Alignment Consensus Annotation

From: jprocter Date: Fri, 24 Nov 2006 10:09:41 +0000 (+0000) Subject: new and corrected docs for 2.2 release X-Git-Tag: Release_2_2~37 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=85fb1c79fd82d7eada801624f745635632be8362;p=jalview.git new and corrected docs for 2.2 release --- diff --git a/help/help.jhm b/help/help.jhm index 41d245d..2e10dbf 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -1,87 +1,89 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 5dec601..c91faff 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -1,86 +1,88 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/help/html/calculations/consensus.html b/help/html/calculations/consensus.html index ce11687..71a1719 100644 --- a/help/html/calculations/consensus.html +++ b/help/html/calculations/consensus.html @@ -1,13 +1,18 @@ - -Alignment Consensus Annotation - -

Alignment Consensus Annotation

The consensus displayed below the alignment is the percentage of the modal - residue per column. By default this calculation takes includes gaps in column. - You can choose to ignore gaps in the calculation by right clicking on the label - "Consensus" to the left of the consensus bar chart. -

If the modal value is shared by more than 1 residue, a "+" symbol - is used in the display for the simple reason that it is not possible to display - multiple characters in a single character space. - - + +Alignment Consensus Annotation + +

Alignment Consensus Annotation

The consensus displayed below the alignment is the percentage of the modal + residue per column. By default this calculation takes includes gaps in column. + You can choose to ignore gaps in the calculation by right clicking on the label + "Consensus" to the left of the consensus bar chart. +

If the modal value is shared by more than 1 residue, a "+" symbol + is used in the display for the simple reason that it is not possible to display + multiple characters in a single character space. +

Copying the consensus sequence

Select the "Copy Consensus Sequence" entry from +the consensus annotation label to copy the alignment's consensus sequence to the +clipboard. +

+ + diff --git a/help/html/calculations/pca.html b/help/html/calculations/pca.html index 32ab81d..af6550e 100755 --- a/help/html/calculations/pca.html +++ b/help/html/calculations/pca.html @@ -1,64 +1,64 @@ - -Principal Component Analysis - -

Principal Component Analysis

This calculation creates a spatial representation of the -similarities within a selected group, or all of the sequences in -an alignment. After the calculation finishes, a 3D viewer displays the -set of sequences as points in 'similarity space', and similar -sequences tend to lie near each other in the space.

Note: The calculation is computationally expensive, and may fail for very large sets of sequences - - usually because the JVM has run out of memory. The next release of - Jalview release will execute this calculation through a web service.

Principal components analysis is a technique for examining the -structure of complex data sets. The components are a set of dimensions -formed from the measured values in the data set, and the principle -component is the one with the greatest magnitude, or length. The -sets of measurements that differ the most should lie at either end of -this principle axis, and the other axes correspond to less extreme -patterns of variation in the data set. -

- -

In this case, the components are generated by an eigenvector -decomposition of the matrix formed from the sum of BLOSUM scores at -each aligned position between each pair of sequences. The basic method -is described in the paper by G. Casari, C. Sander and -A. Valencia. Structural Biology volume 2, no. 2, February 1995 (pubmed) - and implemented at the SeqSpace server at the EBI. -

- -

The PCA Viewer

This is an interactive display of the sequences positioned within - the similarity space. The colour of each sequence point is the same - as the sequence group colours, white if no colour has been - defined for the sequence, and green if the sequence is part of a - the currently selected group. -

The 3d view can be rotated by dragging the mouse with the - left mouse button pressed. The view can also be - zoomed in and out with the up and down arrow - keys. Labels will be shown for each sequence - if the entry in the View menu is checked, and the plot background - colour changed from the View→Background Colour.. dialog - box. The File menu allows the view to be saved (File→Save - submenu) as an EPS or PNG image or printed, and the original - alignment data and matrix resulting from its PCA analysis to be - retrieved. -

A tool tip gives the sequence ID corresponding to a point in the - space, and clicking a point toggles the selection of the - corresponding sequence in the alignment window. Rectangular region - based selection is also possible, by holding the 'S' key whilst - left-clicking and dragging the mouse over the display. -

Initially, the display shows the first three components of the - similarity space, but any eigenvector can be used by changing the selected - dimension for the x, y, or z axis through each ones menu located - below the 3d display. -

- - - + +Principal Component Analysis + +

Principal Component Analysis

This calculation creates a spatial representation of the +similarities within a selected group, or all of the sequences in +an alignment. After the calculation finishes, a 3D viewer displays the +set of sequences as points in 'similarity space', and similar +sequences tend to lie near each other in the space.

Note: The calculation is computationally expensive, and may fail for very large sets of sequences - + usually because the JVM has run out of memory. A future release of + Jalview will be able to avoid this by executing the calculation via a web service.

Principal components analysis is a technique for examining the +structure of complex data sets. The components are a set of dimensions +formed from the measured values in the data set, and the principle +component is the one with the greatest magnitude, or length. The +sets of measurements that differ the most should lie at either end of +this principle axis, and the other axes correspond to less extreme +patterns of variation in the data set. +

+ +

In this case, the components are generated by an eigenvector +decomposition of the matrix formed from the sum of BLOSUM scores at +each aligned position between each pair of sequences. The basic method +is described in the paper by G. Casari, C. Sander and +A. Valencia. Structural Biology volume 2, no. 2, February 1995 (pubmed) + and implemented at the SeqSpace server at the EBI. +

+ +

The PCA Viewer

This is an interactive display of the sequences positioned within + the similarity space. The colour of each sequence point is the same + as the sequence group colours, white if no colour has been + defined for the sequence, and green if the sequence is part of a + the currently selected group. +

The 3d view can be rotated by dragging the mouse with the + left mouse button pressed. The view can also be + zoomed in and out with the up and down arrow + keys (and the roll bar of the mouse if present). Labels + will be shown for each sequence if the entry in the View menu is + checked, and the plot background colour changed from the + View→Background Colour.. dialog box. The File menu allows the + view to be saved (File→Save submenu) as an EPS or PNG image or + printed, and the original alignment data and matrix resulting from + its PCA analysis to be retrieved. +

A tool tip gives the sequence ID corresponding to a point in the + space, and clicking a point toggles the selection of the + corresponding sequence in the alignment window. Rectangular region + based selection is also possible, by holding the 'S' key whilst + left-clicking and dragging the mouse over the display. +

Initially, the display shows the first three components of the + similarity space, but any eigenvector can be used by changing the selected + dimension for the x, y, or z axis through each ones menu located + below the 3d display. +

+ + + diff --git a/help/html/calculations/treeviewer.html b/help/html/calculations/treeviewer.html index bc46771..f05572c 100755 --- a/help/html/calculations/treeviewer.html +++ b/help/html/calculations/treeviewer.html @@ -16,9 +16,15 @@ are also reflected in any other analysis windows associated with the alignment, such as another tree viewer.

- Clicking on an internal node of the tree will rearrange the tree - diagram, inverting the ordering of the branches at that node. +

Moving the mouse over an internal node of the tree will highlight + it. You can then :

Click the highlighted node to select all the sequences in that branch. +
Double-click the highlighted node to rearrange the tree + diagram by inverting the branch ordering at that + node. +
Right-click to open the 'Select Sub-Tree Colour' dialog box, to + pick a new colour for the sub-tree and associated sequences. +

Clicking anywhere along the extent of the tree (but not on a leaf or @@ -47,12 +53,12 @@ retrieved with the 'Input Data...' entry. associated with a tree. Trees calculated by Jalview have branch lengths, which correspond to the distance measure used to construct the tree. Tree imported from outside may also contain bootstrap information, -or additional leaves from sequences not present in the associated +and additional leaves from sequences not present in the associated alignment.

The view menu contains options controlling the way a tree is -rendered and labelled:

Fit to Window
The tree layout will be scaled to fit in the display window. You may need to reduce the font size to minimise the leaf @@ -70,8 +76,14 @@ Labels each branch or leaf with its associated bootstrap value.
Mark unlinked leaves
Toggles the display of a '*' at the beginning of a leaf label to -indicate that there is no sequence corresponding to that leaf in the associated alignment. +indicate that there is no sequence corresponding to that leaf in the +associated alignment.
Leaf Association
+Only visible when there are multiple views of the same +alignment to show and edit which alignment views are associated with +the leaves of the displayed tree. +

Creating and Editing Sequence Features

Creating and Editing Sequence Features

Double clicking on a sequence feature opens the "Amend/Delete Features" dialog box. + +

Sequence feature editing was implemented in Jalview 2.2

Multiple Alignment Views

Multiple Alignment Views

+
Multiple alignment views allow's the same alignment to be viewed in +many different ways, either as multiple alignment tabs, or simultaneously in +linked alignment windows. A view is an independent visualization of +the same alignment, so each may have a different ordering, colouring, +row and column hiding and seuqence feature and annotation display +setting, but alignment, feature and annotation edits are common to +all, since this affects the underlying data. +
+
+A new view is created using the "View→New View" menu item, or by pressing +Control+T. A newly created view will be identical to +the view it was created from, but any changes to the way the alignment +is coloured or displayed will only affect the new view. +
+
A particular view may focus on some specific aspect of an alignment - +for example, hiding all but the region of an alignment containing a +particular domain. Right-clicking a view's tab opens +the View Name dialog box, allowing it to be renamed to something more +meaningful. +
+
Viewing Multiple Views Simultaneously
+
Multiple views of an alignment are, by default, gathered together as tabs +within a single alignment window. They can be viewed simultanously by +pressing X (or via +"View→Expand") to expand each view +into its own linked alignment window. Expanded views are gathered +back into into a single tabbed alignment window by pressing +G, or by selecting "View→Gather"). +
+
Tree Viewers and Multiple Views
+
A tree calculated on a particular view, or loaded onto it, is by +default associated with just that view. However, the Tree Viewer's +"View→Associate leaves" submenu +allows a tree's view association to be changed to to any or all other +views.
+
Multiple Views were introduced in Jalview 2.2
+ \ No newline at end of file diff --git a/help/html/features/reloadSave.html b/help/html/features/reloadSave.html new file mode 100644 index 0000000..ae6b53e --- /dev/null +++ b/help/html/features/reloadSave.html @@ -0,0 +1,20 @@ + + +Reload and Save Alignment + + +
Reload and Save Alignment
+
Jalview remembers the original source of an alignment if it has +been loaded from a file or +URL.
+
"File→Reload" will reload the +alignment from its original source, discarding any edits or applied +colouring and features since the last save.
+
"File→Save" will save the +alignment back to the same filename, with the same format, easing the +the process of editing and updating an alignment file in +place. +
+
+ + \ No newline at end of file diff --git a/help/html/index.html b/help/html/index.html index 60f0bb8..47513c8 100755 --- a/help/html/index.html +++ b/help/html/index.html @@ -1,18 +1,18 @@ - -Home Page - - - -

-Jalview Documentation -

-JalView (1999) is a fast Java multiple alignment editor and analysis tool. It -features many of the functions of AMAS, -for the analysis of sub-families and the prediction of functional sites, but is -fully interactive. -
-
If you use JalView in your work, please cite the bioinformatics paper:
-
Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview - Java Alignment Editor", Bioinformatics, 20, 426-7.
- - + +Home Page + + + +

+Jalview Documentation +

+Jalview (2004) is a fast Java multiple alignment editor and analysis tool. It +features many of the functions of AMAS, +for the analysis of sub-families and the prediction of functional sites, but is +fully interactive. (View the Jalview homepage). +
+
If you use Jalview in your work, please cite the bioinformatics paper:
+
Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), "The Jalview + Java Alignment Editor", Bioinformatics, 20, 426-7.
+ + diff --git a/help/html/keys.html b/help/html/keys.html index ea6a9e8..b49b321 100755 --- a/help/html/keys.html +++ b/help/html/keys.html @@ -1,130 +1,223 @@ - -Key Strokes - -
Key Strokes
-
-Jalview responds a number of key strokes, and has two distinct modes of -keyboard operation. The F2 key switches between 'Normal' and -'Cursor' mode operation. -
- - - - - - - - - - - - - - - As in normal mode, but also cancels any partially entered commands - - - - Show Help Documentation - - - - - - - - - - - - - - Moves selected sequence(s) up the alignment - - - - Moves selected sequence(s) down the alignment. - Cursor Keys
- (Arrow Keys) - - - - - - - - - - - - - - - - - Pastes the contents of the clipboard to a new alignment window. (same as the - Alignment Window menu Edit->Paste command)
- nb. if the paste is from a Jalview alignment, any sequence and alignment - annotations will also be copied over. - - - - - - - - - - - - - - - - - - - - - - - - - -
Key Which Mode Action
Escape Normal Clears the current selection region, highlighted columns and highlghted - residues.
Escape Cursor
F1 Both
F2 Toggle Cursor mode on / off
Control 'Z' Both Undoes the last sequence edit
Up Arrow Normal
Down Arrow Normal
Cursor Move cursor around alignment
Control 'A' Both Selects all sequences in the alignment
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
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
-
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.
Cursor Keys
+ (Arrow Keys) Cursor Move cursor around alignment
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 33c4ead..9d6ed16 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,210 +1,246 @@ - -Release History - -
Release History
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Release
New Features
Issues Resolved
-
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
2.2
+ 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 b099c3b..344c322 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,28 +1,54 @@ - -What's new ? - -
What's new ?
-
Jalview Version 2.1
-
The multiple sequence alignment program MAFFT - is available from the default Web Service list.
-
The sequence feature retrieval system using DBFetch from EBI has been replaced - with DAS Feature fetching capabilities.
-
Hide sequences and columns
-
Export Annotations and Features
-
GFF file reading / writing
-
Associate structures with sequences from local PDB files
-
Add sequences to existing 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
-

-
Issues Resolved
-
Redundancy Panel reinstalled in the Applet
-
Monospaced font - EPS / rescaling bug fixed
-
Annotation files with sequence references bug fixed
-

-
See the Release History page for details of all - new features and resolved issues.
- - + +What's new ? + +
What's new ?
+ +
Jalview Version 2.2
+
Multiple views with different styles, colours, hidden regions for one alignment +
+
Easily add, amend and delete sequence features +
+
"Reload" alignment from File or URL to revert to original +
+
"Save" to current filename or "Save As" to new filename +
+
Set different text colour for dark or light background +
+
Right align sequence ids +
+
Set colour of lower case residues in a user defined colour scheme +
+
Menu Rearrangements: New Format for alignment layout and Select for region selection. +
+
Menu item accelerator keys added +
+
Control-V pastes sequences to active window, Control-Shift-V pastes to a new window. +
+
Raise/Minimise alignment and all associated windows from desktop window's window menu +
+
Select and colour whole branches of a tree
+
'New Window' button on the 'Output to Text box' alignment output +option to open a new alignment window after editing.
+
Issues Resolved
+
+
+Optimisations for large alignments: faster multithreaded calculations and Undo/Redo system. +
+
Remove empty columns - if empty columns exist at the end of the +alignment bug fixed. +
+
DAS feature fetching slowed down, doesn't overload DAS servers +
+
DAS feature fetching can be cancelled +
+
Correct display of > and < symbols for feature descriptions without explicit <html> tags. +
+
Zoom working in PCA viewer +
+
Sequence Descriptions retained after running a web service +
+

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

Key	Which Mode	Action
Escape	Normal	Clears the current selection region, highlighted columns and highlghted - residues.
Escape	Cursor
F1	Both
F2		Toggle Cursor mode on / off
Control 'Z'	Both	Undoes the last sequence edit
Up Arrow	Normal
Down Arrow	Normal
Cursor	Move cursor around alignment
Control 'A'	Both	Selects all sequences in the alignment
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
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

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

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

Release	New Features	Issues Resolved
- 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 -