The Alignment Annotations File

From a05186c1168e5e0a96a8825fe4c53d439079fdb3 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Tue, 6 Feb 2007 17:20:10 +0000 Subject: [PATCH] 2.2.1 updates --- help/html/features/annotationsFormat.html | 207 +++++++----- help/html/releases.html | 502 +++++++++++++++-------------- help/html/whatsNew.html | 75 ++--- 3 files changed, 406 insertions(+), 378 deletions(-) diff --git a/help/html/features/annotationsFormat.html b/help/html/features/annotationsFormat.html index b5a52f5..5a289c9 100755 --- a/help/html/features/annotationsFormat.html +++ b/help/html/features/annotationsFormat.html @@ -1,82 +1,125 @@ - - - -The Alignment Annotations File - - - -

The Alignment Annotations File

Alignment annotations can be imported onto an alignment since -version 2.08 of Jalview, via an annotations file. It is a simple ASCII -text file consisting of tab delimited records similar to the Sequence Features File, and introduced -primarily for use with the Jalview applet.

Alignment annotations files are imported into Jalview in the -following ways:
-

from the command line
- -annotations <Annotations filename>
Dragging an annotations file onto an alignment window
Via the "Load Features / Annotations" entry in the File - menu of an alignment window.

Annotations File Format

The File consists of lines containing an instruction followed by -tab delimited fields, and any lines starting with "#" are -ignored. The first non-commented out line of a valid Annotations file -must begin with :

JALVIEW_ANNOTATION

A row of annotation is added with a line like

GRAPH_TYPE	Label	Values

The GRAPH_TYPE field, which appears first, defines the -appearance of the annotation row when rendered by Jalview. The next field is the row label for the annotation. The final Values field contains a series of "|" -separated value fields. Each value field is itself a comma separated list of fields of a particular type defined by the annotation row's -GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective value fields (with the trailing "|" symbol) are shown below:

BAR_GRAPH
- Plots a histogram with labels below each bar.
- number,text character
LINE_GRAPH
- Draws a line between values on the annotation row.
- number
NO_GRAPH
- For a row consisting of text labels and/or secondary structure symbols.
- {Secondary Structure Symbol},text label
- Currently supported secondary structure structure symbols are H (for helix) and E (for strand)

-Any or all value fields may be left empty, as well as the BAR_GRAPH's -text character field, and either or both of the text-label and secondary -structure symbol fields of the NO_GRAPH type annotation rows. -

You can associate an annotation with a sequence by preceding its -definition with the line:

SEQUENCE_REF	seq_name	[startIndex]

-All Annotations defined after a SEQUENCE_REF command will then be -associated with that sequence, and the first field in the Value field -list will (optionally) be placed at the startIndex'th column.

Sequence associations are turned off for subsequent annotation -definitions by:

SEQUENCE_REF	ALIGNMENT

LINE_GRAPH type annotations can be given a colour -(specified as 24 bit RGB triplet in hexadecimal or comma separated -values), combined onto the same vertical axis, and have ordinate lines -(horizontal lines at a particular vertical axis value) using the -following commands (respectively):

COLOUR	graph_name	colour
-COMBINE	graph_1_name	graph_2_name
-GRAPHLINE	graph_name	value	label	colour

An example Annotation file is given below: -

#Comment lines follow the hash symbol
-JALVIEW_ANNOTATION
-SEQUENCE_REF	FER1_MESCR	5
-BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
-LINE_GRAPH	Green Values	1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
-LINE_GRAPH	Red Values	2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
-BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
-NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
-NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
-COLOUR	Bar Graph 2	blue
-COLOUR	Red Values	255,0,0
-COLOUR	Green Values	green
-COLOUR	Purple Letters	151,52,228
-COMBINE	Green Values	Red Values
-GRAPHLINE	Red Values	2.6	threshold	black
-

- - + + + +The Alignment Annotations File + + + +

The Alignment Annotations File

Alignment annotations can be imported onto an alignment since +version 2.08 of Jalview, via an annotations file. It is a simple ASCII +text file consisting of tab delimited records similar to the Sequence Features File, and introduced +primarily for use with the Jalview applet.

Alignment annotations files are imported into Jalview in the +following ways:
+

from the command line
+ -annotations <Annotations filename>
Dragging an annotations file onto an alignment window
Via the "Load Features / Annotations" entry in the File + menu of an alignment window.

Annotations File Format

The File consists of lines containing an instruction followed by +tab delimited fields, and any lines starting with "#" are +ignored. The first non-commented out line of a valid Annotations file +must begin with :

JALVIEW_ANNOTATION

A row of annotation is added with a line like

GRAPH_TYPE	Label	Values

The GRAPH_TYPE field, which appears first, defines the +appearance of the annotation row when rendered by Jalview. The next field is the row label for the annotation. The final Values field contains a series of "|" +separated value fields. Each value field is itself a comma separated list of fields of a particular type defined by the annotation row's +GRAPH_TYPE. The allowed values of GRAPH_TYPE and the format of their respective value fields (with the trailing "|" symbol) are shown below:

BAR_GRAPH
+ Plots a histogram with labels below each bar.
+ number,text character
LINE_GRAPH
+ Draws a line between values on the annotation row.
+ number
NO_GRAPH
+ For a row consisting of text labels and/or secondary structure symbols.
+ {Secondary Structure Symbol},text label
+ Currently supported secondary structure structure symbols are H (for helix) and E (for strand)

+Any or all value fields may be left empty, as well as the BAR_GRAPH's +text character field, and either or both of the text-label and secondary +structure symbol fields of the NO_GRAPH type annotation rows. +

You can associate an annotation with a sequence by preceding its +definition with the line: +

SEQUENCE_REF	seq_name	[startIndex]

+All Annotations defined after a SEQUENCE_REF command will then be +associated with that sequence, and the first field in the Value field +list will (optionally) be placed at the startIndex'th column.

Sequence associations are turned off for subsequent annotation +definitions by: +

SEQUENCE_REF	ALIGNMENT

LINE_GRAPH type annotations can be given a colour +(specified as 24 bit RGB triplet in hexadecimal or comma separated +values), combined onto the same vertical axis, and have ordinate lines +(horizontal lines at a particular vertical axis value) using the +following commands (respectively): +

COLOUR	graph_name	colour
+COMBINE	graph_1_name	graph_2_name
+GRAPHLINE	graph_name	value	label	colour
+

(Since Jalview 2.2.1) SEQUENCE_GROUP

Groups of sequences can be defined using the tab delimited line

SEQUENCE_GROUP	Group_Name	Group_Start	Group_End	Sequences

The sequences can be defined by alignment index and a range of sequences can + be defined in a comma delimited field such as

2-5,8-15,20,22

Enter * to select all groups.

If the alignment indices are not known, enter -1 then a tab delimited list + of sequence ids.

If the SEQUENCE_REF has been defined, the group_start and group_end will be + relative to the sequence residue numbering, otherwise the group_start and group_end + will be the alignment column indices.

The group can (optionally) be assigned various visualisation properties via + another tab delimited line thus:

PROPERTIES	Group_name	tab_delimited_key_value_pairs
+

The key_value_pairs allow you to define a description and to colour the group + in various ways. All, none or some of the following values could be used for + a group:

description=Text
+ colour=Helix Propensity
+ pidThreshold=0
+ consThreshold=0
+ outlineColour=red
+ displayBoxes=true
+ displayText=false
+ colourText=false
+ textCol1=black
+ textCol2=black
+ textColThreshold=0

An example Annotation file is given below: +

#Comment lines follow the hash symbol
+JALVIEW_ANNOTATION
+SEQUENCE_REF	FER1_MESCR	5
+BAR_GRAPH	Bar Graph 1	||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
+LINE_GRAPH	Green Values	1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
+LINE_GRAPH	Red Values	2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
+BAR_GRAPH	Bar Graph	2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
+NO_GRAPH	Icons 	||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
+NO_GRAPH	Purple Letters	m|y|p|r|o|t|e|i|n
+COLOUR	Bar Graph 2	blue
+COLOUR	Red Values	255,0,0
+COLOUR	Green Values	green
+COLOUR	Purple Letters	151,52,228
+COMBINE	Green Values	Red Values
+GRAPHLINE	Red Values	2.6	threshold	black
+
+SEQUENCE_GROUP Group_A 30 50 *
+SEQUENCE_GROUP Group_B 1 351 2-5
+SEQUENCE_GROUP Group_C 12 14 -1 seq1	seq2	seq3
+PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false	colourText=false textCol1=black textCol2=black textColThreshold=0
+PROPERTIES Group_B outlineColour=red
+PROPERTIES Group_C colour=Clustal
+

+ + diff --git a/help/html/releases.html b/help/html/releases.html index 9d6ed16..8026219 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -1,246 +1,256 @@ - -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 -

- - + +Release History + +

Release History

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

Release	New Features	Issues Resolved
2.2.1 + ?/ 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	+ 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 651292e..c6389d9 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -1,50 +1,25 @@ - - -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

New "New Window" button on the -"Output To Textbox" opens output window for quick 'sequence -editing'.

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.

- - + + +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

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.

+ + -- 1.7.10.2