if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
- pdbentry.setFile("INLINE" + pdb.id);
+ pdbentry.setFile("INLINE" + pdb.getId());
}
} catch (Exception ex)
errorMessage = "Error loading file: " + pdbentry.getId();
return;
}
- pdbentry.setId(pdb.id);
+ pdbentry.setId(pdb.getId());
ssm.addStructureViewerListener(this);
// JUST DEAL WITH ONE SEQUENCE FOR NOW
SequenceI sequence = seq[0];
- for (int i = 0; i < pdb.chains.size(); i++)
+ for (int i = 0; i < pdb.getChains().size(); i++)
{
mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
- + pdb.chains.elementAt(i).sequence.getSequenceAsString());
+ + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
mappingDetails.append("\nNo of residues = "
- + pdb.chains.elementAt(i).residues.size() + "\n\n");
+ + pdb.getChains().elementAt(i).residues.size() + "\n\n");
// Now lets compare the sequences to get
// the start and end points.
// Align the sequence to the pdb
AlignSeq as = new AlignSeq(sequence,
- pdb.chains.elementAt(i).sequence, "pep");
+ pdb.getChains().elementAt(i).sequence, "pep");
as.calcScoreMatrix();
as.traceAlignment();
PrintStream ps = new PrintStream(System.out)
mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
}
- mainchain = pdb.chains.elementAt(maxchain);
+ mainchain = pdb.getChains().elementAt(maxchain);
mainchain.pdbstart = pdbstart;
mainchain.pdbend = pdbend;
// Sort the bonds by z coord
visiblebonds = new Vector<Bond>();
- for (PDBChain chain : pdb.chains)
+ for (PDBChain chain : pdb.getChains())
{
if (chain.isVisible)
{
min[1] = (float) 1e30;
min[2] = (float) 1e30;
- for (PDBChain chain : pdb.chains)
+ for (PDBChain chain : pdb.getChains())
{
if (chain.isVisible)
{
int bsize = 0;
// Find centre coordinate
- for (PDBChain chain : pdb.chains)
+ for (PDBChain chain : pdb.getChains())
{
if (chain.isVisible)
{
PDBChain chain;
if (bysequence && pdb != null)
{
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- chain = pdb.chains.elementAt(ii);
+ chain = pdb.getChains().elementAt(ii);
for (int i = 0; i < chain.bonds.size(); i++)
{
repaint();
if (foundchain != -1)
{
- PDBChain chain = pdb.chains.elementAt(foundchain);
+ PDBChain chain = pdb.getChains().elementAt(foundchain);
if (chain == mainchain)
{
if (fatom.alignmentMapping != -1)
PDBChain chain = null;
if (foundchain != -1)
{
- chain = pdb.chains.elementAt(foundchain);
+ chain = pdb.getChains().elementAt(foundchain);
if (chain == mainchain)
{
mouseOverStructure(fatom.resNumber, chain.id);
}
// Alter the bonds
- for (PDBChain chain : pdb.chains)
+ for (PDBChain chain : pdb.getChains())
{
for (Bond tmpBond : chain.bonds)
{
void drawLabels(Graphics g)
{
- for (PDBChain chain : pdb.chains)
+ for (PDBChain chain : pdb.getChains())
{
if (chain.isVisible)
{
foundchain = -1;
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- PDBChain chain = pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.getChains().elementAt(ii);
int truex;
Bond tmpBond = null;
if (fatom != null) // )&& chain.ds != null)
{ // dead code? value of chain is either overwritten or discarded
- chain = pdb.chains.elementAt(foundchain);
+ chain = pdb.getChains().elementAt(foundchain);
}
}
public void setAllchainsVisible(boolean b)
{
- for (int ii = 0; ii < pdb.chains.size(); ii++)
+ for (int ii = 0; ii < pdb.getChains().size(); ii++)
{
- PDBChain chain = pdb.chains.elementAt(ii);
+ PDBChain chain = pdb.getChains().elementAt(ii);
chain.isVisible = b;
}
mainchain.isVisible = true;