X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=04cc235164ee30368f32b1253282173f3a7016d5;hb=142bf80216af2a15f74fc3956d856bad13b45fc6;hp=1e45aae5d5483f661652d5c9a2ea7494bfe9e275;hpb=ce2fafc54fbec56f100776d81e26fa146ee7d7a1;p=jalview.git
diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 1e45aae..04cc235 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -28,7 +28,7 @@ which are described below. Once initialised,
the applet can be interacted with via its
Javascript API.
Issues arising from tightening of Java Security default settings
JalviewLite is provided as a signed applet with 'sandbox' permissions and wildcards that allow it to be run from any website. Unfortunately, earlier versions of Java may not be compatible with these settings.
- For additional deployment notes, see below.
+ For additional deployment notes, see Applet Deployment.
Applet Parameters
The applet takes the following initialisation parameters.
@@ -91,8 +91,9 @@ the applet can be interacted with via its
jnetfile |
fileName |
Secondary structure predictions from a Jnet Concise
- file will be added to the first sequence in the alignment. |
+ href="http://www.compbio.dundee.ac.uk/~www-jpred/">JPred Concise
+ file will be added to the first sequence in the alignment.
+ jpredfile can be used interchangeably with this parameter.
PDBfile(x) |
@@ -114,7 +115,7 @@ the applet can be interacted with via its
defaultColour |
One of:
Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix
- Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices |
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, Purine/Pyrimidine, T-Coffee Scores, RNA Helices
Default is no colour. |
@@ -158,6 +159,11 @@ the applet can be interacted with via its
Default is true. |
+ showOccupancy |
+ true or false |
+ Default is true. |
+
+
sortBy |
Id , Pairwise Identity, or Length |
Sorts the alignment on startup |
@@ -357,133 +363,4 @@ the applet can be interacted with via its
Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format |
- Notes on applet deployment
-
-
- **NEW FEATURES** in Jalview 2.9
-
- - Split Views for cDNA and Protein alignments
Specify second alignment with 'file2' parameter, and set cDNA/Protein column scaling with scaleProteinAsCdna
-
-
-
- **NEW FEATURES** in Jalview 2.8
-
- **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
-
- - Jmol compatibility updated to Jmol 12.1.x series
- - Jalview 2.6 works only with Jmol version 12.1.13 or later. You can use the JmolApplet.jar from
- the Jmol binary distribution available at the Jmol Sourceforge site,
- or download the Jmol applet from here
- - Minimum recommended version of Java runtime for the applet is now 1.5 (JalviewLite v2.6 without the Jmol viewer may work ok on earlier Java environments but compatibility can no-longer be guaranteed).
-
-
**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
-
- - New applet API methods for feature display control, views, and obtaining current selection via javascript.
- - Group show and hide parameters:
- "showfeaturegroups" and
- "hidefeaturegroups". Both take a list
- of feature group names (separarated by "|" by default) to hide or show on the displayed
- alignment.
-
- - Regular expressions can be used in URL links for sequence IDs.
- - "debug" parameter to control verbosity of the applet's console output.
- - "showbutton" parameter to disable launch button and open JalviewLite immediatly.
- - "nojmol" parameter to disable check for Jmol classes.
-
- **NEW FEATURES** in Jalview 2.3
-
- **NEW FEATURES** in Jalview 2.1
-
- - Jalview Applet can read and display JNet secondary structure annotation
- directly via the jnetfile parameter.
-
- - Param "UserDefinedColour" - specify your own colours for each residue using a semi colon
- separated list. Multiple residues can be assigned the same colour
- using commas. eg:
- <param name="userDefinedColour"
- value="D,E=red; K,R,H=0022FF; C=yellow">
-
- - Param "showFeatureSettings"
- - this will display the feature settings window when the applet starts.
-
- - Param "Application_URL" value="http://www.jalview.org/services/launchApp"
- This calls a servlet which creates a JNLP file with the alignment
- file, annotations file and features file of the applet as arguments.
- If the user has Java installed, the returned JNLP file should start
- up the full Jalview Application. BUT this does not currently work
- for alignment files added to the applet in a zip file.
-
Look at the XML comments in the file downloaded from The LaunchApp page for full documentation.
-
- - Alignment file can be a series of parameters using eg PFAM format
-
- <param name="sequence1"
- value="Q93XJ9_SOLTU/11-26 TSFLPRKPVVTSLKAI">
- <param name="sequence2" value="FER1_PEA/14-29 TSFLRTQPMPMSVTTT">
-
(All the usual Jalview File formats are valid, however each
- new line in an alignment file must be entered as a parameter)
-
-
+