From 3e0101470a0b6d41eac74c129f963a6ed0e69e2f Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 5 Nov 2014 16:04:10 +0000 Subject: [PATCH] JAL-674 Prefences tweaks incl help documentation for Structure tab --- help/html/features/preferences.html | 40 +++++++++++++++++++++++------------ resources/lang/Messages.properties | 2 +- src/jalview/jbgui/GPreferences.java | 8 +++---- 3 files changed, 32 insertions(+), 18 deletions(-) diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 3e45043..1831c3e 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -26,7 +26,7 @@

Preferences

The preferences panel is opened from the Jalview Desktop’s Tools menu.

There are six tabs in the Preferences dialog box: +

There are eight tabs in the Preferences dialog box:

The "Visual" Preferences tab allows you to configure the default display for a new @@ -34,6 +34,8 @@
The "Colours" Preferences tab allows you to configure default colourschemes for a new alignment window.
The "Structure" + Preferences tab allows you to configure options for obtaining and displaying structure information.
The "Connections" Preferences tab allows you to change the links made from Jalview to your default web browser.

Sequence ID Tooltip: Control the display of Database References and Non-positional annotation in the tooltip displayed when the mouse is over a sequence's ID.

Show Unconserved - When this is selected, all consensus sequence +symbols will be rendered as a '.', highlighting mutations in highly conserved alignments.

Sequence Name Italics - select to apply the italicised version of the font to sequence labels.

Smooth Font - Toggles anti-aliasing on / off for faster rendering of the alignment.

Wrap Alignment - Select whether to open new alignment -windows in wrapped mode or not.

Gap Symbol - The default gap symbol may be set to either "-" or "."

Wrap Alignment - Select whether to open new alignment +windows in wrapped mode or not.

Sort alignment by - When the alignment is loaded in, it can be ordered as read (No sort), or sorted by Id or pairwise identity.

Sort annotations by - Annotations can be unsorted, sorted by the order of the related sequences in @@ -104,10 +108,20 @@ will be loaded.

Annotation Shading Default

Colour by - Annotation ..

"Structure" +Preferences tab added in Jalview 2.8.2

Process secondary structure from PDB - if selected, then structure information +read from PDB will be processed to derive secondary structure annotation. +

Use RNAView for secondary structure - if selected, the RNAView service will be +automatically called to derive secondary structure information. +

Add secondary structure annotation to alignment - if selected, PDB secondary structure +annotation will be shown on the alignment when available. +

Add Temperature Factor annotation to alignment - if selected, PDB Temperature Factor +annotation will be shown on the alignment when available. +

Default structure viewer - choose JMOL or CHIMERA for viewing 3D structures. +

"Connections" Preferences tab

URL Link From Sequence ID
@@ -135,6 +149,9 @@ information.

"Prompt each time"
+ Choose this to be asked select between Lineart and Text each time you + make an EPS file.
"Lineart"
EPS files will accurately reproduce the alignment view in Jalview and all characters will be converted into line art. Files generated in this @@ -145,11 +162,7 @@ style for EPS export: files that can be edited easily in programs like Microsoft Word and Adobe Illustrator, but can be problematic if the fonts available to jalview are not accessible by the program reading the EPS file. -
"Prompt each time"
- Choose this to be asked select between Lineart and Text each time you - make an EPS file.

Automatically set ID width
When enabled, the column containing sequence and annotation labels at the left hand side of an exported figure will be made large enough to display each sequence ID and annotation label in its own line. Enable this if you have particularly long sequence IDs and need to generate EPS or PNG figures or web pages.

Figure ID column width
@@ -164,7 +177,6 @@ sequence positions appended to each sequence id:

If the boxes are left unchecked for a particular format, the sequence limits will not be appended to the sequence id.

Use Modeller Output

This option only applies to PIR format output. Jalview automatically reads PIR files with sequence descriptions compatible with @@ -173,16 +185,18 @@ option is selected Jalview will write Modeller style PIR files with correct start/end numbering and PDB file association (if available). The Jalview id/start-end option is ignored if Modeller output is selected. +

Editing Preferences tab

There are currently 2 options available which can be selected / +

There are currently three options available which can be selected / deselected.

AutoCalculate Consensus - For large alignments it can be useful to deselect "Autocalculate Consensus" when editing. This prevents lengthy calculations which are performed after each sequence edit. New alignment windows will have their "Autocalculate Consensus" option set according to this setting.

Pad gaps when editing - New alignment windows will +

Pad Gaps when Editing - New alignment windows will "Pad Gaps" according to this setting.

Sort with New Tree - When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.