import jalview.io.SequenceAnnotationReport;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.util.UrlLink;
import jalview.viewmodel.AlignmentViewport;
import java.awt.BorderLayout;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.util.List;
-import java.util.Vector;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
* @author $author$
* @version $Revision$
*/
-public class IdPanel extends JPanel implements MouseListener,
- MouseMotionListener, MouseWheelListener
+public class IdPanel extends JPanel
+ implements MouseListener, MouseMotionListener, MouseWheelListener
{
private IdCanvas idCanvas;
if (seq > -1 && seq < av.getAlignment().getHeight())
{
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- StringBuffer tip = new StringBuffer(64);
- seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
+ StringBuilder tip = new StringBuilder(64);
+ seqAnnotReport.createTooltipAnnotationReport(tip, sequence,
av.isShowDBRefs(), av.isShowNPFeats(),
sp.seqCanvas.fr.getMinMax());
setToolTipText(JvSwingUtils.wrapTooltip(true,
}
lastid = seq;
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false);
}
/**
{
if (e.isShiftDown())
{
- alignPanel.scrollRight(true);
+ av.getRanges().scrollRight(true);
}
- else
+ else if (!av.getWrapAlignment())
{
- alignPanel.scrollUp(false);
+ av.getRanges().scrollUp(false);
}
}
else
{
if (e.isShiftDown())
{
- alignPanel.scrollRight(false);
+ av.getRanges().scrollRight(false);
}
- else
+ else if (!av.getWrapAlignment())
{
- alignPanel.scrollUp(true);
+ av.getRanges().scrollUp(true);
}
}
}
return;
}
- Vector links = Preferences.sequenceURLLinks;
- if (links == null || links.size() < 1)
- {
- return;
- }
-
int seq = alignPanel.getSeqPanel().findSeq(e);
- String url = null;
- int i = 0;
String id = av.getAlignment().getSequenceAt(seq).getName();
- 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);
- } catch (Exception foo)
- {
- jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'",
- foo);
- url = null;
- continue;
- }
+ String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
- if (urlLink.usesDBAccession())
- {
- // this URL requires an accession id, not the name of a sequence
- url = null;
- continue;
- }
-
- if (!urlLink.isValid())
- {
- jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
- url = null;
- continue;
- }
-
- String urls[] = urlLink.makeUrls(id, true);
- if (urls == null || urls[0] == null || urls[0].length() < 4)
- {
- url = null;
- continue;
- }
- // just take first URL made from regex
- url = urls[1];
- }
try
{
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
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() >= getHeight())
- && (av.getAlignment().getHeight() > av.getEndSeq()))
+ && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
{
scrollThread = new ScrollThread(false);
}
}
if ((av.getSelectionGroup() == null)
- || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() && av
- .getSelectionGroup() != null))
+ || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown()
+ && av.getSelectionGroup() != null))
{
av.setSelectionGroup(new SequenceGroup());
av.getSelectionGroup().setStartRes(0);
av.isSelectionGroupChanged(true);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false);
}
/**
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
// build a new links menu based on the current links + any non-positional
// features
- Vector<String> nlinks = new Vector<String>(Preferences.sequenceURLLinks);
+ List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
if (sfs != null)
{
{
for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
{
- nlinks.addElement(sf.links.elementAt(l));
+ nlinks.add(sf.links.elementAt(l));
}
}
}
for (int i = start; i <= end; i++)
{
- av.getSelectionGroup().addSequence(
- av.getAlignment().getSequenceAt(i), i == end);
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+ i == end);
}
}
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);
}
}
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)