X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=6f44b3d43272c66364c669b808e62b48c88aa38a;hb=0ce9577d119e1cc646f4b0d2e961f698d994fcc5;hp=afa11d9ef3919c716e3431a9c4d79d0b1928eb4b;hpb=85ac8be08a966098ea515abeff242c18dbac3b9e;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index afa11d9..6f44b3d 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -45,6 +45,792 @@
+ |
+
+ |
+
+ General
+
+ -
+ Improved memory usage: sparse arrays used
+ for all consensus calculations
+
+ -
+ Jmol updated to version 14.6.4 (released 3rd Oct 2016)
+
+ - Updated Jalview's Certum code signing certificate
+ for 2016-2017
+
+ 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
+
+
+ |
+
+
+ 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
+
+
+
+ |
+
+
+
+ |
+ 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
+
+ -
+ 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
+
+ -
+ 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.
+
+ |
+
+
+ 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
+
+ -
+ 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
+
+ -
+ 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.
+
+
+ |
+
+
+ |
+
+ |
+ General
+
+ - Time stamps for signed Jalview application and applet
+ jars
+ |
+
+
+ Application
+
+ - Duplicate group consensus and conservation rows
+ shown when tree is partitioned
+ - Erratic behaviour when tree partitions made with
+ multiple cDNA/Protein split views
+
+ |
+
+
+ |
+
+ |
+ General
+
+ - 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
+ |
+
+
+ General
+
+ - Mapping of cDNA to protein in split frames
+ incorrect when sequence start > 1
+ - Broken images in filter column by annotation dialog
+ documentation
+ - Feature colours not parsed from features file
+ - Exceptions and incomplete link URLs recovered when
+ loading a features file containing HTML tags in feature
+ description
+
+
+ Application
+
+ - Annotations corrupted after BioJS export and
+ reimport
+ - Incorrect sequence limits after Fetch DB References
+ with 'trim retrieved sequences'
+ - Incorrect warning about deleting all data when
+ deleting selected columns
+ - Patch to build system for shipping properly signed
+ JNLP templates for webstart launch
+ - EMBL-PDBe fetcher/viewer dialogs do not offer
+ unreleased structures for download or viewing
+ - Tab/space/return keystroke operation of EMBL-PDBe
+ fetcher/viewer dialogs works correctly
+ - Disabled 'minimise' button on Jalview windows
+ running on OSX to workaround redraw hang bug
+ - Split cDNA/Protein view position and geometry not
+ recovered from jalview project
+ - Initial enabled/disabled state of annotation menu
+ sorter 'show autocalculated first/last' corresponds to
+ alignment view
+ - Restoring of Clustal, RNA Helices and T-Coffee
+ color schemes from BioJSON
+
+ Applet
+
+ - Reorder sequences mirrored in cDNA/Protein split
+ frame
+ - Applet with Jmol examples not loading correctly
+
+ |
+
+
|
@@ -109,7 +895,7 @@
region export in flat file generation
Export alignment views for display with the BioJS MSAViewer
+ href="http://msa.biojs.net/">BioJS MSAViewer
Export scrollable SVG in HTML page
Optional embedding of BioJSON data when exporting
@@ -280,27 +1066,6 @@
- |
-
- |
-
-
- |
-
-
-
- - Reinstated the display of default example file on
- startup
- - All pairs shown in Jalview window when viewing
- result of pairwise alignment
-
- |
-
-
|
@@ -606,7 +1371,7 @@
|
@@ -615,7 +1380,7 @@
Certum to the Jalview
open source project).
- - Jalview SRS links replaced by Uniprot and EBI-search
+
- Jalview SRS links replaced by UniProt and EBI-search
- Output in Stockholm format
- Allow import of data from gzipped files
@@ -970,8 +1735,8 @@
current built in colourscheme is saved as new scheme
- AlignFrame->Save in application pops up save
dialog for valid filename/format
- - Cannot view associated structure for Uniprot sequence
- - PDB file association breaks for Uniprot sequence
+
- Cannot view associated structure for UniProt sequence
+ - PDB file association breaks for UniProt sequence
P37173
- Associate PDB from file dialog does not tell you
which sequence is to be associated with the file
@@ -1245,6 +2010,11 @@
- 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
@@ -1288,10 +2058,8 @@
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
@@ -1548,7 +2316,7 @@
- Save works when Jalview project is default format
- Save as dialog opened if current alignment format is
not a valid output format
- - Uniprot canonical names introduced for both das and
+
- UniProt canonical names introduced for both das and
vamsas
- Histidine should be midblue (not pink!) in Zappo
- error messages passed up and output when data read
@@ -1577,7 +2345,7 @@
due to null pointer exceptions
- Secondary structure lines are drawn starting from
first column of alignment
- - Uniprot XML import updated for new schema release in
+
- UniProt XML import updated for new schema release in
July 2008
- Sequence feature to sequence ID match for Features
file is case-insensitive
@@ -1699,6 +2467,11 @@
- Cancel button for DAS Feature Fetching
- 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'
@@ -1713,17 +2486,27 @@
- Fixed Remove Empty Columns Bug (empty columns at end
of alignment)
- Slowed DAS Feature Fetching for increased robustness.
+
+
+
+
+
- Made angle brackets in ASCII feature descriptions
display correctly
- Re-instated Zoom function for PCA
- Sequence descriptions conserved in web service
analysis results
-
- Uniprot ID discoverer uses any word separated by
+
- UniProt ID discoverer uses any word separated by
∣
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
+
+
+
+
+
|