X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=help%2Fhtml%2Freleases.html;h=89a39a32698ac269d7fddac823fb99eef4d647bb;hb=c350f93c6fac69b6a8a65645f0e89e26451df146;hp=e39a4c19197802dcf32f18a48473d19c4f75b1d3;hpb=8a6f2af24f832baf9899c7b0c8f4f723c592bc99;p=jalview.git
diff --git a/help/html/releases.html b/help/html/releases.html
index e39a4c1..89a39a3 100755
--- a/help/html/releases.html
+++ b/help/html/releases.html
@@ -25,24 +25,24 @@
ul {
/* remove bullets, narrower indent */
list-style-type: none;
- margin:0;
+ margin: 0;
padding-left: 10px;
padding-bottom: 4px;
}
li {
/* separate the items from eachother */
- margin-left: -3px;
- padding-bottom: 3px;
- padding-left: 6px;
+ margin-left: -3px;
+ padding-bottom: 3px;
+ padding-left: 6px;
}
+
li:before {
/* doesnt get processed in javahelp */
content: '\00b7 ';
padding: 3px;
margin-left: -14px;
}
-
@@ -70,65 +70,203 @@ li:before {
|
- General
+ Calculations
+
+
+ -
+ Occupancy annotation row shows number of
+ ungapped positions in each column of the alignment.
+
+ -
+ Tree/PCA calculation menu items merged to
+ a calculation dialog box
+
+ -
+ Revised implementation of PCA for speed
+ and memory efficiency (~30x faster)
+
+ -
+ Revised implementation of sequence
+ similarity scores as used by Tree, PCA, Shading Consensus
+ and other calculations
+
+ -
+ Score matrices are stored as resource
+ files within the Jalview codebase
+
+ -
+ Trees computed on Sequence Feature
+ Similarity may have different topology due to increased
+ precision
+
+
+ Rendering
+
+ -
+ More robust colours and shader
+ model for alignments and groups
+
+ -
+ Custom shading schemes created via groovy
+ scripts
+
+
+ Overview
+
+ -
+ Efficiency improvements for interacting
+ with alignment and overview windows
+
+ -
+ Linked scrolling of CDS/Protein views
+ via Overview or sequence motif search operations
+
+ -
+ Scrolling of wrapped alignment views via
+ overview
+
+ -
+ Hidden columns and sequences can be
+ omitted in Overview
+
+ -
+ Click-drag in visible area allows fine
+ adjustment of visible position
+
+
+
+ Data import/export
- - More robust colours and shader model for alignments and groups
- - Custom shading schemes created via groovy scripts
- - linked scrolling of CDS/Protein views via Overview or sequence motif search operations
- - Efficiency improvements for interacting with alignment and overview windows
- - Hidden columns and sequences can be omitted in Overview
-
Posterior probability annotation from
Stockholm files imported as sequence associated annotation
-
+ More robust per-sequence positional
+ annotation input/output via stockholm flatfile
+
+ -
Sequence names don't include file
extension when importing structure files without embedded
names or PDB accessions
- - Amend sequence features dialog box can be opened by double clicking gaps within sequence feature extent
+ -
+ Drag and drop load of AAIndex and NCBI
+ format sequence substitution matrices
+
- Application
+ User Interface
-
-
- Experimental Features Checkbox in Desktop's Tools
- menu to hide or show untested features in the application.
+ Experimental Features Checkbox in
+ Desktop's Tools menu to hide or show untested features in
+ the application.
+
+ -
+ Amend sequence features dialog box can be
+ opened by double clicking gaps within sequence feature
+ extent
+
+ -
+ Status bar message shown when not enough
+ aligned positions were available to create a 3D structure
+ superposition.
- - Warning in alignment status bar when there are not enough columns to superimpose structures in Chimera
- - Faster Chimera/Jalview communication by file-based command exchange
- - URLs for viewing database cross-references provided by identifiers.org and the EMBL-EBI's MIRIAM DB
- - Updated JABAWS client to v2.2
- Experimental features
+ 3D Structure
-
+ Faster Chimera/Jalview communication by
+ file-based command exchange
+
+ -
+ Structure chooser automatically shows
+ Cached Structures rather than querying the PDBe if
+ structures are already available for sequences
+
+ -
+ Structures imported via URL are cached in
+ the Jalview project rather than downloaded again when the
+ project is reopened.
+
+ -
New entries in the Chimera menu
to transfer Chimera's structure attributes as Jalview
- features, and vice-versa.
+ features, and vice-versa (Experimental
+ Feauture)
- Applet
+ Web Services
+
+ -
+ Updated JABAWS client to v2.2
+
+ -
+ Filter non-standard amino acids and nucleotides when submitting to AACon and other MSA Analysis services
+
+ -
+ URLs for viewing database
+ cross-references provided by identifiers.org and the
+ EMBL-EBI's MIRIAM DB
+
+
+
+ Scripting
-
+ -
+ FileFormatI interface for describing and
+ identifying file formats (instead of String constants)
+
+ -
+ FeatureCounter script refactored for
+ efficiency when counting all displayed features (not
+ backwards compatible with 2.10.1)
+
+
+ Example files
+
+ -
+ Graduated feature colour style example
+ included in the example feature file
+
+
+ Documentation
+
+ -
+ Release notes reformatted for readibility
+ with the built-in Java help viewer
+
+ -
+ Find documentation updated with 'search
+ sequence description' option
+
Test Suite
- Added PrivilegedAccessor to test suite
- Prevent or clear modal dialogs raised during tests
-
+
+ -
+ External service integration tests for
+ Uniprot REST Free Text Search Client
+
+ -
+ Added PrivilegedAccessor to test suite
+
+ -
+ Prevent or clear modal dialogs raised
+ during tests
+
- |
- General
+ |
+
- |
+
|
@@ -216,7 +654,8 @@ li:before {
for all consensus calculations
- Jmol updated to version 14.6.4 (released 3rd Oct 2016)
+ Jmol updated to version 14.6.4 (released
+ 3rd Oct 2016)
Updated Jalview's Certum code signing certificate
for 2016-2017
@@ -244,9 +683,9 @@ li:before {
New keystroke (B) and Select highlighted
- columns menu item to mark columns containing
- highlighted regions (e.g. from structure selections or results
- of a Find operation)
+ columns menu item to mark columns containing highlighted
+ regions (e.g. from structure selections or results of a
+ Find operation)
Command line option for batch-generation
@@ -346,73 +785,78 @@ li:before {
lysozyme results in a PDB Client error dialog box
- Structure View's mapping report switched ranges for PDB and sequence for SIFTS
- SIFTS 'Not_Observed' residues mapped to non-existant coordindate data
+ Structure View's mapping report switched
+ ranges for PDB and sequence for SIFTS
+
+
+ SIFTS 'Not_Observed' residues mapped to non-existant
+ coordindate data
+
-
|
-
-
- |
- Application
+ |
+
+ |
+ Application
+
+ - 3D Structure chooser opens with 'Cached structures'
+ view if structures already loaded
+ - Progress bar reports models as they are loaded to
+ structure views
+ |
+
+
+ General
- - 3D Structure chooser opens with 'Cached structures'
- view if structures already loaded
- - Progress bar reports models as they are loaded to
- structure views
- |
-
-
- General
-
- - Colour by conservation always enabled and no tick
- shown in menu when BLOSUM or PID shading applied
- - FER1_ARATH and FER2_ARATH labels were switched in
- example sequences/projects/trees
-
- Application
-
- - Jalview projects with views of local PDB structure
- files saved on Windows cannot be opened on OSX
- - Multiple structure views can be opened and
- superposed without timeout for structures with multiple
- models or multiple sequences in alignment
- - Cannot import or associated local PDB files without
- a PDB ID HEADER line
- - RMSD is not output in Jmol console when
- superposition is performed
- - Drag and drop of URL from Browser fails for Linux
- and OSX versions earlier than El Capitan
- - ENA client ignores invalid content from ENA server
- - Exceptions are not raised in console when ENA
- client attempts to fetch non-existent IDs via Fetch DB
- Refs UI option
- - Exceptions are not raised in console when a new
- view is created on the alignment
- - OSX right-click fixed for group selections:
- CMD-click to insert/remove gaps in groups and CTRL-click
- to open group pop-up menu
-
- Build and deployment
-
- - URL link checker now copes with multi-line anchor
- tags
-
- New Known Issues
-
- - Drag and drop from URL links in browsers do not
- work on Windows
-
-
- |
+ Colour by conservation always enabled and no tick
+ shown in menu when BLOSUM or PID shading applied
+ FER1_ARATH and FER2_ARATH labels were switched in
+ example sequences/projects/trees
+
+ Application
+
+ - Jalview projects with views of local PDB structure
+ files saved on Windows cannot be opened on OSX
+ - Multiple structure views can be opened and superposed
+ without timeout for structures with multiple models or
+ multiple sequences in alignment
+ - Cannot import or associated local PDB files without a
+ PDB ID HEADER line
+ - RMSD is not output in Jmol console when superposition
+ is performed
+ - Drag and drop of URL from Browser fails for Linux and
+ OSX versions earlier than El Capitan
+ - ENA client ignores invalid content from ENA server
+ - Exceptions are not raised in console when ENA client
+ attempts to fetch non-existent IDs via Fetch DB Refs UI
+ option
+ - Exceptions are not raised in console when a new view
+ is created on the alignment
+ - OSX right-click fixed for group selections: CMD-click
+ to insert/remove gaps in groups and CTRL-click to open group
+ pop-up menu
+
+ Build and deployment
+
+ - URL link checker now copes with multi-line anchor
+ tags
+
+ New Known Issues
+
+ - Drag and drop from URL links in browsers do not work
+ on Windows
+
+
+
@@ -423,8 +867,8 @@ li:before {
| General
-
- Updated Spanish translations.
-
+ Updated Spanish translations.
+
-
Jmol now primary parser
for importing structure data to Jalview. Enables mmCIF and
@@ -714,7 +1158,7 @@ li:before {
load even when Consensus calculation is disabled
-
- Remove right on penultimate column of
+ Remove right on penultimate column of
alignment does nothing
@@ -802,7 +1246,8 @@ li:before {
Enable 'Get Cross-References' in menu
- after fetching cross-references, and restoring from project
+ after fetching cross-references, and restoring from
+ project
Mouseover of a copy of a sequence is not
@@ -867,7 +1312,8 @@ li:before {
Unable to read old Jalview projects that
contain non-XML data added after Jalvew wrote project.
- Newly created annotation row reorders
+
+ Newly created annotation row reorders
after clicking on it to create new annotation for a
column.
@@ -939,9 +1385,12 @@ li:before {
Applet
- Split frame example added to applet examples page
- Build and Deployment
+ Build and Deployment
- - New ant target for running Jalview's test suite
+ -
+ New ant target for running Jalview's test
+ suite
+
|
@@ -1329,10 +1778,10 @@ li:before {
Deployment and Documentation
+ General
+ --> Deployment and Documentation
- 2G and 1G options in launchApp have no effect on
memory allocation
@@ -1540,8 +1989,7 @@ li:before {
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
- Export/import group and sequence associated line
@@ -2170,11 +2618,6 @@ li:before {
- URL links generated from description line for
regular-expression based URL links (applet and application)
-
-
-
-
-
- Non-positional feature URL links are shown in link
menu
@@ -2202,8 +2645,8 @@ li:before {
- Enable or disable non-positional feature and database
references in sequence ID tooltip from View menu in
application.
-
+
- Group-associated consensus, sequence logos and
conservation plots
- Symbol distributions for each column can be exported
@@ -2627,11 +3070,6 @@ li:before {
- Cancel button for DAS Feature Fetching
- PCA and PDB Viewers zoom via mouse roller
- User-defined sub-tree colours and sub-tree selection
-
-
-
-
-
- 'New Window' button on the 'Output to Text box'
@@ -2646,11 +3084,6 @@ li:before {
- Fixed Remove Empty Columns Bug (empty columns at end
of alignment)
- Slowed DAS Feature Fetching for increased robustness.
-
-
-
-
-
- Made angle brackets in ASCII feature descriptions
display correctly
@@ -2662,11 +3095,6 @@ li:before {
- WsDbFetch query/result association resolved
- Tree leaf to sequence mapping improved
- Smooth fonts switch moved to FontChooser dialog box.
-
-
-
-
-
|