From: Jim Procter Date: Mon, 13 Jan 2014 14:05:51 +0000 (+0000) Subject: Merge branch 'JAL-1422_srs' into Release_2_8_Branch X-Git-Tag: Release_2_8_0b1~1^2~21^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fe76692596c7d98452e2c93bcd934cb8c0dbf5b5;hp=-c;p=jalview.git Merge branch 'JAL-1422_srs' into Release_2_8_Branch Conflicts: examples/linkedapplets_ng.html --- fe76692596c7d98452e2c93bcd934cb8c0dbf5b5 diff --combined examples/appletParameters.html index 4779046,af1ec87..5f7305d --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@@ -80,11 -80,7 +80,11 @@@ function mcancelclosetime( document.onclick = mclose; // --> - + @@@ -92,10 -88,10 +92,10 @@@ @@@ -104,38 -100,39 +104,38 @@@ @@@ -174,11 -171,6 +174,11 @@@ value=""> Description + + permissions + sandbox + This parameter is necessary, and must have the value sandbox to allow the JalviewLite applet to run. + file fileName @@@ -308,7 -300,7 +308,7 @@@ 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 @@@ -321,12 -313,12 +321,12 @@@
Regex URL links are also applied to the description line (since Jalview 2.4.+).

-


+

+
linkUrl_1


- http://us.expasy.org/cgi-bin/
- niceprot.pl?$SEQUENCE_ID$

+ http://www.ebi.ac.uk/ebisearch/
search.ebi?db=allebi&query=$SEQUENCE_ID$

@@@ -554,7 -546,7 +554,7 @@@
  • 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 2.3 was updated to work with Jmol 11. See the versions archive if you want to download the old Jmol applet.

    •  

    @@@ -607,5 -599,18 +607,5 @@@ Bioinformatics 25 (9) 1189-1191 - - - diff --combined examples/applets.html index 255f104,e88742e..0629af0 --- a/examples/applets.html +++ b/examples/applets.html @@@ -79,11 -79,7 +79,11 @@@ function mcancelclosetime( document.onclick = mclose; // --> - + @@@ -91,10 -87,10 +91,10 @@@ @@@ -103,38 -99,39 +103,38 @@@ @@@ -178,7 -175,6 +178,7 @@@ + - + + value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"> @@@ -204,7 -200,6 +204,7 @@@ + @@@ -216,10 -211,10 +216,10 @@@ - - - + + Displays a features file on the alignment @@@ -228,7 -223,6 +228,7 @@@ + @@@ -241,9 -235,9 +241,9 @@@ - - + + @@@ -255,7 -249,6 +255,7 @@@ + @@@ -269,9 -262,9 +269,9 @@@ - - + + @@@ -288,7 -281,6 +288,7 @@@ + @@@ -327,4 -319,4 +327,4 @@@ Bioinformatics 25 (9) 1189-1191 - + diff --combined examples/embedded.html index eda8a27,b9d26cb..ce6fca5 --- a/examples/embedded.html +++ b/examples/embedded.html @@@ -79,11 -79,7 +79,11 @@@ function mcancelclosetime( document.onclick = mclose; // --> - + @@@ -91,10 -87,10 +91,10 @@@ @@@ -103,38 -99,39 +103,38 @@@ @@@ -169,8 -166,7 +169,8 @@@ - + + @@@ -180,9 -176,9 +180,9 @@@ - - + + diff --combined examples/embeddedWJmol.html index 24f7406,a3a7c3d..af15654 --- a/examples/embeddedWJmol.html +++ b/examples/embeddedWJmol.html @@@ -19,11 -19,6 +19,11 @@@ Embedded JalviewLite talking to externally managed Jmol + @@@ -101,15 -96,14 +101,15 @@@ function genHref( embedded : "true", showFullId : "false", RGB : "F2F2FF", - linkLabel_1 : "SRS", - linkUrl_1 : "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2" + linkLabel_1 : "EMBL-EBI Search", + linkUrl_1 : "http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$" , linkLabel_2 : "Uniprot" , - linkUrl_2 : "http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$", + linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$", APPLICATION_URL : "http://www.jalview.org/services/launchApp", - PDBfile : "1gaq.txt FER1_MAIZE" + PDBfile : "1gaq.txt FER1_MAIZE", + permissions : "sandbox" }; jmolSetCallback("hoverCallback","_jmolhover"); jmolSetCallback("pickCallback","_jmolpick"); @@@ -183,10 -177,10 +183,10 @@@ document.onclick = mclose @@@ -195,38 -189,39 +195,38 @@@ @@@ -274,5 -269,18 +274,5 @@@ Bioinformatics 25 (9) 1189-1191 - - - diff --combined examples/linkedapplets_ng.html index ef43184,3418068..c36f649 --- a/examples/linkedapplets_ng.html +++ b/examples/linkedapplets_ng.html @@@ -23,11 -23,6 +23,11 @@@ + @@@ -273,5 -263,18 +269,5 @@@ Bioinformatics 25 (9) 1189-1191 - - -