X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Freleases.html;h=0e13dabf9d7156685cd54792629403a47abeffb9;hb=19a35562dfd8e4e534681d2d4163e7b07117bd7c;hp=8ef92b9bdabba84b6684a23505450259a4003770;hpb=fa265315cce1d9329ab4db8d464e991847927474;p=jalview.git
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 8ef92b9..0e13dab 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -63,7 +63,32 @@ li:before {
-
+ Jalview Native Application and
+ Installers built with install4j (licensed to the Jalview open
+ source project) rather than InstallAnywhere
+
+ -
+ Jalview Launcher System to auto-configure memory
+ settings, receive over the air updates and launch specific
+ versions via (Three
+ Rings' GetDown)
+
+ -
+ File type associations for
+ formats supported by jalview (including .jvp project files)
+
+ -
+ Jalview launch files (.jvl) to pass command line
+ arguments and switch between different getdown channels
+
+ -
+ Backup files created when saving Jalview project
+ or alignment files
+
+
+ -
Annotate nucleotide alignments from VCF data files
+ - Version of HTSJDK shipped with Jalview updated to version 2.12.0
-
Alternative genetic code tables for
'Translate as cDNA'
@@ -71,6 +96,10 @@ li:before {
Update of Ensembl Rest Client to API v10.0
- Enhanced visualisation and analysis of Sequence Features
+ -
+ IntervalStoreJ (NCList
+ implementation that alows updates) used for Sequence Feature collections
+ -
-
Sequence features can be filtered and
shaded according to any associated attributes (e.g. variant
@@ -86,7 +115,7 @@ li:before {
details
-
- More efficient sequence feature render
+ More efficient sequence feature render
algorithm (Z-sort/transparency and filter aware)
-
@@ -96,10 +125,10 @@ li:before {
-
- Backup files created when saving Jalview project
- or alignment files
-
- - Principal Components Analysis Viewer
+ Symmetric score matrices for faster
+ tree and PCA calculations
+
+ - Principal Components Analysis Viewer
-
Principal Components Analysis results
@@ -112,7 +141,7 @@ li:before {
incrementally
-
- PCA plot is depth cued
+ PCA plot is depth cued
@@ -122,7 +151,7 @@ li:before {
- Speed and Efficiency
-
- More efficient creation of selections and
+ More efficient creation of selections and
multiple groups when working with large alignments
-
@@ -137,7 +166,7 @@ li:before {
view
-
- Alignment Overview now WYSIWIS (What you see is
+ Alignment Overview now WYSIWIS (What you see is
what is shown)
Only visible region of alignment is shown by
default (can be changed in user preferences)
@@ -183,13 +212,10 @@ li:before {
- - Java 11 Support
+
- Jalview Groovy Scripting Console updated to Groovy v2.5
+ - Java 11 Support (not yet on general release)
-
- Java 11 Native Desktop installer, standalone JAR
- and getdown release channels
-
- -
OSX GUI integrations for App menu's 'About' entry and
trapping CMD-Q
@@ -215,149 +241,223 @@ li:before {
Development and Release Processes
- -
- Jalview Native Application and
- Installers built with Install4j (licensed to the Jalview open
- source project) rather than InstallAnywhere
-
- -
- Jalview Launcher System to auto-configure memory
- settings, receive over the air updates and launch specific
- versions via (Three
- Rings' GetDown)
-
- -
- Build system migrated from Ant to Gradle
+
-
+ Build system migrated from Ant to Gradle
+ - Enhanced checks for missing and duplicated keys in Message bundles
-
Eclipse project configuration managed with
gradle-eclipse
- -
+
-
Atlassian Bamboo continuous integration for
unattended Test Suite execution
-
Memory test suite to detect leaks in common
operations
- -
- IntervalStoreJ (NCList
- implementation that alows updates) used for Sequence Feature collections
+ - More unit test coverage, and minor issues resolved.
+ - Developer documentation migrated to markdown (with HTML rendering)
|
-
-
- -
- Timeouts when retrieving data from Ensembl
- -
- 'View [Structure] Mappings' and structure superposition in Jmol fail on Windows
- -
- Text misaligned in EPS or SVG image export with monospaced font
- -
- Warning of 'Duplicate entry' when saving
- 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
- -
- 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
- -
- Table Columns could be re-ordered in
- Feature Settings and Jalview Preferences panels
- -
- Jalview hangs when closing windows
- 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
- -
- Couldn't hide selected columns adjacent
- to a hidden column marker via scale popup menu
- -
- Error message for trying to load in invalid
- URLs doesn't tell users the invalid URL
- -
- Nonpositional features lose feature group
- on export as Jalview features file
+
+
+ -
+ Timeouts when retrieving data from Ensembl
+
+ -
+ 'View [Structure] Mappings' and structure
+ superposition in Jmol fail on Windows
+
+ -
+ Blank error dialog is displayed when discovering
+ structures for sequences with lots of PDB structures
+
+ -
+ Text misaligned in EPS or SVG image export with
+ monospaced font
+
+ -
+ Warning of 'Duplicate entry' when saving 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
+
+ -
+ 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
+
+ -
+ Table Columns could be re-ordered in Feature
+ Settings and Jalview Preferences panels
+
+ -
+ Jalview hangs when closing windows 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
+
+ -
+ Couldn't hide selected columns adjacent to a
+ hidden column marker via scale popup menu
+
+ -
+ Error message for trying to load in invalid URLs
+ doesn't tell users the invalid URL
+
+ -
+ Nonpositional features lose feature group on
+ export as Jalview features file
+
+ -
+ Tooltips displayed for features filtered by
+ score from view
+
-
'Graduated colour' option not offered for
manually created features (where if feature score is Float.NaN)
-
- Blank extra columns drawn or
- printed when columns are hidden
- -
- Regular expression error for '(' in Select Columns by Annotation description
- -
- Scroll doesn't stop on mouse up after
- dragging out of Scale or Annotation Panel
- -
- Column selection incorrect after scrolling out of scale panel
- -
- Left/right drag in annotation can scroll alignment down
- -
- Error if mouse moved before clicking Reveal in scale panel
- -
- Column display is out by one after Page Down, Page Up in wrapped mode
- -
- Finder doesn't skip hidden regions
- -
- Finder searches in minimised alignments
- -
- '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
- -
- Internationalised colour scheme names not shown correctly in menu
- -
- Colour by Annotation can go black at min/max threshold limit
- -
- Value input for graduated feature colour threshold gets 'unrounded'
- -
- PCA image export doesn't respect background colour
- -
- PCA points don't dim when rotated about y axis
- -
- PCA Print dialog continues after Cancel
- -
- Cancel in Tree Font dialog resets alignment, not Tree font
- -
- Associate Tree with All Views not restored from project file
- -
- Scrolling of split frame is sluggish if Overview shown in complementary view
- -
- stop_gained variants not shown correctly on peptide sequence
- -
- Sequence Details report opens positioned to top of report
- -
- Help page can be opened twice
-
- Editing
-
- -
- Start and End should be updated when
- sequence data at beginning or end of alignment added/removed
- via 'Edit' sequence
- -
- Delete/Cut selection doesn't relocate
- sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
- New Known Defects
-
- -
- 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'
+ Blank extra columns drawn or printed
+ when columns are hidden
+
+ -
+ Regular expression error for '(' in Select
+ Columns by Annotation description
+
+ -
+ Scroll doesn't stop on mouse up after dragging
+ out of Scale or Annotation Panel
+
+ -
+ Column selection incorrect after scrolling out of
+ scale panel
+
+ -
+ Left/right drag in annotation can scroll
+ alignment down
+
+ -
+ Error if mouse moved before clicking Reveal in
+ scale panel
+
+ -
+ Column display is out by one after Page Down,
+ Page Up in wrapped mode
+
+ -
+ Finder doesn't skip hidden regions
+
+ -
+ Finder searches in minimised alignments
+
+ -
+ '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
+
+ -
+ Internationalised colour scheme names not shown
+ correctly in menu
+
+ -
+ Colour by Annotation can go black at min/max
+ threshold limit
+
+ -
+ Value input for graduated feature colour
+ threshold gets 'unrounded'
+
+ -
+ PCA image export doesn't respect background
+ colour
+
+ -
+ PCA points don't dim when rotated about y axis
+
+ -
+ PCA Print dialog continues after Cancel
+
+ -
+ Cancel in Tree Font dialog resets alignment, not
+ Tree font
+
+ -
+ Associate Tree with All Views not restored from
+ project file
+
+ -
+ Scrolling of split frame is sluggish if Overview
+ shown in complementary view
+
+ -
+ stop_gained variants not shown correctly on
+ peptide sequence
+
+ -
+ Codon consensus incorrectly scaled when shown
+ without normalisation
+
+ -
+ Sequence Details report opens positioned to top
+ of report
+
+ -
+ Help page can be opened twice
+
+ Editing
+
+ -
+ Start and End should be updated when sequence
+ data at beginning or end of alignment added/removed via 'Edit'
+ sequence
+
+ -
+ Delete/Cut selection doesn't
+ relocate sequence features correctly when start of sequence is
+ removed (Known defect since 2.10)
+
+ -
+ Inserting gap sequence via the Edit Sequence
+ dialog corrupts dataset sequence
+
+ -
+ Structure colours not updated when associated tree
+ repartitions the alignment view (Regression in 2.10.5)
+
+
+
+ New Known Defects
+
+ -
+ Codon consensus logo incorrectly scaled in gapped
+ regions of protein alignment.
+
+ -
+ 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'
+
-
Display is incorrect after removing gapped
columns within hidden columns
@@ -367,9 +467,22 @@ li:before {
window after dragging left to select columns to left of visible
region
+ -
+ Features coloured according to their description
+ string and thresholded by score in earlier versions of Jalview are
+ not shown as thresholded features in 2.11. To workaround please
+ create a Score filter instead.
+
+ - Java 11 Specific defects
+
+ -
+ Jalview Properties file is not sorted alphabetically when saved
+
+
+
- |
-
+ |
+
@@ -542,6 +655,10 @@ li:before {
open URL in the browser can be dropped onto Jalview.
+ New Known Defects
+
+ - Cancel option doesn't reset Colour by Annotation
+
|
@@ -575,12 +692,12 @@ li:before {
Improved performance when rendering lots
of features (particularly when transparency is disabled)
-
- Experimental features in 2.10.2 for
- exchange of Jalview features and Chimera attributes made
- generally available
-
-
+
+ Experimental features in 2.10.2 for
+ exchange of Jalview features and Chimera attributes made
+ generally available
+
+
@@ -701,7 +818,11 @@ li:before {
Sequences' enabled) or Ensembl isoforms (Workaround in
2.10.4 is to fail back to N&W mapping)
-
+
+ Export Annotations from File Menu with CSV
+ option gives blank output
+
+
|
@@ -1453,6 +1574,15 @@ li:before {
User defined gap colour not shown in
overview when features overlaid on alignment
+
+ Feature settings for different views not
+ recovered correctly from Jalview project file
+
+
+ Feature colours in overview when first opened
+ (automatically via preferences) are different to the main
+ alignment panel
+
Data import/export