X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2FappletParameters.html;h=433f5a917f926b4ba361001be86b2a7fb721b813;hb=refs%2Fheads%2Fgroovy%2FJAL-2074_upgradeto2.4.4;hp=976d8f9b40655a0c0b8a1df7ec0b3f9763df670b;hpb=472f47fc68c6f117334a76c0faffed5c86511fcd;p=jalview.git
diff --git a/examples/appletParameters.html b/examples/appletParameters.html
index 976d8f9..433f5a9 100644
--- a/examples/appletParameters.html
+++ b/examples/appletParameters.html
@@ -17,6 +17,9 @@
* The Jalview Authors are detailed in the 'AUTHORS' file.
-->
+
+
Click here to view decorated page
+
JalviewLite Applet Parameter Documentation
@@ -43,11 +46,23 @@ the applet can be interacted with via its
fileName |
The file to open, must be on same server as the applet. |
-
- file2 |
- fileName |
- A second file to open. If one file is nucleotide and the other peptide, and at least one peptide sequence
- is the translation of one of the nucleotide sequences, then alignments will be displayed linked in a split frame (since 2.9). |
+
+ file2 |
+ fileName |
+ A second file to open and show linked in a Split Frame
+ view. If one file is nucleotide and the other peptide, and at
+ least one peptide sequence matches the translation of one of the
+ nucleotide sequences, then gaps will be inserted into the
+ sequences in this file to match the aligned columns for
+ corresponding positions in the primary alignment file. This
+ parameter is ignored if enableSplitFrame is set to false (since
+ 2.9).
+ |
+
+
+ enableSplitFrame |
+ true or false (default true) |
+ Enable or disable the display of linked cDNA and Protein alignments in a split frame (since 2.9). |
sequence1,
@@ -103,6 +118,14 @@ the applet can be interacted with via its
| Default is no colour. |
+ defaultColourNuc |
+ A colour scheme (from the list above) to apply to Nucleotide alignments | This overrides defaultColour if it is specified. |
+
+
+ defaultColourProt |
+ A colour scheme (from the list above) to apply to Peptide alignments | This overrides defaultColour if it is specified. |
+
+
userDefinedColour |
Example:
D,E=red; K,R,H=0022FF; c=yellow |
@@ -334,126 +357,4 @@ 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 2.8
-
- **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)
-
-
+