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JAL-1422 remove SRS and expasy links and replace with EMBL-EBI Search and Uniprot...
author
Jim Procter
<jprocter@compbio.dundee.ac.uk>
Mon, 13 Jan 2014 13:59:55 +0000
(13:59 +0000)
committer
Jim Procter
<jprocter@compbio.dundee.ac.uk>
Mon, 13 Jan 2014 13:59:55 +0000
(13:59 +0000)
examples/appletParameters.html
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examples/applets.html
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examples/embedded.html
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examples/embeddedWJmol.html
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examples/linkedapplets_ng.html
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diff --git
a/examples/appletParameters.html
b/examples/appletParameters.html
index
427c8b7
..
af1ec87
100644
(file)
--- a/
examples/appletParameters.html
+++ b/
examples/appletParameters.html
@@
-300,7
+300,7
@@
document.onclick = mclose;
</tr>
<tr>
<td>linkLabel_1</td>
</tr>
<tr>
<td>linkLabel_1</td>
- <td>Uniprot</td>
+ <td>EMBL-EBI Search</td>
<td rowspan="2"><p>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
<td rowspan="2"><p>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;
<br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
</tr>
<tr>
<br>Regex URL links are also applied to the description line (since Jalview 2.4.+).</em></p></td>
</tr>
<tr>
- <td> <p><br>
+ <td> <p>
+ <br>
linkUrl_1<br>
</p></td>
<td><p><br>
linkUrl_1<br>
</p></td>
<td><p><br>
- http://us.expasy.org/cgi-bin/<br>
- niceprot.pl?$SEQUENCE_ID$</p>
+ http://www.ebi.ac.uk/ebisearch/<br/>search.ebi?db=allebi&query=$SEQUENCE_ID$</p>
</td>
</tr>
<tr>
</td>
</tr>
<tr>
diff --git
a/examples/applets.html
b/examples/applets.html
index
e3e1d3c
..
e88742e
100755
(executable)
--- a/
examples/applets.html
+++ b/
examples/applets.html
@@
-186,9
+186,9
@@
document.onclick = mclose;
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="Expasy">
+ <param name="linkLabel_2" value="EMBL-EBI Search">
<param name="linkUrl_2"
<param name="linkUrl_2"
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp">
</applet></td>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp">
</applet></td>
@@
-211,10
+211,10
@@
document.onclick = mclose;
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="Expasy">
- <param name="linkUrl_2"
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
- <param name="APPLICATION_URL"
+ <param name="linkLabel_2" value="EMBL-EBI Search">
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
+ <param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp">
</applet></td>
<td valign="center">Displays a features file on the alignment</td>
value="http://www.jalview.org/services/launchApp">
</applet></td>
<td valign="center">Displays a features file on the alignment</td>
@@
-235,9
+235,9
@@
document.onclick = mclose;
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="Expasy">
- <param name="linkUrl_2"
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="EMBL-EBI Search">
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp">
<param name="PDBfile" value="1gaq.txt FER1_MAIZE">
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp">
<param name="PDBfile" value="1gaq.txt FER1_MAIZE">
@@
-262,9
+262,9
@@
document.onclick = mclose;
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="Expasy">
- <param name="linkUrl_2"
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="EMBL-EBI Search">
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp">
</applet></td>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp">
</applet></td>
diff --git
a/examples/embedded.html
b/examples/embedded.html
index
2f74116
..
b9d26cb
100644
(file)
--- a/
examples/embedded.html
+++ b/
examples/embedded.html
@@
-176,9
+176,9
@@
document.onclick = mclose;
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
<param name="linkLabel_1" value="Uniprot">
<param name="linkUrl_1"
value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
- <param name="linkLabel_2" value="Expasy">
- <param name="linkUrl_2"
- value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="EMBL-EBI Search">
+ <param name="linkUrl_2"
+ value="http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$">
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp">
</applet>
<param name="APPLICATION_URL"
value="http://www.jalview.org/services/launchApp">
</applet>
diff --git
a/examples/embeddedWJmol.html
b/examples/embeddedWJmol.html
index
86dceea
..
a3a7c3d
100644
(file)
--- a/
examples/embeddedWJmol.html
+++ b/
examples/embeddedWJmol.html
@@
-96,12
+96,12
@@
function genHref()
embedded : "true",
showFullId : "false",
RGB : "F2F2FF",
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"
,
,
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"
};
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
(file)
--- a/
examples/linkedapplets_ng.html
+++ b/
examples/linkedapplets_ng.html
@@
-196,14
+196,12
@@
document.onclick = mclose;
embedded : "true",
showFullId : "false",
RGB : "F2F2FF",
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"
,
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"
};
APPLICATION_URL : "http://www.jalview.org/services/launchApp"
};
@@
-230,15
+228,13
@@
document.onclick = mclose;
embedded : "true",
showFullId : "false",
RGB : "F2F2FF",
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"
,
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');
</script>
};
deployJava.runApplet(attributes, parameters, '1.6');
</script>