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JAL-842; Give Varna frames name for window organizer; always display
[jalview.git]
/
src
/
jalview
/
gui
/
VamsasApplication.java
diff --git
a/src/jalview/gui/VamsasApplication.java
b/src/jalview/gui/VamsasApplication.java
index
abb170f
..
1da1ae9
100644
(file)
--- a/
src/jalview/gui/VamsasApplication.java
+++ b/
src/jalview/gui/VamsasApplication.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@
-27,6
+27,7
@@
import jalview.structure.SelectionListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasListener;
+import jalview.structure.VamsasSource;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
@@
-61,7
+62,7
@@
import uk.ac.vamsas.objects.core.Seg;
* @author jimp
*
*/
* @author jimp
*
*/
-public class VamsasApplication implements SelectionSource
+public class VamsasApplication implements SelectionSource,VamsasSource
{
IClient vclient = null;
{
IClient vclient = null;
@@
-222,14
+223,12
@@
public class VamsasApplication implements SelectionSource
} catch (Error e)
{
Cache.log
} catch (Error e)
{
Cache.log
- .warn(
- "Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
+ .warn("Probable SERIOUS VAMSAS client incompatibility - carrying on regardless",
e);
} catch (Exception e)
{
Cache.log
e);
} catch (Exception e)
{
Cache.log
- .warn(
- "Probable VAMSAS client incompatibility - carrying on regardless",
+ .warn("Probable VAMSAS client incompatibility - carrying on regardless",
e);
}
}
e);
}
}
@@
-241,8
+240,8
@@
public class VamsasApplication implements SelectionSource
*/
private ClientHandle getJalviewHandle()
{
*/
private ClientHandle getJalviewHandle()
{
- return new ClientHandle("jalview.bin.Jalview", jalview.bin.Cache
- .getProperty("VERSION"));
+ return new ClientHandle("jalview.bin.Jalview",
+ jalview.bin.Cache.getProperty("VERSION"));
}
/**
}
/**
@@
-305,8
+304,7
@@
public class VamsasApplication implements SelectionSource
} catch (Exception e)
{
Cache.log
} catch (Exception e)
{
Cache.log
- .warn(
- "Exception whilst refreshing jalview windows after a vamsas document update.",
+ .warn("Exception whilst refreshing jalview windows after a vamsas document update.",
e);
}
}
e);
}
}
@@
-758,8
+756,8
@@
public class VamsasApplication implements SelectionSource
{
final IPickManager pm = vclient.getPickManager();
final StructureSelectionManager ssm = StructureSelectionManager
{
final IPickManager pm = vclient.getPickManager();
final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager();
- final SelectionSource me = this;
+ .getStructureSelectionManager(Desktop.instance);
+ final VamsasApplication me = this;
pm.registerMessageHandler(new IMessageHandler()
{
String last = null;
pm.registerMessageHandler(new IMessageHandler()
{
String last = null;
@@
-791,8
+789,8
@@
public class VamsasApplication implements SelectionSource
// Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
// bound to "+jvobj+" at "+mm.getPosition());
// position is character position in aligned sequence
// Cache.log.debug("Handling Mouse over "+mm.getVorbaID()+"
// bound to "+jvobj+" at "+mm.getPosition());
// position is character position in aligned sequence
- ssm.mouseOverVamsasSequence((SequenceI) jvobj, mm
- .getPosition());
+ ssm.mouseOverVamsasSequence((SequenceI) jvobj,
+ mm.getPosition(), me);
}
}
if (message instanceof uk.ac.vamsas.client.picking.SelectionMessage)
}
}
if (message instanceof uk.ac.vamsas.client.picking.SelectionMessage)
@@
-960,7
+958,7
@@
public class VamsasApplication implements SelectionSource
int i = -1;
int i = -1;
- public void mouseOver(SequenceI seq, int index)
+ public void mouseOver(SequenceI seq, int index, VamsasSource source)
{
if (jv2vobj == null)
return;
{
if (jv2vobj == null)
return;
@@
-1064,8
+1062,8
@@
public class VamsasApplication implements SelectionSource
}
else
{
}
else
{
- int[] intervals = colsel.getVisibleContigs(seqsel
- .getStartRes(), seqsel.getEndRes() + 1);
+ int[] intervals = colsel.getVisibleContigs(
+ seqsel.getStartRes(), seqsel.getEndRes() + 1);
for (int iv = 0; iv < intervals.length; iv += 2)
{
Seg s = new Seg();
for (int iv = 0; iv < intervals.length; iv += 2)
{
Seg s = new Seg();