X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=441b394aedd0acc3cc73d83e7bf73c7f9d85b5ae;hb=12c8641d36171e8c5ce40b0090bb09a8916de28b;hp=4e2502def9e46898e48b771c85d08f4a1b75c452;hpb=2b8019a244c53a24b2a13ea299ba8af02f90ff3b;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 4e2502d..441b394 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,82 +47,712 @@
|
+ |
+
+ General
+
+ -
+ Improved memory usage: sparse arrays used
+ for all consensus calculations
+
+ -
+ Updated Jmol shipped with applet and
+ desktop to 14.6.4
+
+ -
+
+
+
+
+ Application
+
+ -
+ Sequence ID tool tip presents abridged
+ set of database cross-references, sorted alphabetically
+
+ -
+ New replacement token for creating URLs just
+ from database cross references. Users with custom links
+ will receive a warning
+ dialog asking them to update their preferences.
+
+ -
+ Cancel button and escape listener on
+ dialog warning user about disconnecting Jalview from a
+ Chimera session
+
+ -
+ Jalview's Chimera control window closes if
+ the Chimera it is connected to is shut down
+
+ -
+ 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)
+
+ -
+ Command line option for batch-generation
+ of HTML pages rendering alignment data with the BioJS
+ MSAviewer
+
+
+ Applet
+ -->
+ Build and deployment
+
+ - Updated Jalview's Certum code signing certificate
+ for 2016-2017
+
+ |
+
+
+ General
+
+ -
+ Columns with more than one modal residue
+ are not coloured or thresholded according to percent
+ identity (first observed in Jalview 2.8.2)
+
+ -
+ Threonine incorrectly reported as not
+ hydrophobic
+
+ -
+ Updates to documentation pages (above PID
+ threshold, amino acid properties)
+
+ -
+ Lower case residues in sequences are not
+ reported as mapped to residues in a structure file in the
+ View Mapping report
+
+ -
+ Identical features with non-numeric scores
+ could be added multiple times to a sequence
+
+ -
+ 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
+
+ -
+ Custom URL links for database
+ cross-references are matched to database name regardless
+ of case
+
+
+
+ Application
+
+ -
+ Custom URL links for specific database
+ names without regular expressions also offer links from
+ Sequence ID
+
+ -
+ Removing a single configured link in the
+ URL links pane in Connections preferences doesn't actually
+ update Jalview configuration
+
+ -
+ CTRL-Click on a selected region to open
+ the alignment area popup menu doesn't work on El-Capitan
+
+ -
+ Jalview doesn't offer to associate mmCIF
+ files with similarly named sequences if dropped onto the
+ alignment
+
+ -
+ Additional mappings are shown for PDB
+ entries where more chains exist in the PDB accession than
+ are reported in the SIFTS file
+
+ -
+ Certain structures do not get mapped to
+ the structure view when displayed with Chimera
+
+ -
+ No chains shown in the Chimera view
+ panel's View->Show Chains submenu
+
+ -
+ Export as HTML with embedded SVG doesn't
+ work for wrapped alignment views
+
+ -
+ Rename UI components for running JPred
+ predictions from 'JNet' to 'JPred'
+
+ -
+ Export as PNG or SVG is
+ corrupted when annotation panel vertical scroll is not at
+ first annotation row
+
+ -
+ Attempting to view structure for Hen
+ lysozyme results in a PDB Client error dialog box
+
+
+
+ Build and deployment
+
+ -
+ Failing/passing unit tests
+
+
+ New Known Issues
+
+ |
+
+
+
+ |
+ Application
+
+ - 3D Structure chooser opens with 'Cached structures'
+ view if structures already loaded
+ - Progress bar reports models as they are loaded to
+ structure views
+ |
+
+
+ General
+
+ - Colour by conservation always enabled and no tick
+ shown in menu when BLOSUM or PID shading applied
+ - FER1_ARATH and FER2_ARATH labels were switched in
+ example sequences/projects/trees
+
+ Application
+
+ - Jalview projects with views of local PDB structure
+ files saved on Windows cannot be opened on OSX
+ - Multiple structure views can be opened and
+ superposed without timeout for structures with multiple
+ models or multiple sequences in alignment
+ - Cannot import or associated local PDB files without
+ a PDB ID HEADER line
+ - RMSD is not output in Jmol console when
+ superposition is performed
+ - Drag and drop of URL from Browser fails for Linux
+ and OSX versions earlier than El Capitan
+ - ENA client ignores invalid content from ENA server
+ - Exceptions are not raised in console when ENA
+ client attempts to fetch non-existent IDs via Fetch DB
+ Refs UI option
+ - Exceptions are not raised in console when a new
+ view is created on the alignment
+ - OSX right-click fixed for group selections:
+ CMD-click to insert/remove gaps in groups and CTRL-click
+ to open group pop-up menu
+
+ Build and deployment
+
+ - URL link checker now copes with multi-line anchor
+ tags
+
+ New Known Issues
+
+ - Drag and drop from URL links in browsers do not
+ work on Windows
+
+ |
+
+
+ |
+
|
General
- - Jmol now primary parser for importing structure data to Jalview. Enables mmCIF and better PDB parsing.
- - Alignment ruler shows positions relative to reference sequence
- - Position/residue shown in status bar when mousing over sequence associated annotation
- - Default RNA SS symbol to 'matching bracket' for manual entry
- - RNA Structure consensus indicates wc-only '()', canonical '[]' and invalid '{}' base pair populations for each column
- - Feature settings popup menu options for showing or hiding columns containing a feature
+ -
+ Updated Spanish translations.
+
+ -
+ Jmol now primary parser
+ for importing structure data to Jalview. Enables mmCIF and
+ better PDB parsing.
+
+ -
+ Alignment ruler shows positions relative to
+ reference sequence
+
+ -
+ Position/residue shown in status bar when
+ mousing over sequence associated annotation
+
+ -
+ Default RNA SS symbol to 'matching bracket'
+ for manual entry
+
+ -
+ RNA Structure consensus indicates wc-only
+ '()', canonical '[]' and invalid '{}' base pair populations
+ for each column
+
+ -
+ Feature settings popup menu options for
+ showing or hiding columns containing a feature
+
+ -
+ Edit selected group by double clicking on
+ group and sequence associated annotation labels
+
+ -
+ Sequence name added to annotation label in
+ select/hide columns by annotation and colour by annotation
+ dialogs
+
+
Application
-
-
-
-
- - Updated download sites used for Rfam and Pfam sources to xfam.org
- - Disabled Rfam(Full) in the sequence fetcher
- - Show residue labels in Chimera when mousing over sequences in Jalview
- - Support for reverse-complement coding regions in ENA and EMBL
- - Upgrade to EMBL XML 1.2 for ENA record retrieval
- - Support for ENA CDS records with reverse complement operator
- - New 'execute Groovy script' option in an alignment window's Calculate menu
- - Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
- - Support for creating new alignment calculation workers from groovy scripts
- - Store/restore reference sequence in Jalview projects
- - Chain codes for a sequence's PDB associations are now saved/restored from project
- - Double click on an entry in Jalview's database chooser opens a sequence fetcher
- - Free-text search client for UniProt using the UniProt REST API
-
-
- Applet
+
+ Automatically hide introns when opening a
+ gene/transcript view
+
+
+ Uniprot Sequence fetcher Free Text Search
+ dialog
+
+
+ UniProt - PDB protein
+ structure mappings with the EMBL-EBI PDBe SIFTS database
+
+
+ Updated download sites used for Rfam and
+ Pfam sources to xfam.org
+
+
+ Disabled Rfam(Full) in the sequence fetcher
+
+
+ Show residue labels in Chimera when mousing
+ over sequences in Jalview
+
+
+ Support for reverse-complement coding
+ regions in ENA and EMBL
+
+
+ Upgrade to EMBL XML 1.2
+ for record retrieval via ENA rest API
+
+
+ Support for ENA CDS records with reverse
+ complement operator
+
+
+ Update to groovy-2.4.6-indy - for faster
+ groovy script execution
+
+
+ New 'execute Groovy script' option in an
+ alignment window's Calculate menu
+
+
+ Allow groovy scripts that call
+ Jalview.getAlignFrames() to run in headless mode
+
+
+ Support for creating new alignment
+ calculation workers from groovy scripts
+
+
+ Store/restore reference sequence in
+ Jalview projects
+
+
+ Chain codes for a sequence's PDB
+ associations are now saved/restored from project
+
+
+ Database selection dialog always shown
+ before sequence fetcher is opened
+
+
+ Double click on an entry in Jalview's
+ database chooser opens a sequence fetcher
+
+
+ Free-text search client for UniProt using
+ the UniProt REST API
+
+
+ -nonews command line parameter to prevent
+ the news reader opening
+
+
+ Displayed columns for PDBe and Uniprot
+ querying stored in preferences
+
+
+ Pagination for displaying PDBe and Uniprot
+ search results
+
+
+ Tooltips shown on database chooser
+
+
+ Reverse complement function in calculate
+ menu for nucleotide sequences
+
+
+ Alignment sort by feature scores
+ and feature counts preserves alignment ordering (and
+ debugged for complex feature sets).
+
+
+ Chimera 1.11.1 minimum requirement for
+ viewing structures with Jalview 2.10
+
+
+ Retrieve
+ genome, transcript CCDS and gene ids via the Ensembl and
+ Ensembl Genomes REST API
+
+
+ Protein sequence variant annotation
+ computed for 'sequence_variant' annotation on CDS regions
+ (Ensembl)
+
+
+ ENA CDS 'show cross references' for Uniprot
+ sequences
+
+
+ Improved warning messages when DB
+ Ref Fetcher fails to match, or otherwise updates sequence
+ data from external database records.
+
+
+ Revised Jalview Project format for
+ efficient recovery of sequence coding and alignment
+ annotation relationships.
+
+
- |
+
+ -- JAL---
+
+ -->
General
- - reinstate CTRL-click for opening pop-up menu on OSX
- - Export features in Jalview format (again) includes graduated colourschemes
- - More responsive when working with big alignments and lots of hidden columns
- - Hidden column markers not always rendered at right of alignment window
- - Tidied up links in help file table of contents
- - Feature based tree calculation not shown for DNA alignments
- - Hidden columns ignored during feature based tree calculation
- - Alignment view stops updating when show unconserved enabled for group on alignment
- - Cannot insert gaps into sequence when set as reference
- - Alignment column in status incorrectly shown as "Sequence position" when mousing over annotation
- - Incorrect column numbers in ruler when hidden columns present
- - Colour by RNA Helices not enabled when user created annotation added to alignment
- - RNA Structure consensus only computed for '()' base pair annotation
- - Enabling 'Ignore Gaps' results in zero scores for all base pairs in RNA Structure Consensus
- - Extend selection with columns containing feature not working
-
-
+ -
+ reinstate CTRL-click for opening pop-up
+ menu on OSX
+
+ -
+ Export features in Jalview format (again)
+ includes graduated colourschemes
+
+ -
+ More responsive when
+ working with big alignments and lots of hidden columns
+
+ -
+ Hidden column markers not always rendered
+ at right of alignment window
+
+ -
+ Tidied up links in help file table of
+ contents
+
+ -
+ Feature based tree calculation not shown
+ for DNA alignments
+
+ -
+ Hidden columns ignored during feature
+ based tree calculation
+
+ -
+ Alignment view stops updating when show
+ unconserved enabled for group on alignment
+
+ -
+ Cannot insert gaps into sequence when
+ set as reference
+
+ -
+ Alignment column in status incorrectly
+ shown as "Sequence position" when mousing over
+ annotation
+
+ -
+ Incorrect column numbers in ruler when
+ hidden columns present
+
+ -
+ Colour by RNA Helices not enabled when
+ user created annotation added to alignment
+
+ -
+ RNA Structure consensus only computed for
+ '()' base pair annotation
+
+ -
+ Enabling 'Ignore Gaps' results
+ in zero scores for all base pairs in RNA Structure
+ Consensus
+
+ -
+ Extend selection with columns containing
+ feature not working
+
+ -
+ Pfam format writer puts extra space at
+ beginning of sequence
+
+ -
+ Incomplete sequence extracted from pdb
+ entry 3a6s
+
+ -
+ Cannot create groups on an alignment from
+ from a tree when t-coffee scores are shown
+
+ -
+ Cannot import and view PDB
+ structures with chains containing negative resnums (4q4h)
+
+ -
+ ArithmeticExceptions raised when parsing
+ some structures
+
+ -
+ 'Empty' alignment blocks added
+ to Clustal, PIR and PileUp output
+
+ -
+ Reordering sequence features that are
+ not visible causes alignment window to repaint
+
+ -
+ Threshold sliders don't work in
+ graduated colour and colour by annotation row for e-value
+ scores associated with features and annotation rows
+
+ -
+ amino acid physicochemical conservation
+ calculation should be case independent
+
+ -
+ Remove annotation also updates hidden
+ columns
+
+ -
+ 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)
+
+ -
+ Null pointer exceptions and redraw
+ problems when reference sequence defined and 'show
+ non-conserved' enabled
+
+ -
+ Quality and Conservation are now shown on
+ load even when Consensus calculation is disabled
+
+ -
+ Remove right on penultimate column of
+ alignment does nothing
+
Application
-
- - Corrupt preferences for SVG, EPS & HTML output when running on non-gb/us i18n platforms
- - URLs and links can imported by drag'n'drop on OSX webstart
- - InstallAnywhere distribution fails when launching Chimera
- - Jalview very slow to launch via webstart (also hotfix for 2.9.0b2)
- - Cannot save project when view has a reference sequence defined
- - Columns are suddenly selected in other alignments and views when revealing hidden columns
- - Hide columns not mirrored in complement view in a cDNA/Protein splitframe
- - Cannot save/restore representative sequence from project when only one sequence is represented
- - Disabled 'Best Uniprot Coverage' option in Structure Chooser
- - Modifying 'Ignore Gaps' on consensus or structure consensus didn't refresh annotation panel
-
+ -
+ URLs and links can't be imported by
+ drag'n'drop on OSX when launched via webstart (note - not
+ yet fixed for El Capitan)
+
+ -
+ Corrupt preferences for SVG, EPS & HTML
+ output when running on non-gb/us i18n platforms
+
+ -
+ Error thrown when exporting a view with
+ hidden sequences as flat-file alignment
+
+ -
+ InstallAnywhere distribution fails when
+ launching Chimera
+
+ -
+ Jalview very slow to launch via webstart
+ (also hotfix for 2.9.0b2)
+
+ -
+ Cannot save project when view has a
+ reference sequence defined
+
+ -
+ Columns are suddenly selected in other
+ alignments and views when revealing hidden columns
+
+ -
+ Hide columns not mirrored in complement
+ view in a cDNA/Protein splitframe
+
+ -
+ Cannot save/restore representative
+ sequence from project when only one sequence is
+ represented
+
+ -
+ Disabled 'Best Uniprot Coverage' option
+ in Structure Chooser
+
+ -
+ Modifying 'Ignore Gaps' on consensus or
+ structure consensus didn't refresh annotation panel
+
+ -
+ View mapping in structure view shows
+ mappings between sequence and all chains in a PDB file
+
+ -
+ PDB and Uniprot FTS
+ dialogs format columns correctly, don't display array
+ data, sort columns according to type
+
+ -
+ Export complete shown after destination
+ file chooser is cancelled during an image export
+
+ -
+ Error when querying PDB Service with
+ sequence name containing special characters
+
+ -
+ Manual PDB structure querying should be
+ case insensitive
+
+ -
+ Large tooltips with broken HTML
+ formatting don't wrap
+
+ -
+ Figures exported from wrapped view are
+ truncated so L looks like I in consensus annotation
+
+ -
+ Export features should only export the
+ currently displayed features for the current selection or
+ view
+
+ -
+ Enable 'Get Cross-References' in menu
+ after fetching cross-references, and restoring from project
+
+ -
+ Mouseover of a copy of a sequence is not
+ followed in the structure viewer
+
+ -
+ Titles for individual alignments in
+ splitframe not restored from project
+
+ -
+ missing autocalculated annotation at
+ trailing end of protein alignment in transcript/product
+ splitview when pad-gaps not enabled by default
+
+ -
+ amino acid physicochemical conservation
+ is case dependent
+
+ -
+ RSS reader doesn't stay hidden after last
+ article has been read (reopened issue due to
+ internationalisation problems)
+
+ -
+ Only offer PDB structures in structure
+ viewer based on sequence name, PDB and UniProt
+ cross-references
+
+
+ -
+ No progress bar shown during export of
+ alignment as HTML
+
+ -
+ Structures not always superimposed after
+ multiple structures are shown for one or more sequences.
+
+ -
+ Reference sequence characters should not
+ be replaced with '.' when 'Show unconserved' format option
+ is enabled.
+
+ -
+ Cannot specify chain code when entering
+ specific PDB id for sequence
+
+ -
+ File->Export->.. as doesn't work when
+ 'Export hidden sequences' is enabled, but 'export hidden
+ columns' is disabled.
+
+ -
+ Best Quality option in structure chooser
+ selects lowest rather than highest resolution structures
+ for each sequence
+
+ -
+ Incorrect start and end reported for PDB
+ to sequence mapping in 'View Mappings' report
+
+ -
+ Unable to read old Jalview projects that
+ contain non-XML data added after Jalvew wrote project.
+
+ - Newly created annotation row reorders
+ after clicking on it to create new annotation for a
+ column.
+
+
Applet
-
+ -
+ Incorrect columns are selected when
+ hidden columns present before start of sequence
+
+ -
+ Missing dependencies on applet pages
+ (JSON jars)
+
+ -
+ Overview pixel size changes when
+ sequences are hidden in applet
+
+ -
+ Updated instructions for applet
+ deployment on examples pages.
+
|
@@ -163,13 +793,16 @@
Updated Spanish translations of localized text for
2.9
Application
-
+
- Signed OSX InstallAnywhere installer
- Support for per-sequence based annotations in BioJSON
Applet
- Split frame example added to applet examples page
+
Build and Deployment
+
+ - New ant target for running Jalview's test suite
@@ -1399,6 +2032,10 @@
- URL links generated from description line for
regular-expression based URL links (applet and application)
+
+
+
+
- Non-positional feature URL links are shown in link
menu
@@ -1442,7 +2079,8 @@
between different screens.
- New preference items for sequence ID tooltip and
consensus annotation
- - Client to submit sequences and IDs to Envision2 Workflows
+ - Client to submit sequences and IDs to Envision2
+ Workflows
- Vamsas Capabilities
- Improved VAMSAS synchronization (Jalview archive
@@ -1851,6 +2489,10 @@
- PCA and PDB Viewers zoom via mouse roller
- User-defined sub-tree colours and sub-tree selection
+
+
+
+
- 'New Window' button on the 'Output to Text box'
@@ -1866,6 +2508,10 @@
of alignment)
- Slowed DAS Feature Fetching for increased robustness.
+
+
+
+
- Made angle brackets in ASCII feature descriptions
display correctly
@@ -1878,6 +2524,10 @@
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
+
+
+
+
|