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)
{
markCalcIds();
}
+ private static String calcIdPrefix = "JalviewPDB:";
+
+ public static boolean isCalcIdHandled(String calcId)
+ {
+ return calcId != null
+ && (calcId.startsWith(calcIdPrefix) && calcId.indexOf(
+ calcIdPrefix,
+ calcIdPrefix.length() + 1) > -1);
+ }
public static boolean isCalcIdForFile(String calcId, String pdbFile)
{
- return (calcId != null && calcId.startsWith("JalviewPDB:" + pdbFile
- + ":JalviewPDB:"));
+ return (calcId != null && calcId.startsWith(calcIdPrefix + pdbFile
+ + ":" + calcIdPrefix));
+ }
+
+ public static String relocateCalcId(String calcId,
+ Hashtable<String, String> alreadyLoadedPDB) throws Exception
+ {
+ int s = calcIdPrefix.length(), end = calcId.indexOf(calcIdPrefix, s);
+ String between = calcId.substring(s, end - 1);
+ return calcIdPrefix + alreadyLoadedPDB.get(between) + ":"
+ + calcId.substring(end);
}
+
private void markCalcIds()
{
for (SequenceI sq : seqs)
{}).invoke(jmf));
cl.getMethod("addAnnotations", new Class[]
{ Alignment.class }).invoke(jmf, al);
- AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() != null)
+ {
+ sq.getDatasetSequence().getPDBId().clear();
+ }
+ else
+ {
+ sq.getPDBId().clear();
+ }
+ }
+ replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
}
} catch (ClassNotFoundException q)
{
}
}
+ private void replaceAndUpdateChains(ArrayList<SequenceI> prot,
+ AlignmentI al, String pep, boolean b)
+ {
+ List<List<? extends Object>> replaced = AlignSeq
+ .replaceMatchingSeqsWith(seqs,
+ annotations, prot, al, AlignSeq.PEP, false);
+ for (PDBChain ch : chains)
+ {
+ int p = 0;
+ for (SequenceI sq : (List<SequenceI>) replaced.get(0))
+ {
+ p++;
+ if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
+ {
+ p = -p;
+ break;
+ }
+ }
+ if (p < 0)
+ {
+ p = -p - 1;
+ // set shadow entry for chains
+ ch.shadow = (SequenceI) replaced.get(1).get(p);
+ ch.shadowMap = ((AlignSeq) replaced.get(2)
+.get(p))
+ .getMappingFromS1(false);
+ }
+ }
+ }
+
private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna)
throws Exception
{
new Class[]
{ FileParse.class }).invoke(annotate3d, new Object[]
{ new FileParse(getDataName(), type) }));
- AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() != null)
+ {
+ if (sq.getDatasetSequence().getPDBId() != null)
+ {
+ sq.getDatasetSequence().getPDBId().clear();
+ }
+ }
+ else
+ {
+ if (sq.getPDBId() != null)
+ {
+ sq.getPDBId().clear();
+ }
+ }
+ }
+ replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
}
} catch (ClassNotFoundException x)
{
{
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));
}
}