From 78adb95d8a84bd43c948e1550c670fcf74661b8e Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 8 May 2007 14:01:12 +0000 Subject: [PATCH] rightalign and italic ids docs --- help/html/features/preferences.html | 263 ++++++++++++++++++----------------- 1 file changed, 134 insertions(+), 129 deletions(-) diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 0abce06..08e210e 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -1,129 +1,134 @@ - - -Preferences - - -

Preferences

-

There are four tabs in the Preferences dialog box: -

-

-

Visual Preferences tab

-

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

-

Show Overview Window - When this is selected, the alignment overview panel is opened by - default for a new alignment window.

-

Show Annotations - If this is selected the new window will display an annotation - panel below the sequences. This annotation panel may have several rows describing - the whole alignment. The 3 standard annotations Conservation, Quality and Consensus - may be shown or hidden by default.

-

Full Sequence ID - If selected the ID panel will display the name of a sequence - plus the start and end residues in the format name/start-end. If not selected, - the displayed ID will be the name of the sequence.

-

Font - The default font name, size and style can be set for a new - alignment window.

-

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 "."

-

Colour - The default colour scheme for a new alignment window. If - the chosen option is "User Defined" then the last User Defined Colour - loaded or saved via the User Defined Colours panel will be loaded.

-

Sort by - When the alignment is loaded in, it will can be sorted by - Id or pairwise identity.

-

Open file - If this is selected then the default alignment file will - be opened when Jalview is started. You can change the default file by clicking - on file name and either typing in the file path or selecting it from the file - chooser window.

-

"Connections" Preferences tab

-

URL Link From Sequence ID
- Right click a sequence id to see a popup menu with "Link" as one of - the items. By default the item "SRS" is added to this link menu. This - link will show a web page in your default browser with the selected sequence - id as part of the URL.
- Jalview allows you to add your own custom links to other web pages. Click new - to add a new link. You can name the link, this will be displayed on a new menu - item under the "Link" menu when you right click on a sequence id. -
- You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen - sequence id when you click on it.

-

eg.
- UniRef100 = http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
- Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$

-

Default Browser (Unix)
- Its difficult in Java to detect the default web browser for Unix users. If Jalview - can't find your default web browser, enter the name or full path to your web - browser application.

-

Proxy Server
- If you normally use a proxy server for using the internet, you must tick the - box "Use a Proxy Server" and enter the address and port details as - necessary. Web Services will not work if you are using a proxy server and do - not enter the settings here.

-

Output Preferences tab

-

EPS Rendering Style
-This is a selection box which allows the - user to set a default rendering style for EPS export: -

-

-

Sequence//Start-End Numbering
- 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: -

-  >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.

-

-

Use Modeller Output

-

This option only applies to PIR format output. Jalview - automatically reads PIR files with sequence descriptions compatible - with the program Modeller. - If this 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 / 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.

-

DAS Settings

-

See DAS Settings

-

 

-

 

- - + + +Preferences + + +

Preferences

+

There are four tabs in the Preferences dialog box: +

+

+

Visual Preferences tab

+

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

+

Open Overview Window - When this is selected, the alignment overview panel is opened by + default for a new alignment window.

+

Show Annotations - If this is selected the new window will display an annotation + panel below the sequences. This annotation panel may have several rows describing + the whole alignment. The 3 standard annotations Conservation, Quality and Consensus + may be shown or hidden by default.

+

Full Sequence ID - If selected the ID panel will display the name of a sequence + plus the start and end residues in the format name/start-end. If not selected, + the displayed ID will be the name of the sequence.

+

Right Align IDs - select to align all sequence IDs to the +left-hand edge of the sequence alignment, rather than the left-hand +edge of the alignment display window.

+

Font - The default font name, size and style can be set for a new + alignment window.

+

Sequence Name Italics - select to apply the italicised +vbersion 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 "."

+

Colour - The default colour scheme for a new alignment window. If + the chosen option is "User Defined" then the last User Defined Colour + loaded or saved via the User Defined Colours panel will be loaded.

+

Sort by - When the alignment is loaded in, it will can be sorted by + Id or pairwise identity.

+

Open file - If this is selected then the default alignment file will + be opened when Jalview is started. You can change the default file by clicking + on file name and either typing in the file path or selecting it from the file + chooser window.

+

"Connections" Preferences tab

+

URL Link From Sequence ID
+ Right click a sequence id to see a popup menu with "Link" as one of + the items. By default the item "SRS" is added to this link menu. This + link will show a web page in your default browser with the selected sequence + id as part of the URL.
+ Jalview allows you to add your own custom links to other web pages. Click new + to add a new link. You can name the link, this will be displayed on a new menu + item under the "Link" menu when you right click on a sequence id. +
+ You must enter $SEQUENCE_ID$ within your URL. This will be replaced by the chosen + sequence id when you click on it.

+

eg.
+ UniRef100 = http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
+ Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$

+

Default Browser (Unix)
+ Its difficult in Java to detect the default web browser for Unix users. If Jalview + can't find your default web browser, enter the name or full path to your web + browser application.

+

Proxy Server
+ If you normally use a proxy server for using the internet, you must tick the + box "Use a Proxy Server" and enter the address and port details as + necessary. Web Services will not work if you are using a proxy server and do + not enter the settings here.

+

Output Preferences tab

+

EPS Rendering Style
+This is a selection box which allows the + user to set a default rendering style for EPS export: +

+

+

Sequence//Start-End Numbering
+ 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: +

+  >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.

+

+

Use Modeller Output

+

This option only applies to PIR format output. Jalview + automatically reads PIR files with sequence descriptions compatible + with the program Modeller. + If this 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 / 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.

+

DAS Settings

+

See DAS Settings

+

 

+

 

+ + -- 1.7.10.2