X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=475a8da04c862bc642fe85654cbf1ff5ea7a68b7;hb=ac93424cd4c19aa35f7831e4f3da7bbcaf6baf15;hp=afa11d9ef3919c716e3431a9c4d79d0b1928eb4b;hpb=85ac8be08a966098ea515abeff242c18dbac3b9e;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index afa11d9..475a8da 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -45,6 +45,179 @@
+ |
+
+ |
+ 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
+ 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
+ |
+
+
+ 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
+
+
+
+ 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
+
+
+ Applet
+
+ |
+
+
+ |
+
+ |
+ 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
+
+ |
+
+
|
@@ -109,7 +282,7 @@
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 +453,6 @@
- |
-
- |
-
-
- |
-
-
-
- - Reinstated the display of default example file on
- startup
- - All pairs shown in Jalview window when viewing
- result of pairwise alignment
-
- |
-
-
|
@@ -606,7 +758,7 @@
|
@@ -615,7 +767,7 @@
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 +1122,8 @@
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 +1397,7 @@
- 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 +1441,7 @@
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 +1698,7 @@
- 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 +1727,7 @@
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 +1849,7 @@
- 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 +1864,19 @@
- 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.
+
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