import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.urls.UrlProvider;
-import jalview.urls.UrlProviderI;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.applet.AppletUrlProviderFactory;
import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.event.MouseMotionListener;
import java.util.HashMap;
import java.util.List;
-import java.util.Vector;
public class IdPanel extends Panel implements MouseListener,
MouseMotionListener
label = av.applet.getParameter("linkLabel_" + i);
url = av.applet.getParameter("linkURL_" + i);
- urlList.put(label, url);
+ // only add non-null parameters
+ if (label != null)
+ {
+ urlList.put(label, url);
+ }
}
if (!urlList.isEmpty())
{
// set default as first entry in list
String defaultUrl = av.applet.getParameter("linkLabel_1");
- urlProvider = new UrlProvider(defaultUrl, urlList);
+ UrlProviderFactoryI factory = new AppletUrlProviderFactory(
+ defaultUrl, urlList);
+ urlProvider = factory.createUrlProvider();
}
}
}
return;
}
- // DEFAULT LINK IS FIRST IN THE LINK LIST
+ // get the sequence details
int seq = alignPanel.seqPanel.findSeq(e);
SequenceI sq = av.getAlignment().getSequenceAt(seq);
if (sq == null)
return;
}
String id = sq.getName();
- String url = urlProvider.getDefaultUrl(id);
- String target = urlProvider.getDefaultTarget(id);
-
- /* String target = null;
- String url = null;
- int i = 0;
- while (url == null && i < links.size())
- {
- // DEFAULT LINK IS FIRST IN THE LINK LIST
- // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
- url = links.elementAt(i++).toString();
- jalview.util.UrlLink urlLink = null;
- try
- {
- urlLink = new UrlLink(url);
- target = urlLink.getTarget();
- } catch (Exception foo)
- {
- System.err.println("Exception for URLLink '" + url + "'");
- foo.printStackTrace();
- url = null;
- continue;
- }
- if (urlLink.usesDBAccession())
- {
- // this URL requires an accession id, not the name of a sequence
- url = null;
- continue;
- }
-
- if (!urlLink.isValid())
- {
- System.err.println(urlLink.getInvalidMessage());
- url = null;
- continue;
- }
-
- String urls[] = urlLink.makeUrls(id, true);
- if (urls == null || urls[0] == null || urls[0].length() < 1)
- {
- url = null;
- continue;
- }
- // just take first URL made from regex
- url = urls[1];
- }*/
+ // get the default url with the sequence details filled in
+ String url = urlProvider.getPrimaryUrl(id);
+ String target = urlProvider.getPrimaryTarget(id);
try
{
alignPanel.alignFrame.showURL(url, target);
return;
}
- if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
+ if (mouseDragging && e.getY() < 0 && av.getRanges().getStartSeq() > 0)
{
scrollThread = new ScrollThread(true);
}
if (mouseDragging && e.getY() >= getSize().height
- && av.getAlignment().getHeight() > av.getEndSeq())
+ && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
{
scrollThread = new ScrollThread(false);
}
// build a new links menu based on the current links + any non-positional
// features
- Vector<String> nlinks = urlProvider.getLinksForDisplay();
+ List<String> nlinks = urlProvider.getLinksForMenu();
SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
for (int sl = 0; sf != null && sl < sf.length; sl++)
{
for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
{
- nlinks.addElement(sf[sl].links.elementAt(l));
+ nlinks.add(sf[sl].links.elementAt(l));
}
}
}
int index = av.getAlignment().findIndex(list.get(0));
// do we need to scroll the panel?
- if (av.getStartSeq() > index || av.getEndSeq() < index)
+ if (av.getRanges().getStartSeq() > index
+ || av.getRanges().getEndSeq() < index)
{
- alignPanel.setScrollValues(av.getStartRes(), index);
+ alignPanel.setScrollValues(av.getRanges().getStartRes(), index);
}
}
if (alignPanel.scrollUp(up))
{
// scroll was ok, so add new sequence to selection
- int seq = av.getStartSeq();
+ int seq = av.getRanges().getStartSeq();
if (!up)
{
- seq = av.getEndSeq();
+ seq = av.getRanges().getEndSeq();
}
if (seq < lastid)