records for all
data sources</li>
</ul> <em>InstallAnywhere Issues</em>
<ul>
- <li>Dock icon works for Mac OS X java (Mac 1.6 update
+ <li>• Dock icon works for Mac OS X java (Mac 1.6 update
issue with installAnywhere mechanism)</li>
- <li>Command line launching of JARs from InstallAnywhere
+ <li>• Command line launching of JARs from InstallAnywhere
version (java class versioning error fixed)</li>
</ul>
</td>
</td>
<td><em>User Interface</em>
<ul>
- <li>Linked highlighting of codon and amino acid from
+ <li>• Linked highlighting of codon and amino acid from
translation and protein products</li>
- <li>Linked highlighting of structure associated with
+ <li>• Linked highlighting of structure associated with
residue mapping to codon position</li>
- <li>Sequence Fetcher provides example accession numbers
+ <li>• Sequence Fetcher provides example accession numbers
and 'clear' button</li>
- <li>MemoryMonitor added as an option under Desktop's
+ <li>• MemoryMonitor added as an option under Desktop's
Tools menu</li>
- <li>Extract score function to parse whitespace separated
+ <li>• Extract score function to parse whitespace separated
numeric data in description line</li>
- <li>Column labels in alignment annotation can be centred.</li>
- <li>Tooltip for sequence associated annotation give name
+ <li>• Column labels in alignment annotation can be centred.</li>
+ <li>• Tooltip for sequence associated annotation give name
of sequence</li>
</ul> <em>Web Services and URL fetching</em>
<ul>
- <li>JPred3 web service</li>
- <li>Prototype sequence search client (no public services
+ <li>• JPred3 web service</li>
+ <li>• Prototype sequence search client (no public services
available yet)</li>
- <li>Fetch either seed alignment or full alignment from
+ <li>• Fetch either seed alignment or full alignment from
PFAM</li>
- <li>URL Links created for matching database cross
+ <li>• URL Links created for matching database cross
references as well as sequence ID</li>
- <li>URL Links can be created using regular-expressions</li>
+ <li>• URL Links can be created using regular-expressions</li>
</ul> <em>Sequence Database Connectivity</em>
<ul>
- <li>Retrieval of cross-referenced sequences from other
+ <li>• Retrieval of cross-referenced sequences from other
databases</li>
- <li>Generalised database reference retrieval and
+ <li>• Generalised database reference retrieval and
validation to all fetchable databases</li>
- <li>Fetch sequences from DAS sources supporting the
+ <li>• Fetch sequences from DAS sources supporting the
sequence command</li>
</ul> <em>Import and Export</em>
- <li>export annotation rows as CSV for spreadsheet import</li>
- <li>Jalview projects record alignment dataset associations,
+ <li>• export annotation rows as CSV for spreadsheet import</li>
+ <li>• Jalview projects record alignment dataset associations,
EMBL products, and cDNA sequence mappings</li>
- <li>Sequence Group colour can be specified in Annotation
+ <li>• Sequence Group colour can be specified in Annotation
File</li>
- <li>Ad-hoc colouring of group in Annotation File using RGB
+ <li>• Ad-hoc colouring of group in Annotation File using RGB
triplet as name of colourscheme</li>
</ul> <em>VAMSAS Client capabilities (Experimental)</em>
<ul>
- <li>treenode binding for VAMSAS tree exchange</li>
- <li>local editing and update of sequences in VAMSAS
+ <li>• treenode binding for VAMSAS tree exchange</li>
+ <li>• local editing and update of sequences in VAMSAS
alignments (experimental)</li>
- <li>Create new or select existing session to join</li>
- <li>load and save of vamsas documents</li>
+ <li>• Create new or select existing session to join</li>
+ <li>• load and save of vamsas documents</li>
</ul> <em>Application command line</em>
<ul>
- <li>-tree parameter to open trees (introduced for passing
+ <li>• -tree parameter to open trees (introduced for passing
from applet)</li>
- <li>-fetchfrom command line argument to specify nicknames
+ <li>• -fetchfrom command line argument to specify nicknames
of DAS servers to query for alignment features</li>
- <li>-dasserver command line argument to add new servers
+ <li>• -dasserver command line argument to add new servers
that are also automatically queried for features</li>
- <li>-groovy command line argument executes a given groovy
+ <li>• -groovy command line argument executes a given groovy
script after all input data has been loaded and parsed</li>
</ul> <em>Applet-Application data exchange</em>
<ul>
- <li>Trees passed as applet parameters can be passed to
+ <li>• Trees passed as applet parameters can be passed to
application (when using "View in full
application")</li>
</ul> <em>Applet Parameters</em>
<ul>
- <li>feature group display control parameter</li>
- <li>debug parameter</li>
- <li>showbutton parameter</li>
+ <li>• feature group display control parameter</li>
+ <li>• debug parameter</li>
+ <li>• showbutton parameter</li>
</ul> <em>Applet API methods</em>
<ul>
- <li>newView public method</li>
- <li>Window (current view) specific get/set public methods</li>
- <li>Feature display control methods</li>
- <li>get list of currently selected sequences</li>
+ <li>• newView public method</li>
+ <li>• Window (current view) specific get/set public methods</li>
+ <li>• Feature display control methods</li>
+ <li>• get list of currently selected sequences</li>
</ul> <em>New Jalview distribution features</em>
<ul>
- <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
- <li>RELEASE file gives build properties for the latest
+ <li>• InstallAnywhere Installer upgraded to IA 2008 VP1</li>
+ <li>• RELEASE file gives build properties for the latest
Jalview release.</li>
- <li>Java 1.1 Applet build made easier and donotobfuscate
+ <li>• Java 1.1 Applet build made easier and donotobfuscate
property controls execution of obfuscator</li>
- <li>Build target for generating source distribution</li>
- <li>Debug flag for javacc</li>
- <li>.jalview_properties file is documented (slightly) in
+ <li>• Build target for generating source distribution</li>
+ <li>• Debug flag for javacc</li>
+ <li>• .jalview_properties file is documented (slightly) in
jalview.bin.Cache</li>
- <li>Continuous Build Integration for stable and
+ <li>• Continuous Build Integration for stable and
development version of Application, Applet and source
distribution</li>
</ul></td>
<td>
<ul>
- <li>selected region output includes visible annotations
+ <li>• selected region output includes visible annotations
(for certain formats)</li>
- <li>edit label/displaychar contains existing label/char
+ <li>• edit label/displaychar contains existing label/char
for editing</li>
- <li>update PDBEntries when DBRefEntries change (vamsas)</li>
- <li>shorter peptide product names from EMBL records</li>
- <li>Newick string generator makes compact representations</li>
- <li>bootstrap values parsed correctly for tree files with
+ <li>• update PDBEntries when DBRefEntries change (vamsas)</li>
+ <li>• shorter peptide product names from EMBL records</li>
+ <li>• Newick string generator makes compact representations</li>
+ <li>• bootstrap values parsed correctly for tree files with
comments</li>
- <li>pathological filechooser bug avoided by not allowing
+ <li>• pathological filechooser bug avoided by not allowing
filenames containing a ':'</li>
- <li>Fixed exception when parsing GFF files containing
+ <li>• Fixed exception when parsing GFF files containing
global sequence features</li>
- <li>Alignment datasets are finalized only when number of
+ <li>• Alignment datasets are finalized only when number of
references from alignment sequences goes to zero</li>
- <li>Close of tree branch colour box without colour
+ <li>• Close of tree branch colour box without colour
selection causes cascading exceptions</li>
- <li>occasional negative imgwidth exceptions</li>
- <li>better reporting of non-fatal warnings to user when
+ <li>• occasional negative imgwidth exceptions</li>
+ <li>• better reporting of non-fatal warnings to user when
file parsing fails.</li>
- <li>Save works when Jalview project is default format</li>
- <li>Save as dialog opened if current alignment format is
+ <li>• Save works when Jalview project is default format</li>
+ <li>• Save as dialog opened if current alignment format is
not a valid output format</li>
- <li>UniProt canonical names introduced for both das and
+ <li>• UniProt canonical names introduced for both das and
vamsas</li>
- <li>Histidine should be midblue (not pink!) in Zappo</li>
- <li>error messages passed up and output when data read
+ <li>• Histidine should be midblue (not pink!) in Zappo</li>
+ <li>• error messages passed up and output when data read
fails</li>
- <li>edit undo recovers previous dataset sequence when
+ <li>• edit undo recovers previous dataset sequence when
sequence is edited</li>
- <li>allow PDB files without pdb ID HEADER lines (like
+ <li>• allow PDB files without pdb ID HEADER lines (like
those generated by MODELLER) to be read in properly</li>
- <li>allow reading of JPred concise files as a normal
+ <li>• allow reading of JPred concise files as a normal
filetype</li>
- <li>Stockholm annotation parsing and alignment properties
+ <li>• Stockholm annotation parsing and alignment properties
import fixed for PFAM records</li>
- <li>Structure view windows have correct name in Desktop
+ <li>• Structure view windows have correct name in Desktop
window list</li>
- <li>annotation consisting of sequence associated scores
+ <li>• annotation consisting of sequence associated scores
can be read and written correctly to annotation file</li>
- <li>Aligned cDNA translation to aligned peptide works
+ <li>• Aligned cDNA translation to aligned peptide works
correctly</li>
- <li>Fixed display of hidden sequence markers and
+ <li>• Fixed display of hidden sequence markers and
non-italic font for representatives in Applet</li>
- <li>Applet Menus are always embedded in applet window on
+ <li>• Applet Menus are always embedded in applet window on
Macs.</li>
- <li>Newly shown features appear at top of stack (in
+ <li>• Newly shown features appear at top of stack (in
Applet)</li>
- <li>Annotations added via parameter not drawn properly
+ <li>• Annotations added via parameter not drawn properly
due to null pointer exceptions</li>
- <li>Secondary structure lines are drawn starting from
+ <li>• Secondary structure lines are drawn starting from
first column of alignment</li>
- <li>UniProt XML import updated for new schema release in
+ <li>• UniProt XML import updated for new schema release in
July 2008</li>
- <li>Sequence feature to sequence ID match for Features
+ <li>• Sequence feature to sequence ID match for Features
file is case-insensitive</li>
- <li>Sequence features read from Features file appended to
+ <li>• Sequence features read from Features file appended to
all sequences with matching IDs</li>
- <li>PDB structure coloured correctly for associated views
+ <li>• PDB structure coloured correctly for associated views
containing a sub-sequence</li>
- <li>PDB files can be retrieved by applet from Jar files</li>
- <li>feature and annotation file applet parameters
+ <li>• PDB files can be retrieved by applet from Jar files</li>
+ <li>• feature and annotation file applet parameters
referring to different directories are retrieved correctly</li>
- <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
- <li>Fixed application hang whilst waiting for
+ <!--<li>• DAS Histogram Features display ( (Prlic et al) </li>-->
+ <li>• Fixed application hang whilst waiting for
splash-screen version check to complete</li>
- <li>Applet properly URLencodes input parameter values
+ <li>• Applet properly URLencodes input parameter values
when passing them to the launchApp service</li>
- <li>display name and local features preserved in results
+ <li>• display name and local features preserved in results
retrieved from web service</li>
- <li>Visual delay indication for sequence retrieval and
+ <li>• Visual delay indication for sequence retrieval and
sequence fetcher initialisation</li>
- <li>updated Application to use DAS 1.53e version of
+ <li>• updated Application to use DAS 1.53e version of
dasobert DAS client</li>
- <li>Re-instated Full AMSA support and .amsa file
+ <li>• Re-instated Full AMSA support and .amsa file
association</li>
- <li>Fixed parsing of JNet Concise annotation <em>sans</em>
+ <li>• Fixed parsing of JNet Concise annotation <em>sans</em>
sequences
</li>
</ul>
</td>
<td>
<ul>
- <li>Jmol 11.0.2 integration</li>
- <li>PDB views stored in Jalview XML files</li>
- <li>Slide sequences</li>
- <li>Edit sequence in place</li>
- <li>EMBL CDS features</li>
- <li>DAS Feature mapping</li>
- <li>Feature ordering</li>
- <li>Alignment Properties</li>
- <li>Annotation Scores</li>
- <li>Sort by scores</li>
- <li>Feature/annotation editing in applet</li>
+ <li>• Jmol 11.0.2 integration</li>
+ <li>• PDB views stored in Jalview XML files</li>
+ <li>• Slide sequences</li>
+ <li>• Edit sequence in place</li>
+ <li>• EMBL CDS features</li>
+ <li>• DAS Feature mapping</li>
+ <li>• Feature ordering</li>
+ <li>• Alignment Properties</li>
+ <li>• Annotation Scores</li>
+ <li>• Sort by scores</li>
+ <li>• Feature/annotation editing in applet</li>
</ul>
</td>
<td>
<ul>
- <li>Headless state operation in 2.2.1</li>
- <li>Incorrect and unstable DNA pairwise alignment</li>
- <li>Cut and paste of sequences with annotation</li>
- <li>Feature group display state in XML</li>
- <li>Feature ordering in XML</li>
- <li>blc file iteration selection using filename # suffix</li>
- <li>Stockholm alignment properties</li>
- <li>Stockhom alignment secondary structure annotation</li>
- <li>2.2.1 applet had no feature transparency</li>
- <li>Number pad keys can be used in cursor mode</li>
- <li>Structure Viewer mirror image resolved</li>
+ <li>• Headless state operation in 2.2.1</li>
+ <li>• Incorrect and unstable DNA pairwise alignment</li>
+ <li>• Cut and paste of sequences with annotation</li>
+ <li>• Feature group display state in XML</li>
+ <li>• Feature ordering in XML</li>
+ <li>• blc file iteration selection using filename # suffix</li>
+ <li>• Stockholm alignment properties</li>
+ <li>• Stockhom alignment secondary structure annotation</li>
+ <li>• 2.2.1 applet had no feature transparency</li>
+ <li>• Number pad keys can be used in cursor mode</li>
+ <li>• Structure Viewer mirror image resolved</li>
</ul>
</td>
</td>
<td>
<ul>
- <li>Non standard characters can be read and displayed
- <li>Annotations/Features can be imported/exported to the
+ <li>• Non standard characters can be read and displayed
+ <li>• Annotations/Features can be imported/exported to the
applet via textbox
- <li>Applet allows editing of sequence/annotation/group
+ <li>• Applet allows editing of sequence/annotation/group
name & description
- <li>Preference setting to display sequence name in
+ <li>• Preference setting to display sequence name in
italics
- <li>Annotation file format extended to allow
+ <li>• Annotation file format extended to allow
Sequence_groups to be defined
- <li>Default opening of alignment overview panel can be
+ <li>• Default opening of alignment overview panel can be
specified in preferences
- <li>PDB residue numbering annotation added to associated
+ <li>• PDB residue numbering annotation added to associated
sequences
</ul>
</td>
<td>
<ul>
- <li>Applet crash under certain Linux OS with Java 1.6
+ <li>• Applet crash under certain Linux OS with Java 1.6
installed
- <li>Annotation file export / import bugs fixed
- <li>PNG / EPS image output bugs fixed
+ <li>• Annotation file export / import bugs fixed
+ <li>• PNG / EPS image output bugs fixed
</ul>
</td>
</tr>
</td>
<td>
<ul>
- <li>Multiple views on alignment
- <li>Sequence feature editing
- <li>"Reload" alignment
- <li>"Save" to current filename
- <li>Background dependent text colour
- <li>Right align sequence ids
- <li>User-defined lower case residue colours
- <li>Format Menu
- <li>Select Menu
- <li>Menu item accelerator keys
- <li>Control-V pastes to current alignment
- <li>Cancel button for DAS Feature Fetching
- <li>PCA and PDB Viewers zoom via mouse roller
- <li>User-defined sub-tree colours and sub-tree selection
+ <li>• Multiple views on alignment
+ <li>• Sequence feature editing
+ <li>• "Reload" alignment
+ <li>• "Save" to current filename
+ <li>• Background dependent text colour
+ <li>• Right align sequence ids
+ <li>• User-defined lower case residue colours
+ <li>• Format Menu
+ <li>• Select Menu
+ <li>• Menu item accelerator keys
+ <li>• Control-V pastes to current alignment
+ <li>• Cancel button for DAS Feature Fetching
+ <li>• PCA and PDB Viewers zoom via mouse roller
+ <li>• User-defined sub-tree colours and sub-tree selection
- <li>'New Window' button on the 'Output to Text box'
+ <li>• 'New Window' button on the 'Output to Text box'
</ul>
</td>
<td>
<ul>
- <li>New memory efficient Undo/Redo System
- <li>Optimised symbol lookups and conservation/consensus
+ <li>• New memory efficient Undo/Redo System
+ <li>• Optimised symbol lookups and conservation/consensus
calculations
- <li>Region Conservation/Consensus recalculated after
+ <li>• Region Conservation/Consensus recalculated after
edits
- <li>Fixed Remove Empty Columns Bug (empty columns at end
+ <li>• Fixed Remove Empty Columns Bug (empty columns at end
of alignment)
- <li>Slowed DAS Feature Fetching for increased robustness.
+ <li>• Slowed DAS Feature Fetching for increased robustness.
- <li>Made angle brackets in ASCII feature descriptions
+ <li>• Made angle brackets in ASCII feature descriptions
display correctly
- <li>Re-instated Zoom function for PCA
- <li>Sequence descriptions conserved in web service
+ <li>• Re-instated Zoom function for PCA
+ <li>• Sequence descriptions conserved in web service
analysis results
- <li>UniProt ID discoverer uses any word separated by
+ <li>• UniProt ID discoverer uses any word separated by
∣
- <li>WsDbFetch query/result association resolved
- <li>Tree leaf to sequence mapping improved
- <li>Smooth fonts switch moved to FontChooser dialog box.
+ <li>• WsDbFetch query/result association resolved
+ <li>• Tree leaf to sequence mapping improved
+ <li>• Smooth fonts switch moved to FontChooser dialog box.
</td>
<td>
<ul>
- <li>Copy consensus sequence to clipboard</li>
+ <li>• Copy consensus sequence to clipboard</li>
</ul>
</td>
<td>
<ul>
- <li>Image output - rightmost residues are rendered if
+ <li>• Image output - rightmost residues are rendered if
sequence id panel has been resized</li>
- <li>Image output - all offscreen group boundaries are
+ <li>• Image output - all offscreen group boundaries are
rendered</li>
- <li>Annotation files with sequence references - all
+ <li>• Annotation files with sequence references - all
elements in file are relative to sequence position</li>
- <li>Mac Applet users can use Alt key for group editing</li>
+ <li>• Mac Applet users can use Alt key for group editing</li>
</ul>
</td>
</tr>
</td>
<td>
<ul>
- <li>MAFFT Multiple Alignment in default Web Service list</li>
- <li>DAS Feature fetching</li>
- <li>Hide sequences and columns</li>
- <li>Export Annotations and Features</li>
- <li>GFF file reading / writing</li>
- <li>Associate structures with sequences from local PDB
+ <li>• MAFFT Multiple Alignment in default Web Service list</li>
+ <li>• DAS Feature fetching</li>
+ <li>• Hide sequences and columns</li>
+ <li>• Export Annotations and Features</li>
+ <li>• GFF file reading / writing</li>
+ <li>• Associate structures with sequences from local PDB
files</li>
- <li>Add sequences to exisiting alignment</li>
- <li>Recently opened files / URL lists</li>
- <li>Applet can launch the full application</li>
- <li>Applet has transparency for features (Java 1.2
+ <li>• Add sequences to exisiting alignment</li>
+ <li>• Recently opened files / URL lists</li>
+ <li>• Applet can launch the full application</li>
+ <li>• Applet has transparency for features (Java 1.2
required)</li>
- <li>Applet has user defined colours parameter</li>
- <li>Applet can load sequences from parameter
+ <li>• Applet has user defined colours parameter</li>
+ <li>• Applet can load sequences from parameter
"sequence<em>x</em>"
</li>
</ul>
</td>
<td>
<ul>
- <li>Redundancy Panel reinstalled in the Applet</li>
- <li>Monospaced font - EPS / rescaling bug fixed</li>
- <li>Annotation files with sequence references bug fixed</li>
+ <li>• Redundancy Panel reinstalled in the Applet</li>
+ <li>• Monospaced font - EPS / rescaling bug fixed</li>
+ <li>• Annotation files with sequence references bug fixed</li>
</ul>
</td>
</tr>
</td>
<td>
<ul>
- <li>Change case of selected region from Popup menu</li>
- <li>Choose to match case when searching</li>
- <li>Middle mouse button and mouse movement can compress /
+ <li>• Change case of selected region from Popup menu</li>
+ <li>• Choose to match case when searching</li>
+ <li>• Middle mouse button and mouse movement can compress /
expand the visible width and height of the alignment</li>
</ul>
</td>
<td>
<ul>
- <li>Annotation Panel displays complete JNet results</li>
+ <li>• Annotation Panel displays complete JNet results</li>
</ul>
</td>
</tr>
<td> </td>
<td>
<ul>
- <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
- <li>Righthand label on wrapped alignments shows correct
+ <li>• Java 1.5 bug - InternalMessageDialog fix for threads</li>
+ <li>• Righthand label on wrapped alignments shows correct
value</li>
</ul>
</td>
</td>
<td>
<ul>
- <li>Editing can be locked to the selection area</li>
- <li>Keyboard editing</li>
- <li>Create sequence features from searches</li>
- <li>Precalculated annotations can be loaded onto
+ <li>• Editing can be locked to the selection area</li>
+ <li>• Keyboard editing</li>
+ <li>• Create sequence features from searches</li>
+ <li>• Precalculated annotations can be loaded onto
alignments</li>
- <li>Features file allows grouping of features</li>
- <li>Annotation Colouring scheme added</li>
- <li>Smooth fonts off by default - Faster rendering</li>
- <li>Choose to toggle Autocalculate Consensus On/Off</li>
+ <li>• Features file allows grouping of features</li>
+ <li>• Annotation Colouring scheme added</li>
+ <li>• Smooth fonts off by default - Faster rendering</li>
+ <li>• Choose to toggle Autocalculate Consensus On/Off</li>
</ul>
</td>
<td>
<ul>
- <li>Drag & Drop fixed on Linux</li>
- <li>Jalview Archive file faster to load/save, sequence
+ <li>• Drag & Drop fixed on Linux</li>
+ <li>• Jalview Archive file faster to load/save, sequence
descriptions saved.</li>
</ul>
</td>
</td>
<td>
<ul>
- <li>PDB Structure Viewer enhanced</li>
- <li>Sequence Feature retrieval and display enhanced</li>
- <li>Choose to output sequence start-end after sequence
+ <li>• PDB Structure Viewer enhanced</li>
+ <li>• Sequence Feature retrieval and display enhanced</li>
+ <li>• Choose to output sequence start-end after sequence
name for file output</li>
- <li>Sequence Fetcher WSDBFetch@EBI</li>
- <li>Applet can read feature files, PDB files and can be
+ <li>• Sequence Fetcher WSDBFetch@EBI</li>
+ <li>• Applet can read feature files, PDB files and can be
used for HTML form input</li>
</ul>
</td>
<td>
<ul>
- <li>HTML output writes groups and features</li>
- <li>Group editing is Control and mouse click</li>
- <li>File IO bugs</li>
+ <li>• HTML output writes groups and features</li>
+ <li>• Group editing is Control and mouse click</li>
+ <li>• File IO bugs</li>
</ul>
</td>
</tr>
</td>
<td>
<ul>
- <li>View annotations in wrapped mode</li>
- <li>More options for PCA viewer</li>
+ <li>• View annotations in wrapped mode</li>
+ <li>• More options for PCA viewer</li>
</ul>
</td>
<td>
<ul>
- <li>GUI bugs resolved</li>
- <li>Runs with -nodisplay from command line</li>
+ <li>• GUI bugs resolved</li>
+ <li>• Runs with -nodisplay from command line</li>
</ul>
</td>
</tr>
</td>
<td>
<ul>
- <li>Choose EPS export as lineart or text</li>
- <li>Jar files are executable</li>
- <li>Can read in Uracil - maps to unknown residue</li>
+ <li>• Choose EPS export as lineart or text</li>
+ <li>• Jar files are executable</li>
+ <li>• Can read in Uracil - maps to unknown residue</li>
</ul>
</td>
<td>
<ul>
- <li>Known OutOfMemory errors give warning message</li>
- <li>Overview window calculated more efficiently</li>
- <li>Several GUI bugs resolved</li>
+ <li>• Known OutOfMemory errors give warning message</li>
+ <li>• Overview window calculated more efficiently</li>
+ <li>• Several GUI bugs resolved</li>
</ul>
</td>
</tr>
</td>
<td>
<ul>
- <li>Edit and annotate in "Wrapped" view</li>
+ <li>• Edit and annotate in "Wrapped" view</li>
</ul>
</td>
<td>
<ul>
- <li>Several GUI bugs resolved</li>
+ <li>• Several GUI bugs resolved</li>
</ul>
</td>
</tr>
</td>
<td>
<ul>
- <li>Hold down mouse wheel & scroll to change font
+ <li>• Hold down mouse wheel & scroll to change font
size</li>
</ul>
</td>
<td>
<ul>
- <li>Improved JPred client reliability</li>
- <li>Improved loading of Jalview files</li>
+ <li>• Improved JPred client reliability</li>
+ <li>• Improved loading of Jalview files</li>
</ul>
</td>
</tr>
</td>
<td>
<ul>
- <li>Set Proxy server name and port in preferences</li>
- <li>Multiple URL links from sequence ids</li>
- <li>User Defined Colours can have a scheme name and added
+ <li>• Set Proxy server name and port in preferences</li>
+ <li>• Multiple URL links from sequence ids</li>
+ <li>• User Defined Colours can have a scheme name and added
to Colour Menu</li>
- <li>Choose to ignore gaps in consensus calculation</li>
- <li>Unix users can set default web browser</li>
- <li>Runs without GUI for batch processing</li>
- <li>Dynamically generated Web Service Menus</li>
+ <li>• Choose to ignore gaps in consensus calculation</li>
+ <li>• Unix users can set default web browser</li>
+ <li>• Runs without GUI for batch processing</li>
+ <li>• Dynamically generated Web Service Menus</li>
</ul>
</td>
<td>
<ul>
- <li>InstallAnywhere download for Sparc Solaris</li>
+ <li>• InstallAnywhere download for Sparc Solaris</li>
</ul>
</td>
</tr>
<td> </td>
<td>
<ul>
- <li>Copy & Paste order of sequences maintains
+ <li>• Copy & Paste order of sequences maintains
alignment order.</li>
</ul>
</td>
</td>
<td>
<ul>
- <li>Use delete key for deleting selection.</li>
- <li>Use Mouse wheel to scroll sequences.</li>
- <li>Help file updated to describe how to add alignment
+ <li>• Use delete key for deleting selection.</li>
+ <li>• Use Mouse wheel to scroll sequences.</li>
+ <li>• Help file updated to describe how to add alignment
annotations.</li>
- <li>Version and build date written to build properties
+ <li>• Version and build date written to build properties
file.</li>
- <li>InstallAnywhere installation will check for updates
+ <li>• InstallAnywhere installation will check for updates
at launch of Jalview.</li>
</ul>
</td>
<td>
<ul>
- <li>Delete gaps bug fixed.</li>
- <li>FileChooser sorts columns.</li>
- <li>Can remove groups one by one.</li>
- <li>Filechooser icons installed.</li>
- <li>Finder ignores return character when searching.
+ <li>• Delete gaps bug fixed.</li>
+ <li>• FileChooser sorts columns.</li>
+ <li>• Can remove groups one by one.</li>
+ <li>• Filechooser icons installed.</li>
+ <li>• Finder ignores return character when searching.
Return key will initiate a search.<br>
</li>
</ul>
</td>
<td>
<ul>
- <li>New codebase</li>
+ <li>• New codebase</li>
</ul>
</td>
<td> </td>
git://source.jalview.org / jalview.git / commitdiff