import jalview.io.vamsas.DatastoreItem;
import jalview.io.vamsas.DatastoreRegistry;
import jalview.io.vamsas.Rangetype;
+import jalview.project.Jalview2XML;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
// client data is shared over all app clients
try
{
- jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+ // jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+ Jalview2XML fromxml = new Jalview2XML();
fromxml.attemptversion1parse = false;
fromxml.setUniqueSetSuffix("");
fromxml.setObjectMappingTables(vobj2jv, jv2vobj); // mapKeysToString
// user data overrides data shared over all app clients ?
try
{
- jalview.gui.Jalview2XML fromxml = new jalview.gui.Jalview2XML();
+ Jalview2XML fromxml = new Jalview2XML();
fromxml.attemptversion1parse = false;
fromxml.setUniqueSetSuffix("");
fromxml.setSkipList(skipList);
{
try
{
- jalview.gui.Jalview2XML jxml = new jalview.gui.Jalview2XML();
+ Jalview2XML jxml = new Jalview2XML();
jxml.setObjectMappingTables(mapKeysToString(vobj2jv),
mapValuesToString(jv2vobj));
jxml.setSkipList(skipList);
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));
}
}
}