Sequence Feature Settings Dialog Box

From: amwaterhouse Date: Mon, 14 Aug 2006 10:18:22 +0000 (+0000) Subject: 2.1 updates X-Git-Tag: Release_2_1~81 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=20bddfcf8ef1a53bce455b7599f8066b8ccba0d4;p=jalview.git 2.1 updates --- diff --git a/help/help.jhm b/help/help.jhm index 210933b..3790abe 100755 --- a/help/help.jhm +++ b/help/help.jhm @@ -12,11 +12,11 @@ + - @@ -24,15 +24,16 @@ - + + - + diff --git a/help/helpTOC.xml b/help/helpTOC.xml index 09c7125..9265599 100755 --- a/help/helpTOC.xml +++ b/help/helpTOC.xml @@ -3,34 +3,28 @@ - - - - - - - - - + + + - - - - - - - - + + + + - + + + + + @@ -57,6 +51,12 @@ + + + + + + diff --git a/help/html/editing/index.html b/help/html/editing/index.html index a33dea7..b0e8103 100755 --- a/help/html/editing/index.html +++ b/help/html/editing/index.html @@ -38,9 +38,19 @@ href="../keys.html">keystrokes table.

contain only space characters ("-" or "." or " ")

Removing gaps - Removes all gaps from the alignment. Gaps are "-" or "." or " ".

Set gap character - Switches the gap character between "." - and "-". If the "Render Gaps" option from the "View" +

Set gap character - Switches the gap character between "." + and "-". If the "Render Gaps" option from the "View" menu is unticked all gaps will appear as blank spaces.

Editing In Selection Areas

+Editing can be restricted to the current selection area. +This allows the user to "Lock" the alignment either side of the selection +area. Any gap insertions or deletions will only affect the current selection area. +

In this example, if Sequence IL2RA_MACMU has gaps removed from position 98-104, + the same number of gaps will be inserted at position 116, (between M and L). +

Locked selection area based editing was introduced in Jalview 2.08

diff --git a/help/html/features/featureSettings.gif b/help/html/features/featureSettings.gif index 87de549..29b1db0 100755 Binary files a/help/html/features/featureSettings.gif and b/help/html/features/featureSettings.gif differ diff --git a/help/html/features/featuresettings.html b/help/html/features/featuresettings.html index 31369d8..81af8d0 100755 --- a/help/html/features/featuresettings.html +++ b/help/html/features/featuresettings.html @@ -1,43 +1,45 @@ - - -Sequence Feature Settings Dialog Box - - -

Sequence Feature Settings Dialog Box

Select View→Feature Settings... menu entry in -an alignment window to open the feature settings dialog box, which -allows you to precisely control the presence and appearance of -sequence features for the current alignment.

Sequence Feature - Settings for the Jalview Application -

The top section of the dialog box lists all the sequence feature - groups, along with a tickbox for each that controls whether its - features are displayed. The table in the middle lists all the - features in the currently selected groups, along with their display - colour and whether they are currently being displayed (only the - ticked features and groups are displayed). You can change the - colour used for a feature in the associated alignment by clicking on - its colour box.

Transparency and Feature Ordering

- It is important to realise that sequence features are often not - distinct and often overlap (for example, a metal binding site - feature may be attached to one position along a stretch of sequence - marked with a secondary structure feature).

The ordering of the sequence features in the dialog box list is the - order used by jalview for rendering sequence features. A feature at - the bottom of the list is rendered below a feature higher - up in the list.
You can change the order of a feature - by dragging it up and down the list with the - mouse.

- The transparency slider setting (currently only available - in the application version) controls the visibility of features - rendered below other features. Reducing the transparency will mean - that features at the top of the list can obscure features lower - down, and increasing it allows the user to 'see through' the upper - layers of a set of features.

You can save all features, with their current colours and visibility - in a Jalview format file. -

- - + + +Sequence Feature Settings Dialog Box + + +

Sequence Feature Settings Dialog Box

Select View→Feature Settings... menu entry in +an alignment window to open the feature settings dialog box, which +allows you to precisely control the presence and appearance of +sequence features for the current alignment.

+ +

+ Sequence Feature + Settings for the Jalview Application +

The top section of the dialog box lists all the sequence feature + groups, along with a tickbox for each that controls whether its + features are displayed. The table in the middle lists all the + features in the currently selected groups, along with their display + colour and whether they are currently being displayed (only the + ticked features and groups are displayed). You can change the + colour used for a feature in the associated alignment by clicking on + its colour box.

Transparency and Feature Ordering

+ It is important to realise that sequence features are often not + distinct and often overlap (for example, a metal binding site + feature may be attached to one position along a stretch of sequence + marked with a secondary structure feature).

The ordering of the sequence features in the dialog box list is the + order used by jalview for rendering sequence features. A feature at + the bottom of the list is rendered below a feature higher + up in the list.
You can change the order of a feature + by dragging it up and down the list with the + mouse.

+ The transparency slider setting (currently only available + in the application version) controls the visibility of features + rendered below other features. Reducing the transparency will mean + that features at the top of the list can obscure features lower + down, and increasing it allows the user to 'see through' the upper + layers of a set of features.

You can save all features, with their current colours and visibility + in a Jalview format file. +

+ + diff --git a/help/html/io/export.html b/help/html/io/export.html index f0f615b..943451b 100755 --- a/help/html/io/export.html +++ b/help/html/io/export.html @@ -17,9 +17,15 @@ diagrams and powerpoint presentations diagrams and publications. -

Tips for working with EPS Files

The EPS file generated by jalview contains vector - graphics which are directly editable in graphics applications such as - Adobe Illustrator.

Tips for working with EPS Files

The EPS file generated by jalview contains vector graphics which are directly + editable in graphics applications such as Adobe Illustrator.

EPS files can be produced as "Text" or "Lineart". Use + "Text" if you want the final document to be MUCH smaller in diskspace + and be able to search, edit and select text. Use "Lineart" if you + want an exact image of the alignment as displayed in Jalview. This is useful + if a 3rd Party EPS viewer does not have the same Font which the EPS file was + created with.

When importing an EPS into to a Microsoft office document, a snapshot image of the file will be displayed which often looks blurred. Right-click the image and choose "Edit image." to convert it to word diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 7d88e7f..5bb50f9 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -2,54 +2,26 @@ What's new ?

What's new ?

Jalview Version 2.08

Editing can be locked to the - selection area so that any edits made within the locked area do - not unexpectedly shift other parts of the alignment.

Keyboard editing - press F2 to toggle cursor mode On / Off. For a full list - of keyboard controls, look here.

Create sequence features from searches. - Previously, the regions of sequences highlighted as the result of - searches were added as new regions in the alignment. Now, the sequence region - selected by a search can be used to define named sequences features - attached to the sequence, rather than the alignment. -

Sequence feature display and rendering has also been enhanced, with - the addition of sequence feature groups (which can be used to show - or hide a set of features en masse) and user defined - feature colours as well as transparency controls, using the Sequence Feature Settings - window. The Features file - has also been extended to accomodate these enhancements.

Alignment annotation and colouring is also considerably - enhanced. Precalculated symbolic and quantitative annotations (text labels, - secondary structure symbols and multiple scalar graphs) can now be - loaded onto alignments via the Annotation - File. Additionally, the Annotation - Colouring dialog box allows an alignment to be coloured based on - any of the graphed quantities with which it is annotated.

Rendering speed has been improved by disabling anti-aliasing via - the Smooth Fonts - option in the View - menu (its default set in Preferences). In addition, response - times when editing alignments can be reduced by turning off the automatic - calculation of amino acid property Consensus (which has been - reintroduced to the Calculate menu as Autocalculate Consensus).
-

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 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

Issues Resolved

Drag & Drop now works on common Linux desktops (at least KDE -and Gnome)
Jalview XML Archive Input/Output is now faster (using an -internal Jalview schema), and sequence description strings are now -preserved in the archive.
Jalview can now correctly read and write MODELLER style -PIR files. -

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.