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JAL-2089 patch broken merge to master for Release 2.10.0b1
[jalview.git]
/
src
/
jalview
/
gui
/
VamsasApplication.java
diff --git
a/src/jalview/gui/VamsasApplication.java
b/src/jalview/gui/VamsasApplication.java
index
6444667
..
afb6df4
100644
(file)
--- a/
src/jalview/gui/VamsasApplication.java
+++ b/
src/jalview/gui/VamsasApplication.java
@@
-156,7
+156,9
@@
public class VamsasApplication implements SelectionSource, VamsasSource
{
if (sess != null)
{
{
if (sess != null)
{
- throw new Error(MessageManager.getString("error.implementation_error_cannot_import_vamsas_doc"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_import_vamsas_doc"));
}
try
{
}
try
{
@@
-176,8
+178,10
@@
public class VamsasApplication implements SelectionSource, VamsasSource
.showInternalMessageDialog(
Desktop.desktop,
.showInternalMessageDialog(
Desktop.desktop,
- MessageManager.getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
- MessageManager.getString("label.vamsas_document_import_failed"),
+ MessageManager
+ .getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
+ MessageManager
+ .getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
}
JOptionPane.ERROR_MESSAGE);
}
@@
-263,7
+267,9
@@
public class VamsasApplication implements SelectionSource, VamsasSource
{
if (!inSession())
{
{
if (!inSession())
{
- throw new Error(MessageManager.getString("error.implementation_error_vamsas_operation_not_init"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_vamsas_operation_not_init"));
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
@@
-315,6
+321,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
Thread udthread = new Thread(new Runnable()
{
Thread udthread = new Thread(new Runnable()
{
+ @Override
public void run()
{
Cache.log.info("Jalview updating to the Vamsas Session.");
public void run()
{
Cache.log.info("Jalview updating to the Vamsas Session.");
@@
-348,7
+355,9
@@
public class VamsasApplication implements SelectionSource, VamsasSource
{
if (!inSession())
{
{
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
@@
-631,6
+640,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
final VamsasApplication client = this;
vclient.addDocumentUpdateHandler(new PropertyChangeListener()
{
final VamsasApplication client = this;
vclient.addDocumentUpdateHandler(new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
Cache.log.debug("Dealing with document update event.");
public void propertyChange(PropertyChangeEvent evt)
{
Cache.log.debug("Dealing with document update event.");
@@
-648,6
+658,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE,
new PropertyChangeListener()
{
uk.ac.vamsas.client.Events.DOCUMENT_REQUESTTOCLOSE,
new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (client.promptUser)
public void propertyChange(PropertyChangeEvent evt)
{
if (client.promptUser)
@@
-717,7
+728,9
@@
public class VamsasApplication implements SelectionSource, VamsasSource
return;
}
return;
}
- throw new Error(MessageManager.getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
@@
-764,6
+777,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
{
String last = null;
{
String last = null;
+ @Override
public void handleMessage(Message message)
{
if (vobj2jv == null)
public void handleMessage(Message message)
{
if (vobj2jv == null)
@@
-988,6
+1002,7
@@
public class VamsasApplication implements SelectionSource, VamsasSource
selecter = new SelectionListener()
{
selecter = new SelectionListener()
{
+ @Override
public void selection(SequenceGroup seqsel,
ColumnSelection colsel, SelectionSource source)
{
public void selection(SequenceGroup seqsel,
ColumnSelection colsel, SelectionSource source)
{
@@
-1013,9
+1028,9
@@
public class VamsasApplication implements SelectionSource, VamsasSource
if (source instanceof AlignViewport)
{
// the empty selection.
if (source instanceof AlignViewport)
{
// the empty selection.
- sm = new SelectionMessage("jalview", new String[]
- { ((AlignmentViewport) source).getSequenceSetId() }, null,
- true);
+ sm = new SelectionMessage("jalview",
+ new String[] { ((AlignmentViewport) source)
+ .getSequenceSetId() }, null, true);
}
else
{
}
else
{
@@
-1055,11
+1070,10
@@
public class VamsasApplication implements SelectionSource, VamsasSource
{
// gather selected columns outwith the sequence positions
// too
{
// gather selected columns outwith the sequence positions
// too
- for (Object obj : colsel.getSelected())
+ for (Integer ival : colsel.getSelected())
{
{
- int ival = ((Integer) obj).intValue();
Pos p = new Pos();
Pos p = new Pos();
- p.setI(ival + 1);
+ p.setI(ival.intValue() + 1);
range.addPos(p);
}
}
range.addPos(p);
}
}