Mapping Between Different Sequences

From 83b541e967d19e6aeb5b02f476a77399f5f79d22 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 7 May 2007 15:16:54 +0000 Subject: [PATCH] 2.3 updates --- help/html/features/seqmappings.html | 13 +- help/html/features/viewingpdbs.html | 78 ++--- help/html/keys.html | 467 ++++++++++++++-------------- help/html/releases.html | 583 ++++++++++++++++++----------------- 4 files changed, 581 insertions(+), 560 deletions(-) diff --git a/help/html/features/seqmappings.html b/help/html/features/seqmappings.html index 46fcd59..7a25e3c 100644 --- a/help/html/features/seqmappings.html +++ b/help/html/features/seqmappings.html @@ -1,13 +1,12 @@ - + Mapping Between Different Sequences - +

Mapping Between Different Sequences

A new feature in Jalview 2.8 is the ability to map -between sequences in different domains, based on alignment, -or by the use of explicit mappings provided by databases. -

A new feature in Jalview 2.3 is the ability to map between sequences in different + domains, based on alignment, or by the use of explicit mappings provided by + databases.

The most familiar mapping is the one used to identify the coordinates corresponding to a displayed sequence when viewing a PDB file associated with a sequence (see @@ -18,5 +17,5 @@ correspondence between DNA and protein sequences. This mapping can be imported directly from EMBL and EMBLCDS database records retrieved by the Sequence Fetcher, or by the definition of coding regions. - + \ No newline at end of file diff --git a/help/html/features/viewingpdbs.html b/help/html/features/viewingpdbs.html index 6e47707..353ca09 100755 --- a/help/html/features/viewingpdbs.html +++ b/help/html/features/viewingpdbs.html @@ -1,37 +1,41 @@ - -PDB Viewing - -

Viewing PDB Structures

Jalview has a simple 3D structure viewer which can visualize polypeptide backbone - structures associated with a sequence in a particular alignment view. It is - accessed via the "Sequence→View PDB - entry:" entry from the sequence's pop-up menu.

To associate PDB files with a sequence, right click on a sequence ID and select - "Associate Structure with Sequence", and one of the submenus:

From File - You can load a PDB file from the local machine or network and - associate it with the selected sequence. PDB files associated in this way - will also be saved in the Jalview Archive file.
-
Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch - the PDB file with the entered Id.
-
Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover - PDB ids for all the sequences in the alignment which have valid Uniprot names - / accession ids.

Note: You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with this - service are automatically associated with their source database entry. For PDB - sequences, simply select PDB as the database and enter your known PDB id (appended - with ':' and a chain code, if desired).

Sequences which have PDB File associations are annotated with sequence features - from the group 'PDBFile' giving the corresponding PDB Residue Number for each - mapped residue in the seuqence. The display of these features is controlled through - the "View→Sequence Features" menu item and the - Feature Settings dialog box.

See the PDB Viewer help page for more information.

- - + +PDB Viewing + +

Viewing PDB Structures

Jalview has a simple 3D structure viewer which + can visualize polypeptide backbone structures associated with a sequence in + a particular alignment view. It is accessed via the "Sequence→View + PDB entry:" entry from the sequence's pop-up menu.

Since Jalview 2.3, Jmol has been integrated into the application and will also + run in the applet in all latest web browsers. For more help using Jmol, see + http://jmol.sourceforge.net/docs/JmolUserGuide/ +

To associate PDB files with a sequence, right click on a sequence ID and select + "Associate Structure with Sequence", and one of the submenus:

From File - You can load a PDB file from the local machine or network and + associate it with the selected sequence. PDB files associated in this way + will also be saved in the Jalview Archive file.
+
Enter PDB Id - Jalview will use WSDBFetch, provided by the EBI, to fetch + the PDB file with the entered Id.
+
Discover PDB Ids - Jalview uses WSDBFetch, provided by the EBI, to discover + PDB ids for all the sequences in the alignment which have valid Uniprot names + / accession ids.

Note: You can retrieve sequences from the PDB using the Sequence Fetcher. Any sequences retrieved with this + service are automatically associated with their source database entry. For PDB + sequences, simply select PDB as the database and enter your known PDB id (appended + with ':' and a chain code, if desired).

Sequences which have PDB File associations are annotated with sequence features + from the group 'PDBFile' giving the corresponding PDB Residue Number for each + mapped residue in the seuqence. The display of these features is controlled through + the "View→Sequence Features" menu item and the + Feature Settings dialog box.

See the PDB Viewer help page for more information.

+ + diff --git a/help/html/keys.html b/help/html/keys.html index 586f436..61c55cc 100755 --- a/help/html/keys.html +++ b/help/html/keys.html @@ -1,225 +1,242 @@ - -Key Strokes - -

Key Strokes

-Jalview has two distinct modes of keyboard operation - in 'Normal' - mode, single keystrokes (including those shown next to menu items) - provide short cuts to common commands. In 'Cursor' mode (enabled by - F2), some of these are disabled and more complex 'Compound - Keystrokes' can be entered to perform precise navigation, selection - and editing operations. -

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Key	Which Mode	Action
Escape	Normal	Clears the current selection region, highlighted columns and highlghted - residues.
Escape	Cursor	As in normal mode, but also cancels any partially entered commands
F1	Both	Show Help Documentation
F2		Toggle Cursor mode on / off
Control 'Z'	Both	Undoes the last sequence edit
Control 'Y'	Both	Redo the last sequence edit undone.
Up Arrow	Normal	Moves selected sequence(s) up the alignment
Down Arrow	Normal	Moves selected sequence(s) down the alignment.
Cursor Keys - (Arrow Keys)	Cursor	Move cursor around alignment
Page Up	Both	Scroll up the alignment view
Page Down	Both	Scroll down the alignment view
Control 'A'	Both	Selects all sequences in the alignment
Control 'I'	Both -	Invert sequence selection. -
Control Alt 'I'	Both -	Invert column selection. -
Control 'C'	Both	Copies the selected region into the clipboard as a Fasta format file - nb. not available in applet, as no clipboard is available
Control 'V'	Both	- Paste the contents of the clipboard to the current alignment - window. (Alignment Window->Edit->Paste->Add to this Alignment) - nb. if the paste is from a Jalview alignment, any sequence and alignment - annotations will also be copied over.
Control Shift 'V'	Both	Paste the contents of the clipboard to a new alignment - window. (Alignment Window->Edit->Paste->To New Alignment)
Control 'X'	Both	Cuts the (fully) selected sequences from the alignment. - -
Control 'F'	Both	Launches the search window
H	Both	Hides / Reveals selected columns and sequences
Control 'H'	Both	Hides / Reveals selected columns
Shift 'H'	Both	Hides / Reveals selected sequences
Control 'O'	Both	Input new alignment from file
Control 'S'	Both	Save alignment with current filename and format
Control Shift 'S'	Both	Save alignment as a new file or with a different format
Control 'P'	Both	Opens the print dialog box to print the current view
Control 'W'	Both	Closes the current view or the current alignment
Backspace	Normal	Delete the currently selected rows or columns from the alignment.
Control 'L'	Left	Remove columns to left of left-most column marker.
Control 'R'	Both	Remove columns to right of right-most column marker.
Control 'E'	Both	Remove gapped columns
Control Shift 'E'	Both	Remove all gaps
Control 'D'	Both	Open the 'Remove redundancy' Dialog box.
	Normal

The compound commands available in the Cursor mode are summarised -below. Single letter commands can be prefixed by digits to specify a repetition -number, and some more complex commands take one or more numeric -parameters (prefixing the command key and separated by commas).

- - - - - - - - - - - -

Compound -Command	Mode	Action (and parameter description)
0-9	Cursor	Begin entering a -numeric parameter (p) or repetition number for a cursor movement or edit -command.
,	Cursor	Separates one or -more numeric parameters (e.g. p1,p2) for a command.
p1,p2 Return	Cursor	Move cursor to a particular column (p1) and row (p2) in the alignment. e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.
pS	Cursor	Jump to the p'th sequence in the alignment.
pP	Cursor	Jump to p'th amino acid in current sequence.
pC	Cursor	Jump to p'th column in the alignment.
Q	Cursor	Marks the top left corner of the selection area
M	Cursor	Marks the bottom right corner of the selection area
[p] Space	Cursor	Inserts -one (or optionally p) gaps at the current position. Hold down Control or Shift to insert gaps over a sequence group
[p] Delete	Cursor	Removes -one (or optionally p) gaps at the cursor position. Hold down Control or Shift to insert gaps over a sequence group
[p] Backspace	Cursor	Removes -one (or optionally p) gaps at the cursor position. Hold down Control or Shift to insert gaps over a sequence group

- - + +Key Strokes + +

Key Strokes

+Jalview has two distinct modes of keyboard operation - in 'Normal' + mode, single keystrokes (including those shown next to menu items) + provide short cuts to common commands. In 'Cursor' mode (enabled by + F2), some of these are disabled and more complex 'Compound + Keystrokes' can be entered to perform precise navigation, selection + and editing operations. +

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

Key	Which Mode	Action
Escape	Normal	Clears the current selection region, highlighted columns and highlghted + residues.
Escape	Cursor	As in normal mode, but also cancels any partially entered commands
F1	Both	Show Help Documentation
F2		Toggle Cursor mode on / off
Control 'Z'	Both	Undoes the last sequence edit
Control 'Y'	Both	Redo the last sequence edit undone.
Up Arrow	Normal	Moves selected sequence(s) up the alignment
Down Arrow	Normal	Moves selected sequence(s) down the alignment.
Left Arrow	Normal	Slides selected sequence(s) left. Press Alt key to slide in cursor mode
Right Arrow	Normal	Slides selected sequence(s) right. Press Alt key to slide in cursor mode
Cursor Keys + (Arrow Keys)	Cursor	Move cursor around alignment
Page Up	Both	Scroll up the alignment view
Page Down	Both	Scroll down the alignment view
Control 'A'	Both	Selects all sequences in the alignment
Control 'I'	Both	Invert sequence selection.
Control Alt 'I'	Both	Invert column selection.
Control 'C'	Both	Copies the selected region into the clipboard as a Fasta format file + nb. not available in applet, as no clipboard is available
Control 'V'	Both	Paste the contents of the clipboard to the current alignment window. + (Alignment Window->Edit->Paste->Add to this Alignment) nb. if the + paste is from a Jalview alignment, any sequence and alignment annotations + will also be copied over.
Control Shift 'V'	Both	Paste the contents of the clipboard to a new alignment window. (Alignment + Window->Edit->Paste->To New Alignment)
Control 'X'	Both	Cuts the (fully) selected sequences from the alignment. + +
Control 'F'	Both	Launches the search window
H	Both	Hides / Reveals selected columns and sequences
Control 'H'	Both	Hides / Reveals selected columns
Shift 'H'	Both	Hides / Reveals selected sequences
Control 'O'	Both	Input new alignment from file
Control 'S'	Both	Save alignment with current filename and format
Control Shift 'S'	Both	Save alignment as a new file or with a different format
Control 'P'	Both	Opens the print dialog box to print the current view
Control 'W'	Both	Closes the current view or the current alignment
Backspace	Normal	Delete the currently selected rows or columns from the alignment.
Control 'L'	Left	Remove columns to left of left-most column marker.
Control 'R'	Both	Remove columns to right of right-most column marker.
Control 'E'	Both	Remove gapped columns
Control Shift 'E'	Both	Remove all gaps
Control 'D'	Both	Open the 'Remove redundancy' Dialog box.
	Normal

The compound commands available in the Cursor mode are summarised +below. Single letter commands can be prefixed by digits to specify a repetition +number, and some more complex commands take one or more numeric +parameters (prefixing the command key and separated by commas).

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

Compound +Command	Mode	Action (and parameter description)
0-9	Cursor	Begin entering a +numeric parameter (p) or repetition number for a cursor movement or edit +command.
,	Cursor	Separates one or +more numeric parameters (e.g. p1,p2) for a command.
p1,p2 Return	Cursor	Move cursor to a particular column (p1) and row (p2) in the alignment. e.g. '5,6<Return>' moves the cursor to the 5th column in the 6th sequence.
pS	Cursor	Jump to the p'th sequence in the alignment.
pP	Cursor	Jump to p'th amino acid in current sequence.
pC	Cursor	Jump to p'th column in the alignment.
Q	Cursor	Marks the top left corner of the selection area
M	Cursor	Marks the bottom right corner of the selection area
[p] Space	Cursor	Inserts +one (or optionally p) gaps at the current position. Hold down Control or Shift to insert gaps over a sequence group
[p] Delete	Cursor	Removes +one (or optionally p) gaps at the cursor position. Hold down Control or Shift to insert gaps over a sequence group
[p] Backspace	Cursor	Removes +one (or optionally p) gaps at the cursor position. Hold down Control or Shift to insert gaps over a sequence group

+ + diff --git a/help/html/releases.html b/help/html/releases.html index 6b5f99a..477141d 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,291 +1,292 @@ - -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 -

- - + +Release History + +

Release History

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

Release	New Features	Issues Resolved
2.3 + 8/5/07	+ Jmol 11 integration + PDB views stored in Jalview XML files + 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 + Number pad keys can be used in cursor mode + +
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 +

+ + -- 1.7.10.2