*/
package jalview.appletgui;
-import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.util.UrlProvider;
-import jalview.util.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.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
-import java.util.Vector;
public class IdPanel extends Panel implements MouseListener,
MouseMotionListener
UrlProviderI urlProvider = null;
- public IdPanel(AlignViewport av, AlignmentPanel parent)
+ public IdPanel(AlignViewport viewport, AlignmentPanel parent)
{
- this.av = av;
+ this.av = viewport;
alignPanel = parent;
- idCanvas = new IdCanvas(av);
+ idCanvas = new IdCanvas(viewport);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
idCanvas.addMouseListener(this);
// make a list of label,url pairs
HashMap<String, String> urlList = new HashMap<String, String>();
- if (av.applet != null)
+ if (viewport.applet != null)
{
for (int i = 1; i < 10; i++)
{
- label = av.applet.getParameter("linkLabel_" + i);
- url = av.applet.getParameter("linkURL_" + i);
+ label = viewport.applet.getParameter("linkLabel_" + i);
+ url = viewport.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);
+ String defaultUrl = viewport.applet.getParameter("linkLabel_1");
+ UrlProviderFactoryI factory = new AppletUrlProviderFactory(
+ defaultUrl, urlList);
+ urlProvider = factory.createUrlProvider();
}
}
}
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- // look for non-pos features
StringBuffer tooltiptext = new StringBuffer();
- if (sequence != null)
+ if (sequence == null)
+ {
+ return;
+ }
+ if (sequence.getDescription() != null)
+ {
+ tooltiptext.append(sequence.getDescription());
+ tooltiptext.append("\n");
+ }
+
+ for (SequenceFeature sf : sequence.getFeatures()
+ .getNonPositionalFeatures())
{
- if (sequence.getDescription() != null)
+ boolean nl = false;
+ if (sf.getFeatureGroup() != null)
{
- tooltiptext.append(sequence.getDescription());
- tooltiptext.append("\n");
+ tooltiptext.append(sf.getFeatureGroup());
+ nl = true;
}
-
- SequenceFeature sf[] = sequence.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
+ if (sf.getType() != null)
{
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
- {
- boolean nl = false;
- if (sf[sl].getFeatureGroup() != null)
- {
- tooltiptext.append(sf[sl].getFeatureGroup());
- nl = true;
- }
- ;
- if (sf[sl].getType() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getType());
- nl = true;
- }
- ;
- if (sf[sl].getDescription() != null)
- {
- tooltiptext.append(" ");
- tooltiptext.append(sf[sl].getDescription());
- nl = true;
- }
- ;
- if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
- {
- tooltiptext.append(" Score = ");
- tooltiptext.append(sf[sl].getScore());
- nl = true;
- }
- ;
- if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
- {
- tooltiptext.append(" (");
- tooltiptext.append(sf[sl].getStatus());
- tooltiptext.append(")");
- nl = true;
- }
- ;
- if (nl)
- {
- tooltiptext.append("\n");
- }
- }
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getType());
+ nl = true;
+ }
+ if (sf.getDescription() != null)
+ {
+ tooltiptext.append(" ");
+ tooltiptext.append(sf.getDescription());
+ nl = true;
+ }
+ if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
+ {
+ tooltiptext.append(" Score = ");
+ tooltiptext.append(sf.getScore());
+ nl = true;
+ }
+ if (sf.getStatus() != null && sf.getStatus().length() > 0)
+ {
+ tooltiptext.append(" (");
+ tooltiptext.append(sf.getStatus());
+ tooltiptext.append(")");
+ nl = true;
+ }
+ if (nl)
+ {
+ tooltiptext.append("\n");
}
}
+
if (tooltiptext.length() == 0)
{
// nothing to display - so clear tooltip if one is visible
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
+ if (urlProvider == null)
+ {
+ return;
+ }
+ 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);
}
if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sq = av.getAlignment().getSequenceAt(seq);
- // build a new links menu based on the current links + any non-positional
- // features
- Vector<String> nlinks = urlProvider.getLinksForDisplay();
+ /*
+ * build a new links menu based on the current links
+ * and any non-positional features
+ */
+ List<String> nlinks;
+ if (urlProvider != null)
+ {
+ nlinks = urlProvider.getLinksForMenu();
+ }
+ else
+ {
+ nlinks = new ArrayList<String>();
+ }
- SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
- for (int sl = 0; sf != null && sl < sf.length; sl++)
+ for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
{
- if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+ if (sf.links != null)
{
- if (sf[sl].links != null && sf[sl].links.size() > 0)
+ for (String link : sf.links)
{
- for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
- {
- nlinks.addElement(sf[sl].links.elementAt(l));
- }
+ nlinks.add(link);
}
}
}
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);
+ av.getRanges().setStartSeq(index);
}
}
boolean up = true;
- public ScrollThread(boolean up)
+ public ScrollThread(boolean isUp)
{
- this.up = up;
+ this.up = isUp;
start();
}
running = true;
while (running)
{
- if (alignPanel.scrollUp(up))
+ if (av.getRanges().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)
git://source.jalview.org / jalview.git / blobdiff