X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=475a8da04c862bc642fe85654cbf1ff5ea7a68b7;hb=ac93424cd4c19aa35f7831e4f3da7bbcaf6baf15;hp=6802f698a4dfdd37f88a98e89f6c3a8c17647a8e;hpb=c6083a0519c5d89bbe63a1112acdc9af07ef27a8;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 6802f69..475a8da 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,32 +47,81 @@
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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
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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
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+
+ - 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
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@@ -233,7 +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
@@ -718,7 +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
@@ -1073,8 +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
@@ -1649,7 +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
@@ -1678,7 +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
@@ -1822,7 +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