<html>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
<tr>
<td width="60" nowrap>
<div align="center">
- <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
- <em>6/10/2015</em></strong>
+ <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
+ <em>25/10/2016</em></strong>
</div>
</td>
+ <td><em>Application</em>
+ <ul>
+ <li>3D Structure chooser opens with 'Cached structures'
+ view if structures already loaded</li>
+ <li>Progress bar reports models as they are loaded to
+ structure views</li>
+ </ul></td>
<td>
- <em>General</em>
- <ul>
- <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</li></ul>
- <em>Applet</em>
- <ul><li>Split frame example added to applet examples page</li>
- </ul>
+ <div align="left">
+ <em>General</em>
+ <ul>
+ <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
+ example sequences/projects/trees</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <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
+ superposed without timeout for structures with multiple
+ models or multiple sequences in alignment</li>
+ <li>Cannot import or associated local PDB files without
+ a PDB ID HEADER line</li>
+ <li>RMSD is not output in Jmol console when
+ superposition is performed</li>
+ <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
+ client attempts to fetch non-existent IDs via Fetch DB
+ Refs UI option</li>
+ <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:
+ 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
+ tags</li>
+ </ul>
+ <em>New Known Issues</em>
+ <ul>
+ <li>Drag and drop from URL links in browsers do not
+ work on Windows</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
+ </div>
+ </td>
+ <td><em>General</em>
+ <ul>
+ <li>
+ <!-- JAL-2124 -->Updated Spanish translations.
+ </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>
+ <!-- JAL-192 --->Alignment ruler shows positions relative to
+ reference sequence
+ </li>
+ <li>
+ <!-- JAL-2202 -->Position/residue shown in status bar when
+ mousing over sequence associated annotation
+ </li>
+ <li>
+ <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
+ for manual entry
+ </li>
+ <li>
+ <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
+ '()', canonical '[]' and invalid '{}' base pair populations
+ for each column
+ </li>
+ <li>
+ <!-- JAL-2092 -->Feature settings popup menu options for
+ showing or hiding columns containing a feature
+ </li>
+ <li>
+ <!-- JAL-1557 -->Edit selected group by double clicking on
+ group and sequence associated annotation labels
+ </li>
+ <li>
+ <!-- JAL-2236 -->Sequence name added to annotation label in
+ select/hide columns by annotation and colour by annotation
+ dialogs
+ </li>
+
+ </ul> <em>Application</em>
+ <ul>
+ <li>
+ <!-- JAL-2050-->Automatically hide introns when opening a
+ gene/transcript view
+ </li>
+ <li>
+ <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
+ dialog
+ </li>
+ <li>
+ <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
+ structure mappings with the EMBL-EBI PDBe SIFTS database
+ </li>
+ <li>
+ <!-- JAL-2079 -->Updated download sites used for Rfam and
+ Pfam sources to xfam.org
+ </li>
+ <li>
+ <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
+ </li>
+ <li>
+ <!-- JAL-2123 -->Show residue labels in Chimera when mousing
+ over sequences in Jalview
+ </li>
+ <li>
+ <!-- JAL-2027-->Support for reverse-complement coding
+ regions in ENA and EMBL
+ </li>
+ <li>
+ <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
+ for record retrieval via ENA rest API
+ </li>
+ <li>
+ <!-- JAL-2027 -->Support for ENA CDS records with reverse
+ complement operator
+ </li>
+ <li>
+ <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
+ groovy script execution
+ </li>
+ <li>
+ <!-- JAL-1812 -->New 'execute Groovy script' option in an
+ alignment window's Calculate menu
+ </li>
+ <li>
+ <!-- JAL-1812 -->Allow groovy scripts that call
+ Jalview.getAlignFrames() to run in headless mode
+ </li>
+ <li>
+ <!-- JAL-2068 -->Support for creating new alignment
+ calculation workers from groovy scripts
+ </li>
+ <li>
+ <!-- JAL-1369 --->Store/restore reference sequence in
+ Jalview projects
+ </li>
+ <li>
+ <!-- JAL-1803 -->Chain codes for a sequence's PDB
+ associations are now saved/restored from project
+ </li>
+ <li>
+ <!-- JAL-1993 -->Database selection dialog always shown
+ before sequence fetcher is opened
+ </li>
+ <li>
+ <!-- JAL-2183 -->Double click on an entry in Jalview's
+ database chooser opens a sequence fetcher
+ </li>
+ <li>
+ <!-- JAL-1563 -->Free-text search client for UniProt using
+ the UniProt REST API
+ </li>
+ <li>
+ <!-- JAL-2168 -->-nonews command line parameter to prevent
+ the news reader opening
+ </li>
+ <li>
+ <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
+ querying stored in preferences
+ </li>
+ <li>
+ <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
+ search results
+ </li>
+ <li>
+ <!-- JAL-1977-->Tooltips shown on database chooser
+ </li>
+ <li>
+ <!-- JAL-391 -->Reverse complement function in calculate
+ menu for nucleotide sequences
+ </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>
+ <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
+ viewing structures with Jalview 2.10
+ </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>
+ <!-- JAL-2049 -->Protein sequence variant annotation
+ computed for 'sequence_variant' annotation on CDS regions
+ (Ensembl)
+ </li>
+ <li>
+ <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
+ sequences
+ </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>
+ <!-- JAL-2154 -->Revised Jalview Project format for
+ efficient recovery of sequence coding and alignment
+ annotation relationships.
+ </li>
+ </ul> <!-- <em>Applet</em>
+ <ul>
+ <li>
+ -- JAL---
+ </li>
+ </ul> --></td>
+ <td>
+ <div align="left">
+ <em>General</em>
+ <ul>
+ <li>
+ <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
+ menu on OSX
+ </li>
+ <li>
+ <!-- JAL-2018-->Export features in Jalview format (again)
+ includes graduated colourschemes
+ </li>
+ <li>
+ <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
+ working with big alignments and lots of hidden columns
+ </li>
+ <li>
+ <!-- JAL-2053-->Hidden column markers not always rendered
+ at right of alignment window
+ </li>
+ <li>
+ <!-- JAL-2067 -->Tidied up links in help file table of
+ contents
+ </li>
+ <li>
+ <!-- JAL-2072 -->Feature based tree calculation not shown
+ for DNA alignments
+ </li>
+ <li>
+ <!-- JAL-2075 -->Hidden columns ignored during feature
+ based tree calculation
+ </li>
+ <li>
+ <!-- JAL-2065 -->Alignment view stops updating when show
+ unconserved enabled for group on alignment
+ </li>
+ <li>
+ <!-- JAL-2086 -->Cannot insert gaps into sequence when
+ set as reference
+ </li>
+ <li>
+ <!-- JAL-2146 -->Alignment column in status incorrectly
+ shown as "Sequence position" when mousing over
+ annotation
+ </li>
+ <li>
+ <!-- JAL-2099 -->Incorrect column numbers in ruler when
+ hidden columns present
+ </li>
+ <li>
+ <!-- JAL-1577 -->Colour by RNA Helices not enabled when
+ user created annotation added to alignment
+ </li>
+ <li>
+ <!-- JAL-1841 -->RNA Structure consensus only computed for
+ '()' base pair annotation
+ </li>
+ <li>
+ <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
+ in zero scores for all base pairs in RNA Structure
+ Consensus
+ </li>
+ <li>
+ <!-- JAL-2174-->Extend selection with columns containing
+ feature not working
+ </li>
+ <li>
+ <!-- JAL-2275 -->Pfam format writer puts extra space at
+ beginning of sequence
+ </li>
+ <li>
+ <!-- JAL-1827 -->Incomplete sequence extracted from pdb
+ entry 3a6s
+ </li>
+ <li>
+ <!-- JAL-2238 -->Cannot create groups on an alignment from
+ from a tree when t-coffee scores are shown
+ </li>
+ <li>
+ <!-- JAL-1836,1967 -->Cannot import and view PDB
+ structures with chains containing negative resnums (4q4h)
+ </li>
+ <li>
+ <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
+ some structures
+ </li>
+ <li>
+ <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
+ to Clustal, PIR and PileUp output
+ </li>
+ <li>
+ <!-- JAL-2008 -->Reordering sequence features that are
+ not visible causes alignment window to repaint
+ </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>
+ <!-- JAL-1797 -->amino acid physicochemical conservation
+ calculation should be case independent
+ </li>
+ <li>
+ <!-- JAL-2173 -->Remove annotation also updates hidden
+ columns
+ </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>
+ <!-- JAL-2065 -->Null pointer exceptions and redraw
+ problems when reference sequence defined and 'show
+ non-conserved' enabled
+ </li>
+ <li>
+ <!-- JAL-1306 -->Quality and Conservation are now shown on
+ load even when Consensus calculation is disabled
+ </li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <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>
+ <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
+ output when running on non-gb/us i18n platforms
+ </li>
+ <li>
+ <!-- JAL-1944 -->Error thrown when exporting a view with
+ hidden sequences as flat-file alignment
+ </li>
+ <li>
+ <!-- JAL-2030-->InstallAnywhere distribution fails when
+ launching Chimera
+ </li>
+ <li>
+ <!-- JAL-2080-->Jalview very slow to launch via webstart
+ (also hotfix for 2.9.0b2)
+ </li>
+ <li>
+ <!-- JAL-2085 -->Cannot save project when view has a
+ reference sequence defined
+ </li>
+ <li>
+ <!-- JAL-1011 -->Columns are suddenly selected in other
+ alignments and views when revealing hidden columns
+ </li>
+ <li>
+ <!-- JAL-1989 -->Hide columns not mirrored in complement
+ view in a cDNA/Protein splitframe
+ </li>
+ <li>
+ <!-- JAL-1369 -->Cannot save/restore representative
+ sequence from project when only one sequence is
+ represented
+ </li>
+ <li>
+ <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
+ in Structure Chooser
+ </li>
+ <li>
+ <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
+ structure consensus didn't refresh annotation panel
+ </li>
+ <li>
+ <!-- JAL-1962 -->View mapping in structure view shows
+ mappings between sequence and all chains in a PDB file
+ </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>
+ <!-- JAL-1975 -->Export complete shown after destination
+ file chooser is cancelled during an image export
+ </li>
+ <li>
+ <!-- JAL-2025 -->Error when querying PDB Service with
+ sequence name containing special characters
+ </li>
+ <li>
+ <!-- JAL-2024 -->Manual PDB structure querying should be
+ case insensitive
+ </li>
+ <li>
+ <!-- JAL-2104 -->Large tooltips with broken HTML
+ formatting don't wrap
+ </li>
+ <li>
+ <!-- JAL-1128 -->Figures exported from wrapped view are
+ truncated so L looks like I in consensus annotation
+ </li>
+ <li>
+ <!-- JAL-2003 -->Export features should only export the
+ currently displayed features for the current selection or
+ view
+ </li>
+ <li>
+ <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
+ after fetching cross-references, and restoring from project
+ </li>
+ <li>
+ <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
+ followed in the structure viewer
+ </li>
+ <li>
+ <!-- JAL-2163 -->Titles for individual alignments in
+ splitframe not restored from project
+ </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>
+ <!-- JAL-1797 -->amino acid physicochemical conservation
+ is case dependent
+ </li>
+ <li>
+ <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
+ article has been read (reopened issue due to
+ internationalisation problems)
+ </li>
+ <li>
+ <!-- JAL-1960 -->Only offer PDB structures in structure
+ viewer based on sequence name, PDB and UniProt
+ cross-references
+ </li>
+
+ <li>
+ <!-- JAL-1976 -->No progress bar shown during export of
+ alignment as HTML
+ </li>
+ <li>
+ <!-- JAL-2213 -->Structures not always superimposed after
+ multiple structures are shown for one or more sequences.
+ </li>
+ <li>
+ <!-- JAL-1370 -->Reference sequence characters should not
+ be replaced with '.' when 'Show unconserved' format option
+ is enabled.
+ </li>
+ <li>
+ <!-- JAL-1823 -->Cannot specify chain code when entering
+ specific PDB id for sequence
+ </li>
+ <li>
+ <!-- JAL-1944 -->File->Export->.. as doesn't work when
+ 'Export hidden sequences' is enabled, but 'export hidden
+ columns' is disabled.
+ </li>
+ <li>
+ <!--JAL-2026-->Best Quality option in structure chooser
+ selects lowest rather than highest resolution structures
+ for each sequence
+ </li>
+ <li>
+ <!-- JAL-1887 -->Incorrect start and end reported for PDB
+ to sequence mapping in 'View Mappings' report
+ </li>
+ <!-- may exclude, this is an external service stability issue JAL-1941
+ -- > RNA 3D structure not added via DSSR service</li> -->
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>
+ <!-- JAL-2151 -->Incorrect columns are selected when
+ hidden columns present before start of sequence
+ </li>
+ <li>
+ <!-- JAL-1986 -->Missing dependencies on applet pages
+ (JSON jars)
+ </li>
+ <li>
+ <!-- JAL-1947 -->Overview pixel size changes when
+ sequences are hidden in applet
+ </li>
+ <li>
+ <!-- JAL-1996 -->Updated instructions for applet
+ deployment on examples pages.
+ </li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
+ <em>16/10/2015</em></strong>
+ </div>
</td>
+ <td><em>General</em>
+ <ul>
+ <li>Time stamps for signed Jalview application and applet
+ jars</li>
+ </ul></td>
<td>
<div align="left">
- <em>General</em>
+ <em>Application</em>
+ <ul>
+ <li>Duplicate group consensus and conservation rows
+ shown when tree is partitioned</li>
+ <li>Erratic behaviour when tree partitions made with
+ multiple cDNA/Protein split views</li>
+ </ul>
+ </div>
+ </td>
+ </tr>
+ <tr>
+ <td width="60" nowrap>
+ <div align="center">
+ <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
+ <em>8/10/2015</em></strong>
+ </div>
+ </td>
+ <td><em>General</em>
+ <ul>
+ <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>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Split frame example added to applet examples page</li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>General</em>
<ul>
- <li>Mapping of cDNA to protein in split frames incorrect when sequence start > 1</li>
- <li>Broken images in filter column by annotation dialog documentation</li>
+ <li>Mapping of cDNA to protein in split frames
+ incorrect when sequence start > 1</li>
+ <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 loading a features file containing HTML tags in feature description</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 reimport</li>
- <li>Incorrect sequence limits after Fetch DB References with 'trim retrieved sequences'</li>
- <li>Incorrect warning about deleting all data when deleting selected columns</li>
- <li>Patch to build system for shipping properly signed JNLP templates for webstart launch</li>
- <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 fetcher/viewer dialogs works correctly</li>
- <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 recovered from jalview project</li>
- <li>Initial enabled/disabled state of annotation menu sorter 'show autocalculated first/last' corresponds to alignment view</li>
- </ul>
- <em>Applet</em><ul>
- <li>Reorder sequences mirrored in cDNA/Protein split frame</li>
+ <em>Application</em>
+ <ul>
+ <li>Annotations corrupted after BioJS export and
+ reimport</li>
+ <li>Incorrect sequence limits after Fetch DB References
+ with 'trim retrieved sequences'</li>
+ <li>Incorrect warning about deleting all data when
+ deleting selected columns</li>
+ <li>Patch to build system for shipping properly signed
+ JNLP templates for webstart launch</li>
+ <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
+ fetcher/viewer dialogs works correctly</li>
+ <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
+ recovered from jalview project</li>
+ <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
+ color schemes from BioJSON</li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>Reorder sequences mirrored in cDNA/Protein split
+ frame</li>
<li>Applet with Jmol examples not loading correctly</li>
- </ul>
+ </ul>
</div>
</td>
</tr>
region export in flat file generation</li>
<li>Export alignment views for display with the <a
- href="http://biojs.io/d/msa">BioJS MSAViewer</a></li>
+ 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
<tr>
<td><div align="center">
<strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
- <em>30/1/2014</em></strong>
+ <em>30/1/2014</em></strong>
</div></td>
<td>
<ul>
<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>
current built in colourscheme is saved as new scheme</li>
<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
which sequence is to be associated with the file</li>
<ul>
<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
menu</li>
between different screens.</li>
<li>New preference items for sequence ID tooltip and
consensus annotation</li>
- <li>Client to submit sequences and IDs to <a
- href="webServices/index.html#envision2">Envision2</a>
- Workflows
- </li>
+ <li>Client to submit sequences and IDs to Envision2
+ Workflows</li>
<li><em>Vamsas Capabilities</em>
<ul>
<li>Improved VAMSAS synchronization (Jalview archive
<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
due to null pointer exceptions</li>
<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
file is case-insensitive</li>
<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'
</ul>
<li>Fixed Remove Empty Columns Bug (empty columns at end
of alignment)
<li>Slowed DAS Feature Fetching for increased robustness.
+
+
+
+
+
<li>Made angle brackets in ASCII feature descriptions
display correctly
<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.
+
+
+
+
+
</ul>
</td>
git://source.jalview.org / jalview.git / blobdiff