X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=c4a8bab9d1fd1e9905f225b33c0955a4f23120ca;hb=d0771875f23ab994c4f85fb6cd604378768df10e;hp=6f1c35122c30432ac35a193a52991ab49cddaf7a;hpb=f56c23d8432153bda35721d78325afcd7ce3dc86;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 6f1c351..c4a8bab 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -47,32 +47,63 @@
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General
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+
+ - Alignment ruler shows positions relative to reference sequence
Application
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+
+
+
+
+
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+ - 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
+ - Store/restore reference sequence in Jalview projects
+
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
+
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
+
Applet
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@@ -233,7 +264,7 @@
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 +749,7 @@
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 +1104,8 @@
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 +1680,7 @@
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 +1709,7 @@
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 +1853,7 @@
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