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=17d3ea2201aefcedab0ed6513cbd420f87f8b999;p=jalview.git Merge branch 'JAL-1422_srs' into Release_2_8_Branch Conflicts: examples/linkedapplets_ng.html --- diff --git a/examples/appletParameters.html b/examples/appletParameters.html index 4779046..5f7305d 100644 --- a/examples/appletParameters.html +++ b/examples/appletParameters.html @@ -308,7 +308,7 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr 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 +321,12 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr
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 255f104..0629af0 100755 --- a/examples/applets.html +++ b/examples/applets.html @@ -190,9 +190,9 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - + + value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"> @@ -216,10 +216,10 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - - - + + Displays a features file on the alignment @@ -241,9 +241,9 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - - + + @@ -269,9 +269,9 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - - + + diff --git a/examples/embedded.html b/examples/embedded.html index eda8a27..ce6fca5 100644 --- a/examples/embedded.html +++ b/examples/embedded.html @@ -180,9 +180,9 @@ var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_tr - - + + diff --git a/examples/embeddedWJmol.html b/examples/embeddedWJmol.html index 24f7406..af15654 100644 --- a/examples/embeddedWJmol.html +++ b/examples/embeddedWJmol.html @@ -101,12 +101,12 @@ 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", permissions : "sandbox" diff --git a/examples/linkedapplets_ng.html b/examples/linkedapplets_ng.html index ef43184..c36f649 100644 --- a/examples/linkedapplets_ng.html +++ b/examples/linkedapplets_ng.html @@ -200,15 +200,13 @@ 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?$SEQUENCE_ID$", permissions : 'sandbox', + linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$", APPLICATION_URL : "http://www.jalview.org/services/launchApp" }; @@ -235,16 +233,14 @@ 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?$SEQUENCE_ID$", permissions : 'sandbox', - 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'); diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index 3adaa14..070004f 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -73,10 +73,21 @@ public class IdPanel extends Panel implements MouseListener, } } + { + // upgrade old SRS link + int srsPos = links + .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); + if (srsPos > -1) + { + links.setElementAt( + "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$", + srsPos); + } + } if (links.size() < 1) { links = new java.util.Vector(); - links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); + links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"); } } diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index a0fa216..0f23ecd 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -58,7 +58,7 @@ public class Preferences extends GPreferences String string = Cache .getDefault( "SEQUENCE_LINKS", - "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); + "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$"); sequenceURLLinks = new Vector(); try @@ -80,6 +80,18 @@ public class Preferences extends GPreferences { System.out.println(ex + "\nError parsing sequence links"); } + { + // upgrade old SRS link + int srsPos = sequenceURLLinks + .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry"); + if (srsPos > -1) + { + sequenceURLLinks.setElementAt( + "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$", + srsPos); + } + } + /** * TODO: reformulate groupURL encoding so two or more can be stored in the * .properties file as '|' separated strings