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 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.
-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.
- -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.
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.
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 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. - -
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.
--
- - + + +
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.
+ +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.
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. +
+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.
+ +See DAS Settings
++
+ +