Preferences
-There are four tabs in the Preferences dialog box: +
There are six 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.
+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 + href="overview.html">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 +for the alignment may be shown or hidden by default using the checkboxes +below.
+Show group: Conservation and Consensus controls the +display of per-group automatic annotation.
+Consensus: Histogram and Logo checkboxes control the +display of the consensus histogram and sequence logo for consensus +annotation rows.
+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.
+Font - The default font name, size and style can be set +for a new alignment window.
+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.
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.
- +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 "."
+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.
+ +Alignment 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.
++ Annotation Shading Default - set the default minimum + and maximum colours used when Colour by + Annotation .. is selected from the alignment window's colours menu. +
+"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/$SEQUENCE_ID$
-
- Links will also be made for any database cross references
- associated with the sequence where the database name exactly
- matches a URL link name. In this case, the $SEQUENCE_ID$ string will be replaced with
- the accession string for the database cross-reference, rather than the
- sequence ID for the sequence (since Jalview 2.4).
-
- Regular Expression Substitution
- A url may contain a string of the form $SEQUENCE_ID=/regular expression/=$. In this case, the regular expression will be applied to the full sequence ID string and the resulting match will be inserted into the URL.
- Groups of parentheseses can be used to specify which regions of the regular expression will be used to generate the URL:
-
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.
Usage statistics, Questionnaire and Version checks
+Uncheck these options to prevent Jalview from submitting usage
+statistics to google analytics, checking for jalview questionnaires or
+retrieving details of the latest release version (at www.jalview.org).
+See the user privacy statement for more
+information.
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:
-
+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.
+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. +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
+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.