X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpreferences.html;h=08e210ed8a86b7e6682a4552700f51ef897373c7;hb=78adb95d8a84bd43c948e1550c670fcf74661b8e;hp=943728f84725eaa5d6e11ad3677f382c5d58fd7f;hpb=c7c9ce5fb38118f2509c10c81661614d7edeb57b;p=jalview.git diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 943728f..08e210e 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -1,29 +1,134 @@ - - -Preferences - - -

Preferences

-

The "Visual" tab on the preferences window allows you to configure - the default display for a new alignment window.

-

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

-

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.

-

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.

-

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.

- - + + +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

+

 

+

 

+ +