@@ -25,7 +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.
| 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, @@ -76,8 +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.
| PDBfile(x) | @@ -99,10 +115,18 @@ the applet can be interacted with via itsdefaultColour | 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. |
| 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: |
@@ -135,6 +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 | @@ -334,126 +363,4 @@ the applet can be interacted with via itsMultiple 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 2.8
-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">
-