X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=554419ca48e764105da1b2b2b1c07b5bc5cc8fbb;hb=bbc3577d8579b3abef464ddbcce36075202831ec;hp=5078c69e4ae1179e915175c61d2d67d819322c58;hpb=6fa12685f5a274baad0f65db6241de29b7e5dbbf;p=jalview.git
diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 5078c69..554419c 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -3,7 +3,7 @@
|
|
Download the applet jar file from here. Parameters are described
- below, and the javascript API is described here.
+ below, and the javascript API is described here.
Useful to know!!
@@ -22,7 +22,7 @@
button by setting the embed parameter to true;
<param name="embedded"
value="true">
-
**NEW FEATURES** in Jalview 2.6
+
**NEW FEATURES** in Jalview 2.7
- Javascript callbacks capabilities
- oninit parameter and methods for registering javascript handlers for selections, mouseovers and linking to Jmol applets on the page.
- To use javascript callbacks, ensure the applet tag includes the 'mayscript' attribute - either as a parameter (<param name="mayscript" value="true"/;gt;) or as a bare attribute in the applet html tag).
- New jalviewLite java api methods for selecting, highlighting, scrolling and reordering sequences in an alignment view.
**NEW FEATURES** in Jalview 2.6
**NEW FEATURES** in Jalview 2.5
- New parameters to control display of tree annotation, width of alignment columns, and to disable the jalview button and check for Jmol on startup.
**NEW FEATURES** in Jalview 2.4
|
sortByTree |
true or false (default is false) |
automatically sort the associated alignment view by the tree when a new tree is opened. |
showTreeBootstraps | true or false (default is true) | show or hide branch bootstraps |
showTreeDistances | true or false (default is true) | show or hide branch lengths |
showUnlinkedTreeNodes | true or false (default is false) | indicate if unassociated nodes should be highlighted in the tree view |
heightScale |
1.0 or greater |
Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. |
- widthScale |
1.0 or greater |
Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. |
+
sortByTree |
true or false (default is false) |
automatically sort the associated alignment view by the tree when a new tree is opened. |
showTreeBootstraps | true or false (default is true) | show or hide branch bootstraps |
showTreeDistances | true or false (default is true) | show or hide branch lengths |
showUnlinkedTreeNodes | true or false (default is false) | indicate if unassociated nodes should be highlighted in the tree view |
heightScale |
1.0 or greater |
Adjust the height of each cell in the alignment grid relative to the height of a character in the alignment font. (since 2.5.1) |
+
widthScale |
1.0 or greater |
Adjust the width of each cell in the alignment grid relative to the width of a character in the alignment font. (since 2.5.1) |
centrecolumnlabels |
true of false (default is false) |
When true, text labels associated with a column in the alignment will be shown centered with respect to the column. (since 2.4) |
showUnconserved |
true of false (default is false) |
When true, only gaps and symbols different to the consensus sequence for a column will be shown. Useful for visualizing alignments exhibiting low sequence variation, where it is important to highlight mutations. (since 2.5) |
upperCase |
bold or other value |
Indicate a text style to apply to uppercase sequence symbols. Currently, only bold is supported. |
automaticScrolling |
true of false (default is false) |
When true, alignment panels will automatically scroll to show any regions of the alignment highlighted due to javascript events or when mousing over a position in an associated structure. (since 2.6) |
showGroupConsensus |
true of false (default is false) |
When true, shows consensus annotation row for any groups on the alignment. (since 2.7) |
showGroupConservation |
true of false (default is false) |
When true, shows amino-acid property conservation annotation row for any groups on the alignment. (since 2.7) |
showConsensusHistogram |
true of false (default is true) |
When true, shows the percentage occurence of the consensus symbol for each column as a histogram above the consensus sequence row. (since 2.7) |
showSequenceLogo |
true of false (default is false) |
When true, shows a sequence logo above the consensus sequence (overlaid above the Consensus Histogram, if visible, with symbols coloured using the alignment's default colourscheme). (since 2.7) |
oninit |
after_init() |
name of javascript function that will be called after the jalviewLite instance has completed its initialisation. (since 2.7) |
relaxedidmatch |
true or false (default is false) |
When true, use stem based matching to identify sequences that match features imported from a GFF or Jalview sequence features file, and for associating PDB data (passed on PDBfile parguments) with sequences (based on a given destination sequence ID). (since 2.7) |
alignpdbfiles |
true or false (default is false) |
When true, and jalviewLite is able to use jmol as a structure viewer, attempt to show a superposition of all structures loaded onto the alignment, superimposed using the aligned regions of corresponding sequences. [experimental] (since 2.7) |
externalstructureviewer |
true or false (default is false) |
re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] (since 2.7) |
annotationcolour_max |
colour name or RGB hex triplet (default is red) |
Default colour used for maximum value when shading by annotation. (since 2.7) |
annotationcolour_min |
colour name or RGB hex triplet (default is orange) |
Default colour used for minimum value when shading by annotation. (since 2.7) |
jalviewhelpurl |
absolute or relative url or javascript function prefixed by javascript: (default is http://www.jalview.org/help.html) |
Optional parameter allowing modification of the default Jalview Help URL normally opened when JalviewLite's 'Help' menu item is selected. (since 2.7) |
resolvetocodebase |
True or False (False) |
Set to true to re-instate pre-JalviewLite 2.7 behaviour where relative URLs were prepended with the applet 'codebase' rather than the current document base URL before resolution. (since 2.7) |