import jalview.io.vamsas.Rangetype;
import jalview.project.Jalview2XML;
import jalview.util.MessageManager;
+import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.AlignmentViewport;
+import java.io.File;
import java.io.IOException;
import java.util.Enumeration;
import java.util.HashMap;
// /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++)
// and
// mapValuesToString
fromxml.setSkipList(skipList);
- jalview.util.jarInputStreamProvider jprovider = new jalview.util.jarInputStreamProvider()
+ jarInputStreamProvider jprovider = new jarInputStreamProvider()
{
@Override
"Returning client input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getClientInputStream());
}
+
+ @Override
+ public File getFile()
+ {
+ return null;
+ }
};
if (dojvsync)
{
fromxml.setSkipList(skipList);
fromxml.setObjectMappingTables(mapKeysToString(vobj2jv),
mapValuesToString(jv2vobj));
- jalview.util.jarInputStreamProvider jarstream = new jalview.util.jarInputStreamProvider()
+ jarInputStreamProvider jarstream = new jarInputStreamProvider()
{
@Override
"Returning user input stream for Jalview from Vamsas Document.");
return new JarInputStream(cappdata.getUserInputStream());
}
+
+ @Override
+ public File getFile()
+ {
+ return null;
+ }
};
if (dojvsync)
{
if (mappings != null)
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.registerMappings(mappings);
}
}
Float val = null;
try
{
- val = new Float(props[p].getContent());
+ val = Float.valueOf(props[p].getContent());
} catch (Exception e)
{
Cache.log.warn("Failed to parse threshold property");
int se_end = se[1 - se[2]] + (se[2] == 0 ? 1 : -1);
for (int p = se[se[2]]; p != se_end; p += se[2] == 0 ? 1 : -1)
{
- posList.add(new Integer(p));
+ posList.add(Integer.valueOf(p));
}
}
}
for (int p = 0, pSize = dseta.getPosCount(); p < pSize; p++)
{
pos = dseta.getPos(p).getI();
- posList.add(new Integer(pos));
+ posList.add(Integer.valueOf(pos));
}
}
}