X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=475a8da04c862bc642fe85654cbf1ff5ea7a68b7;hb=fd102a4945da5c62de156159c98a6a2c51f1ebbc;hp=2b2184b9e92d986363c6df36423f20ed2bb00922;hpb=e75cf5f98eb75a8b23056c73e198ca9e75b8d6c8;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 2b2184b..475a8da 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,17 +47,38 @@
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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
@@ -69,10 +90,18 @@
- 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
+ - 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
@@ -82,6 +111,12 @@
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
@@ -247,7 +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
@@ -732,7 +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
@@ -1087,8 +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
@@ -1663,7 +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
@@ -1692,7 +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
@@ -1836,7 +1871,7 @@
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
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