From 76417f8a84ca46eab2f7c07dca76d13017715829 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 13 Jan 2014 13:59:55 +0000 Subject: [PATCH] JAL-1422 remove SRS and expasy links and replace with EMBL-EBI Search and Uniprot links in applet examples --- examples/appletParameters.html | 8 ++++---- examples/applets.html | 24 ++++++++++++------------ examples/embedded.html | 6 +++--- examples/embeddedWJmol.html | 6 +++--- examples/linkedapplets_ng.html | 18 +++++++----------- 5 files changed, 29 insertions(+), 33 deletions(-) diff --git a/examples/appletParameters.html b/examples/appletParameters.html index 427c8b7..af1ec87 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -300,7 +300,7 @@ document.onclick = mclose; 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 @@ -313,12 +313,12 @@ document.onclick = mclose;
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=$SEQUENCE_ID$

diff --git a/examples/applets.html b/examples/applets.html index e3e1d3c..e88742e 100755 --- a/examples/applets.html +++ b/examples/applets.html @@ -186,9 +186,9 @@ document.onclick = mclose; - + + value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"> @@ -211,10 +211,10 @@ document.onclick = mclose; - - - + + Displays a features file on the alignment @@ -235,9 +235,9 @@ document.onclick = mclose; - - + + @@ -262,9 +262,9 @@ document.onclick = mclose; - - + + diff --git a/examples/embedded.html b/examples/embedded.html index 2f74116..b9d26cb 100644 --- a/examples/embedded.html +++ b/examples/embedded.html @@ -176,9 +176,9 @@ document.onclick = mclose; - - + + diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html index 86dceea..a3a7c3d 100644 --- a/examples/embeddedWJmol.html +++ b/examples/embeddedWJmol.html @@ -96,12 +96,12 @@ 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" }; diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html index 4296146..3418068 100644 --- a/examples/linkedapplets_ng.html +++ b/examples/linkedapplets_ng.html @@ -196,14 +196,12 @@ document.onclick = mclose; 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" }; @@ -230,15 +228,13 @@ document.onclick = mclose; 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?$SEQUENCE_ID$", - APPLICATION_URL : "http://www.jalview.org/services/launchApp" + linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$", + APPLICATION_URL : "http://www.jalview.org/services/launchApp" }; deployJava.runApplet(attributes, parameters, '1.6'); -- 1.7.10.2