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JAL-1563 JAL-2071 Update and completed implementation for UniProt FTS support
[jalview.git]
/
src
/
jalview
/
gui
/
VamsasApplication.java
diff --git
a/src/jalview/gui/VamsasApplication.java
b/src/jalview/gui/VamsasApplication.java
index
6daaf68
..
7588e07
100644
(file)
--- a/
src/jalview/gui/VamsasApplication.java
+++ b/
src/jalview/gui/VamsasApplication.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-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;
@@
-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();
@@
-347,7
+353,11
@@
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
{
@@
-715,7
+725,9
@@
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();
@@
-958,11
+970,14
@@
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
+1013,7
@@
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)
@@
-1008,9
+1023,9
@@
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[]
- { ((AlignViewport) source).getSequenceSetId() }, null,
- true);
+ sm = new SelectionMessage("jalview",
+ new String[] { ((AlignmentViewport) source)
+ .getSequenceSetId() }, null, true);
}
else
{
}
else
{
@@
-1050,10
+1065,9
@@
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);