import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import jalview.util.DBRefUtils;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.Hashtable;
import java.util.LinkedHashMap;
void addFeatureLinks(final SequenceI seq, List<String> links)
{
JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- List<String> linkset = new ArrayList<String>();
+ Map<String, String[]> linkset = new LinkedHashMap<String, String[]>();
+
for (String link : links)
{
UrlLink urlLink = null;
Cache.log.error("Exception for URLLink '" + link + "'", foo);
continue;
}
- ;
+
if (!urlLink.isValid())
{
Cache.log.error(urlLink.getInvalidMessage());
continue;
}
- final String label = urlLink.getLabel();
-
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr != null && descr.length() < 1)
- {
- descr = null;
- }
-
- if (seq != null && urlLink.usesSeqId()) // link is ID
- {
- // collect matching db-refs
- DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { urlLink.getTarget() });
-
- // if there are any dbrefs which match up with the link
- if (dbr != null)
- {
- for (int r = 0; r < dbr.length; r++)
- {
- if (id != null && dbr[r].getAccessionId().equals(id))
- {
- // suppress duplicate link creation for the bare sequence ID
- // string with this link
- id = null;
- }
- // create Bare ID link for this URL
- createBareURLLink(urlLink, dbr[r].getAccessionId(), linkset,
- linkMenu, label, true);
- }
- }
- // Create urls from description but only for URL links which are regex
- // links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description where regex matches
- createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
- }
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
- }
- else if (seq != null && !urlLink.usesSeqId()) // link is name
- {
- if (id != null)
- {
- // create Bare ID link for this URL
- createBareURLLink(urlLink, id, linkset, linkMenu, label, false);
- }
- // Create urls from description but only for URL links which are regex
- // links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description where regex matches
- createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
- }
- }
- else
- {
- if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
- {
- linkset.add(label + "|" + urlLink.getUrl_prefix());
- // Add a non-dynamic link
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());
- }
- }
+ addshowLinks(linkMenu, linkset.values());
- }
if (sequence != null)
{
sequenceMenu.add(linkMenu);
}
}
- /*
- * Create a bare URL Link
- */
- private void createBareURLLink(UrlLink urlLink, String id,
- List<String> linkset, JMenu linkMenu, String label,
- Boolean addSepToLabel)
- {
- String[] urls = urlLink.makeUrls(id, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.add(urls[u] + "|" + urls[u + 1]);
- if (addSepToLabel)
- {
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
- }
- else
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- }
+
/**
* Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
}
}
+ private void addshowLinks(JMenu linkMenu, Collection<String[]> linkset)
+ {
+ for (String[] linkstrset : linkset)
+ {
+ // split linkstr into label and url
+ addshowLink(linkMenu, linkstrset[1], linkstrset[3]);
+ }
+ }
+
/**
* add a show URL menu item to the given linkMenu
*