X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=6eb42bc7d90a51d5a90ec2ac2a6fc7dcd20f919e;hb=e5ff0544866ec954e311b7401f5c3989c0016a5e;hp=3c265faa4e3a0c97c84f7f641cf2382a22d501da;hpb=a49ce69b89678b3e6ba3c1a61b62d61cc9ee7342;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 3c265fa..6eb42bc 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -45,6 +45,299 @@
+ |
+
+ |
+ 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
+ - 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
+ -
+
+
+ -
+
+
+
+
+ Applet
+ |
+
+
+ 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
+ -
+
+
+ -
+
+
+ -
+
+
+
+ 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
+ - 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
+ - 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
+
+ -
+ Improved warning messages when DB Ref Fetcher fails to match, or otherwise updates sequence data from external database records.
+
+ -
+ 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
+
+ -
+
+
+ -
+
+
+
+
+
+ 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
+ |
+
+
+ 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
+
+ |
+
+
|
@@ -65,7 +358,7 @@
Jmol integration updated to Jmol v14.2.14
Import and export of Jalview alignment views as BioJSON
+ href="features/bioJsonFormat.html">BioJSON
New alignment annotation file statements for
reference sequences and marking hidden columns
Reference sequence based alignment shading to
@@ -109,7 +402,7 @@
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 +573,6 @@
- |
-
- |
-
-
- |
-
-
-
- - Reinstated the display of default example file on
- startup
- - All pairs shown in Jalview window when viewing
- result of pairwise alignment
-
- |
-
-
|
@@ -606,7 +878,7 @@
|
@@ -615,7 +887,7 @@
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 +1242,8 @@
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 +1517,7 @@
- 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 +1561,7 @@
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 +1818,7 @@
- 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 +1847,7 @@
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 +1969,7 @@
- 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 +1984,19 @@
- 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.
+
|