Release History

From f37dc08487781352739364a3977a43e9fa4d9176 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 1 May 2007 09:51:03 +0000 Subject: [PATCH] 2.3 what's new --- help/html/releases.html | 552 +++++++++++++++++++++++++---------------------- help/html/whatsNew.html | 63 +++--- 2 files changed, 328 insertions(+), 287 deletions(-) diff --git a/help/html/releases.html b/help/html/releases.html index e16e119..6b5f99a 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,261 +1,291 @@ - -Release History - -

Release History

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Release	New Features	Issues Resolved
2.2.1 - 12/2/07	- Non standard characters can be read and displayed - Annotations/Features can be imported/exported to the applet via textbox - Applet allows editing of sequence/annotation/group name & description - Preference setting to display sequence name in italics - Annotation file format extended to allow Sequence_groups - to be defined - Default opening of alignment overview panel can be specified in - preferences - PDB residue numbering annotation added to associated sequences -	- Applet crash under certain Linux OS with Java 1.6 installed - Annotation file export / import bugs fixed - PNG / EPS image output bugs fixed
2.2 - 27/11/06	- Multiple views on alignment - Sequence feature editing - "Reload" alignment - "Save" to current filename - Background dependent text colour - Right align sequence ids - User-defined lower case residue colours - Format Menu - Select Menu - Menu item accelerator keys - Control-V pastes to current alignment - 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'	- New memory efficient Undo/Redo System - Optimised symbol lookups and conservation/consensus calculations - Region Conservation/Consensus recalculated after edits - 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 - Re-instated Zoom function for PCA - Sequence descriptions conserved in web service analysis results - Uniprot ID discoverer uses any word separated by ∣ - WsDbFetch query/result association resolved - Tree leaf to sequence mapping improved - Smooth fonts switch moved to FontChooser dialog box.
2.1.1 - 12/9/06	- Copy consensus sequence to clipboard -	- Image output - rightmost residues are rendered if sequence id panel - has been resized - Image output - all offscreen group boundaries are rendered - Annotation files with sequence references - all elements in file are - relative to sequence position - Mac Applet users can use Alt key for group editing -
2.1 - 22/8/06	- MAFFT Multiple Alignment in default Web Service list - DAS Feature fetching - Hide sequences and columns - Export Annotations and Features - GFF file reading / writing - Associate structures with sequences from local PDB files - Add sequences to exisiting alignment - Recently opened files / URL lists - Applet can launch the full application - Applet has transparency for features (Java 1.2 required) - Applet has user defined colours parameter - Applet can load sequences from parameter "sequencex" -	- Redundancy Panel reinstalled in the Applet - Monospaced font - EPS / rescaling bug fixed - Annotation files with sequence references bug fixed -
2.08.1 - 2/5/06	- Change case of selected region from Popup menu - Choose to match case when searching - Middle mouse button and mouse movement can compress / expand the visible - width and height of the alignment -	- Annotation Panel displays complete JNet results -
2.08b - 18/4/06		- Java 1.5 bug - InternalMessageDialog fix for threads - Righthand label on wrapped alignments shows correct value -
2.08 - 10/4/06	- Editing can be locked to the selection area - Keyboard editing - Create sequence features from searches - Precalculated annotations can be loaded onto alignments - Features file allows grouping of features - Annotation Colouring scheme added - Smooth fonts off by default - Faster rendering - Choose to toggle Autocalculate Consensus On/Off -	- Drag & Drop fixed on Linux - Jalview Archive file faster to load/save, sequence descriptions saved. - -
2.07 - 12/12/05	- PDB Structure Viewer enhanced - Sequence Feature retrieval and display enhanced - Choose to output sequence start-end after sequence name for file output - Sequence Fetcher WSDBFetch@EBI - Applet can read feature files, PDB files and can be used for HTML - form input -	- HTML output writes groups and features - Group editing is Control and mouse click - File IO bugs -
2.06 - 28/9/05	- View annotations in wrapped mode - More options for PCA viewer -	- GUI bugs resolved - Runs with -nodisplay from command line -
2.05b - 15/9/05	- Choose EPS export as lineart or text - Jar files are executable - Can read in Uracil - maps to unknown residue -	- Known OutOfMemory errors give warning message - Overview window calculated more efficiently - Several GUI bugs resolved -
2.05 - 30/8/05	- Edit and annotate in "Wrapped" view -	- Several GUI bugs resolved -
2.04 - 24/8/05	- Hold down mouse wheel & scroll to change font size -	- Improved JPred client reliability - Improved loading of Jalview files -
2.03 - 18/8/05	- Set Proxy server name and port in preferences - Multiple URL links from sequence ids - User Defined Colours can have a scheme name and added to Colour Menu - Choose to ignore gaps in consensus calculation - Unix users can set default web browser - Runs without GUI for batch processing - Dynamically generated Web Service Menus -	- InstallAnywhere download for Sparc Solaris -
2.02 - 18/7/05		- Copy & Paste order of sequences maintains alignment order. -
2.01 - 12/7/05	- Use delete key for deleting selection. - Use Mouse wheel to scroll sequences. - Help file updated to describe how to add alignment annotations. - Version and build date written to build properties file. - InstallAnywhere installation will check for updates at launch of Jalview. -	- Delete gaps bug fixed. - FileChooser sorts columns. - Can remove groups one by one. - Filechooser icons installed. - Finder ignores return character when searching. Return key will initiate - a search. - -
2.0 - 20/6/05	- New codebase -

- - + +Release History + +

Release History

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

Release	New Features	Issues Resolved
2.3 + 2/5/07	+ Jmol 11 integration + PDB views in Jalview XML + Slide sequences + Edit sequence in place + EMBL CDS features + DAS Feature mapping + Feature ordering + Alignment Properties + Annotation Scores + Sort by scores + Feature/annotation editing in applet +	+ + Headless state operation in 2.2.1 + Incorrect and unstable DNA pairwise alignment + Cut and paste of sequences with annotation + Feature group display state in XML + Feature ordering in XML + blc file iteration selection using filename # suffix + Stockholm alignment properties + Stockhom alignment secondary structure annotation + 2.2.1 applet had no feature transparency + +
2.2.1 + 12/2/07	+ Non standard characters can be read and displayed + Annotations/Features can be imported/exported to the applet via textbox + Applet allows editing of sequence/annotation/group name & description + Preference setting to display sequence name in italics + Annotation file format extended to allow Sequence_groups + to be defined + Default opening of alignment overview panel can be specified in + preferences + PDB residue numbering annotation added to associated sequences +	+ Applet crash under certain Linux OS with Java 1.6 installed + Annotation file export / import bugs fixed + PNG / EPS image output bugs fixed
2.2 + 27/11/06	+ Multiple views on alignment + Sequence feature editing + "Reload" alignment + "Save" to current filename + Background dependent text colour + Right align sequence ids + User-defined lower case residue colours + Format Menu + Select Menu + Menu item accelerator keys + Control-V pastes to current alignment + 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'	+ New memory efficient Undo/Redo System + Optimised symbol lookups and conservation/consensus calculations + Region Conservation/Consensus recalculated after edits + 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 + Re-instated Zoom function for PCA + Sequence descriptions conserved in web service analysis results + Uniprot ID discoverer uses any word separated by ∣ + WsDbFetch query/result association resolved + Tree leaf to sequence mapping improved + Smooth fonts switch moved to FontChooser dialog box.
2.1.1 + 12/9/06	+ Copy consensus sequence to clipboard +	+ Image output - rightmost residues are rendered if sequence id panel + has been resized + Image output - all offscreen group boundaries are rendered + Annotation files with sequence references - all elements in file are + relative to sequence position + Mac Applet users can use Alt key for group editing +
2.1 + 22/8/06	+ MAFFT Multiple Alignment in default Web Service list + DAS Feature fetching + Hide sequences and columns + Export Annotations and Features + GFF file reading / writing + Associate structures with sequences from local PDB files + Add sequences to exisiting alignment + Recently opened files / URL lists + Applet can launch the full application + Applet has transparency for features (Java 1.2 required) + Applet has user defined colours parameter + Applet can load sequences from parameter "sequencex" +	+ Redundancy Panel reinstalled in the Applet + Monospaced font - EPS / rescaling bug fixed + Annotation files with sequence references bug fixed +
2.08.1 + 2/5/06	+ Change case of selected region from Popup menu + Choose to match case when searching + Middle mouse button and mouse movement can compress / expand the visible + width and height of the alignment +	+ Annotation Panel displays complete JNet results +
2.08b + 18/4/06		+ Java 1.5 bug - InternalMessageDialog fix for threads + Righthand label on wrapped alignments shows correct value +
2.08 + 10/4/06	+ Editing can be locked to the selection area + Keyboard editing + Create sequence features from searches + Precalculated annotations can be loaded onto alignments + Features file allows grouping of features + Annotation Colouring scheme added + Smooth fonts off by default - Faster rendering + Choose to toggle Autocalculate Consensus On/Off +	+ Drag & Drop fixed on Linux + Jalview Archive file faster to load/save, sequence descriptions saved. + +
2.07 + 12/12/05	+ PDB Structure Viewer enhanced + Sequence Feature retrieval and display enhanced + Choose to output sequence start-end after sequence name for file output + Sequence Fetcher WSDBFetch@EBI + Applet can read feature files, PDB files and can be used for HTML + form input +	+ HTML output writes groups and features + Group editing is Control and mouse click + File IO bugs +
2.06 + 28/9/05	+ View annotations in wrapped mode + More options for PCA viewer +	+ GUI bugs resolved + Runs with -nodisplay from command line +
2.05b + 15/9/05	+ Choose EPS export as lineart or text + Jar files are executable + Can read in Uracil - maps to unknown residue +	+ Known OutOfMemory errors give warning message + Overview window calculated more efficiently + Several GUI bugs resolved +
2.05 + 30/8/05	+ Edit and annotate in "Wrapped" view +	+ Several GUI bugs resolved +
2.04 + 24/8/05	+ Hold down mouse wheel & scroll to change font size +	+ Improved JPred client reliability + Improved loading of Jalview files +
2.03 + 18/8/05	+ Set Proxy server name and port in preferences + Multiple URL links from sequence ids + User Defined Colours can have a scheme name and added to Colour Menu + Choose to ignore gaps in consensus calculation + Unix users can set default web browser + Runs without GUI for batch processing + Dynamically generated Web Service Menus +	+ InstallAnywhere download for Sparc Solaris +
2.02 + 18/7/05		+ Copy & Paste order of sequences maintains alignment order. +
2.01 + 12/7/05	+ Use delete key for deleting selection. + Use Mouse wheel to scroll sequences. + Help file updated to describe how to add alignment annotations. + Version and build date written to build properties file. + InstallAnywhere installation will check for updates at launch of Jalview. +	+ Delete gaps bug fixed. + FileChooser sorts columns. + Can remove groups one by one. + Filechooser icons installed. + Finder ignores return character when searching. Return key will initiate + a search. + +
2.0 + 20/6/05	+ New codebase +

+ + diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 6989dd4..8484a26 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,26 +1,37 @@ - - -What's new ? - - -

What's new ?

- -

Jalview Version 2.2.1

Non standard characters can be read and displayed

Annotations/Features can be imported/exported to the applet via textbox

Applet allows editing of sequence/annotation/group name & description

Preference setting to display sequence name in italics

Annotation file format extended to allow Sequence_groups to be defined

Default opening of alignment overview panel can be specified in preferences

Issues Resolved

- Applet crash under certain Linux OS with Java 1.6 installed

Annotation file export / import bugs fixed

PNG / EPS image output bugs fixed
-

See the Release History page for -details of all new features and resolved issues.

- - + + +What's new ? + + +

What's new ?

+ +

Jalview Version 2.3

Issues Resolved

+Headless state operation in 2.2.1 +
Incorrect and unstable DNA pairwise alignment +
+Cut and paste of sequences with annotation +
+Feature group display state in XML
+Feature ordering in XML
+2.2.1 applet had no feature transparency
+

See the Release History page for +details of all new features and resolved issues.

+ + -- 1.7.10.2