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Merge develop to Release_2_8_3_Branch
[jalview.git]
/
src
/
jalview
/
gui
/
VamsasApplication.java
diff --git
a/src/jalview/gui/VamsasApplication.java
b/src/jalview/gui/VamsasApplication.java
index
3671b39
..
6444667
100644
(file)
--- a/
src/jalview/gui/VamsasApplication.java
+++ b/
src/jalview/gui/VamsasApplication.java
@@
-32,12
+32,12
@@
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasListener;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.structure.VamsasListener;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.IOException;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.IOException;
-import java.util.Enumeration;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
@@
-347,7
+347,9
@@
public class VamsasApplication implements SelectionSource, VamsasSource
public void end_session(boolean promptUser)
{
if (!inSession())
public void end_session(boolean promptUser)
{
if (!inSession())
+ {
throw new Error(MessageManager.getString("error.jalview_no_connected_vamsas_session"));
throw new Error(MessageManager.getString("error.jalview_no_connected_vamsas_session"));
+ }
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
{
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
{
@@
-958,11
+960,14
@@
public class VamsasApplication implements SelectionSource, VamsasSource
int i = -1;
int i = -1;
- public void mouseOver(SequenceI seq, int index,
+ @Override
+ public void mouseOverSequence(SequenceI seq, int index,
VamsasSource source)
{
if (jv2vobj == null)
VamsasSource source)
{
if (jv2vobj == null)
+ {
return;
return;
+ }
if (seq != last || i != index)
{
VorbaId v = (VorbaId) jv2vobj.get(seq);
if (seq != last || i != index)
{
VorbaId v = (VorbaId) jv2vobj.get(seq);
@@
-998,7
+1003,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
AlignmentI visal = null;
if (source instanceof AlignViewport)
{
AlignmentI visal = null;
if (source instanceof AlignViewport)
{
- visal = ((AlignViewport) source).getAlignment();
+ visal = ((AlignmentViewport) source).getAlignment();
}
SelectionMessage sm = null;
if ((seqsel == null || seqsel.getSize() == 0)
}
SelectionMessage sm = null;
if ((seqsel == null || seqsel.getSize() == 0)
@@
-1009,7
+1014,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
{
// the empty selection.
sm = new SelectionMessage("jalview", new String[]
{
// the empty selection.
sm = new SelectionMessage("jalview", new String[]
- { ((AlignViewport) source).getSequenceSetId() }, null,
+ { ((AlignmentViewport) source).getSequenceSetId() }, null,
true);
}
else
true);
}
else
@@
-1050,10
+1055,9
@@
public class VamsasApplication implements SelectionSource, VamsasSource
{
// gather selected columns outwith the sequence positions
// too
{
// gather selected columns outwith the sequence positions
// too
- Enumeration cols = colsel.getSelected().elements();
- while (cols.hasMoreElements())
+ for (Object obj : colsel.getSelected())
{
{
- int ival = ((Integer) cols.nextElement()).intValue();
+ int ival = ((Integer) obj).intValue();
Pos p = new Pos();
p.setI(ival + 1);
range.addPos(p);
Pos p = new Pos();
p.setI(ival + 1);
range.addPos(p);