X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Freleases.html;h=cffa10f692c88b13d3b8400aae8ab9556f447153;hb=07addcb8a9c7904b60e19f637c5258849987c2a6;hp=91ba69cc3e9cf180b4b564c3b93f1dd09073708a;hpb=6764c7be2ae71536ef150f5753ab36e585d56e5c;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index 91ba69c..cffa10f 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -70,46 +70,75 @@ li:before {
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-
+ Optional automatic backups when saving
+ Jalview project or alignment files
+ -
Principal Components Analysis and
Viewer state is saved in Jalview Project
The 'Change
- parameters' option has also been removed from the PCA
- viewer.
-
+ parameters' option has also been removed from the PCA viewer
+ -
+ New 'Colour by Sequence ID' (subgroup) option
+ -
+ Alternative genetic code tables supported for
+ 'Translate as cDNA'
+ -
+ Finder panel remembers last position in each view
-
More efficient creation of selections and
- multiple groups when working with large alignments
-
+ multiple groups when working with large alignments
-
Speedier import of annotation rows when
- parsing stockholm files
-
+ parsing stockholm files
-
- Update of Ensembl Rest Client to API v9.0
-
+ Update of Ensembl Rest Client to API v10.0
-
- Sequence features can be filtered and
+ Sequence features can be filtered and
shaded according to any associated attributes (e.g. variant
attributes from VCF file, or key-value pairs imported from
- column 9 of GFF file)
-
+ column 9 of GFF file)
-
- More efficient sequence feature render
- algorithm (Z-sort/transparency and filter aware)
-
+ More efficient sequence feature render
+ algorithm (Z-sort/transparency and filter aware)
-
Alignment Overview now by default shows
only visible region of alignment (this can be changed in
- user preferences)
-
- -
-
+ user preferences)
+ -
+ File Chooser stays open after Cancel overwrite
+ -
+ Better popup menu behaviour when
+ all sequences are hidden
+ -
+ Status bar shows bounds when dragging a selection
+ region, and gap count when inserting or deleting gaps
+ -
+ Status bar updates over sequence and annotation labels
+ -
+ Show annotation tooltips and popup menus in wrapped mode
+ -
+ Can select columns by dragging left/right in annotations
+ -
+ Improved tooltips in Feature Settings dialog
+ -
+ Help button on Uniprot and PDB search panels
+ -
+ Cursor changes over draggable box in Overview panel
+ -
+ Overview panel default changed to not show hidden regions
+ -
+ Consistent ordering of links in sequence id popup menu
+ -
+ Sequence Details report opens positioned to top of report
+ -
+ Scale panel popup menu allows Hide selected columns adjacent
+ to a hidden column marker
Deprecations
@@ -120,86 +149,104 @@ li:before {
Release Processes
- - Atlassian Bamboo continuous integration server for
+
-
+ Atlassian Bamboo continuous integration server for
unattended Test Suite execution
-
Memory test suite to detect leaks in common
- operations
-
+ operations
-
IntervalStoreJ (new updatable NCList
- implementation) used for Sequence Feature collections
-
+ implementation) used for Sequence Feature collections
-
Castor library for XML marshalling and
unmarshalling has been replaced by JAXB for Jalview projects
- and XML based data retrieval clients
-
- -
-
-
+ and XML based data retrieval clients
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-
+ Timeouts when retrieving data from Ensembl
+ -
Warning of 'Duplicate entry' when saving
- Jalview project involving multiple views
-
+ Jalview project involving multiple views
-
Overview for complementary view in a linked
CDS/Protein alignment is not updated when Hide Columns by
- Annotation dialog hides columns
-
+ Annotation dialog hides columns
-
Selection highlighting in the complement of
a CDS/Protein alignment stops working after making a
selection in one view, then making another selection in the
- other view.
-
- - Annotations tooltip changes beyond visible columns
+ other view
+ -
+ Annotations tooltip changes beyond visible columns
-
Table Columns could be re-ordered in
- Feature Settings and Jalview Preferences panels
-
+ Feature Settings and Jalview Preferences panels
-
Jalview hangs when closing windows
- or the overview updates with large alignments.
-
+ or the overview updates with large alignments
-
Tree and PCA calculation fails for selected
region if columns were selected by dragging right-to-left
- and the mouse moved to the left of the first column.
-
+ and the mouse moved to the left of the first column
-
Error message for trying to load in invalid
- URLs doesn't tell users the invalid URL
-
+ URLs doesn't tell users the invalid URL
+ -
+ Nonpositional features lose feature group
+ on export as Jalview features file
+ -
+ Status bar updates beyond visible columns
+ -
+ Blank extra columns drawn or
+ printed when columns are hidden
+ -
+ Regular expression error in Select Columns by Annotation description
+ -
+ Scroll doesn't stop on mouse up after
+ dragging out of Scale or Annotation Panel
+ -
+ Display is incorrect after Page Down and Up in wrapped mode
+ -
+ Help page can be opened twice
+ -
+ Finder doesn't skip hidden regions
+ -
+ Column selection incorrect after scrolling out of scale panel
+ -
+ Tree calculation fails on a selection dragged to left of alignment
+ -
+ 'Apply Colour to All Groups' not always selected on
+ opening an alignment
+ -
+ 'Colour by Annotation' not marked selected in Colour menu
+ -
+ Per-group Clustal colour scheme changes when
+ different groups in the alignment are selected
+ -
+ Value input for graduated feature colour threshold gets 'unrounded'
Editing
-
Start and End should be updated when
sequence data at beginning or end of alignment added/removed
- via 'Edit' sequence
-
+ via 'Edit' sequence
-
Delete/Cut selection doesn't relocate
sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
-
- -
-
-
+ removed (Known defect since 2.10)
New Known Defects
-
- Nonpositional features lose feature group
- on export as jalview features file
-
- - Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
+ Input Data menu entry is greyed out when PCA View is restored from a Jalview 2.11 project
+ -
+ Alignment panel height can be too small after 'New View'
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