X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=examples%2FappletParameters.html;h=8daa4ee59a71be6659de2609bfc644511716871e;hb=b0842a6ddaef0ceb4de3e1534c3772515d4b103d;hp=5078c69e4ae1179e915175c61d2d67d819322c58;hpb=6fa12685f5a274baad0f65db6241de29b7e5dbbf;p=jalview.git diff --git a/examples/appletParameters.html b/examples/appletParameters.html index 5078c69..8daa4ee 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -1,106 +1,69 @@ -
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- Download the applet jar file from here. Parameters are described - below, and the javascript API is described here. - -Useful to know!!-
**NEW FEATURES** in Jalview 2.6
**NEW FEATURES** in Jalview 2.5
**NEW FEATURES** in Jalview 2.4 -
- **NEW FEATURES** in Jalview 2.3 -
- -
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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. (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) | +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
scaleProteinAsCdna | true or false (default is false) | +Set true to shown protein residues the same width as their encoding codons. + For use with parameter file2 when showing a split frame of cDNA and protein. (since 2.9) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
centrecolumnlabels | +true or 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 or 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 or false (default is true) | +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 or false (default is false) | +When true, shows consensus annotation row for any groups on the alignment. (since 2.7) | +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
showGroupConservation | +true or false (default is false) | +When true, shows amino-acid property conservation annotation row for any groups on the alignment. (since 2.7) | +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
showConsensusHistogram | +true or 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 or 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) | +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
normaliseSequenceLogo | +true or false (default is false) | +When true, all sequence logos will be normalised (all symbol stacks add up to full height of annotation row), rather than being scaled according to the fraction of symbols identical to the consensus. (since 2.8) | +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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) | +|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
scoreFile | +file | +Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format | +
<applet code="jalview.bin.JalviewLite" + archive="jalviewApplet.jar, mydata.zip">
+
**NEW FEATURES** in Jalview 2.9
+**NEW FEATURES** in Jalview 2.8
+archive="jalviewApplet.jar,Jmol-12.2.4.jar"+
**NEW FEATURES** in Jalview 2.7
+**NEW FEATURES** in Jalview 2.6
++ <param name="PDBFile" value="First.pdb SeqA SeqB + SeqC">+
+ <param name="PDBFile2" value="Second.pdb + A=SeqA B=SeqB C=SeqC">
+ <param name="PDBFile3" value="Third.pdb + D=SeqX B=SeqY C=SeqZ">
+
+ +
<param name="userDefinedColour" + value="D,E=red; K,R,H=0022FF; C=yellow">+
<param name="sequence1" + value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI">(All the usual Jalview File formats are valid, however each + new line in an alignment file must be entered as a parameter)
+ <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT">
+