</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
<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>
- 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>
<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"
- 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="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>
<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="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="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>
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"
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/$SEQUENCE_ID$",
permissions : 'sandbox',
APPLICATION_URL : "http://www.jalview.org/services/launchApp"
};
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?$SEQUENCE_ID$",
+ linkLabel_2 : "Uniprot",
+ linkUrl_2 : "http://www.uniprot.org/uniprot/$SEQUENCE_ID$",
permissions : 'sandbox',
- APPLICATION_URL : "http://www.jalview.org/services/launchApp"
+ APPLICATION_URL : "http://www.jalview.org/services/launchApp"
};
deployJava.runApplet(attributes, parameters, '1.6');
</script>
}
}
+ {
+ // 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=$SEQUENCE_ID$");
}
}
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
{
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