import jalview.datamodel.*;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.util.UrlLink;
/**
* DOCUMENT ME!
for (int i = 0; i < links.size(); i++)
{
String link = links.elementAt(i).toString();
- final String label = link.substring(0, link.indexOf("|"));
-
-
- if (link.indexOf("$SEQUENCE_ID$") > -1)
+ UrlLink urlLink = new UrlLink(link);
+ if (!urlLink.isValid())
+ {
+ jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ if (urlLink.isDynamic())
{
- // Substitute SEQUENCE_ID string and any matching database reference accessions
- String url_pref = link.substring(link.indexOf("|") + 1,
- link.indexOf("$SEQUENCE_ID$"));
-
- String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
// collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{label});
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{urlLink.getTarget()});
// collect id string too
String id = seq.getName();
- if (id.indexOf("|") > -1)
- {
- id = id.substring(id.lastIndexOf("|") + 1);
- }
-
if (dbr!=null)
{
for (int r=0;r<dbr.length; r++)
{
- if (dbr[r].getAccessionId().equals(id))
+ if (id!=null && dbr[r].getAccessionId().equals(id))
{
// suppress duplicate link creation for the bare sequence ID string with this link
id = null;
}
- addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(),
- url_pref+dbr[r].getAccessionId()+url_suff);
+ // create Bare ID link for this RUL
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
+ if (urls!=null)
+ {
+ for (int u=0; u<urls.length; u+=2)
+ {
+ addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]);
+ }
+ }
}
}
if (id!=null)
{
// create Bare ID link for this RUL
- addshowLink(linkMenu, label, url_pref + id + url_suff);
+ String[] urls = urlLink.makeUrls(id, true);
+ if (urls!=null)
+ {
+ for (int u=0; u<urls.length; u+=2)
+ {
+ addshowLink(linkMenu, label, urls[u+1]);
+ }
+ }
}
- }
- else
+ } else
{
// Add a non-dynamic link
- addshowLink(linkMenu, label, link.substring(link.lastIndexOf("|") + 1));
+ addshowLink(linkMenu, label, urlLink.getUrl_prefix());
}
}
if (sequence != null)
private void addshowLink(JMenu linkMenu, String label, final String url)
{
JMenuItem item = new JMenuItem(label);
+ item.setToolTipText("open URL: "+url);
item.addActionListener(new java.awt.event.ActionListener()
{
public void actionPerformed(ActionEvent e)