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Merge branch 'develop' into features/JAL-2393customMatrices
[jalview.git]
/
src
/
jalview
/
gui
/
IdPanel.java
diff --git
a/src/jalview/gui/IdPanel.java
b/src/jalview/gui/IdPanel.java
index
fb9bcbb
..
2074900
100755
(executable)
--- a/
src/jalview/gui/IdPanel.java
+++ b/
src/jalview/gui/IdPanel.java
@@
-36,9
+36,7
@@
import java.awt.event.MouseMotionListener;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.util.List;
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;
import javax.swing.JPanel;
import javax.swing.SwingUtilities;
import javax.swing.ToolTipManager;
@@
-108,8
+106,8
@@
public class IdPanel extends JPanel implements MouseListener,
if (seq > -1 && seq < av.getAlignment().getHeight())
{
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
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,
av.isShowDBRefs(), av.isShowNPFeats(),
sp.seqCanvas.fr.getMinMax());
setToolTipText(JvSwingUtils.wrapTooltip(true,
@@
-200,17
+198,17
@@
public class IdPanel extends JPanel implements MouseListener,
int seq = alignPanel.getSeqPanel().findSeq(e);
String id = av.getAlignment().getSequenceAt(seq).getName();
int seq = alignPanel.getSeqPanel().findSeq(e);
String id = av.getAlignment().getSequenceAt(seq).getName();
- String url = Preferences.sequenceUrlLinks.getDefaultUrl(id);
+ String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
try
{
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
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"),
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
}
ex.printStackTrace();
}
}
@@
-244,13
+242,14
@@
public class IdPanel extends JPanel implements MouseListener,
return;
}
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())
{
scrollThread = new ScrollThread(true);
}
if (mouseDragging && (e.getY() >= getHeight())
- && (av.getAlignment().getHeight() > av.getEndSeq()))
+ && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
{
scrollThread = new ScrollThread(false);
}
{
scrollThread = new ScrollThread(false);
}
@@
-328,7
+327,7
@@
public class IdPanel extends JPanel implements MouseListener,
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
// build a new links menu based on the current links + any non-positional
// features
Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
// build a new links menu based on the current links + any non-positional
// features
- Vector<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+ List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
if (sfs != null)
{
SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
if (sfs != null)
{
@@
-340,7
+339,7
@@
public class IdPanel extends JPanel implements MouseListener,
{
for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
{
{
for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
{
- nlinks.addElement(sf.links.elementAt(l));
+ nlinks.add(sf.links.elementAt(l));
}
}
}
}
}
}
@@
-444,9
+443,10
@@
public class IdPanel extends JPanel implements MouseListener,
int index = av.getAlignment().findIndex(list.get(0));
// do we need to scroll the panel?
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);
}
}
}
}
@@
-488,11
+488,11
@@
public class IdPanel extends JPanel implements MouseListener,
if (alignPanel.scrollUp(up))
{
// scroll was ok, so add new sequence to selection
if (alignPanel.scrollUp(up))
{
// scroll was ok, so add new sequence to selection
- int seq = av.getStartSeq();
+ int seq = av.getRanges().getStartSeq();
if (!up)
{
if (!up)
{
- seq = av.getEndSeq();
+ seq = av.getRanges().getEndSeq();
}
if (seq < lastid)
}
if (seq < lastid)