X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=4779046313e6892d99f7aabae2807513e89b0874;hb=524f1bc53749f18e8217ec14b72d3a2a444c072f;hp=286c26dacf6af24742e564b51a902071f02a39b2;hpb=92d3ddd8e9cf6f34759557f3ed85a12a1dd91c34;p=jalview.git
diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 286c26d..4779046 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -80,7 +80,11 @@ function mcancelclosetime()
document.onclick = mclose;
// -->
-
+
@@ -88,10 +92,10 @@ document.onclick = mclose;
@@ -100,39 +104,38 @@ document.onclick = mclose;
@@ -148,8 +151,8 @@ document.onclick = mclose;
Applet Parameters
Javascript API
in-page API demo
-Two JalviewLites demo
-Sequence And Structure demo
+Two JalviewLites demo
+Jalview and Jmol demo
@@ -163,134 +166,19 @@ document.onclick = mclose;
href="jalviewLiteJs.html">here
-
- Useful to know!!
-
- - Package all your data files into a single (or multiple) zip / jar
- files. This is very useful to reduce download time of large data files.
- The applet archive tag can take multiple entries separated by commas,
- eg
- <applet code="jalview.bin.JalviewLite"
- archive="jalviewApplet.jar, mydata.zip">
-
- - Use Jalview for input to a HTML form. For an example of how to
- code this using Javascript, click here.
-
-
- - Embed Jalview into the web page, without the "Start Jalview"
- button by setting the embed parameter to true;
- <param name="embedded"
- value="true">
-
- **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
-
- - Note that Parameter "PDBFile" now takes
- the PDB file followed by a space separated list of alignment sequence
- ids to associate the structure to. It is also possible to associate
- multiple PDB files by adding an incremental value to PDBFile (up to
- 10). It is also possible to map specific sequences to specific chains
- by using the following notation:
-
- <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">
-
- - Note parameter "PDBSeq" is no longer required.
-
- - Jalview 2.3 was updated to work with Jmol 11. See the versions archive if you want to download the old Jmol applet.
-
-
-
- **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.
-
- - 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)
-
-
-
+ Additional applet deployment notes are below.
+ Applet Parameters
The applet takes the following initialisation parameters.
+
| <param name="" |
value=""> |
Description |
+
+ | permissions |
+ sandbox |
+ This parameter is necessary, and must have the value sandbox to allow the JalviewLite applet to run. |
+
| file |
fileName |
@@ -578,11 +466,134 @@ document.onclick = mclose;
Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format |
+ Notes on applet deployment
+
+ **NEW FEATURES** in Jalview 2.8
+
+ **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)
+
+
+
-