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Merge branch 'Jalview-JS/develop' into merge_js_develop
[jalview.git]
/
src
/
jalview
/
io
/
VamsasAppDatastore.java
diff --git
a/src/jalview/io/VamsasAppDatastore.java
b/src/jalview/io/VamsasAppDatastore.java
index
387dbfa
..
15c481d
100644
(file)
--- a/
src/jalview/io/VamsasAppDatastore.java
+++ b/
src/jalview/io/VamsasAppDatastore.java
@@
-35,8
+35,10
@@
import jalview.io.vamsas.DatastoreRegistry;
import jalview.io.vamsas.Rangetype;
import jalview.project.Jalview2XML;
import jalview.util.MessageManager;
import jalview.io.vamsas.Rangetype;
import jalview.project.Jalview2XML;
import jalview.util.MessageManager;
+import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.AlignmentViewport;
+import java.io.File;
import java.io.IOException;
import java.util.Enumeration;
import java.util.HashMap;
import java.io.IOException;
import java.util.Enumeration;
import java.util.HashMap;
@@
-720,9
+722,9
@@
public class VamsasAppDatastore
// /SAVE THE TREES
// /////////////////////////////////
// FIND ANY ASSOCIATED TREES
// /SAVE THE TREES
// /////////////////////////////////
// FIND ANY ASSOCIATED TREES
- if (Desktop.desktop != null)
+ if (Desktop.getDesktopPane() != null)
{
{
- javax.swing.JInternalFrame[] frames = Desktop.instance
+ javax.swing.JInternalFrame[] frames = Desktop.getInstance()
.getAllFrames();
for (int t = 0; t < frames.length; t++)
.getAllFrames();
for (int t = 0; t < frames.length; t++)
@@
-1320,7
+1322,7
@@
public class VamsasAppDatastore
// and
// mapValuesToString
fromxml.setSkipList(skipList);
// and
// mapValuesToString
fromxml.setSkipList(skipList);
- jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
+ jarInputStreamProvider jprovider = new jarInputStreamProvider()
{
@Override
{
@Override
@@
-1338,6
+1340,12
@@
public class VamsasAppDatastore
"Returning client input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getClientInputStream());
}
"Returning client input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getClientInputStream());
}
+
+ @Override
+ public File getFile()
+ {
+ return null;
+ }
};
if (dojvsync)
{
};
if (dojvsync)
{
@@
-1368,7
+1376,7
@@
public class VamsasAppDatastore
fromxml.setSkipList(skipList);
fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
mapValuesToString(jv2vobj));
fromxml.setSkipList(skipList);
fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
mapValuesToString(jv2vobj));
- jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
+ jarInputStreamProvider jarstream = new jarInputStreamProvider()
{
@Override
{
@Override
@@
-1386,6
+1394,12
@@
public class VamsasAppDatastore
"Returning user input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getUserInputStream());
}
"Returning user input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getUserInputStream());
}
+
+ @Override
+ public File getFile()
+ {
+ return null;
+ }
};
if (dojvsync)
{
};
if (dojvsync)
{
@@
-1479,7
+1493,7
@@
public class VamsasAppDatastore
if (mappings != null)
{
jalview.structure.StructureSelectionManager
if (mappings != null)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.registerMappings(mappings);
}
}
.registerMappings(mappings);
}
}