From 2a436b9052affcfeb6f3748a40de53f6b8a7e9ef Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Mon, 10 Apr 2006 13:15:18 +0000 Subject: [PATCH] Editing tab --- help/html/features/preferences.html | 63 ++++++++++++++++++++++++----------- 1 file changed, 43 insertions(+), 20 deletions(-) diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index e08837a..5f88d62 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -4,21 +4,23 @@

Preferences

There are three tabs in the Preferences dialog box: -

The "Visual" - Preferences tab allows - you to configure the default display for a new alignment - window.
The "Connections" - Preferences tab allows you to change the links - made from Jalview to your default web browser. -
The "Output" - Preferences tab contains settings affecting the export of sequence -alignments and EPS files. -

There are four tabs in the Preferences dialog box: +

The "Visual" Preferences + tab allows you to configure the default display for a new alignment window. +
The "Connections" Preferences + tab allows you to change the links made from Jalview to your default web browser. +
The "Output" Preferences + tab contains settings affecting the export of sequence alignments and EPS + files.
The "Editing" Preferences + tab contains settings affecting the export of sequence alignments and EPS + f

Visual Preferences tab

Maximise Window - If this is selected, a new alignment window will stretch to fit the available space.

@@ -81,15 +83,36 @@ the program reading the EPS file.

Sequence//Start-End Numbering
-The output tab also has a group of checkboxes for each file format. If these + The output tab also has a group of checkboxes for each file format. If these are ticked, then Jalview will write files with the start and end sequence positions - appended to each sequence id:
+ appended to each sequence id:

-  >ID//1-10
+  >ID/1-10
   AACDEAAFEA

-
If the boxes are left unchecked for a particular - format, the sequence limits will not be appended to the 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 can now read and write + PIR files with sequence descriptions compatible with the program Modeller. + If this option is selected Jalview will write the sequence description in the + following format:

>P1;O80429_MAIZE
+sequence:O80429_MAIZE:1:.:140:.:.

+If a sequence description existed before the file was saved, it will be appended +to the new Modeller style desciption. 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 / 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" + according to this setting.

-- 1.7.10.2