{
dssmods.addElement(sequence);
}
+ ;
}
if (dssmods.size() > 0)
{
(AlignmentSequence) alsref, aa[i]);
break;
}
+ ;
}
}
}
// /SAVE THE TREES
// /////////////////////////////////
// FIND ANY ASSOCIATED TREES
- if (Desktop.getDesktopPane() != null)
+ if (Desktop.desktop != null)
{
- javax.swing.JInternalFrame[] frames = Desktop.getInstance()
+ javax.swing.JInternalFrame[] frames = Desktop.instance
.getAllFrames();
for (int t = 0; t < frames.length; t++)
// active
if (mappings != null)
{
- Desktop.getInstance().getStructureSelectionManager()
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
.registerMappings(mappings);
}
}
}
// bitfields - should be a template in j1.5
- private static final int HASSECSTR = 0;
+ private static int HASSECSTR = 0;
- private static final int HASVALS = 1;
+ private static int HASVALS = 1;
- private static final int HASHPHOB = 2;
+ private static int HASHPHOB = 2;
- private static final int HASDC = 3;
+ private static int HASDC = 3;
- private static final int HASDESCSTR = 4;
+ private static int HASDESCSTR = 4;
- private static final int HASTWOSTATE = 5; // not used yet.
+ private static int HASTWOSTATE = 5; // not used yet.
/**
* parses the AnnotationElements - if they exist - into
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));
}
}
}