X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=examples%2FappletParameters.html;h=3cc5403106efa65925d59d49281253af5af057a8;hb=f54983a4b00eeeba75854bee6d4d2de6a24856e0;hp=3b2edfbf6ea9a40166afe278eac3a72e51af9c53;hpb=17d9f091cda339850a7cdfd87dd17b6b1244ed51;p=jalview.git diff --git a/examples/appletParameters.html b/examples/appletParameters.html index 3b2edfb..3cc5403 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -1,10 +1,7 @@
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- Download the applet jar file from here. Parameters are described - below, and the javascript API is described here. - +Quick Links: Useful to know!!
**NEW FEATURES** in Jalview 2.7
**NEW FEATURES** in Jalview 2.6
** NEW FEATURES ** in Jalview 2.7.1
**NEW FEATURES** in Jalview 2.7
**NEW FEATURES** in Jalview 2.6
**NEW FEATURES** in Jalview 2.5
**NEW FEATURES** in Jalview 2.4
showbutton |
true |
Show the jalview button on the page. When false, JalviewLite will open immediately. |
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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. | |||||||||||||||
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. | |||||||||||||||
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. | |||||||||||||||
upperCase | bold or other value | Indicate a text style to apply to uppercase sequence symbols. Currently, only bold is supported. | |||||||||||||||
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. | |||||||||||||||
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. | |||||||||||||||
showGroupConsensus | true of false (default is false) | When true, shows consensus annotation row for any groups on the alignment. | |||||||||||||||
showGroupConservation | true of false (default is false) | When true, shows amino-acid property conservation annotation row for any groups on the alignment. | |||||||||||||||
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. | |||||||||||||||
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). | |||||||||||||||
oninit | after_init() | name of javascript function that will be called after the jalviewLite instance has completed its initialisation. | |||||||||||||||
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). | |||||||||||||||
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] | |||||||||||||||
externalstructureviewer | true or false (default is false) | re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] | |||||||||||||||
externalstructureviewer | true or false (default is false) | re-route jmol colouring commands, selection and mouseover events to an external viewer using javascript callbacks. [experimental] | |||||||||||||||
annotationcolour_max | colour name or RGB hex triplet (default is red) | Default colour used for maximum value when shading by annotation. | |||||||||||||||
annotationcolour_min | colour name or RGB hex triplet (default is orange) | Default colour used for minimum value when shading by annotation. |