</td>
<td><em>General</em>
<ul>
- <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>
-
+ <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-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- -->
+ </li>
+ <li>
+ <!-- JAL- -->
+ </li>
+
+
+ </ul> <em>Applet</em>
+ <ul>
+ <li>
+ <!-- JAL--->
+ </li>
+ </ul></td>
+ <td>
+ <div align="left">
+ <em>General</em>
+ <ul>
<li>
- <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores and feature counts preserves alignment ordering (and debugged for complex feature sets).
+ <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
+ menu on OSX
</li>
<li>
- <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for viewing structures with Jalview 2.10
+ <!-- JAL-2018-->Export features in Jalview format (again)
+ includes graduated colourschemes
</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
+ <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
+ working with big alignments and lots of hidden columns
</li>
<li>
- <!-- JAL-2049 -->Protein sequence variant annotation computed for 'sequence_variant' annotation on CDS regions (Ensembl)
+ <!-- JAL-2053-->Hidden column markers not always rendered
+ at right of alignment window
</li>
- <li><!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot sequences</li>
<li>
- <!-- JAL- -->
+ <!-- JAL-2067 -->Tidied up links in help file table of
+ contents
</li>
<li>
- <!-- JAL- -->
+ <!-- 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>
-
-
- </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
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)
+ <!-- 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
+ <!-- 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>
- <li><!-- JAL-1306 -->Quality and Conservation are now shown on load even when Consensus calculation is disabled</li>
<li>
<!-- -->
</li>
</ul>
<em>Application</em>
<ul>
- <li><!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment--></li>
- <li><!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms</li>
- <li><!-- JAL-1552-->URLs and links can imported by drag'n'drop on OSX webstart</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</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
+ <!-- JAL-1944 not yet fixed Error thrown when exporting a view with hidden sequences as flat-file alignment-->
+ </li>
+ <li>
+ <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
+ output when running on non-gb/us i18n platforms
+ </li>
+ <li>
+ <!-- JAL-1552-->URLs and links can imported by drag'n'drop
+ on OSX webstart
+ </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-1797 -->amino acid physicochemical conservation is case dependent
+ <!-- JAL-1011 -->Columns are suddenly selected in other
+ alignments and views when revealing hidden columns
</li>
<li>
- <!-- JAL-1448 -->RSS reader doesn't stay hidden after last article has been read (reopened issue due to internationalisation problems)
+ <!-- JAL-1989 -->Hide columns not mirrored in complement
+ view in a cDNA/Protein splitframe
</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
+ <!-- JAL-1369 -->Cannot save/restore representative
+ sequence from project when only one sequence is
+ represented
</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.
+ <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
+ in Structure Chooser
</li>
<li>
- <!-- JAL-2213 -->Structures not always superimposed after multiple structures are shown for one or more sequences.
+ <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
+ structure consensus didn't refresh annotation panel
</li>
<li>
- <!-- JAL-1370 -->Reference sequence characters should not be replaced with '.' when 'Show unconserved' format option is enabled.
+ <!-- JAL-1962 -->View mapping in structure view shows
+ mappings between sequence and all chains in a PDB file
</li>
<li>
- <!-- JAL-1823 -->Cannot specify chain code when entering specific PDB id for sequence
+ <!-- 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-1944 -->File->Export->.. as doesn't work when 'Export hidden sequences' is enabled, but 'export hidden columns' is disabled.
+ <!-- JAL-1975 -->Export complete shown after destination
+ file chooser is cancelled during an image export
</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
+ <!-- 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
+ </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,JAL-1856 -->Improved warning messages when
+ DB Ref Fetcher fails to match, or otherwise updates
+ sequence data from external database records.
+ </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>
<li>
<!-- JAL- -->
</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
+ <!-- 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-1996 -->Updated instructions for applet deployment on examples pages.
+ <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>
<li>Updated Spanish translations of localized text for
2.9</li>
</ul> <em>Application</em>
- <ul>
+ <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>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 Envision2 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>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>
of alignment)
<li>Slowed DAS Feature Fetching for increased robustness.
+
<li>Made angle brackets in ASCII feature descriptions
display correctly
<li>Tree leaf to sequence mapping improved
<li>Smooth fonts switch moved to FontChooser dialog box.
+
</ul>
</td>
git://source.jalview.org / jalview.git / commitdiff