- Quick Links: -
- -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
--
-
- Normalised sequence logo display - -
- RNA secondary structure annotation row - -
- Jmol compatibility updated to Jmol 12.2.x series - download the JmolApplet here -
- To use Jmol as the structure viewer for Jalview, you must include
- the jar file in the applet archive argument thus:
-archive="jalviewApplet.jar,Jmol-12.2.4.jar"
-
- - Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have
- Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the
- original Jalview structure viewer will still be available.
-
-
-
**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. -
- -
-
-
- 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)
-
-
| <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 | @@ -346,7 +236,7 @@ document.onclick = mclose;defaultColour | One of: Clustal, Blosum62, % Identity, Hydrophobic, Zappo, Taylor, Helix - Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide |
+ Propensity, Strand Propensity, Turn Propensity, Buried Index, Nucleotide, T-Coffee Scores, RNA Helices
Default is no colour. |
| linkLabel_1 | -Uniprot | +EMBL-EBI Search | Right click on sequence id to see list of available
links. Any new links MUST have $SEQUENCE_ID$ as part of the linkURL_n
value. For multiple links, increment the label and url name by
@@ -433,12 +323,12 @@ document.onclick = mclose;
|
|
|
|
+ |
search.ebi?db=allebi&query=$SEQUENCE_ID$ |
||
| Multiple sequences aligment scores file. Currently is supported only the T-Coffee score_ascii file format |
Notes on applet deployment
+
-
+
- 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
+-
+
- Normalised sequence logo display + +
- RNA secondary structure annotation row + +
- Jmol compatibility updated to Jmol 12.2.x series - download the JmolApplet here +
- To use Jmol as the structure viewer for Jalview, you must include
+ the jar file in the applet archive argument thus:
+archive="jalviewApplet.jar,Jmol-12.2.4.jar"
+
+ - Jmol 12.2.x requires at least Java 1.6 to run in the clients web browser. If the client does not have
+ Java 1.6, or if the Jmol-12.2.jar is not added to the archive, the
+ original Jalview structure viewer will still be available.
+
+
+
**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. +
+ +
-
+
- 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">
(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">
+
+