X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=6eb42bc7d90a51d5a90ec2ac2a6fc7dcd20f919e;hb=e5ff0544866ec954e311b7401f5c3989c0016a5e;hp=25830822b6630f5880288f73c4c9937a0370ad5f;hpb=54df37fffa15c0fe522b96ba5a443f3ba21e54d3;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 2583082..6eb42bc 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,19 +47,65 @@
|
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 ENA record retrieval
- - New 'execute Groovy script' option in an alignment window's Calculate menu
- - Allow groovy scripts that call Jalview.getAlignFrames() to run in headless mode
+ - 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
@@ -71,14 +117,55 @@
- 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
+ - 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
@@ -87,11 +174,74 @@
- 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.
+
|
@@ -252,7 +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
@@ -737,7 +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
@@ -1092,8 +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
@@ -1668,7 +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
@@ -1697,7 +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
@@ -1841,7 +1991,7 @@
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