X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fpreferences.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fpreferences.html;h=8c6b699e00a56dfcd813392a4493069265425af9;hb=44d68d55d9c85bf7b28853feeebc4b901c4a8392;hp=0000000000000000000000000000000000000000;hpb=6f9d7b98943ecba292a9c0dd65b30c4d8150c98f;p=jalview.git diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html new file mode 100755 index 0000000..8c6b699 --- /dev/null +++ b/help/help/html/features/preferences.html @@ -0,0 +1,388 @@ + + +
++ Preferences +
++ The preferences panel is opened from the Jalview Desktop’s Tools + menu. +
+There are eight 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 4 + standard annotations Conservation, Quality, + Occupancy and Consensus for the alignment may + be shown or hidden by default using the checkboxes adjacent and + 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. +
++ 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. +
++ Show Unconserved - When this is selected, all consensus + sequence symbols will be rendered as a '.', highlighting mutations + in highly conserved alignments. +
++ Sequence Name Italics - select to apply the italicised + version of the font to sequence labels. +
++ 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 "." +
++ Wrap Alignment - Select whether to open new alignment + windows in wrapped mode or not. +
++ Sort alignment by - When the alignment is loaded in, it can + be ordered as read (No sort), or sorted by Id or pairwise identity. +
++ Sort annotations by - Annotations can be unsorted, sorted + by the order of the related sequences in the alignment, or by label. + Autocalculated annotations (e.g. Consensus) can be shown either last + (below sequence annotations) or first (above sequence annotations). + Since Jalview 2.8.2. +
+
+ 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.
Note:
+ The default example alignment is updated periodically to
+ demonstrate new features in Jalview.
+
+ "Colours" + Preferences tab +
++ 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. +
++ "Overview" + Preferences tab +
++ Use legacy gap colouring (gaps are white) - when enabled, + Jalview's overview shows gaps as white, and sequences with no + colourscheme applied as grey. +
++ Show Hidden regions when opening overview - default setting + for inclusion of hidden regions. +
++ Gap Colour - When legacy gap colouring is not enabled, this + configures the default colour for gaps in the overview. +
++ Hidden Colour - colour used to highlight regions in the + overview that are hidden in the alignment. +
++ Gap 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. +
++ "Structure" + Preferences tab added in Jalview 2.8.2 +
++ Process secondary structure from PDB - if selected, then + structure information read from PDB will be processed and annotation + added to associated sequences. +
+ Use RNAView for secondary structure - if selected, the + pyRNA RNAView service (https://github.com/fjossinet/PyRNA) + will be called to derive secondary structure information for RNA + chains. +
+ Add secondary structure annotation to alignment - if + selected, Jmol's + implementation DSSP will be used to add annotation to polypeptide + chains in the structure. +
+ Add Temperature Factor annotation to alignment - if + selected, values extracted from the Temperature Factor column for + the backbone atoms in the PDB file will be extracted as annotation + lines shown on the alignment. +
+ Default structure viewer - choose Jmol or CHIMERA for + viewing 3D structures. +
+ Path to Chimera program - Optional, as Jalview will search + standard installation paths for Windows, Linux or MacOS. If you have + installed Chimera in a non-standard location, you can specify it + here, by entering the full path to the Chimera executable program. + Double-click this field to open a file chooser dialog. +
+ "Connections" + Preferences tab +
+
+ Default Browser (Unix)
It's 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.
+
+ The "Links" Preferences + tab +
++ This panel shows a table, and two sections - Edit and Filter. + The table shows the available URL link definitions (consisting of a + database, Name, and URL template string), a checkbox In + Menu which indicates if the link is enabled, and Double + Click which marks the link that will be opened if a sequence's ID + is double clicked. The table can be sorted by clicking on the column headers. +
+Edit Links
This section contains three buttons,
+ New, Edit and Delete, which allow you to
+ create, modify and remove user-defined URL links from the Sequence
+ ID's links submenu.
+
+ Filter
The Filter text box allows you to
+ quickly show rows in the table containing a particular text string.
+ The Custom only button limits the entries in the table to
+ just those you have configured yourself via the Edit
+ Links buttons. Press Show all to clear any filters.
+
The links table is prepopulated with persistent URLs for many common + bioinformatics databases (since 2.10.2). These links are downloaded by Jalview from + the identifiers.org website, and the names and URLs are not + user editable. + Read more about configuring + URL links. +
+ +
+ EPS Rendering Style
This is a selection box which
+ allows the user to set a default rendering style for EPS export:
+
+ Automatically set ID width
When enabled, the
+ column containing sequence and annotation labels at the left hand
+ side of an exported figure will be made large enough to display each
+ sequence ID and annotation label in its own line. Enable this if you
+ have particularly long sequence IDs and need to generate EPS or PNG
+ figures or web pages.
+
+ Figure ID column width
Manually specify the width
+ of the left hand column where sequence IDs and annotation labels
+ will be rendered in exported alignment figures. This setting will be
+ ignored if "Automatically set ID width" is set.
+
+ 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.
++ Embed BioJSON to HTML export +
++ When this option is enabled, Jalview embeds BioJSON data within HTML files + exported from Jalview at generation time. This enables the exported + HTML files to be extracted and imported back into the Jalview + desktop application at a later time. +
+ 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 three 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. +
++ Sort with New Tree - When selected, any trees calculated or + loaded onto the alignment will automatically sort the alignment. +
++
+ +