import java.io.IOException;
import java.util.ArrayList;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
public class PDBfile extends jalview.io.AlignFile
{
- public Vector chains;
+ public Vector<PDBChain> chains;
public String id;
}
for (int i = 0; i < chains.size(); i++)
{
- SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
+ SequenceI dataset = chains.elementAt(i).sequence;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
entry.setProperty(new Hashtable());
- if (((PDBChain) chains.elementAt(i)).id != null)
+ if (chains.elementAt(i).id != null)
{
entry.getProperty().put("CHAIN",
- ((PDBChain) chains.elementAt(i)).id);
+ chains.elementAt(i).id);
}
if (inFile != null)
{
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).makeResidueList();
+ chains.elementAt(i).makeResidueList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
+ chains.elementAt(i).makeCaBondList();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- if (((PDBChain) chains.elementAt(i)).id.equals(id))
+ if (chains.elementAt(i).id.equals(id))
{
- return (PDBChain) chains.elementAt(i);
+ return chains.elementAt(i);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChargeColours();
+ chains.elementAt(i).setChargeColours();
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+ chains.elementAt(i).setChainColours(cs);
}
}
{
for (int i = 0; i < chains.size(); i++)
{
- ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+ chains.elementAt(i).setChainColours(Color.getHSBColor(
1.0f / i, .4f, 1.0f));
}
}